gebhart/patrepeval huggingface dataset:
Neurofeedback fMRI‐mediated learning and consolidation of regional brain activation during motor imagery (2008)

Abstract We report the long‐term effect of real‐time functional MRI (rtfMRI) training on voluntary regulation of the level of activation from a hand motor area. During the performance of a motor imagery task of a right hand, blood‐oxygenation‐level‐dependent (BOLD) signal originating from a primary motor area was presented back to the subject in real‐time. Demographically‐matched individuals also received the same procedure without valid feedback information. Followed by the initial rtfMRI sessions, both groups underwent 2‐week long, daily‐practice of the task. Off‐line data analysis revealed that the individuals in the experimental group were able to increase the level of BOLD signal from the regulatory target to a greater degree compared with the control group. Furthermore, the learned level of activation was maintained after the 2‐week period, with the recruitment of additional neural circuitries such as the hippocampus and the limbo‐thalamo‐cortical pathway. The activation obtained from the control group, in the absence of proper feedback, was indifferent across the training conditions. The level of BOLD activity from the target regulatory region was positively correlated with a self evaluative score within the experimental group, while the majority of control subjects had difficulty adopting a strategy to attain the desired level of functional regulation. Our results suggest that rtfMRI helped individuals learn how to increase region‐specific cortical activity associated with a motor imagery task, and the level of increased activation in motor areas was consolidated after the 2‐week self‐practice period, with the involvement of neural circuitries implicated in motor skill learning. © 2008 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 18, 69–78, 2008
The Variational Fair Autoencoder (2016)

We investigate the problem of learning representations that are invariant to certain nuisance or sensitive factors of variation in the data while retaining as much of the remaining information as possible. Our model is based on a variational autoencoding architecture with priors that encourage independence between sensitive and latent factors of variation. Any subsequent processing, such as classification, can then be performed on this purged latent representation. To remove any remaining dependencies we incorporate an additional penalty term based on the "Maximum Mean Discrepancy" (MMD) measure. We discuss how these architectures can be efficiently trained on data and show in experiments that this method is more effective than previous work in removing unwanted sources of variation while maintaining informative latent representations.
Writing Stories with Help from Recurrent Neural Networks (2016)

This thesis explores the use of a recurrent neural network model for a novel story generation task. In this task, the model analyzes an ongoing story and generates a sentence that continues the story.
High-throughput method for analyzing methylation of CpGs in targeted genomic regions (2010)

A unique microarray-based method for determining the extent of DNA methylation has been developed. It relies on a selective enrichment of the regions to be assayed by target amplification by capture and ligation (mTACL). The assay is quantitatively accurate, relatively precise, and lends itself to high-throughput determination using nanogram amounts of DNA. The measurements using mTACLs are highly reproducible and in excellent agreement with those obtained by sequencing (r = 0.94). In the present work, the methylation status of >145,000 CpGs from 5,472 promoters in 221 samples was measured. The methylation levels of nearby CpGs are correlated, but the correlation falls off dramatically over several hundred base pairs. In some instances, nearby CpGs have very different levels of methylation. Comparison of normal and tumor samples indicates that in tumors, the promoter regions of genes involved in differentiation and signaling are preferentially hypermethylated, whereas those of housekeeping genes remain hypomethylated. mTACL is a platform for profiling the state of methylation of a large number of CpG in many samples in a cost-effective fashion, and is capable of scaling to much larger numbers of CpGs than those collected here.
Eddy currents in windings of switched reluctance machines (2008)

This thesis analyzes eddy currents in windings of switched reluctance machines. Since common design tools neglect these losses, the performance of new machine designs is often overestimated. To calculate the eddy current losses a complex two-dimensional finite element model is presented. The model can simulate any transient operating point, considering all relevant machine losses. An automated generation process allows the detailed modeling of any number of individual winding conductors. Besides the determination of converter, iron and copper losses the model also contains a new method to consider the so-called end-effects. Using the implemented finite element tool, the winding geometry of a traction machine is optimized. By changing the conductor dimensions, the losses are significantly reduced and efficiency accordingly increases. Based on numerous simulation results it is analyzed in how far analytic loss calculations are reasonable for switched reluctance machines. Finally, it is investigated to what extent the eddy currents influence the general electromagnetic machine behavior.
Hypoxia limits antioxidant capacity in red blood cells by altering glycolytic pathway dominance (2009)

