gebhart/patrepeval huggingface dataset:
Fully Automatic Left Ventricle Segmentation in Cardiac Cine MR Images Using Registration and Minimum Surfaces (2009)

This paper describes a fully automatic system to segment the left ventricle in all slices and all phases of a magnetic resonance cardiac cine study. After localizing the left ventricle blood pool using motion, thresholding and clustering, slices are segmented sequentially. For each slice, deformable registration is used to align all the phases, candidate contours are recovered in the average image using shortest paths, and a minimal surface is built to generate the final contours. The advantage of our method is that the resulting contours follow the edges in each phase and are consistent over time. As part of the MICCAI grand challenge on left ventricle segmentation, we demonstrate using 15 training datasets and 15 validation datasets that the results are very good with average errors around 2 mm and the method is ready for clinical routine.
Real-Time Data Quality Analysis (2020)

Data quality is critically important for big data and machine learning applications. Data quality systems can analyze data sets for quality and detection of potential errors. They can also provide remediation to fix problems encountered in analyzing data sets. This paper discusses key features that of data quality analysis systems. We also present new algorithms for efficiently maintaining updated data quality metrics on changing data sets. Our algorithms consider anomalies in data regions in determining how much different regions of data contribute to overall data metrics. We also make intelligent choices of which data metrics to update and how frequently to do so in order to limit the overhead for data quality metric updates.
Synthetic Social Media Data Generation (2018)

This paper presents a novel system, synthetic high-fidelity social media data generator (SHIELD), for generating the synthetic social media data. SHIELD jointly generates time-varying, directed and weighted interaction graph structures and topic-driven text features similar to the input social media data. A synthetic interaction graph is generated by a social network model to minimize the distance to real graph and is enhanced by adding various patterns, such as anomalies and information cascades, interaction types, and temporal dynamics. A synthetic text generator based on the <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$n$ </tex-math></inline-formula> -gram Markov model is trained under each topic identified by topic modeling. Synthetic text and graph structures are combined through the assignment of synthetic social media entities. Extensive performance evaluation via a graph and text analysis is provided to demonstrate the statistical fidelity of large-scale synthetic data generated by SHIELD. A data evaluation exercise with human participants is executed to identify how difficult it is for a human to distinguish between tweets that were generated by SHIELD and tweets that were posted by real users. Experimental results followed by a statistical significance analysis showed that human participants cannot reliably distinguish between real and synthetic tweets.
In vivo non-invasive monitoring of dystrophin correction in a new Duchenne muscular dystrophy reporter mouse (2019)

Duchenne muscular dystrophy (DMD) is a fatal genetic disorder caused by mutations in the dystrophin gene. To enable the non-invasive analysis of DMD gene correction strategies in vivo, we introduced a luciferase reporter in-frame with the C-terminus of the dystrophin gene in mice. Expression of this reporter mimics endogenous dystrophin expression and DMD mutations that disrupt the dystrophin open reading frame extinguish luciferase expression. We evaluated the correction of the dystrophin reading frame coupled to luciferase in mice lacking exon 50, a common mutational hotspot, after delivery of CRISPR/Cas9 gene editing machinery with adeno-associated virus. Bioluminescence monitoring revealed efficient and rapid restoration of dystrophin protein expression in affected skeletal muscles and the heart. Our results provide a sensitive non-invasive means of monitoring dystrophin correction in mouse models of DMD and offer a platform for testing different strategies for amelioration of DMD pathogenesis.
Gesture connect (2007)

The Gesture Connect system streamlines the process of connecting to and/or controlling objects from a user's personal mobile device. Typically, in order to connect two devices together they users must follow a two-step process that consists of first selecting which devices should be connected, and then specifying what the devices should do once they are connected. By combining contact-based connections with gesture-based selection, the Gesture Connect system combines these two steps into a single physical action for simple actions, greatly simplifying the common case. In order to demonstrate and test the underlying concept, a hardware extension comprising Near Field Communication (NFC) and accelerometer capability has been developed for standard commercial mobile phone devices, along with the associated tagging and gesture recognition software. This system greatly reduces overall interaction time for common-case interaction, enhancing the overall user experience.
Poly(Vinyl Alcohol) (Core)-Polyurethane (Shell) Nanofibers Produced by Coaxial Electrospinning (2016)

