Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Salmonella and simultaneous detection of Salmonella and Shiga‐like toxin‐producing Escherichia coli using the magnetic capture hybridization polymerase chain reaction

J. CHEN AND M.W. GRIFFITHS. 2001. The magnetic capture hybridization polymerase chain reaction (MCH‐PCR) was used to detect Salmonella and also to simultaneously detect Salmonella and Shiga‐like toxin‐producing Escherichia coli (SLTEC). Fifty‐seven Salmonella and 41 SLTEC were included in the study. Salmonella were detected either individually by a single MCH‐PCR assay targeting the inv gene or simultaneously with SLTEC by a multiplex MCH‐PCR in which SLTEC were detected using primers for the slt genes. Both single and multiplex assays were found to be specific for tested pathogens. The results indicate that MCH‐PCR can be used as means of detecting single or multiple bacterial pathogen(s).
A GPU OpenCL based cross-platform Monte Carlo dose calculation engine (goMC)

Monte Carlo (MC) simulation has been recognized as the most accurate dose calculation method for radiotherapy. However, the extremely long computation time impedes its clinical application. Recently, a lot of effort has been made to realize fast MC dose calculation on graphic processing units (GPUs). However, most of the GPU-based MC dose engines have been developed under NVidia’s CUDA environment. This limits the code portability to other platforms, hindering the introduction of GPU-based MC simulations to clinical practice. The objective of this paper is to develop a GPU OpenCL based cross-platform MC dose engine named goMC with coupled photon–electron simulation for external photon and electron radiotherapy in the MeV energy range. Compared to our previously developed GPU-based MC code named gDPM (Jia et al Phys. Med. Biol. 57 7783–97), goMC has two major differences. First, it was developed under the OpenCL environment for high code portability and hence could be run not only on different GPU cards but also on CPU platforms. Second, we adopted the electron transport model used in EGSnrc MC package and PENELOPE’s random hinge method in our new dose engine, instead of the dose planning method employed in gDPM. Dose distributions were calculated for a 15 MeV electron beam and a 6 MV photon beam in a homogenous water phantom, a water-bone-lung-water slab phantom and a half-slab phantom. Satisfactory agreement between the two MC dose engines goMC and gDPM was observed in all cases. The average dose differences in the regions that received a dose higher than 10% of the maximum dose were 0.48–0.53% for the electron beam cases and 0.15–0.17% for the photon beam cases. In terms of efficiency, goMC was ~4–16% slower than gDPM when running on the same NVidia TITAN card for all the cases we tested, due to both the different electron transport models and the different development environments. The code portability of our new dose engine goMC was validated by successfully running it on a variety of different computing devices including an NVidia GPU card, two AMD GPU cards and an Intel CPU processor. Computational efficiency among these platforms was compared.
EXCHANGE TRANSFUSION IN VERY SMALL INFANTS

The mother's history, the infant's Rh-positive blood group and a positive result of the direct Coombs test, as well as the level of the maternal antibodies, provided the indications for exchange transfusion in cases of erythroblastosis fretalis; it was hoped thus to prevent hyperbilirubinremia. In group II a serum bilirubin level of 15 to 20 mg. per 100 ml. , especially if associated with early cerebral signs, was taken as an indication for exchange transfusion.
Development and characterisation of high electrical performances TSV for 3D applications

Today, a new trend in wafer level packaging is to add more than one die in the same package and, sometimes, to use the third dimension in order to : • Decrease the form factor of the final system • Improve the thermal and electrical performances of the device • Decrease the cost of the final product In order to stack the heterogeneous components in the third dimension, TSV (Through Silicon Vias) is a very promising technology compare to wire bonding. In this paper, the technological bricks specifically developed for 3D integration demonstrator will be presented. The integration flow was based on the 45 nm technology top chip stacked on a 130 nm technology active bottom wafer [1] [2]. This flow needed to develop specific wafer level packaging technologies such as: • Top chip & bottom chip interconnections • High aspect ratio TSV included into the bottom wafer • Backside interconnections for subsequent packaging step • Temporary bonding and debonding of bottom wafer [3] [4] • Top chip stacking on bottom wafer In the first part of the paper, the complete process flow will be presented. Then, a technical focus will be done on the specific steps developed for the improvement of the TSV's electrical performances. Finally, the electrical results achieved on a specific test vehicle, similar to the demonstrator will be discussed. The electrical results obtained on a technological test vehicle will be firtly presented. Those results include electrical continuity, pillars resistance, TSV resistance and capacitance and TSV insulation and current losses. Then, the electrical results obtained with the “high electrical performances” process on the functionnal demonstrator will be showed, including a specific focus on the TSV capacitance measurements.
Resource management for maximum spectrum utilization in D2D cellular communication

