Miracle-dz/UniFAR-FTUs huggingface dataset:
Reliability of confocal choroidal laser Doppler flowmetry.

PURPOSE To assess the variability in choroidal laser Doppler flowmetry (LDF). METHODS Five measurements of choroidal blood flow were obtained on 5 days in both eyes of 10 subjects. Reliability, sensitivity, and sample size calculations were performed. Yield, the intensity of the returning light (direct current [DC]) divided by the signal amplification (gain) used during recording, was calculated (yield = DC/gain). The correlation between yield and the LDF parameters velocity, volume, and flux was analyzed. Reliability, sensitivity, and sample size calculations were repeated after correcting for this relationship. The influence of different light-scattering properties on the returning signal was assessed in a model eye. RESULTS Yield and the LDF parameters, velocity, volume, and flux, correlated significantly in a regression model. After the influence of yield was partialized out, reliability, reproducibility, sensitivity, and statistical power improved markedly. The high reliability of yield in a given eye (87%) suggests, that, besides varying recording settings on different days, individual specific scattering properties within the eye influence LDF measurements. Comparison of model eye data with human data disclosed a low signal-to-noise ratio with decreasing yield. Correcting for yield did not affect the sensitivity to blood flow changes induced by hypercapnia or a suction cup. CONCLUSIONS Tissue-scattering properties alter the characteristics of the returning light, and recording settings affect the outcome of the analysis of the returning light during LDF measurements. Partializing out the influence of yield markedly improves the reproducibility of choroidal LDF.
An Application of the Latent p Value Method to Assess Linkage in Asthma Pedigrees

Objective: The latent p value is a recently proposed empirical method for assessing evidence against a null hypothesis in a stochastic system involving latent, unobservable variables. It is particularly applicable to genome-wide genetic linkage analysis for test statistics with poorly defined analytical distributions. Methods: We describe an implementation of the latent p value method and its application to a linkage analysis of asthma in 81 extended pedigrees containing 1,858 people genotyped at 533 microsatellite markers. We compare the performance of the latent p value method to a more conventional p value calculation. We also compare the performance of various linkage statistics within this pedigree resource. Results: Using a novel linkage score referred to as the C-link statistic, our analysis provides strong evidence for a recessive gene influencing asthma on chromosome 5q13 (median latent p value = 0.03). We also demonstrate remarkable improvement in computational requirements compared to a more conventional empirical p value calculation. Conclusions: The latent p value method is indeed feasible and provides a computationally efficient means to evaluate evidence for linkage regardless of the choice of linkage statistic.
Does the use of lidocaine affect the culture of percutaneous bone biopsy specimens obtained to diagnose osteomyelitis? An in vitro and in vivo study.

OBJECTIVE When percutaneous bone biopsy is done by radiologists, local anesthetics such as lidocaine are routinely used. Although percutaneous bone biopsy of neoplasms is well accepted, it has been suggested that this procedure not be used to diagnose osteomyelitis because of a reported bactericidal effect of lidocaine and related drugs on certain organisms. The purposes of this study were to determine if lidocaine is bactericidal in vitro and to determine if it has an effect on the culture of bacteria in specimens obtained by percutaneous bone biopsy in vivo. SUBJECTS AND METHODS The minimal inhibitory concentration and minimal bactericidal concentration of 1% lidocaine hydrochloride (10 mg/ml preserved with methylparaben) were determined in vitro for seven bacteria known to be frequent causes of osteomyelitis by using conventional clinical microbiologic methods. Percutaneous core bone biopsy for suspected osteomyelitis was done in 28 patients: 21 with and seven without the use of lidocaine. Sites sampled included vertebrae (14); calcanei, pubis, and ischia (two each); and intervertebral disks (eight). Six of the 21 patients who had percutaneous biopsy with lidocaine also had an open surgical biopsy without lidocaine. The results of cultures of the specimens were compared. Histologic evaluation and radiographic follow-up were used to identify false-negative results. RESULTS The minimal inhibitory and the minimal bactericidal concentrations, respectively, of lidocaine (in milligrams per milliliter) were as follows: Klebsiella pneumoniae, 5.0 and > 5.0; group B streptococci, 2.5 and 5.0; Staphylococcus aureus, > 5.0; and > 5.0; methicillin-resistant S. aureus, > 5.0 and > 5.0; Escherichia coli, 2.5 and > 5.0; Pseudomonas aeruginosa, 5.0 and 5.0; Salmonella species, 5.0 and > 5.0. We found no difference in bacterial growth and the number of false-negative results between patients who had biopsies with and those who had biopsies without lidocaine. Fifty percent of patients who had growth on cultures of specimens from percutaneous biopsies done with lidocaine had no growth on cultures of specimens from surgical biopsies done without lidocaine. This likely occurred because the surgical specimens were not obtained under cross-sectional imaging guidance. CONCLUSION Up to a 50% mixture of lidocaine has no significant effect in vitro on the bacterial growth of the seven organisms that cause osteomyelitis most frequently, and no inhibitory effect on bacterial growth was seen in biopsies done with lidocaine in vivo. The inhibitory effect of lidocaine therefore occurs at a greater concentration than is used clinically. We conclude that lidocaine used for biopsy does not interfere with the diagnosis of osteomyelitis.
Strong recursive feasibility in model predictive control of biped walking

