gebhart/patrepeval huggingface dataset:
Applications of strategically acquired gradient echo imaging to neurodegenerative diseases (2022)

Background: One major thrust in radiology today is image standardization with a focus on rapid, quantitative, multi-contrast data collection and processing. Methods: Strategically acquired gradient echo (STAGE) imaging1-4 is one such method that uses multiple flip angles and multiple echo times. It can provide 8 qualitative and 7 quantitative images as well as transmit field B1 transmit field and B1 receive field maps in 4-6 minutes or less on a 3T magnetic resonance (MR) scanner. STAGE provides qualitative images in the form of proton density-weighted images, T1 weighted images and T2* weighted images. STAGE provides quantitative data in the form of proton spin density (PSD), T1, T2* and susceptibility maps as well as segmentation of white matter, gray matter and cerebrospinal fluid via simulated double inversion recovery (sDIR) images. STAGE has been tested using the NIST phantom and yields intrasubject errors of only 1-2% and intrasubject variation of 2 to 5%. Contrast-to-noise ratio (CNR) measurements show that the T1WE images are comparable to the conventional T1W MP-RAGE images. Today these quantitative measures are providing new biomarkers for imaging a variety of neurodegenerative diseases (Figure 1). Results: During the last few years, we have focused on measuring iron content and neuromelanin (NM) in the substantia nigra (SN) for comparing idiopathic Parkinson’s disease (PD) with healthy controls and patients with other movement disorders. We have found that the volume of NM, the iron content of the SN, the volume of the SN and the N1 sign all together can provide an area under the curve of 95% in distinguishing PD from healthy controls.5 We have developed a template of the midbrain to allow for automatic detection and quantification of these properties. We use tSWI to enhance the N1 sign visibility. We have also used STAGE to study multiple sclerosis (MS) lesions. QSM can be used to map changes in white matter susceptibility and potentially correlated with demyelination. We provide a composite image using tSWI combined with fluid-attenuated inversion recovery (FLAIR) to highlight those lesions that are purely inflammatory from inflammatory demyelinating lesions. Recently we have begun to study the use of absolute water content as a measure of lesion atrophy. Higher water content means a higher likelihood of tissue damage. This also explains why the presence of “black holes” seen in T1W images of MS patients tends to correlate with the expanded disability status score. Conclusions: In summary, STAGE provides a comprehensive clinical imaging protocol that, combined with diffusion-weighted imaging (DWI) and FLAIR, can yield a standardized 10-minute (3T) o 15-minute (1.5T) imaging protocol of the entire brain across all manufacturers.
Synergistic anticryptosporidial potential of the combination alpha-1-antitrypsin and paromomycin (1997)

The combined effect of the serine protease inhibitor alpha-1-antitrypsin (AAT) and the aminoglycoside paromomycin on Cryptosporidium parvum infection in vitro was investigated. AAT and paromomycin were mixed with C. parvum oocysts as either single or combined treatments and used to inoculate epithelial cell cultures. Single- and combined-treatment groups had significantly lower (P < 0.01) parasite numbers than untreated controls. The mean fractional inhibitory concentration indices suggested significant synergistic activity.
Long-wavelength, InAsSb strained-layer superlattice photovoltaic infrared detectors (1989)

Long-wavelength infrared photodiodes were fabricated using InAs/sub 1-x/Sb/sub x//InSb (x=0.82-0.85) strained-layer superlattices (SLSs). These structures can be grown using either molecular-beam epitaxy or metalorganic chemical vapor deposition. These photodiodes display broad spectral responses up to wavelengths greater than or approximately equal to 10 mu m, and detectivities of 1*10/sup 9/ cm-Hz/sup 1/2//W at 10 mu m.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Hybrid Electro-Plasmonic Neural Stimulation with Visible-Light-Sensitive Gold Nanoparticles (2020)

