gebhart/patrepeval huggingface dataset:
Model-observer based quality measures for decomposed medical images (2005)

This paper provides the fundamental basis for model observers on decompressed images by the understanding of compression noise statistics. In medical applications, model observers have been successfully used to predict human observer performance and to empirically evaluate image quality for detection tasks on various backgrounds. To derive closed-form expressions for model observers, however, requires closed-form expressions for noise statistics. This paper views a decompressed image as the sum of the original image and compression noise. The statistics of compression noise depend on the compression algorithms. One of the most efficient image compression techniques is transform coding, on which the JPEG image compression standard is based. By analyzing transform coding, this paper derives probability density functions (PDF), and the first and second moments of compression noise. Those statistics are used to derive closed-form representations for the ideal and channelized Hotelling observers on decompressed images. It provides the closed-form decompressed image quality measurements in terms of model observer performance.
A comparison between multi-channel audio equalization filters using warping (2004)

Typically, room equalization techniques do not focus on designing filters that equalize the room responses at perceptually relevant frequencies. Thus, by performing Bark warping of the room responses and using lower order spectral models, it is possible to design low order psycho-acoustically motivated equalization filters. We compare the performance, through experiments, between the traditional RMS averaging filter (with and without warping to the Bark scale) and our pattern recognition based multiple listener equalization filter with warping (Bharitkar, S. and Kyriakakis, C., Proc. 36th Asilomar Conf. on Signals, Systems and Computers, 2002). It is shown that our pattern recognition filter, using warping, outperforms the RMS averaging filter (with and without warping to the Bark scale).
Rational Design of a New Trypanosoma rangeli Trans-Sialidase for Efficient Sialylation of Glycans (2014)

This paper reports rational engineering of Trypanosoma rangeli sialidase to develop an effective enzyme for a potentially important type of reactivity: production of sialylated prebiotic glycans. The Trypanosoma cruzi trans-sialidase and the homologous T. rangeli sialidase has previously been used to investigate the structural requirements for trans-sialidase activity. We observed that the T. cruzi trans-sialidase has a seven-amino-acid motif (197-203) at the border of the substrate binding cleft. The motif differs substantially in chemical properties and substitution probability from the homologous sialidase, and we hypothesised that this motif is important for trans-sialidase activity. The 197-203 motif is strongly positively charged with a marked change in hydrogen bond donor capacity as compared to the sialidase. To investigate the role of this motif, we expressed and characterised a T. rangeli sialidase mutant, Tr13. Conditions for efficient trans-sialylation were determined, and Tr13's acceptor specificity demonstrated promiscuity with respect to the acceptor molecule enabling sialylation of glycans containing terminal galactose and glucose and even monomers of glucose and fucose. Sialic acid is important in association with human milk oligosaccharides, and Tr13 was shown to sialylate a number of established and potential prebiotics. Initial evaluation of prebiotic potential using pure cultures demonstrated, albeit not selectively, growth of Bifidobacteria. Since the 197-203 motif stands out in the native trans-sialidase, is markedly different from the wild-type sialidase compared to previous mutants, and is shown here to confer efficient and broad trans-sialidase activity, we suggest that this motif can serve as a framework for future optimization of trans-sialylation towards prebiotic production.
A single non‐invasive model to diagnose non‐alcoholic fatty liver disease (<scp>NAFLD</scp>) and non‐alcoholic steatohepatitis (<scp>NASH</scp>) (2014)

The ION model was superior in predicting NASH and mortality compared with the FLI model. Studies are needed to validate ION.
A novel CRIg‐targeted complement inhibitor protects cells from complement damage (2014)