Given the steadily growing importance of D2D communication, a resource allocation scheme aimed at maximizing the spectrum utilization by minimizing transmission length of D2D link is proposed. The proposed scheme illustrates the existence of RBs in time and frequency domain and performs power control within set Cellular to Device (C2D) and Device to Cellular (D2C) Constraints. Mixed integer programming (MIP) which is an NP complete problem is suggested to formulate interference issues. Proposed column generation method is the solution for NP problem which is achieved by reducing it to a pricing problem that focus to solve restricted master problem before proceeding for the next step. The pricing issue is iteratively solved by a combination of a distance based and greedy heuristic algorithm. The numerical results represented optimum minimum distance between suggested cellular user and device to device link user.
Long‐term decrease in satellite vegetation indices in response to environmental variables in an iconic desert riparian ecosystem: the Upper San Pedro, Arizona, United States

The Upper San Pedro River is one of the few remaining undammed rivers that maintain a vibrant riparian ecosystem in the southwest United States. However, its riparian forest is threatened by diminishing groundwater and surface water inputs, due to either changes in watershed characteristics such as changes in riparian and upland vegetation, or human activities such as regional groundwater pumping. We used satellite vegetation indices to quantify the green leaf density of the groundwater‐dependent riparian forest from 1984 to 2012. The river was divided into a southern, upstream (mainly perennial flow) reach and a northern, downstream (mainly intermittent and ephemeral flow) reach. Pre‐monsoon (June) Landsat normalized difference vegetation index (NDVI) values showed a 20% drop for the northern reach (P < 0·001) and no net change for the southern reach (P > 0·05). NDVI and enhanced vegetation index values were positively correlated (P < 0·05) with river flows, which decreased over the study period in the northern reach, and negatively correlated (P < 0·05) with air temperatures in both reaches, which have increased by 1·4 °C from 1932 to 2012. NDVI in the uplands around the river did not increase from 1984 to 2012, suggesting that increased evapotranspiration in the uplands was not a factor in reducing river flows. Climate change, regional groundwater pumping, changes in the intensity of monsoon rain events and lack of overbank flooding are feasible explanations for deterioration of the riparian forest in the northern reach. Copyright © 2014 John Wiley & Sons, Ltd.
Wideband wide-scan millimeter-wave phased arrays for enhanced security/privacy and performance in 5G mobile wireless

Millimeter wave (mmWave) phased arrays have been demonstrated recently as the technology that enables 5G mobile's grand vision of high data rate and low latency, as well as provides a physical layer security stemming from mmWave's high propagation loss in the air interface. This paper explores the fundamental issues in both capacity and security/privacy of 5G wireless, and proposes a solution to enhance its capacity and cyberspace security/privacy by employing wideband wide-scan mmWave phased arrays. Implementation on small mobile platforms such as smartphones and tablets is discussed.
miRNAs and cancer: New research developments and potential clinical applications

miRNAs are small non-protein coding transcripts that regulate gene expression post-transcriptionally by binding to the 3' UTRs (untranslated regions) of messenger RNAs (mRNAs). The number of newly discovered miRNAs and our understanding of their biological roles continue to grow. In addition to their roles in important biological processes such as development, differentiation, proliferation, and cell death, deregulated expression of miRNAs has been implicated in a wide range of pathologies, especially in cancer. We now understand that miRNA expression is often deregulated in cancer cells and that a vast number of genes, including tumor suppressor genes and oncogenes, are regulated by these small RNAs. The small size of miRNAs and sequence similarity of miRNA family members pose some challenges in routine molecular detection and quantification techniques. Therefore, methods are being modified to specifically and sensitively detect miRNAs in cancer cells. Our current knowledge and the ever increasing pace of new discoveries clearly show that miRNAs are quite important in normal and in cancer cells in surprisingly diverse aspects. The better we understand how miRNAs contribute to cancer, the more likely we will be able to exploit them as tumor classifiers, biomarkers and, potentially, as unique targets for therapeutic applications.
Properties of single motor units in medial gastrocnemius muscles of adult and old rats.

