Miracle-dz/UniFAR-FTUs huggingface dataset:
Purple sweet potato pigments protect murine thymocytes from 60Co γ-ray-induced mitochondria-mediated apoptosis

Purpose: Purple sweet potato (PSP) pigments have been widely accepted as antioxidants but their radioprotective effect still remains unclear. In this study we investigated the effect of PSP pigments on 60Co γ-ray-induced mitochondria-mediated apoptosis in murine thymocytes. Materials and methods: The murine thymocytes were pretreated by PSP pigments before exposure to 4 Gy 60Co γ-rays. Flow cytometry analysis was used to measure apoptotic cells and mitochondrial membrane potential. Reactive oxygen species (ROS) were detected using 2′,7′,-dichlorofluorescein diacetate (DCFH-DA) probe and the activity of antioxidant enzymes was tested by biochemical assay after irradiation. Cytochrome c, caspase-3 and poly ADP-ribose polymerase (PARP) were measured by Western blotting. Results: After treatment with PSP pigments and exposure to 4 Gy radiation the apoptosis of thymocytes was reduced and the mitochondrial transmembrane potential was maintained compared to control cells. In the presence of PSP pigments, ROS were reduced and the activities of glutathione peroxidase (GSH-px) and superoxide dismutase (SOD) were protected and in some cases increased. All the pro-apoptotic proteins (cytochrome oxidase, caspase 3 and PARP) decreased in PSP pigments pretreated thymocytes compared to irradiated cells in the absence of PSP pigments. Conclusions: Pre-treatment with PSP pigments significantly inhibited 60Co γ-ray-induced mitochondria-mediated apoptosis. This radioprotective effect might be related to ROS scavenging, the enhancement of the activity of antioxidant enzymes, the maintenance of mitochondrial transmembrane potential, and the sequential inhibition of cytochrome c release and downstream caspase and PARP cleavage.
Wrist-Worn Accelerometer-Brand Independent Posture Classification.

INTRODUCTION Access to raw acceleration data should facilitate comparisons between accelerometer outputs regardless of monitor brand. PURPOSE To evaluate the accuracy of posture classification using the Sedentary Sphere in data from two widely used wrist-worn triaxial accelerometers. METHODS Laboratory: Thirty-four adults wore a GENEActiv and an ActiGraph GT3X+ on their nondominant wrist while performing four lying, seven sitting, and five upright activities. Free-living: The same participants wore both accelerometers on their nondominant wrist and an activPAL3 on their right thigh during waking hours for 2 d. RESULTS Laboratory: Using the Sedentary Sphere with 15-s epoch GENEActiv data, sedentary and upright postures were correctly identified 74% and 91% of the time, respectively. Corresponding values for the ActiGraph data were 75% and 90%. Free-living: Total sedentary time was estimated at 534 ± 144, 523 ± 143, and 528 ± 137 min by the activPAL, the Sedentary Sphere with GENEActiv data and with ActiGraph data, respectively. The mean bias, relative to the activPAL, was small with moderate limits of agreement (LoA) for both the GENEActiv (mean bias = -12.5 min, LoA = -117 to 92 min) and ActiGraph (mean bias = -8 min, LoA = -103 to 88 min). Strong intraclass correlations (ICC) were evident for the activPAL with the GENEActiv (0.93, 0.84-0.97 (95% confidence interval) and the ActiGraph (0.94, 0.86-0.97). Agreement between the GENEActiv and ActiGraph posture classifications was very high (ICC = 0.98 (0.94-0.99), mean bias = +3 min, LoA = -58 to 63 min). CONCLUSIONS These data support the efficacy of the Sedentary Sphere for classification of posture from a wrist-worn accelerometer in adults. The approach is equally valid with data from both the GENEActiv and ActiGraph accelerometers.
Ionic Currents and Spontaneous Firing in Neurons Isolated from the Cerebellar Nuclei