The inappropriate activation of complement may contribute to various immune diseases. The alternative pathway (AP) predominates during complement activation regardless of the initiating pathways. Hence, the main AP regulator factor H (FH) holds great potential as an attractive therapeutic intervention. In addition, complement receptor of the immunoglobulin superfamily (CRIg) has been demonstrated to inhibit AP and, more notably, still specifically binds to C3b/iC3b. We thus developed novel CRIg-targeted complement inhibitors by connecting the functional domains of CRIg and FH, which we termed CRIg-FH and CRIg-L-FH. CRIg-L-FH, slightly more potent than CRIg-FH, considerably inhibited both AP- and also classical pathway (CP)-mediated hemolysis and successfully eliminated the deposition of C3b/iC3b. Kinetic analysis further revealed that the binding affinity constant (KD) of CRIg/FH was in the micromolar range, consistent with its long-lasting binding to complement-attacked cells. CRIg-L-FH efficiently protected aberrant erythrocytes of patients with paroxysmal nocturnal hemoglobinuria (PNH) from AP- and CP-mediated complement damage (IC50 was 22.43 and 64.69 nM, respectively). Moreover, CRIg-L-FH was found to inhibit complement activation induced by the anti-Thy1 antibody in a mesangioproliferative glomerulonephritis (MPGN) rat model. Hence, CRIg-L-FH protects glomerular mesangial cells (GMCs) from complement-mediated injury and proliferative lesions. These findings strongly suggest that CRIg/FH is a potential therapeutic drug candidate for a range of complement-mediated diseases.
<title>Real-time motion detection using an analog VLSI zero-crossing chip</title> (1991)

The authors have designed and tested a one-dimensional 64 pixel, analog CMOS VLSI chip which localizes intensity edges in real-time. This device exploits on-chip photoreceptors and the natural filtering properties of resistive networks to implement a scheme similar to and motivated by the Difference of Gaussians (DOG) operator proposed by Marr and Hildreth (1980). The chip computes the zero-crossings associated with the difference of two exponential weighting functions and reports only those zero-crossings at which the derivative is above an adjustable threshold. A real-time motion detection system based on the zero- crossing chip and a conventional microprocessor provides linear velocity output over two orders of magnitude of light intensity and target velocity.
Establishment of human embryonic stem cell lines from frozen-thawed blastocysts using STO cell feeder layers (2004)

This study indicates that establishment of hES cells from frozen-thawed blastocysts minimizes the ethical problem associated with the use of human embryos in research and that the STO cell feeder layer can be used for the culture of hES cells.
Polymerase chain reaction for detection of invasive Shigella flexneri in food (1990)

The polymerase chain reaction (PCR) was used to amplify a 760-base-pair (bp) fragment with the 220-kbp invasive plasmids of enteroinvasive Escherichia coli, Shigella flexneri, Shigella dysenteriae, Shigella boydii, and Shigella sonnei as templates. This PCR product was easily detected by agarose gel electrophoresis. A 210-bp AccI-PstI fragment lying within the amplified region was used as a probe in Southern hybridization blots and showed that the PCR-generated product was derived from the invasive plasmid. The application of PCR as a rapid method to detect enteroinvasive bacteria in foods was tested by inoculating lettuce with 10(4) S. flexneri cells per g in shigella broth base. Plasmid DNA was isolated from cultures of inoculated and uninoculated lettuce in broth after 0, 4, and 24 h of incubation. With the PCR, the 760-bp fragment was generated only from lettuce inoculated with S. flexneri, as shown by gel electrophoresis and confirmed both by Southern blotting and by nucleotide sequencing of the amplified region. Because the isolation of plasmid DNA, the performance of PCR, and gel electrophoresis all can be completed in 6 to 7 h, invasive enteric bacteria can be detected in less than 1 day.
Development of low-loss IR transmitting chalcogenide glass fibers (1995)

We have fabricated long lengths of low loss sulphide and telluride glass fibers for the 1 - 6 and 3 - 12 micrometers regions, respectively. Minimum losses for core/clad fibers are approximately 0.6 and 0.7 dB/m, respectively, while core-only fibers have exhibited losses of about 0.1 dB/m. The measurements have been performed on long lengths, typically 7 - 50 meters. Fiber strengths are reasonable for many short length applications, but improved processing will lead to stronger fibers for long length applications. These fibers are candidates for chemical sensors and for IR laser power delivery.
Rapid communication A trafficking defective, Brugada syndrome-causing SCN5A mutation rescued by drugs (2004)