Nanoweb fabricated by electrospinning has a large specific area and a small pore size which can be controlled through a spinning process to enable a strong adsorption and selective permeability. It is required to produce nanofiber of different polymer mixture with a limited miscibility for improvement of physical, chemical, or biological properties. In this study, poly (vinyl alcohol) (PVA)/polyurethane (PU) nanofibers were produced by coaxial electrospinning. PVA (core)/PU (shell) nanofibers were defect-free and had a uniform thickness. The pseudo core/shell structure of PVA/PU nanofibers was confirmed by transmission electron microscopy. The presence of PVA and PU in the nanofibers was identified by 13 C solid state nuclear magnetic resonance spectroscopy, fourier transform infrared spectroscopy, and X-ray diffraction analysis. Water contact angle was reduced by incorporation of PVA in a core of PU nanofiber. For variety of biomedical applications, bioactive substances such as antibiotics and proteins can be incorporated in a core of hydrophobic PU nanofiber by coaxial electrospinning of water-soluble polymer/bioactive substance mixture.
Biodegradation of Degradable Plastic Polyethylene by <i>Phanerochaete</i> and <i>Streptomyces</i> Species (1991)

The ability of lignin-degrading microorganisms to attack degradable plastics was investigated in pure shake flask culture studies. The degradable plastic used in this study was produced commercially by using the Archer-Daniels-Midland POLYCLEAN masterbatch and contained pro-oxidant and 6% starch. The known lignin-degrading bacteria Streptomyces viridosporus T7A, S. badius 252, and S. setonii 75Vi2 and fungus Phanerochaete chrysosporium were used. Pro-oxidant activity was accelerated by placing a sheet of plastic into a drying oven at 70 degrees C under atmospheric pressure and air for 0, 4, 8, 12, 16, or 20 days. The effect of 2-, 4-, and 8-week longwave UV irradiation at 365 nm on plastic biodegradability was also investigated. For shake flask cultures, plastics were chemically disinfected and incubated-shaken at 125 rpm at 37 degrees C in 0.6% yeast extract medium (pH 7.1) for Streptomyces spp. and at 30 degrees C for the fungus in 3% malt extract medium (pH 4.5) for 4 weeks along with an uninoculated control for each treatment. Weight loss data were inconclusive because of cell mass accumulation. For almost every 70 degrees C heat-treated film, the Streptomyces spp. demonstrated a further reduction in percent elongation and polyethylene molecular weight average when compared with the corresponding uninoculated control. Significant (P < 0.05) reductions were demonstrated for the 4- and 8-day heat-treated films by all three bacteria. Heat-treated films incubated with P. chrysosporium consistently demonstrated higher percent elongation and molecular weight average than the corresponding uninoculated controls, but were lower than the corresponding zero controls (heat-treated films without 4-week incubation). The 2- and 4-week UV-treated films showed the greatest biodegradation by all three bacteria. Virtually no degradation by the fungus was observed. To our knowledge, this is the first report demonstrating bacterial degradation of these oxidized polyethylenes in pure culture.
Physical and genetic map of the Lactobacillus sakei 23K chromosome The GenBank accession numbers for the sequences reported in this paper are given in Table 2 and the legend to Fig. 3. (2002)

The Lactobacillus sakei 23K chromosome was analysed by pulsed-field gel electrophoresis after digestion with the restriction enzymes AscI, NotI and SfiI. The chromosome size was estimated to be 1845+/-80 kb. The use of I-CeuI, specific for rrn genes encoding 23S rRNAs, showed that seven rrn loci were present, on 40% of the chromosome. The seven rrn clusters were mapped and their orientation was determined, allowing the position of the replication origin to be estimated. Partial I-CeuI digestions were used to construct a backbone and the different restriction fragments obtained with AscI, NotI and SfiI were assembled to a physical map by Southern hybridization. Eleven L. sakei gene clusters previously identified were mapped, as well as 25 new loci located randomly on the chromosome and 11 regions flanking the rrn gene clusters. A total of 47 clusters were thus mapped on L. sakei chromosome. The new loci were sequenced, allowing the identification of 73 complete or incomplete coding sequences. Among these 73 new genes of L. sakei, the function of 36 could be deduced from their similarity to known genes described in databases. However, 10 genes had no homologues, 10 encoded proteins similar to proteins of unknown function and 17 were similar to hypothetical proteins.
Treatment of Diabetes and Obesity by Rationally Designed Peptide Agonists Functioning at Multiple Metabolic Receptors (2017)