The erythrocyte membrane is a newly appreciated platform for thiol-based circulatory signaling, and it requires robust free thiol maintenance. We sought to define physiological constraints on erythrocyte antioxidant defense. Hemoglobin (Hb) conformation gates glycolytic flux through the hexose monophosphate pathway (HMP), the sole source of nicotinamide adenine dinucleotide phosphate (NADPH) in erythrocytes. We hypothesized elevated intraerythrocytic deoxyHb would limit resilience to oxidative stress. Human erythrocytes were subjected to controlled oxidant (superoxide) loading following independent manipulation of oxygen tension, Hb conformation, and glycolytic pathway dominance. Sufficiency of antioxidant defense was determined by serial quantification of GSH, NADPH, NADH redox couples. Hypoxic erythrocytes demonstrated greater loss of reduction potential [Delta GSH E(hc) (mV): 123.4+/-9.7 vs. 57.2+/-11.1] and reduced membrane thiol (47.7+/-5.7 vs. 20.1+/-4.3%) (hypoxia vs. normoxia, respectively; P<0.01), a finding mimicked in normoxic erythrocytes after HMP blockade. Rebalancing HMP flux during hypoxia restored resilience to oxidative stress at all stages of the system. Cell-free studies assured oxidative loading was not altered by oxygen tension, heme ligation, or the inhibitors employed. These data indicate that Hb conformation controls coupled glucose and thiol metabolism in erythrocytes, and implicate hypoxemia in the pathobiology of erythrocyte-based vascular signaling.
Source Contribution Evaluation of Mechanical Vibration Signals via Enhanced Independent Component Analysis (2012)

Extraction of effective information from measured vibration signals is a fundamental task for the machinery condition monitoring and fault diagnosis. As a typical blind source separation (BSS) method, independent component analysis (ICA) is known to be able to effectively extract the latent information in complex signals even when the mixing mode and sources are unknown. In this paper, we propose a novel approach to overcome two major drawbacks of the traditional ICA algorithm: lack of robustness and source contribution evaluation. The enhanced ICA algorithm is established to escalate the separation performance and robustness of ICA algorithm. This algorithm repeatedly separates the mixed signals multiple times with different initial parameters and evaluates the optimal separated components by the clustering evaluation method. Furthermore, the source contributions to the mixed signals can also be evaluated. The effectiveness of the proposed method is validated through the numerical simulation and experiment studies.
Spatial registration for functional near-infrared spectroscopy: From channel position on the scalp to cortical location in individual and group analyses (2013)

Functional near-infrared spectroscopy (fNIRS) has now become widely accepted as a common functional imaging modality. In order for fNIRS to achieve genuine neuroimaging citizenship, it would ideally be equipped with functional and structural image analyses. However, fNIRS measures cortical activities from the head surface without anatomical information of the object being measured. In this review article, we will present a methodological overview of spatial registration of fNIRS data to overcome this technical drawback of fNIRS. We first introduce and explore the use of standard stereotaxic space and anatomical labeling. Second, we explain different ways of describing scalp landmarks using 10-20 based systems. Third, we describe the simplest case of fNIRS data co-registration to a subject's own MRI. Fourth, we extend the concept to fNIRS data registration of group data. Fifth, we describe probabilistic registration methods, which use a reference-MRI database instead of a subject's own MRIs, and thus enable MRI-free registration for standalone fNIRS data. Sixth, we further extend the concept of probabilistic registration to three-dimensional image reconstruction in diffuse optical tomography. Seventh, we describe a 3D-digitizer-free method for the virtual registration of fNIRS data. Eighth, we provide practical guidance on how these techniques are implemented in software. Finally, we provide information on current resources and limitations for spatial registration of child and infant data. Through these technical descriptions, we stress the importance of presenting fNIRS data on a common platform to facilitate both intra- and inter-modal data sharing among the neuroimaging community.
Effects of papillary muscles and trabeculae on left ventricular quantification: increased impact of methodological variability in patients with left ventricular hypertrophy (2008)