Neurons of the cerebellar nuclei fire spontaneous action potentials both in vitro, with synaptic transmission blocked, andin vivo, in resting animals, despite ongoing inhibition from spontaneously active Purkinje neurons. We have studied the intrinsic currents of cerebellar nuclear neurons isolated from the mouse, with an interest in understanding how these currents generate spontaneous activity in the absence of synaptic input as well as how they allow firing to continue during basal levels of inhibition. Current-clamped isolated neurons fired regularly (∼20 Hz), with shallow interspike hyperpolarizations (approximately −60 mV), much like neurons in more intact preparations. The spontaneous firing frequency lay in the middle of the dynamic range of the neurons and could be modulated up or down with small current injections. During step or action potential waveform voltage-clamp commands, the primary current active at interspike potentials was a tetrodotoxin-insensitive (TTX), cesium-insensitive, voltage-independent, cationic flux carried mainly by sodium ions. Although small, this cation current could depolarize neurons above threshold voltages. Voltage- and current-clamp recordings suggested a high level of inactivation of the TTX-sensitive transient sodium currents that supported action potentials. Blocking calcium currents terminated firing by preventing repolarization to normal interspike potentials, suggesting a significant role for K(Ca) currents. Potassium currents that flowed during action potential waveform voltage commands had high activation thresholds and were sensitive to 1 mmTEA. We propose that, after the decay of high-threshold potassium currents, the tonic cation current contributes strongly to the depolarization of neurons above threshold, thus maintaining the cycle of firing.
Treatment Effect of Clopidogrel Plus Aspirin Within 12 Hours of Acute Minor Stroke or Transient Ischemic Attack

Background The aim of this study was to analyze the benefits and safety associated with the combination therapy of clopidogrel and aspirin among minor stroke or transient ischemic attack patients treated within 12 hours. Methods and Results This was a subanalysis of the CHANCE (Clopidogrel in High‐Risk Patients with Acute Nondisabling Cerebrovascular Events) trial, mainly limited to the prespecified group of patients randomized within 12 hours to either the combination of clopidogrel plus aspirin or aspirin alone. The primary outcome was ischemic stroke during 90‐day follow‐up. Recurrent ischemic stroke and progressive ischemic stroke were analyzed. Multivariable Cox modeling showed that randomization within 12 hours was an independent predictor of ischemic stroke events (hazard ratio [95% CI] 1.25 [1.04–1.49], P=0.02). Among 2573 patients randomized within 12 hours, 282 (10.96%) patients had ischemic stroke events. Among them, 158 (12.34%) of 1280 patients taking aspirin experienced ischemic stroke compared with 124 (9.59%) of 1293 patients taking clopidogrel–aspirin (P=0.02). The dual antiplatelet was more effective than aspirin alone in reducing the risk of recurrent ischemic stroke (6.57% versus 8.91%, P=0.03) but not progressive ischemic stroke (3.02% versus 3.43%, P=0.28). There was no significant difference in hemorrhagic events (P=0.39). Conclusions Among patients treated within 12 hours, the combination of clopidogrel and aspirin was more effective than aspirin alone in reducing the risk of recurrent ischemic stroke during the 90‐day follow‐up and did not increase the hemorrhagic risk. Clinical Trial Registration URL: https://www.clinicaltrials. gov/. Unique identifier: NCT00979589.
Photorealism and Non-Photorealism in Virtual Heritage Representation

The area of virtual heritage has long been concentrated on generating digital reconstructions of historical or archaeological artefacts and sites with enough fidelity to be truly accurate representations of their real-world counterparts. In some cases, the advancement of tools and techniques for achieving greater visual realism has distracted from the development of other directions that enhance a virtual experience, such as interactivity, sound or touch. Recent trends in the area of non-photorealistic rendering shift focus to the development of more "believable" environments, while maintaining the accuracy and validity of the visualised data, which is significant for archaeological research. In this paper we argue that it is important to enhance the perception of realism, achieved both through photorealistic and non-photorealistic visualisation approaches, with interactivity. This is illustrated by two example projects which develop prototype virtual environments created for specialists as well as novice users.
Use of Specific Chemical Reagents for Detection of Modified Nucleotides in RNA