Biomedical prosthetics utilizing electrical stimulation have limited, effective spatial resolution due to spread of electrical currents to surrounding tissue, causing nonselective stimulation. So, precise spatial resolution is not possible for traditional neural prosthetic devices, such as cochlear implants. More recently, alternative methods utilize optical stimulation, mainly infrared, sometimes paired with nanotechnology for stimulating action potentials. Infrared stimulation has its own drawbacks, as it may cause collateral heating of surrounding tissue. In previous work, we employed a plasmonic method for stimulation of an electrically excitable neuroblastoma cell line, which had limited success. Here, we report the development of a hybrid electro-plasmonic stimulation platform for spatially and temporally precise neural excitation to address the above deficiencies. Primary trigeminal neurons were costimulated <i>in vitro</i> in a whole-cell patch-clamp configuration with subthreshold-level short-duration (1-5 ms) electrical and visible light pulses (1-5 ms). The visible light pulses were aimed at a gold-nanoparticle-coated nanoelectrode placed alongside the neuron, within 2 μm distance. Membrane action potentials were recorded with a 3-fold higher success rate and 5-fold better poststimulation cell recovery rate than with pure optical stimulation alone. Also, electrical stimulus current input was being reduced by up to 40%. The subthreshold levels of electrical stimuli in conjunction with visible light (532 nm) reliably triggered trains of action potentials. This single-cell hybrid activation was reliable and repeatable, without any damage as observed with pure optical stimulation. This work represents an empirical cellular study of the membrane action potential response produced by the cultured primary sensory trigeminal neurons when costimulated with plasmonic and electrical (hybrid) stimulation. Our hybrid neurostimulation method can be used toward development of high-acuity neural modulation prosthetic devices, tunable for individual needs, which would qualify as a preferred alternative over traditional electrical stimulation technologies.
A frequency error resistant blind interference-mitigating CDMA detector (2002)

This paper presents an enhanced version of the previously-proposed blind adaptive interference detector (BAID) for direct-sequence code division multiple access (DS-CDMA) transmission. Such a new detector, named extended complex BAID (EC-BAID), reveals resistance to a possible large frequency shift (e.g., Doppler shift) on interfering carriers, and features invariance to the phase error on the useful channel's carrier. The EC-BAID is also shown to bear a sensitivity to residual carrier frequency errors on the desired channel which is lower by three orders of magnitude with respect to the data-aided minimum mean square error (DA-MMSE) receiver. The performance of the EC-BAID was numerically assessed by computer simulations and successfully compared to analytical findings under a variety of system configurations. It turned out that the EC-BAID, despite its blind operating mode, bears an uncoded symbol error rate (SER) performance that closely approaches the DA-MMSEs. Finally, a few implementation aspects of the new interference-mitigating detector are also discussed.
High-energy cast Pr-Fe-B magnets (1988)

A new process has been developed to produce high-energy bulk Pr-Fe-B magnets directly from the melt without the handling of magnetic powder or powderlike ribbons. The process mainly consists of only three steps—casting/hot pressing/annealing—and minimizes the oxygen contamination of magnets. A typical composition of cast alloy is Pr17 Fe76.5 B5 Cu1.5 . Using this type of alloy, a magnetic alignment is easily introduced by hot pressing. Copper plays two important roles: high coercivity and excellent magnetic alignment are achieved simultaneously by the addition of copper. Magnetic properties of hot-pressed Pr17 Fe76.5 B5 Cu1.5 magnets are as follows: Br=12.5 kG, i Hc =10.0 kOe, and (BH)max =36.2 MGOe. The cast alloy of this composition also has an i Hc of 7.4 kOe and a (BH)max of 8.8 MGOe after annealing at 1000 °C for 24 h. The steep rise in the initial magnetization curve indicates a type of nucleation-controlled coercivity mechanism.
Recovery of frequency-sparse signals from compressive measurements (2010)