Background: The human cardiac SCN5A gene encodes for the a subunit of the human cardiac voltage-dependent sodium channel hNav1.5 [Neuron 28 (2) (2000) 365] and carries inward Na current (INa). Mutations in SCN5A cause arrhythmia syndromes including Brugada syndrome (BrS) and congenital long QT syndrome subtype 3 (LQT3). Here, we report a trafficking defective BrS-causing SCN5A mutation that was drug-rescued. Methods and Results: A 14-year-old Caucasian male was diagnosed with BrS with typical ECG pattern for BrS and ventricular fibrillation was easily induced. He also had significant HV interval delay (f65 ms) and high (31 J) defibrillation thresholds (DFTs). Genomic analysis revealed the SCN5A mutation (G1743R). We engineered G1743R into the cardiac Na channel and transfected HEK-293 cells for functional studies. The mutant channel yielded nearly undetectable sodium channel currents. Coexpression with the h1 subunit, or incubation at low temperature did not increase current density. However, mexiletine, a sodium channel blocker, increased current density 93-fold in G1743R, but only twofold in WT. Conclusions: This study identifies an expression-defective BrS mutation in SCN5A with pharmacological rescue. The profoundly decreased sodium current associated with the G1743R suggests a molecular basis for the delayed His-Purkinje conduction and elevated DFTs observed in the proband. Whether the mutant channel may be rescued in vivo by mexiletine and normalize the patient’s electrophysiologic parameters remains to be tested.
An Immunogenic <i>Onchocerca volvulus</i> Antigen: a Specific and Early Marker of Infection (1991)

Onchocerciasis (river blindness) is a serious health problem and a severe obstacle to social and economic development, especially in Africa. A complementary DNA fragment coding for an Onchocerca volvulus antigen (OV-16) was cloned and expressed in the plasmid vector pCG808fx. Immune responses to this O. volvulus-specific recombinant antigen were detectable in patients with documented onchocerciasis; the antibody response was also detectable at 3 months and at more than 1 year before infection could otherwise be detected in humans and in chimpanzees experimentally infected with O. volvulus third-stage larvae.
High-Performance Servo Channel for Nanometer Head Positioning and Longitudinal Position Symbol Detection in Tape Systems (2015)

In a tape system, the core of the reel-to-reel and track-following servomechanisms is the servo channel, which processes the servo signal generated by a servo reader reading a timing-based servo pattern. The servo channel estimates essential servo parameters, including tape velocity, head lateral position, and longitudinal tape position. The achievable precision of the various estimates determines how densely data can be placed on tape. In this paper, the architecture and the design of a high-performance synchronous servo channel (SSC) are presented. The channel performance is evaluated by means of analytical bounds on the estimation error, simulations, and experimental results, which demonstrate that the proposed servo channel is instrumental to achieve head positioning with nanometer accuracy and reliable detection of longitudinal position information in tape systems. Methods for the estimation of servo parameters with enhanced precision and of dynamic tape-to-head skew by dual SSCs operating on adjacent servo bands are also presented and their performance evaluated.
Automatic Vertebra Labeling in Large-Scale 3D CT using Deep Image-to-Image Network with Message Passing and Sparsity Regularization (2017)

Automatic localization and labeling of vertebra in 3D medical images plays an important role in many clinical tasks, including pathological diagnosis, surgical planning and postoperative assessment. However, the unusual conditions of pathological cases, such as the abnormal spine curvature, bright visual imaging artifacts caused by metal implants, and the limited field of view, increase the difficulties of accurate localization. In this paper, we propose an automatic and fast algorithm to localize and label the vertebra centroids in 3D CT volumes. First, we deploy a deep image-to-image network (DI2IN) to initialize vertebra locations, employing the convolutional encoder-decoder architecture together with multi-level feature concatenation and deep supervision. Next, the centroid probability maps from DI2IN are iteratively evolved with the message passing schemes based on the mutual relation of vertebra centroids. Finally, the localization results are refined with sparsity regularization. The proposed method is evaluated on a public dataset of 302 spine CT volumes with various pathologies. Our method outperforms other state-of-the-art methods in terms of localization accuracy. The run time is around 3 seconds on average per case. To further boost the performance, we retrain the DI2IN on additional 1000+ 3D CT volumes from different patients. To the best of our knowledge, this is the first time more than 1000 3D CT volumes with expert annotation are adopted in experiments for the anatomic landmark detection tasks. Our experimental results show that training with such a large dataset significantly improves the performance and the overall identification rate, for the first time by our knowledge, reaches 90 %.
Cell Therapy for Cardiovascular Regeneration (2013)