Established cardiac magnetic resonance methods yield differences in left ventricular quantification due to variable exclusion of papillary muscles and trabeculae from myocardium. The relative impact of papillary muscles and trabeculae exclusion on calculated mass and ejection fraction is increased among patients with hypertrophy-associated left ventricular remodeling.
An extension to the SCI flow control protocol for increased network efficiency (1996)

The scalable coherent interface (SCI) is a newly established IEEE standard that provides bus-like services to a network of nodes without actually using a physical bus. Rather, it utilizes very fast, unidirectional links that can be arranged into a variety of topologies. SCI provides a novel fairness protocol that equally allocates bandwidth to all nodes on the network. When global fairness is not required, it is often desirable to relax its enforcement, in exchange for increased network utilization and better load balancing. This paper presents an extension to the SCI flow control protocol that increases network utilization and, hence, attainable system throughput by enforcing fairness only among nodes whose transmissions interfere with one another. The enhanced protocol grants a node as much bandwidth as it requires, as long as its transmissions do not inhibit those of other nodes. Although this is commonly known as max-min fairness, we more descriptively refer to it as relaxed fairness. We present extensive simulation results and compare them to the standard SCI protocol and to our desired performance, which has been preciously derived in the literature. The comparisons show that, on average, this enhancement can provide a substantial increase in performance over the original protocol.
Comparison of methods for diagnosing bacterial vaginosis among pregnant women (1989)

The diagnosis of bacterial vaginosis is usually based on clinical criteria including homogeneous vaginal discharge, an elevated vaginal pH, the presence of clue cells, and an amine odor. We have evaluated the vaginal flora and clinical signs for 593 pregnant women. Gardnerella vaginalis, Bacteroides spp., and Mycoplasma hominis were isolated more frequently among women with clinical signs than among those without clinical signs of bacterial vaginosis in multivariable analyses that controlled for other bacteria. To determine the laboratory method that best predicted bacterial vaginosis, we calculated the sensitivity, specificity, and predictive value of positive and negative tests for Gram-stained vaginal smears, gas-liquid chromatography of vaginal fluid, and G. vaginalis cultures compared with clinical signs. G. vaginalis culture was sensitive (92%) and both gas-liquid chromatography (78%) and Gram-stained vaginal smears (62%) were moderately sensitive in identifying women with three of the four clinical signs of bacterial vaginosis. However, the Gram-stained vaginal smear (95%) was more specific than G. vaginalis culture (69%) or gas-liquid chromatography (81%). The predictive value of a positive test was also higher for the Gram staining (76%) than for G. vaginalis culture (41%) or gas-liquid chromatography (48%).
Preparation of cell nuclei from fresh tissues for high‐quality DNA flow cytometry (1993)

An easy method for preparation of bare cell nuclei from fresh solid tissues for DNA flow cytometry is described. Pieces of up to 2 x 2 x 2 mm3 size from fresh tissues were fixed in formalin. After removal of formalin by washing with ethanol and rehydration with tap water, the tissue pieces were incubated with subtilisin Carlsberg (pronase, Sigma protease XXIV) and then stained directly with DAPI. Staining with ethidium bromide gave unsatisfactory results. Neither mechanical disaggregation nor centrifugation were used. The resulting cell nucleus suspensions had extremely low frequencies of debris particles and of clumped cell nuclei. A good yield, a minimized loss, and a good stainability of cell nuclei were obtained. The applicability of the method was exemplified by the analysis of biopsies from the colon-rectum in patients with ulcerative colitis and of biopsies from the bladder in patients with bladder cancer and compared to the standard method of this laboratory, which uses mechanical disaggregation, ethanol fixation, pepsin treatment, and staining with ethidium bromide. The formalin-subtilisin Carlsberg technique resulted in good agreement of ploidy measurements compared to the standard method, a higher number of evaluable histograms, an improved detectability of aneuploid cell populations, and an improved accuracy of the S- and G2-phase analysis, particularly in samples with low proliferation. The method also makes it possible to use long-term storage and to transport samples by post.
Visually Imperceptible Liquid‐Metal Circuits for Transparent, Stretchable Electronics with Direct Laser Writing (2018)