Compressive sensing (CS) is a new approach to simultaneous sensing and compression for sparse and compressible signals. While the discrete Fourier transform has been widely used for CS of frequency-sparse signals, it provides optimal sparse representations only for signals with components at integral frequencies. There exist redundant frames that provide compressible representations for frequency-sparse signals, but such frames are highly coherent and severely affect the performance of standard CS recovery. In this paper, we show that by modifying standard CS recovery algorithms to prevent coherent frame elements from being present in the signal estimate, it is possible to bypass the shortcomings introduced by the coherent frame. The resulting algorithm comes with theoretical guarantees and is shown to perform significantly better for frequency-sparse signal recovery than its standard counterparts. The algorithm can also be extended to similar settings that use coherent frames.
Cross lingual text classification by mining multilingual topics from wikipedia (2011)

This paper investigates how to effectively do cross lingual text classification by leveraging a large scale and multilingual knowledge base, Wikipedia. Based on the observation that each Wikipedia concept is described by documents of different languages, we adapt existing topic modeling algorithms for mining multilingual topics from this knowledge base. The extracted topics have multiple types of representations, with each type corresponding to one language. In this work, we regard such topics extracted from Wikipedia documents as universal-topics, since each topic corresponds with same semantic information of different languages. Thus new documents of different languages can be represented in a space using a group of universal-topics. We use these universal-topics to do cross lingual text classification. Given the training data labeled for one language, we can train a text classifier to classify the documents of another language by mapping all documents of both languages into the universal-topic space. This approach does not require any additional linguistic resources, like bilingual dictionaries, machine translation tools, or labeling data for the target language. The evaluation results indicate that our topic modeling approach is effective for building cross lingual text classifier.
Molecular Cloning and Characterization of a cDNA Encoding the Third Putative Mammalian Hyaluronan Synthase (1997)

We report the isolation of a cDNA encoding the third putative hyaluronan synthase, HAS3. Partial cDNAs and genomic fragments of mouse Has3 were obtained using a degenerate polymerase chain reaction approach. Partial clones facilitated the isolation of genomic and cDNA clones representing the mouse Has3 open reading frame. The open reading frame of 554 amino acids predicted a protein of 63.3 kDa with multiple transmembrane domains and several consensus HA binding motifs. Sequence comparisons indicated that mouse Has3 is most closely related to Has2 (71% amino acid identity) and also related to Has1 (57% identity), Xenopus laevis DG42 (56% identity), and Streptococcus pyogenes HasA (28% identity). Isolation of a genomic fragment of human HAS3 indicated high conservation between mouse and human sequences, similar to those observed for HAS1 and HAS2. Expression of the mouse Has3 open reading frame in transfected COS-1 cells led to high levels of hyaluronan synthesis, as determined through a classical particle exclusion assay, and by in vitro HA synthase assays. These results suggest that there are three putative mammalian hyaluronan synthases encoded by three separate but related genes which comprise a mammalian hyaluronan synthase (HAS) gene family.
BPEL4WS unit testing: framework and implementation (2008)

The Business Process Execution Language for Web Services (BPEL4WS) offers a new standards-based approach to building flexible business processes by orchestrating multiple Web Services. Unit testing is critical to guarantee the creation of correct and reliable BPEL4WS business processes. Yet, this is a topic that is still to be explored, both in research and industry. Lack of unit test tooling support has affected BPEL4WS process development in terms of quality and efficiency. This paper proposes a BPEL4WS unit test framework, which includes a BPEL4WS process composition model, a test architecture, a lifecycle management schema, a test design outline and a test adequacy/coverage criterion. An example implementation of the framework illustrates the whole approach. By adopting this test framework, the experience of developing, testing and debugging a BPEL4WS processes will be greatly improved.
Microfluidic formation of lipid bilayer array for membrane transport analysis (2008)

We present a highly parallel and reproducible method for reconstituting an array of lipid bilayers to analyze membrane transport. We infuse buffer/lipid/buffer solutions sequentially into a microchannel with numerous microchambers in its walls and seal each chamber by a lipid bilayer containing membrane proteins. Due to the small volume of the chamber (2 pL), membrane transport of confined fluorescent molecules across the bilayer through the proteins is readily observed as changes in fluorescent intensity. We successfully perform quantitative measurement of the transport flux of fluorescent molecules (Calcein) through α-Hemolysin antibiotic pores.
Photorealistic Facial Texture Inference Using Deep Neural Networks (2017)