Naturally occurring cellular RNAs contain an impressive number of chemically distinct modified residues which appear posttranscriptionally, as a result of specific action of the corresponding RNA modification enzymes. Over 100 different chemical modifications have been identified and characterized up to now. Identification of the chemical nature and exact position of these modifications is typically based on 2D-TLC analysis of nucleotide digests, on HPLC coupled with mass spectrometry, or on the use of primer extension by reverse transcriptase. However, many modified nucleotides are silent in reverse transcription, since the presence of additional chemical groups frequently does not change base-pairing properties. In this paper, we give a summary of various chemical approaches exploiting the specific reactivity of modified nucleotides in RNA for their detection.
Immunosuppression status of liver transplant recipients with hepatitis C affects biopsy-proven acute rejection

Background/Aims The relationship between patient survival and biopsy-proven acute rejection (BPAR) in liver transplant recipients with hepatitis C remains unclear. The aims of this study were to compare the characteristics of patients with and without BPAR and to identify risk factors for BPAR. Methods We retrospectively reviewed the records of 169 HCV-RNA-positive patients who underwent LT at three centers. Results BPAR occurred in 39 (23.1%) of the HCV-RNA-positive recipients after LT. The 1-, 3-, and 5-year survival rates were 92.1%, 90.3%, and 88.5%, respectively, in patients without BPAR, and 75.7%, 63.4%, and 58.9% in patients with BPAR (P<0.001). Multivariate analyses showed that BPAR was associated with the non-use of basiliximab and tacrolimus and the use of cyclosporin in LT recipients with HCV RNA-positive. Conclusion The results of the present study suggest that the immunosuppression status of HCV-RNA-positive LT recipients should be carefully determined in order to prevent BPAR and to improve patient survival.
The relation of empathy to prosocial and related behaviors.

In a prior review involving a meta-analysis (Underwood & Moore, 1982), no relation between affective empathy and prosocial behavior was found. In this article, the literature relevant to this issue is reexamined. The studies were organized according to the method used to assess empathy. When appropriate, meta-analyses were computed. In contrast to the earlier review, low to moderate positive relations generally were found between empathy and both prosocial behavior and cooperative/socially competent behavior. The method of assessing empathy did influence the strength of the relations; picture/story measures of empathy were not associated with prosocial behavior, whereas nearly all other measures were. Several possible explanations for the pattern of findings are discussed, as are the implications of the findings.
Text-Aided Image Classification: Using Labeled Text from Web to Help Image Classification

As more and more multimedia data become available on the Web, mining on those data is playing an increasingly important role in Web applications. In this paper, we investigate the interplay between multimedia data mining and text data mining. Specifically, in an approach we called text-aided image classification (TAIC), we address the problem of image classification with very limited amount of labeled images and a large amount of auxiliary labeled text data. This problem is important in practice, since currently on the Web, labeled text data are usually much more than image data. To solve the problem, based on the “bag-of-words” view and the Naive Bayes classification model, we focus our attention on the estimation of the image feature distribution under given concept. We extend the Naive Bayes algorithm by considering a mapping that maps the most discriminative text features into the image feature space. This feature mapping is estimated based on the text-image cooccurrence data on the Web, acting like a bridge that connects text and image knowledge. With this process, we estimate target image feature distribution from a text model based on sufficient labeled data. Our empirical results on real world data sets show that our method makes a good approximation of the image feature distribution when trained with abundant labeled images. In the case amount of labeled images is very limited, the classification performance is improved by using auxiliary labeled text data, which shows that our method can indeed integrate text and image knowledge in a simple yet effective way.
Successful Control of Nosocomial VRE Outbreak: Experiences of Hospital Infection Control Committee