A great numbers of cardiovascular disease patients all over the world are suffering in the poor outcomes. Under this situation, cardiac regeneration therapy to reorganize the postnatal heart that is defined as a terminal differentiated-organ is a very important theme and mission for human beings. However, the temporary success of several clinical trials using usual cell types with uncertain cell numbers has provided the transient effect of cell therapy to these patients. We therefore should redevelop the evidence of cell-based cardiovascular regeneration therapy, focusing on targets (disease, patient's status, cardiac function), materials (cells, cytokines, genes), and methodology (transplantation route, implantation technology, tissue engineering). Meanwhile, establishment of the induced pluripotent stem (iPS) cells is an extremely innovative technology which should be proposed as embryonic stem (ES) cellularization of post natal somatic cells, and this application have also showed the milestones of the direct conversion to reconstruct cardiomyocyte from the various somatic cells, which does not need the acquisition of the re-pluripotency. This review discusses the new advance in cardiovascular regeneration therapy from cardiac regeneration to cardiac re-organization, which is involved in recent progress of on-going clinical trials, basic research in cardiovascular regeneration, and the possibility of tissue engineering technology.
Compact, high average power, fiber-pumped terahertz source for active real-time imaging of concealed objects (2007)

We have modeled and demonstrated a scalable, compact, fiber-pumped terahertz source based on difference frequency mixing (DFM) in zinc germanium phosphide (ZGP) capable of producing high average and peak-power pulses. Currently, our terahertz source produces 2 mW of average THz power and >40 W of peak power with sub-nanosecond pulses at a repetition rate of 100 kHz in the range of 2-3 THz without cryogenic cooling or ultra-fast optics. This high average power laser-based terahertz output enables the real-time imaging of concealed objects using an off-the-shelf uncooled microbolometer focal-plane array. With this THz system, we have imaged objects obscured inside in a common shipping envelope, demonstrating the potential of compact laser-based terahertz sources for use in security screening applications.
Degradation of cocaine by a mixed culture of Pseudomonas fluorescens MBER and Comamonas acidovorans MBLF (1996)

A mixed culture that could utilize cocaine as the sole source of carbon and energy for growth was isolated by selective enrichment. The individual microorganisms within this mixed culture were identified as Pseudomonas fluorescens (termed MBER) and Comamonas acidovorans (termed MBLF). Each microorganism was shown to be unable to grow to any appreciable extent on 10 mM cocaine in the absence of the other. C. acidovorans MBLF was found to possess an inducible cocaine esterase which catalyzed the hydrolysis of cocaine to ecgonine methyl ester and benzoate. C. acidovorans was capable of growth on benzoate at concentrations below 5 mM but was unable to metabolize ecgonine methyl ester. P. fluorescens MBER was capable of growth on either benzoate as the sole source of carbon or ecgonine methyl ester as the sole source of carbon and nitrogen. P. fluorescens MBER was found to initiate the degradation of ecgonine methyl ester via ecgonine, pseudoecgonine, and pseudoecgonyl-coenzyme A. Subcellular studies resulted in the identification of an ecgonine methyl esterase, an ecgonine epimerase, and a pseudoecgonyl-coenzyme A synthetase which were induced by growth on ecgonine methyl ester or ecgonine. Further metabolism of the ecgonine moiety is postulated to involve nitrogen debridging, with the production of carbonyl-containing intermediates.
An anti-TL1A antibody for the treatment of asthma and inflammatory bowel disease (2018)