We present a data-driven inference method that can synthesize a photorealistic texture map of a complete 3D face model given a partial 2D view of a person in the wild. After an initial estimation of shape and low-frequency albedo, we compute a high-frequency partial texture map, without the shading component, of the visible face area. To extract the fine appearance details from this incomplete input, we introduce a multi-scale detail analysis technique based on mid-layer feature correlations extracted from a deep convolutional neural network. We demonstrate that fitting a convex combination of feature correlations from a high-resolution face database can yield a semantically plausible facial detail description of the entire face. A complete and photorealistic texture map can then be synthesized by iteratively optimizing for the reconstructed feature correlations. Using these high-resolution textures and a commercial rendering framework, we can produce high-fidelity 3D renderings that are visually comparable to those obtained with state-of-the-art multi-view face capture systems. We demonstrate successful face reconstructions from a wide range of low resolution input images, including those of historical figures. In addition to extensive evaluations, we validate the realism of our results using a crowdsourced user study.
Property-based design of a glucosylceramide synthase inhibitor that reduces glucosylceramide in the brain (2011)

Synthesis inhibition is the basis for the treatment of type 1 Gaucher disease by the glucosylceramide synthase (GCS) inhibitor eliglustat tartrate. However, the extended use of eliglustat and related compounds for the treatment of glycosphingolipid storage diseases with CNS manifestations is limited by the lack of brain penetration of this drug. Property modeling around the D-threo-1-phenyl-2-decanoylamino-3-morpholino-propanol (PDMP) pharmacophore was employed in a search for compounds of comparable activity against the GCS but lacking P-glycoprotein (MDR1) recognition. Modifications of the carboxamide N-acyl group were made to lower total polar surface area and rotatable bond number. Compounds were screened for inhibition of GCS in crude enzyme and whole cell assays and for MDR1 substrate recognition. One analog, 2-(2,3-dihydro-1H-inden-2-yl)-N-((1R,2R)-1-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-1-hydroxy-3-(pyrrolidin-1-yl)propan-2-yl)acetamide (CCG-203586), was identified that inhibited GCS at low nanomolar concentrations with little to no apparent recognition by MDR1. Intraperitoneal administration of this compound to mice for 3 days resulted in a significant dose dependent decrease in brain glucosylceramide content, an effect not seen in mice dosed in parallel with eliglustat tartrate.
Provable Fast Greedy Compressive Summarization with Any Monotone Submodular Function (2018)

Shinsaku Sakaue, Tsutomu Hirao, Masaaki Nishino, Masaaki Nagata. Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers). 2018.
Context-aware packet switching in ad hoc networks (2008)

We present the design and performance of a new approach to packet switching for MANETs, which we call context aware protocol engines (CAPE). With CAPE, nodes disseminate information in the network by means of context-aware packet switching that enables the statistical multiplexing of bandwidth, processing and storage resources using integrated signaling covering channel access, routing and other functions, to share and store the context within which information is disseminated. Data packet headers consist of simple pointers to their context, and elections and opportunistic reservations integrated with routing are used to attain high throughput and low channel-access delay.
Gene Transfer of Drug Resistance Genes Implications for Cancer Therapy (1994)