1. The purpose of this study was to determine the role of motor unit remodelling in the deficit that develops in the maximum isometric tetanic force (Fo) of whole medial gastrocnemius (MGN) muscles in old compared with adult rats. The Fo values and morphological data were determined for MGN muscles and eighty‐two single motor units in muscles of adult (10‐12 months) and sixty‐two units in those of old (24‐26 months) F344 rats. During an unfused tetanus, fast and slow (S) motor units were identified by the presence and absence of sag, respectively. Fast‐fatigable (FF) and fast‐fatigue‐resistant (FR) units were classified by fatigue indices less than or greater than 0.50, respectively. 2. For old rats, whole MGN muscle Fo was 29% less than the value of 11.2 N measured for adult rats. The deficit in whole muscle Fo of old rats resulted from equivalent decreases in the number of motor units, 16% smaller than the adult value of ninety‐seven, and in the mean motor unit Fo value, 14% less than the adult value of 117 mN. 3. With ageing, little motor unit remodelling occurred in FR units, whereas the S and FF motor units demonstrated dramatic, but opposing, changes. For S units, the number of units remained constant, but the number of fibres per motor unit increased 3‐fold from 57 to 165. In contrast, the number of FF units decreased by 34% and the number of fibres per motor unit of the remaining units decreased to 86% of the adult value of 333. The age‐related remodelling of motor units appeared to involve denervation of fast muscle fibres with reinnervation of denervated fibres by axonal sprouting from slow fibres.
Design, testing and modelling of a novel robotic system for trans‐oesophageal ultrasound

Trans‐oesophageal echocardiography (TOE) has been widely utilized for cardiac disease diagnosis and interventional procedure guidance. However, the TOE operator is required to manually manipulate the probe, often for long periods of time and sometimes in an X‐ray environment where there is exposure to ionizing radiation.
Generation of 50-TW femtosecond pulses in a Ti:sapphire/Nd:glass chain.

Femtosecond pulses in the 50–60-TW power range have been generated at 1064 nm by using the chirped-pulse-amplification technique applied to a Ti:sapphire/Nd:silicate glass (90-mm output aperture) power chain. We have identified the spectral gain narrowing to be one of the main issues, and we show how to solve it.
Barriers to E-Commerce Adoption: Consumers’ Perspectives from a Developing Country

Although e-commerce has become a familiar retail channel for businesses in developed countries, it is still considered an innovation in developing countries. Specifically, electronic commerce (e-commerce) in Saudi Arabia is still in the first stage despite its advance and fast growth in ICT marketplace, the highest increase in Internet penetration in the world, strong retail sector, and young population. This research study aims to identify tangible barriers influencing consumers in Saudi Arabia to adopt e-commerce. An exploratory research design is used to shed light on the tangible barriers facing Saudi consumers when shopping online. This research study identified key tangible barriers and their relative importance for both e-commerce adapters and non-adapters facing Saudi consumer when shopping online. Practical as well as managerial implications are discussed.
Catheterization of the Carotid Artery and Jugular Vein to Perform Hemodynamic Measures, Infusions and Blood Sampling in a Conscious Rat Model

The success of a small animal model to study critical illness is, in part, dependent on the ability of the model to simulate the human condition. Intra-tracheal inoculation of a known amount of bacteria has been successfully used to reproduce the pathogenesis of pneumonia which then develops into sepsis. Monitoring hemodynamic parameters and providing standard clinical treatment including infusion of antibiotics, fluids and drugs to maintain blood pressure is critical to simulate routine supportive care in this model but to do so requires both arterial and venous vascular access. The video details the surgical technique for implanting carotid artery and common jugular vein catheters in an anesthetized rat. Following a 72 hr recovery period, the animals will be re-anesthetized and connected to a tether and swivel setup attached to the rodent housing which connects the implanted catheters to the hemodynamic monitoring system. This setup allows free movement of the rat during the study while continuously monitoring pressures, infusing fluids and drugs (antibiotics, vasopressors) and performing blood sampling.
Ipsilateral primary sensorimotor cortical response to mechanical tactile stimuli