Address for Correspondence/Yaz›flma Adresi: Dr. Guven Celebi, Zonguldak Karaelmas Universitesi Tip Fakultesi, Enfeksiyon Hastaliklari ve Klinik Mikrobiyoloji Anabilim Dali, Zonguldak, Turkey Phone: +90 533 352 02 54 e.mail: guvencelebi@yahoo.com doi:10.5152/dcbybd.2011. 10 Aim: The aim of this study is to describe the methods used to control the first monoclonal vancomycin resistant enterococcus (VRE) outbreak which emerged in September 2005 in a university hospital in Turkey. Material and Methods: Following detection of the first VRE positive case, surveillance with stool or rectal swab cultures from all the hospital inpatients was performed. Patients were categorized according to their potential risk of exposure to VRE; VRE positive cases, primary contacts and secondary contacts. Isolation and cohortion of the patients were performed according to this categorization. Hospital wide information and training programs were conducted for healthcare workers (HCW) and strict contact isolation precautions were implemented in the hospital. Results: Apart from the index case, three additional cases were detected. The recommendations of the Center for Disease Control and Prevention (CDC) were adopted and implemented in our hospital and the outbreak was controlled within one month. Conclusion: Categorization of patients according to their possible risk of exposure to VRE may be useful in determining the form and extent of control measures, especially in the hospitals with limited resources. (Yogun Bakim Derg 2011; 2: 44-8)
Electro-Optical Properties of Sputtered Calcium Lead Titanate Thin Films for Pyroelectric Detection

Pyroelectric detectors are the class of thermal detectors which change their spontaneous polarization when there is a change in temperature. The change in the spontaneous polarization occurs due to the absorption of infrared radiation which eventually produces a voltage. This work demonstrates the deposition and characterization of calcium modified lead titatante (Pb1-xCaxTiO3, PCT) thin films for using them as materials of pyroelectric thermal detectors. The PCT thin films were sputtered using an RF sputter system in Ar:O2 environment at room temperature. The thin films were grown on Au electrode. The capacitance was formed by using Au electrodes on top of PCT thin films which were fabricated by sputtering and liftoff. The PCT films were annealed at 450, 500, 550 and 600 °C in O2 environment for 15 minutes. Energy dispersive spectroscopy was done to determine the atomic composition of PCT films. Variations of capacitance, pyroelectric voltage, loss tangent and pyroelectric current between the temperature range 303 K to 353 K were determined. The PCT films were annealed at 550 °C showed the highest value of pyroelectric current and pyroelectric coefficient of 2.45 × 10-12 A and 1.99 μC/m2K respectively at room temperature. The loss tangent did not change much with temperature for all the PCT samples.
ARCH domain of XPD, an anchoring platform for CAK that conditions TFIIH DNA repair and transcription activities

The xeroderma pigmentosum group D (XPD) helicase is a subunit of transcription/DNA repair factor, transcription factor II H (TFIIH) that catalyzes the unwinding of a damaged DNA duplex during nucleotide excision repair. Apart from two canonical helicase domains, XPD is composed of a 4Fe-S cluster domain involved in DNA damage recognition and a module of uncharacterized function termed the “ARCH domain. ” By investigating the consequences of a mutation found in a patient with trichothiodystrophy, we show that the ARCH domain is critical for the recruitment of the cyclin-dependent kinase (CDK)-activating kinase (CAK) complex. Indeed, this mutation not only affects the interaction with the MAT1 CAK subunit, thereby decreasing the in vitro basal transcription activity of TFIIH itself and impeding the efficient recruitment of the transcription machinery on the promoter of an activated gene, but also impairs the DNA unwinding activity of XPD and the nucleotide excision repair activity of TFIIH. We further demonstrate the role of CAK in downregulating the XPD helicase activity within TFIIH. Taken together, our results identify the ARCH domain of XPD as a platform for the recruitment of CAK and as a potential molecular switch that might control TFIIH composition and play a key role in the conversion of TFIIH from a factor active in transcription to a factor involved in DNA repair.
Integrated Assessment of Heavy Metal Pollution in the Surface Sediments of the Laizhou Bay and the Coastal Waters of the Zhangzi Island, China: Comparison among Typical Marine Sediment Quality Indices