A material architecture and laser-based microfabrication technique is introduced to produce electrically conductive films (sheet resistance = 2.95 Ω sq<sup>-1</sup> ; resistivity = 1.77 × 10<sup>-6</sup> Ω m) that are soft, elastic (strain limit >100%), and optically transparent. The films are composed of a grid-like array of visually imperceptible liquid-metal (LM) lines on a clear elastomer. Unlike previous efforts in transparent LM circuitry, the current approach enables fully imperceptible electronics that have not only high optical transmittance (>85% at 550 nm) but are also invisible under typical lighting conditions and reading distances. This unique combination of properties is enabled with a laser writing technique that results in LM grid patterns with a line width and pitch as small as 4.5 and 100 µm, respectively-yielding grid-like wiring that has adequate conductivity for digital functionality but is also well below the threshold for visual perception. The electrical, mechanical, electromechanical, and optomechanical properties of the films are characterized and it is found that high conductivity and transparency are preserved at tensile strains of ≈100%. To demonstrate their effectiveness for emerging applications in transparent displays and sensing electronics, the material architecture is incorporated into a couple of illustrative use cases related to chemical hazard warning.
Speech-picking for speech systems with auditory attention ability (2015)

Currently, a natural speech-picking mode is badly needed in speech communication and in human-computer interaction systems. However, speech is usually corrupted by attenuation, multi-path propagation, and various interferences before it is received, especially when there exist several speech systems and users. It is important for practical speech systems to pick the correct speech signal within complex environments. In this paper, the mechanism of auditory attention ability is simulated through a target speech-picking system in which the a priori knowledge of the target speech and interference of sound sources are used carefully to detect and improve the target speech. The technologies of microphone arrays, wake-up-words, target speech detection, speech enhancement, and dereverberation are combined in this strategy to ful ll the task of robust target speech-picking.
Historical films as reenactments of the past: A case study of 'The last emperor' (2014)

Recent decades have witnessed the proliferation of historical films by Hollywood. This is in part due to the growth of the interest in the past. This desire for an imagined, idyllic past of simplicity, order and virtue, which came to represent the essence of an antiquarian past 'contaminated' by modernisation and industrialisation, 'derive their nostalgic impetus' from the uncertainty resulting from a rapidly changing, globalised, post-Fordist, consumerist society'. Indeed, the box office success of films such as Titanic and Dances with Wolves lends credence to this craving for history by audiences. Both films won several Academy awards.
Virtual PCF: Improving VoIP over WLAN performance with legacy clients (2009)

Abstract\nVoice over IP (VoIP) is one of the fastest growing applications on the Internet.\nConcurrently, 802.11 Wireless LANs (WLANs) have become ubiquitous in residential, enterprise, campus and public networks. Currently the majority of traffic on\nWLANs is data traffic but as more people use wireless networks as their primary\naccess medium, a greater portion of traffic will be real-time traffic such as VoIP traffic. Unfortunately 802.11 networks are designed to handle delay-insensitive, bursty\ntraffic and perform poorly for VoIP streams. Experimental and analytical results\nhave shown that a single 802.11b access point operating at the maximum 11 Mbps\nrate can support only 5 to 10 VoIP connections simultaneously. Intuitively, an 11 Mbps link should support approximately 85 bi-directional 64Kbps (G.711) streams.\nThe reason for this under-utilization lies primarily in the Distributed Coordination\nFunction (DCF) used by 802.11 MAC layer. The problem can be addressed by using the optional Point Coordination Function (PCF). However PCF is not widely\nimplemented in commodity hardware nor likely to be. There is a similar problem\nwith the proposed 802.11e standard for quality of service. To solve these problems\nwe propose Virtual PCF, a legacy-client compatible solution to increase the number\nof simultaneous VoIP calls. We implement Virtual PCF, a scheme which employs\na variety of techniques to improve both uplink and downlink VoIP QoS. This alleviates delays and packet loss due to DCF contention and doubles the number of\nsupported VoIP sessions.
A 50–59 GHz CMOS Injection Locking Power Amplifier (2014)