We studied somatosensory-evoked fields elicited by mechanical versus electrical stimuli to index finger of healthy participants. Mechanical stimulation was index pulp compression and decompression by using nonmagnetic mechanical stimulator. Electrical stimulation was three times of sensory threshold and delivered to index pulp by using ball-shaped electrodes. Mechanical/electrical stimuli evoked contralateral primary somatosensory cortical responses in all respective participants. Compressive stimuli evoked ipsilateral primary sensorimotor cortical responses in all respective participants, with dipole strengths less than contralateral primary somatosensory cortical responses of compressive stimuli. Mechanical/electrical stimuli evoked secondary somatosensory (SII) cortical responses bilaterally; electrical-stimuli SII dipole strengths were relatively stronger than compressive-stimuli SII responses. It is concluded that the use of mechanical stimulation may improve our understanding of functional sensory cortical responses compared with electrical stimulation.
Supplemental Data Cardiac Fibroblasts Regulate Myocardial Proliferation through β 1 Integrin Signaling

SUPPLEMENTAL EXPERIMENTAL PROCEDURES HL1 Cell Culture HL1 cells were cultured at a density of 2.5x10/ cm in Claycomb medium containing 10% FBS on fibronectin/gelatin-coated or laminin-coated dish as described (Claycomb et al., 1998). To determine the cell number, HL1 cells were dissociated with trypsin and counted by hemocytometer. Cell cycle analyses were done as described (Ichii et al., 2002). Briefly, HL1 cells were incubated in hypotonic lysis buffer that contained PI (0.1% sodium citrate, 0.01% Triton X and 0.1 mg/ml of PI). The DNA content in each nucleus was analyzed on a FACS Calibur with FlowJo software.
MR‐monitored focused ultrasound using the acoustic‐coupling water bath as an intrinsic high‐mode dielectric resonator

The conventional set‐up for MR‐monitored focused ultrasound surgery includes a piezoelectric transducer and an acoustic‐coupling water bath integrated into the MR patient table; a large surface RF coil is placed close to the patient or, alternatively, the body coil is used as the MR receiver. Potential disadvantages of this approach are that the body coil has low sensitivity because of its low filling factor and the local RF coil can interfere with and cause reflections of the ultrasound irradiation. In this article, a completely new approach is presented, in which an MR transmit/receive coil is not needed at all. Instead, the dimensions of the water bath are adjusted so that a high‐order dielectric mode is excited, resulting in efficient MR excitation and reception at the transducer focal point. An example of monitoring ultrasound‐mediated heating in a phantom is shown on a 7‐T human system, although the new method can also be applied at lower fields. Copyright © 2014 John Wiley & Sons, Ltd.
Bagged Biclustering for Microarray Data

One of the major tools of transcriptomics is the biclustering that simultaneously constructs a partition of both examples and genes. Several methods have been proposed for microarray data analysis that enables to identify groups of genes with similar expression profiles only under a subset of examples. We propose to improve the quality of these biclustering methods by using an ensemble approach. Our bagged biclustering method generates a collection of biclusters using the bootstrap samples of the original data and aggregate them into new biclusters. Our method improve the performance of biclustering on artificial and real datasets.
Preconditioning with cyclosporine a or fk506 differentially regulates mitogen-activated protein kinase expression in rat kidneys with ischemia/reperfusion injury12