The total concentrations and chemical forms of heavy metals (Cd, Cr, Cu, Ni, Pb and Zn) in the surface sediments of the Laizhou Bay and the surrounding marine area of the Zhangzi Island (hereafter referred to as Zhangzi Island for short) were obtained and multiple indices and guidelines were applied to assess their contamination and ecological risks. The sedimentary conditions were fine in both of the two studied areas according to the marine sediment quality of China. Whereas the probable effects level guideline suggested that Ni might cause adverse biological effects to occur frequently in some sites. All indices used suggested that Cd posed the highest environmental risk in both the Laizhou Bay and the Zhangzi Island, though Cd may unlikely be harmful to human and ecological health due to the very low total concentrations. The enrichment factor (EF) showed that a substantial portion of Cr was delivered from anthropogenic sources, whereas the risk assessment code (RAC) indicated that most Cr was in an inactive state that it may not have any adverse effect either. Moreover, the results of EF and geoaccumulation index were consistent with the trend of the total metal concentrations except for Cd, while the results of RAC and potential ecological risk factor did not follow the same trend of their corresponding total metal concentrations. We also evaluated the effects of using different indices to assess the environmental impact of these heavy metals.
Mechanics of limb bone loading during terrestrial locomotion in river cooter turtles (Pseudemys concinna)

SUMMARY Studies of limb bone loading during terrestrial locomotion have focused primarily on birds and mammals. However, data from a broader functional and phylogenetic range of species are critical for understanding the evolution of limb bone function and design. Turtles are an interesting lineage in this context. Although their slow walking speeds and robust limb bones might lead to low locomotor forces and limb bone stresses similar to other non-avian reptiles, their highly sprawled posture could produce high bending loads, leading to high limb bone stresses similar to those of avian and mammalian species, as well as high torsion. To test between these possibilities, we evaluated stresses experienced by the femur of river cooter turtles (Pseudemys concinna) during terrestrial walking by synchronizing measurements of three-dimensional joint kinematics and ground reaction forces (GRFs) during isolated hindlimb footfalls. Further, we evaluated femoral safety factors for this species by comparing our locomotor stress calculations with the results of mechanical property tests. The net GRF magnitude at peak tensile bone stress averaged 0.35 BW (body weight) and was directed nearly vertically for the middle 40–65% of the contact interval, essentially orthogonal to the femur. Peak bending stresses experienced by the femur were low (tensile: 24.9±9.0 MPa; compressive: –31.1±9.1 MPa) and comparable to those in other reptiles, yet peak shear stresses were higher than those in other reptiles, averaging 13.7±4.2 MPa. Such high torsion is present despite cooters lacking a large tail, a feature that has been hypothesized to contribute to torsion in other reptiles in which the tail is dragged along the ground. Comparison of femoral stresses to measurements of limb bone mechanical properties in cooters indicates safety factors to yield of 13.9 in bending and 6.3 in torsion, considerably higher than values typical for birds and mammals, and closer to the elevated values calculated for other reptile species. Thus, not only do turtle limb bones seem considerably `over-designed' for resisting the loads that they encounter, but comparisons of bone loading across tetrapod lineages are consistent with the hypothesis that low limb bone loads, elevated torsion and high safety factors may be primitive features of limb bone design.
Using Decision Trees to Predict the Certification Result of a Build

Large teams of practitioners (developers, testers, etc.) usually work in parallel on the same code base. A major concern when working in parallel is the introduction of integration bugs in the latest shared code. These latent bugs are likely to slow down the project unless they are discovered as soon as possible. Many companies have adopted daily or weekly processes which build the latest source code and certify it by executing simple manual smoke/sanity tests or extensive automated integration test suites. Other members of a team can then use the certified build to develop new features or to perform additional analysis, such as performance or usability testing. For large projects the certification process may take a few days. This long certification process forces team members to either use outdated or uncertified (possibly buggy) versions of the code. In this paper, we create decision trees to predict ahead of time the certification result of a build. By accurately predicting the outcome of the certification process, members of large software teams can work more effectively in parallel. Members can start using the latest code without waiting for the certification process to be completed. To perform our study, we mine historical information (code changes and certification results) for a large software project which is being developed at the IBM Toronto Labs. Our study shows that using a combination of project attributes (such as the number of modified subsystems in a build and certification results of previous builds), we can correctly predict 69% of the time that a build will fail certification. We can as well correctly predict 95% of the time if a build will pass certification