The injection-locked power amplifier (ILPA) has demonstrated relatively high gain and high efficiency at millimeter-wave frequency. However, their application is still limited by its sensitivity to loading effect and narrow injection locking bandwidth. In this letter, a wide injection locking ILPA using buffered input and output has been proposed and implemented on 65 nm CMOS technology. The buffered input and output can improve the injection locking range and avoid load-to-tank pulling. The measured injection locking range is from 50 GHz to 59 GHz and the peak Power Added Efficiency (PAE) is 16.1% with a maximum output power of 11.39 dBm. Moreover, the die size is merely 260 μm×400 μm excluding pads.
Changes in the spectral powers of finger photoplethysmographic waveform variability in hemodialysis patients (2009)

This paper reports changes in the spectral powers of finger photoplethysmographic waveform variability (PPGV) following hemodialysis compared to pre-dialysis. The results are based on data collected from 12 hemodynamically stable patients having regular hemodialysis thrice weekly. Six minutes of continuous electrocardiogram (ECG) and finger infra-red photoplethysmographic (PPG) signals were collected at pre-dialysis and at end of dialysis. A four minute artefact free segment was selected and baseline and amplitude variabilities were derived from PPG waveform. Heart rate variability was derived from ECG R-R interval. Frequency spectrum analysis was then applied to these variability signals. The spectral powers were then calculated from low frequency (LF), mid frequency (MF) and high frequency (HF) bands. The results indicate that LF (p=0.01) and MF (p=0.02) powers of baseline PPGV (expressed in mean-scaled units) and LF (p=0.006), MF (p=0.003) and HF (p=0.017) powers of amplitude PPGV (expressed in mean-scaled units) showed a significant increase at the end of dialysis compared to pre-dialysis. HRV spectral measures did not show any significant change. The increase in LF and MF powers in PPGV may suggest the recovery and further enhancement of peripheral sympathetic vascular modulation as a result of volume unloading in initially hypervolemic dialysis patients, at the same time the increase in respiratory HF power in PPGV may indicate preload reduction.
Improved photosynthetic capacity and photosystem I oxidation via heterologous metabolism engineering in cyanobacteria (2021)

Cyanobacteria must prevent imbalances between absorbed light energy (source) and the metabolic capacity (sink) to utilize it to protect their photosynthetic apparatus against damage. A number of photoprotective mechanisms assist in dissipating excess absorbed energy, including respiratory terminal oxidases and flavodiiron proteins, but inherently reduce photosynthetic efficiency. Recently, it has been hypothesized that some engineered metabolic pathways may improve photosynthetic performance by correcting source/sink imbalances. In the context of this subject, we explored the interconnectivity between endogenous electron valves, and the activation of one or more heterologous metabolic sinks. We coexpressed two heterologous metabolic pathways that have been previously shown to positively impact photosynthetic activity in cyanobacteria, a sucrose production pathway (consuming ATP and reductant) and a reductant-only consuming cytochrome P450. Sucrose export was associated with improved quantum yield of phtotosystem II (PSII) and enhanced electron transport chain flux, especially at lower illumination levels, while cytochrome P450 activity led to photosynthetic enhancements primarily observed under high light. Moreover, coexpression of these two heterologous sinks showed additive impacts on photosynthesis, indicating that neither sink alone was capable of utilizing the full "overcapacity" of the electron transport chain. We find that heterologous sinks may partially compensate for the loss of photosystem I (PSI) oxidizing mechanisms even under rapid illumination changes, although this compensation is incomplete. Our results provide support for the theory that heterologous metabolism can act as a photosynthetic sink and exhibit some overlapping functionality with photoprotective mechanisms, while potentially conserving energy within useful metabolic products that might otherwise be "lost."