Two general approaches to the gene therapy of cancer have been proposed: (1) strategies that use exogenous genes to modify cancer cells so that they are less malignant or more susceptible to host defenses or to killing by exogenous agents; and (2) approaches that modify host cells so that they are more effective in eliminating cancer cells or more resistant to agents that are used to treat cancer. In both cases, the development of vectors that encode in vivo selectable phenotypes, such as drug resistance, would be extremely valuable because of the inherent inefficiency of gene transfer and the potential of such vectors to protect normal tissues against toxic agents. To allow the selection of cells in vivo that have been transduced with vectors for gene therapy, we have utilized the human multidrug resistance (MDR1) gene. The product of this gene is a 170,000-dalton glycoprotein known as P-glycoprotein, which acts as an energy-dependent efflux pump for a great many cytotoxic anticancer drugs, including doxorubicin, daunorubicin, etoposide, teniposide, actinomycin D, and taxol. Vectors encoding an MDR1 cDNA are able to transduce many cell types, including bone marrow cells, with high efficiency to allow selection of drug resistance in vitro and in vivo in mouse models. Thus, it should be possible to protect the bone marrow of patients undergoing intensive chemotherapy by transduction of their bone marrow with MDR1 vectors. Furthermore, the ability to select for the presence of the MDR1 cDNA in vivo means that it can be used to introduce otherwise nonselectable genes into the bone marrow for therapy of cancer and other diseases.
Development and application of computed tomography in the inspection of reinforced concrete (2004)

As an alternative, THASA has developed, improved beyond the previous state-of-the-art, and applied over a decade, Reinforced Concrete Tomography (RCT), a non-destructive inspection technique of the highest precision, based on the use of gamma-rays. This technique has found a wide range of practical applications in buildings, bridges, under-water pillars, oil-filled ducts, statues and tunnels involving well over a thousand inspected structural elements. Beneficiaries of this technology are primarily civil engineers who are responsible for issuing technical reports on the condition of structures and need data to base their reports on. Port, highway and railway authorities rely on this technology to meet maintenance requirements. Construction companies interested in quality controlling the work of subcontractors, insurance companies and landowners are also beneficiaries of this technology. The ultimate beneficiary is the general public, through safety improvements of buildings and other structures, and also through less disruption, no noise and absolute cleanliness during the inspection procedures. An important initial motivation for the development of RCT was a tragedy that took place in 1992 at a beach resort on the Atlantic shore, 250 miles south of Buenos Aires. Four young people were killed when a balcony in a high-rise building where they were standing broke off. The ensuing investigation showed that just about every kind of malpractice was present: insufficient number of rebars of appropriate size, severe corrosion due to chlorine in the unwashed sand from the beach used in the construction of these balconies and steel bars placed too low. It was disturbing that there was no technical solution to detect these defects in balconies. RCT now provides the most complete answer to these kinds of problems.
An On-Line Chinese Character Recognition System (1981)

This paper describes an experimental system for the on-line recognition of handwritten Chinese characters. Constituent shapes of the characters are recognized as they are formed on an electronic tablet. The 72 constituent shapes can define a very large set of Chinese characters. The implementation described recognizes more than 2200 Chinese characters. More symbols can be added with relative ease. Experimental results are given for two writer populations.
Intrinsic frequency for a systems approach to haemodynamic waveform analysis with clinical applications (2014)

The reductionist approach has dominated the fields of biology and medicine for nearly a century. Here, we present a systems science approach to the analysis of physiological waveforms in the context of a specific case, cardiovascular physiology. Our goal in this study is to introduce a methodology that allows for novel insight into cardiovascular physiology and to show proof of concept for a new index for the evaluation of the cardiovascular system through pressure wave analysis. This methodology uses a modified version of sparse time-frequency representation (STFR) to extract two dominant frequencies we refer to as intrinsic frequencies (IFs; ω1 and ω2). The IFs are the dominant frequencies of the instantaneous frequency of the coupled heart + aorta system before the closure of the aortic valve and the decoupled aorta after valve closure. In this study, we extract the IFs from a series of aortic pressure waves obtained from both clinical data and a computational model. Our results demonstrate that at the heart rate at which the left ventricular pulsatile workload is minimized the two IFs are equal (ω1 = ω2). Extracted IFs from clinical data indicate that at young ages the total frequency variation (Δω = ω1 - ω2) is close to zero and that Δω increases with age or disease (e.g. heart failure and hypertension). While the focus of this paper is the cardiovascular system, this approach can easily be extended to other physiological systems or any biological signal.