Background. The signaling pathways of mitogen-activated protein kinases (MAPKs) are important molecular components responsible for ischemia/reperfusion (I/R) injury in the kidneys. Preconditioning with cyclosporine A (CsA) or FK506 reduces subsequent I/R injury. We studied the effect of preconditioning with CsA or FK506 on MAPK expression in ischemic rat kidneys. Methods. Two separate studies were performed using Sprague-Dawley rats. First, MAPK (extracellular signal-regulated kinase [ERK], jun N-terminal kinase [JNK], p38) expressions were observed at 0, 10, 20, 30, 60, 120, and 1,440 min after I/R injury. Second, the effects of preconditioning with CsA or FK506 on MAPK expressions were observed in rat kidneys with I/R injury. I/R injury was induced by clamping both renal arteries for 45 min. Rats were pretreated with intravenous (IV) CsA (3 mg/kg) or IV FK506 (0.3 mg/kg) 6 hr before I/R injury and killed 30 min later. Expression of MAPK was measured using immunoblot and immunohistochemistry. Results. MAPK (ERK, JNK, p38) expressions were significantly increased in kidneys with I/R injury compared with sham-operated controls, and immunohistochemistry revealed increased MAPK immunoreactivity in renal tubules of the outer medulla. Kidneys preconditioned with low-dose CsA or FK506 showed significantly increased ERK expression compared with kidneys with I/R injury alone (CsA, 9.5- vs. 4.5-fold; FK506 10.4- vs. 4.5-fold:P <0.05) but showed decreased JNK (CsA, 3.8- vs. 5.3-fold; FK506, 3.4- vs. 5.3-fold:P <0.05) and p38 expression (CsA, 2.5- vs. 3.7-fold; FK506, 2.1- vs. 3.7-fold:P <0.05). Conclusions. Preconditioning with CsA or FK506 differentially regulates the expression of MAPK in rat kidneys with I/R injury, and this may explain the remarkable protective effects of these agents.
Active Magnetic Bearings Robust Control Design based on Symmetry Properties

This paper describes an Hinfin robust control design for an electromechanical system consisting of a rotary flexible spindle hovered by active magnetic bearings (AMB), whose potential uses in the machine-tool industry have been well documented. Symmetry properties are utilized to perform a model reduction avoiding the ill-conditioning of the matrices when Hinfin algorithms are solved and hence, facilitating the design of the controller. The better behavior of the system is probed by simulation in a complete model of a real device.
Effects of Erythropoietin on Neuronal Activity

Abstract: Recently, erythropoietin (EPO) receptors and synthesis of EPO have been identified in the brain. To clarify the effects of EPO on neuronal cells, we investigated the effects of EPO on Ca2+ uptake, intracellular Ca2+ concentration, membrane potential, cell survival, release and biosynthesis of dopamine, and nitric oxide (NO) production in differentiated PC12 cells, which possess EPO receptors. EPO (10‐12‐10‐10M) increased 45Ca2+ uptake and intracellular Ca2+ concentration in PC12 cells in a dose‐related manner; these increases were inhibited by nicardipine (1 μM) or anti‐EPO antibody (1:100 dilution). EPO induced membrane depolarization in PC12 cells. After a 5‐day culture without serum and nerve growth factor (NGF), viable cell number decreased to 50% of that of the control cells cultured with serum and NGF. EPO (10‐13‐10‐10M) increased the number of viable cells cultured without serum and NGF; this increase was blunted by nicardipine or anti‐EPO antibody. Incubation with EPO (10‐13‐10‐10M) stimulated mitogen‐activated protein kinase activity in PC12 cells. EPO (10‐13‐10‐10M) increased dopamine release from PC12 cells and tyrosine hydroxylase activity; these increases were sensitive to nicardipine or anti‐EPO antibody. Following a 4‐h incubation with EPO (10‐14‐10‐10M), NO production was increased, which was blunted by nicardipine and anti‐EPO antibody. In contrast, maximal NO synthase activity was not changed by EPO. These results suggest that EPO stimulates neuronal function and viability via activation of Ca2+ channels.
Quantitative RT-PCR: limits and accuracy.

In this paper we determine the limits and accuracy of quantitative reverse transcription (RT)-PCR using a modification of the original protocol. The quantification of mRNA with this procedure requires a preliminary estimation of the target molecule (TM) concentration, established from experiments with an internal control molecule (ICM). A definitive quantification is then attained from serial dilutions of the reverse transcription reaction. The success of this latter step is dependent on maintaining an equivalent number of TM and ICM in the reaction. The purpose of our study was to evaluate the influence of the deviation between the TM and the ICM on the result. We show here that we can control the accuracy of the assay by fixing the limit of the TM/ICM ratio. Indeed, when the TM/ICM ratio is between 0.66 and 1.5 (i.e., the difference between TM and ICM is 1.5-fold), the final result has an error of approximately 10%. Exceeding this limit produces errors approaching 60%, as in the case of TM/ICM = 2. When the above conditions are respected, a difference as small as 20% between two samples can be determined with an accuracy of 95%.