TL1A is an attractive therapeutic target for the treatment of mucosal inflammation associated with inflammatory bowel disease (IBD) and asthma. Blockade of the TL1A pathway has been shown to reduce inflammatory responses while leaving baseline immunity intact, and to be beneficial in animal models of colitis and asthma. Given the therapeutic potential of blocking this pathway in IBD and asthma, we developed C03V, a human antibody that binds with high affinity to soluble and membrane-bound TL1A. In an assay measuring apoptosis induced by exogenous TL1A, C03V was 43-fold more potent than the next most potent anti-TL1A antibody analyzed. C03V also potently inhibited endogenous TL1A activity in a primary cell-based assay. This potency was linked to the C03V-binding epitope on TL1A, encompassing the residue R32. This residue is critical for the binding of TL1A to its signaling receptor DR3 but not to its decoy receptor DcR3, and explains why C03V inhibited TL1A-DR3 binding to a much greater extent than TL1A-DcR3 binding. This characteristic may be advantageous to preserve some of the homeostatic functions of DcR3, such as TL1A antagonism. In colitis models, C03V significantly ameliorated microscopic, macroscopic and clinical aspects of disease pathology, and in an asthma model it significantly reduced airways inflammation. Notable in both types of disease model was the reduction in fibrosis observed after C03V treatment. C03V has the potential to address unmet medical needs in asthma and IBD.
Hourglass schemes (2012)

We consider the following challenge: How can a cloud storage provider prove to a tenant that it's encrypting files at rest, when the provider itself holds the corresponding encryption keys? Such proofs demonstrate sound encryption policies and file confidentiality. (Cheating, cost-cutting, or misconfigured providers may bypass the computation/management burdens of encryption and store plaintext only.)
Acoustic diode (2012)

Usually, waves can travel just as easily in either direction along a given path. The invention of electric diode, which acts as a one-way filter for the current flux, has marked the beginning of modern electronics and eventually led to worldwide revolutions in many aspects. Similar devices also exist for light and heat transmission. However, it is much more difficult to make such one-way devices for sound waves, another important form of classical wave with even longer research history than electric waves, because of the way sound waves move though a material. Recently, the first model of “acoustic diode” has been demonstrated both theoretically and experimentally to allow the acoustic energy to flow in only one direction. This device was fabricated by coupling a superlattice with a layer of ultrasound contrast agent microbubble suspension. A significant rectifying effect could be observed within two frequency bands at locations that agreed well with theoretical predictions. The development of the “acoustic diode” prototype will inspire the interests and investigations in the more practical and efficient acoustic rectifiers, which should have substantial significance for the applications of ultrasound devices in many practical areas such as medical ultrasound therapy and high resolution imaging.
High efficiency coronary MR angiography with nonrigid cardiac motion correction (2016)

Purpose To improve the coronary visualization quality of four‐dimensional (4D) coronary MR angiography (MRA) through cardiac motion correction and iterative reconstruction. Methods A contrast‐enhanced, spoiled gradient echo sequence with 3D radial trajectory and self‐gating was used for 4D coronary MRA data acquisition at 3 Tesla. A whole‐heart 16‐phase cine series was reconstructed with respiratory motion correction. Nonrigid registration was performed between the identified quiescent phases and a reference. The motion information of all included phases was then used along with the corresponding k‐space data to iteratively reconstruct the final image. Healthy volunteer studies (N = 13) were conducted to compare the proposed method with the conventional strategy, which accepts data from a single, contiguous window out of the original 16‐phase data. Apparent signal‐to‐noise ratio (aSNR) and coronary sharpness were used as the image quality metrics. Results The proposed method significantly improved aSNR (11.89 ± 3.76 to 13.97 ± 5.21; P = 0.005) and scan efficiency (18.8% ± 6.0% to 40.9% ± 9.7%; P < 0.001), compared with the conventional strategy. Sharpness of left main ( P = 0.002), proximal ( P = 0.04), and middle ( P = 0.02) right coronary artery, and proximal left anterior descending ( P = 0.04) was also significantly improved. Conclusion The proposed cardiac motion‐corrected reconstruction significantly improved the achievable quality of coronary visualization from 4D coronary MRA. Magn Reson Med 76:1345–1353, 2016. © 2016 International Society for Magnetic Resonance in Medicine