Realizing a stable walking motion requires satisfying a set of constraints. Model Predictive Control (MPC) is one of few suitable methods to handle such constraints. The capacity to satisfy constraints, which is usually called feasibility, is classically guaranteed recursively. In our applications, an important aspect is that the MPC scheme has to adapt continuously to the dynamic environment of the robot (e.g. collision avoidance, physical interaction). We aim therefore at guaranteeing recursive feasibility for all possible scenarios, which is called strong recursive feasibility. Recursive feasibility is classically obtained by introducing a terminal constraint at the end of the prediction horizon. Between two standard approaches for legged robot, in our applications we favor a capturable terminal constraint. When the robot is not really planning to stop and considers actually making a new step, recursive feasibility is not guaranteed anymore. We demonstrate numerically that recursive feasibility is actually guaranteed, even when a new step is added in the prediction horizon.
Study of the coupling between human head and cellular phone helical antennas

The interaction between normal-mode helical antennas and human head models is analyzed, using both a novel accurate semi-analytical method and finite-difference time-domain (FDTD) simulations. The semi-analytical method is based on the combination of Green's functions theory with the method of moments (Green/MoM) and is able to model arbitrarily shaped wire antennas radiating in the close proximity of layered lossy dielectric spheres representing simplified models of the human head. The purpose of the development of the Green/MoM technique is to provide a reliable tool for preliminary (worst case) estimation of human head exposure to the field generated by different antenna configurations with emphasis on the helical antenna, representing the most diffused antenna type used in modern cellular handsets. Furthermore, the accurate semi-analytical character of the Green/MoM technique permits the accuracy assessment of purely numerical techniques, such as the FDTD, which is currently the most widely used computational method in mobile communication dosimetric problems, since it allows modeling of anatomically based head models. After appropriate benchmarking, FDTD simulations are used to study the interaction between a heterogeneous anatomically correct model of the human head exposed to a normal-mode helix monopole operating at 1710 MHz mounted on the top of a metal box representing a realistic mobile communication terminal. The study of both canonical and realistic exposure problems includes computations of specific absorption rates (SARs) inside the human head, total power absorbed by the head and assessment of antenna performance. Emphasis is placed on the comparative dosimetric assessment between adults and children head models.
The cost of virtualization implementation in volunteer computing

The advantages of using virtualization can be impaired if it can not deliver sufficient performance. Running applications in virtualized environment incur performance overheads regarding to the virtualization functionalities like initialization virtual machine image, the booting time of virtual machine, starting, pausing and turning off the virtual machine. Virtualization functionality has implication on the host performance and when it is mixed with volunteer computing in order to undertake the execution of jobs, it becomes a serious challenge as volunteer computing aims to use public dedicated resources in an efficient manner to maximize the work done. In order to adopt virtualization technology in volunteer computing, the performance impact of virtualization on volunteer computing middleware needs to be distinguished. In this paper, we experimentally evaluate the virtualization functionalities overhead by comparing the job application execution in two scenarios: 1) executing job application in a virtualized environment by using vboxwrapper (The latest BOINC virtualization approach) and 2) executing job application directly on the host OS. Based on the result, virtualization fashion imposed up to 5 minutes pre-execution overhead when three jobs performed in parallel. The storage overhead ranged from 13% to 26%, depending on the number of jobs that are executing in parallel. This amount of overhead for memory ranged from 6.5% to 20%.
Morphological and functional reorganization of rat medial prefrontal cortex in neuropathic pain

Neuropathic pain is a chronic pain that results from lesion or dysfunction of the nervous system. Depression and cognitive decline are often coupled to chronic pain, suggesting the involvement of cortical areas associated with higher cognitive functions. We investigated layer 2/3 pyramidal neurons in acute slices of the contralateral medial prefrontal cortex (mPFC) in the rat spared nerve injury (SNI) model of neuropathic pain and found morphological and functional differences between the mPFC of SNI and sham-operated animals. Basal, but not apical, dendrites of neurons from SNI rats are longer and have more branches than their counterparts in sham-operated animals; spine density is also selectively increased in basal dendrites of neurons from SNI rats; the morphological changes are accompanied by increased contribution to synaptic currents of the NMDA component. Interestingly, the NMDA/AMPA ratio of the synaptic current elicited in mPFC neurons by afferent fiber stimulation shows linear correlation with the rats' tactile threshold in the injured (but not in the contralateral) paw. Our results not only provide evidence that neuropathic pain leads to rearrangement of the mPFC, which may help defining the cellular basis for cognitive impairments associated with chronic pain, but also show pain-associated morphological changes in the cortex at single neuron level.
Pilot-Aided Optical Signal-to-Noise Ratio Estimation for Direct-Detection OFDM Systems

We propose an optical signal-to-noise ratio (OSNR) estimation method for direct-detection optical orthogonal frequency division multiplexing (DDO-OFDM) systems by calculating the electrical SNR of one pilot subcarrier based on correlation. Simulation and experiment are conducted to verify this OSNR estimation method in a 15-Gb/s DDO-OFDM system. The maximum OSNR estimation error is 0.8 dB within an OSNR range of 8-28 dB for 100- and 200-km transmission distances.
Arterial and cardiac disease in young adults with childhood-onset end-stage renal disease-impact of calcium and vitamin D therapy.

BACKGROUND Studies in patients with childhood-onset end-stage renal disease (ESRD) provide a diagnostic window to the evolution of cardiovascular disease (CVD) in this population. Hyperphosphataemia and renal osteodystrophy are particularly difficult to treat in paediatric patients, but there is only limited information regarding the effect of calcium-containing phosphate binders and vitamin D preparations on the development of CVD in the young. METHODS We studied 40 adult patients (mean age 23.6 years) who developed ESRD at the age of 11.5 +/- 4 years and 40 matched healthy control subjects. Nine patients were on dialysis and 31 had a functioning kidney transplant. Measurements included intima-media thickness (IMT) of the common carotid artery, electron beam computed tomography (EBCT) for the detection of coronary artery calcifications (CAC), echocardiography and post-ischaemic arterial blood flow by venous occlusion plethysmography. Patient characteristics, atherosclerotic risk factors and a complete account of prescribed medications were analysed for correlations with arterial and cardiac changes. RESULTS The IMT was not significantly different in patients and controls; four patients (10%) had coronary calcifications on EBCT. Twenty-five patients (62.5%) had left ventricular hypertrophy. Patients had a 40% reduction of post-ischaemic arterial flow. Morphological alterations of the heart and arteries were significantly correlated with the duration of ESRD and dialysis time, and with the cumulative intake of calcium-containing phosphate binders and active vitamin D preparations. Functional changes (vascular reactivity) were correlated with duration of ESRD and non-traditional risk factors. CONCLUSIONS Young adults with ESRD since childhood have systemic CVD characterized by a decrease in arterial elasticity, the occurrence of CAC and changes in left ventricular morphology. Treatment with calcium-containing phosphate binders and active vitamin D preparations is independently associated in a dose-dependent manner with surrogate markers for CVD.
Preserved Catalytic Activity in an Engineered Ribonucleotide Reductase R2 Protein with a Nonphysiological Radical Transfer Pathway

A hydrogen-bonded catalytic radical transfer pathway in Escherichia coli ribonucleotide reductase (RNR) is evident from the three-dimensional structures of the R1 and R2 proteins, phylogenetic studies, and site-directed mutagenesis experiments. Current knowledge of electron transfer processes is difficult to apply to the very long radical transfer pathway in RNR. To explore the importance of the hydrogen bonds between the participating residues, we converted the protein R2 residue Asp237, one of the conserved residues along the radical transfer route, to an asparagine and a glutamate residue in two separate mutant proteins. In this study, we show that the D237E mutant is catalytically active and has hydrogen bond connections similar to that of the wild type protein. This is the first reported mutant protein that affects the radical transfer pathway while catalytic activity is preserved. The D237N mutant is catalytically inactive, and its tyrosyl radical is unstable, although the mutant can form a diferric-oxo iron center and a R1-R2 complex. The data strongly support our hypothesis that an absolute requirement for radical transfer during catalysis in ribonucleotide reductase is an intact hydrogen-bonded pathway between the radical site in protein R2 and the substrate binding site in R1. Our data thus strongly favor the idea that the electron transfer mechanism in RNR is coupled with proton transfer, i.e. a radical transfer mechanism.
The Interpretive Power of Infraorbital Foramen Area in Making Dietary Inferences in Extant Apes

The infraorbital foramen (IOF) is located below the orbit and transmits the sensory infraorbital nerve (ION) to mechanoreceptors located throughout the maxillary region. The size of the IOF correlates with the size of the ION; thus, the IOF appears to indicate relative touch sensitivity of maxillary region. In primates, IOF size correlates well with diet. Frugivores have relatively larger IOFs than folivores or insectivores because fruit handling/processing requires increased touch sensitivity. However, it is unknown if the IOF can be used to detect subtle dietary differences among closely related hominoid species. Hominoids are traditionally grouped into broad dietary categories, despite the fact that hominoid diets are remarkably diverse. This study examines whether relative IOF size is capable of differentiating among the dietary preferences of closely related species with overlapping, yet divergent diets. We measured IOF area in Hylobates lar, Symphalangus syndactulus, Pongo pygmaeus spp. , Pan troglodytes, Gorilla gorilla, Gorilla beringei graueri, and Gorilla beringei beringei. We classified each species as a dedicated folivore, mixed folivore/frugivore, soft object frugivore, or hard object frugivore. The IOF is documented to be larger in more frugivorous species and smaller in more folivorous taxa. Interestingly, G.b. beringei, had the largest relative IOF of any gorilla, despite being a dedicated folivore. G.b. beringei does have unique food processing behavior that relies heavily on maxillary mechanoreception, thus this finding is not entirely unsupported behaviorally. The results of this study provide evidence that the IOF is an informative feature in interpretations of fossil apes. Anat Rec, 297:1377–1384, 2014. © 2014 Wiley Periodicals, Inc.
Different types of ganglion cell in the cardiac plexus of guinea‐pigs.

1. Intracellular recordings were made from the parasympathetic ganglion cells that lie in the epicardium of the left atrium of guinea‐pig heart near the interatrial septum. 2. Three distinct types of neurone were identified on the basis of their electrophysiological properties. In one group of neurones, S cells, somatic action potentials were followed by brief after‐hyperpolarizations. In the other two sets of neurones, somatic action potentials were followed by prolonged after‐hyperpolarizations. The neurones with prominent after‐hyperpolarization were further subdivided: one group of neurones, P cells, showed inward rectification at membrane potentials near the resting membrane potential whilst neurones in the other group, SAH cells, did so only at more negative potentials. 3. In the group of neurones that displayed inward rectification at potentials near rest, rectification resulted from the activation of an inward current, which resembled the hyperpolarization‐activated inward current present in cardiac muscle pacemaker cells. 4. The three different types of neurone received different patterns of synaptic input. Each SAH cell received a synaptic excitatory connection from the vagus which in most cells released sufficient transmitter to initiate an action potential in that cell; several SAH cells also received a separate connection, which could be activated by local stimulation. Although most S cells failed to receive a synaptic input from the vagus, all of those tested received an excitatory synaptic input which could be activated by local stimulation. Virtually all P cells failed to receive a synaptic input from the vagus; in addition, local stimulation failed to initiate synaptic potentials in P cells. 5. When the structure of cardiac ganglion cells was determined, by loading the cells with either biocytin or neurobiotin, it was found that most cells lacked extensive dendritic processes. S cells were invariably monopolar, most P cells were dipolar or pseudodipolar, whereas many SAH cells were multipolar. 6. In many neurones an on‐going discharge of action potentials was detected in the absence of obvious stimulation. In S and SAH cells, the action potentials resulted from an on‐going discharge of excitatory synaptic potentials. However, when a spontaneous discharge of action potentials was detected in P cells a discharge of excitatory synaptic potentials was not detected. 7. The results are discussed in relation to the idea that the three different types of cell may have different functions and that some of the cells may be organized in such a way as to permit the local handling of neuronal information within the heart.
Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats

ABSTRACT Pathogenic biofilms have been associated with persistent infections due to their high resistance to antimicrobial agents, while commensal biofilms often fortify the host's immune system. Hence, controlling biofilm formation of both pathogenic bacteria and commensal bacteria is important in bacterium-related diseases. We investigated the effect of plant flavonoids on biofilm formation of enterohemorrhagic Escherichia coli O157:H7. The antioxidant phloretin, which is abundant in apples, markedly reduced E. coli O157:H7 biofilm formation without affecting the growth of planktonic cells, while phloretin did not harm commensal E. coli K-12 biofilms. Also, phloretin reduced E. coli O157:H7 attachment to human colon epithelial cells. Global transcriptome analyses revealed that phloretin repressed toxin genes (hlyE and stx 2), autoinducer-2 importer genes (lsrACDBF), curli genes (csgA and csgB), and dozens of prophage genes in E. coli O157:H7 biofilm cells. Electron microscopy confirmed that phloretin reduced fimbria production in E. coli O157:H7. Also, phloretin suppressed the tumor necrosis factor alpha-induced inflammatory response in vitro using human colonic epithelial cells. Moreover, in the rat model of colitis induced by trinitrobenzene sulfonic acid (TNBS), phloretin significantly ameliorated colon inflammation and body weight loss. Taken together, our results suggest that the antioxidant phloretin also acts as an inhibitor of E. coli O157:H7 biofilm formation as well as an anti-inflammatory agent in inflammatory bowel diseases without harming beneficial commensal E. coli biofilms.