Obesity and its comorbidities such as type 2 diabetes constitute major worldwide health threats, and the identification of an effective medical intervention has emerged as a global priority. The limited effectiveness of historical, anti-obesity treatments is commonly attributed to the complexity of the disease and the redundancy of metabolic regulatory mechanisms that sustain body weight. At the forefront of obesity research is the development of combinational drug therapies that simultaneously target multiple regulatory pathways, which promote dysfunctional metabolism. Recently, molecularly crafted unimolecular "multi-agonism" of balanced activity at 3 key receptors involved in metabolism and specifically the glucagon-like peptide (GLP)-1 receptor, glucose-dependent insulinotropic polypeptide (GIP) receptor and glucagon receptor was reported as superior to conventional monoagonist therapy. These mixed peptide agonists are designed to pharmacologically integrate the insulinotropic and anorexigenic effects of GLP-1, the thermogenic and lipolytic activities of glucagon, and the insulinotropic and insulin sensitizing properties of GIP. The molecular mechanism of these purposefully promiscuous ligands is not completely understood, however, recent studies in pancreatic beta cells point to the prospect of a complex signaling network that can magnify the signaling of multi-agonist ligands. The activation of this signalosome might explain the additional therapeutic benefit inherent to simultaneous cellular activation through multiple metabolic receptors.
Red‐Light‐Induced Cationic Photopolymerization: Perylene Derivatives as Efficient Photoinitiators (2013)

Nine different perylene derivatives are prepared and their ability to initiate, when combined with an iodonium salt (and optionally N-vinylcarbazole), a ring-opening cationic photopolymerization of epoxides under very soft halogen lamp irradiation is investigated. One of them is particularly efficient under a red laser diode exposure at 635 nm and belongs now to the very few systems available at this wavelength. The photochemical mechanisms are studied by steady-state photolysis, electron spin resonance spin trapping, fluorescence, cyclic voltammetry, and laser flash photolysis techniques.
Jointly optimal near-end and far-end multi-microphone speech intelligibility enhancement based on mutual information (2016)

The processing required for the global maximization of the intelligibility of speech acquired by multiple microphones and rendered by a single loudspeaker, is considered in this paper. The intelligibility is quantized, based on the mutual information rate between the message spoken by the talker and the message as interpreted by the listener. We prove that then, in each of a set of narrow-band channels, the processing can be decomposed into a minimum variance distortionless response (MVDR) beamforming operation that reduces the noise in the talker environment, followed by a gain operation that, given the far-end noise and beamforming operation, accounts for the noise at the listener end. Our experiments confirm that both processing steps are necessary for the effective conveyance ofa message and, importantly, that the second step must be aware of the first step.
Microstructures and Mechanical Properties of Highly Electrically Conductive Cu&ndash;0.5, Cu&ndash;1 and Cu&ndash;2 at%Zr Alloy Wires (2012)

Hypoeutectic Cu–Zr binary alloys have originally been studied in order to develop wires with both high strengths and high electrical conductivities. This study aimed to improve the electrical conductivities of Cu–0.5, Cu–1 and Cu–2 at% Zr alloys, which have Zr contents lower than those of high-strength Cu–3, Cu–4 and Cu–5 at% Zr alloys. Cast rod samples, whose lengths and diameters were 180 and 12 mm, respectively, were prepared by copper-mold casting and wire-drawn to diameters in the range of 1–0.031 mm (drawing ratio, η = 4.8–11.1). The microstructures and mechanical properties of the obtained wires were investigated and compared to those of Cu–3, Cu–4 and Cu–5 at%Zr alloy wires that had been investigated in a previous study.The eutectic phases found in the cast rods consisted of α-Cu primary phases and phases of the intermetallic compound Cu5Zr. The eutectic phases became isolated, like small islands, in the matrices, and their volume fractions decreased with a decrease in the Zr content. The orientations of the α-Cu and Cu5Zr phases around the boundaries of these eutectic phases were similar. After the wiredrawing process, the intermetallic compound in the eutectic phases transformed into Cu9Zr2 in the case of the Cu–0.5 at%Zr alloy and into Cu8Zr3 in the case of the Cu–1 at%Zr alloy. The electrical conductivity (EC) and ultimate tensile strength (UTS) values of the alloys depended on the volume fractions of their eutectic phases. However, the changes in these properties with the change in the drawing ratio were smaller than those in the case of the high-strength Cu–3, Cu–4 and Cu5 at%Zr alloy wires. The EC and UTS values of the Cu–0.5, Cu–1 and Cu–2 at%Zr alloy wires drawn at values of η greater than 8.0 were 61–83% IACS (International Annealed Copper Standard) and 690–1010 MPa, respectively. When combined together, wires of the resulting hypoeutectic Cu–Zr binary alloy exhibited EC and UTS values of 16–83% IACS and 690–2234 MPa, respectively. These results showed that instead of there being a tradeoff between these properties, the values of both these properties increased at the same time.
Measuring frequency and quality of pathogen-specific T cells (2016)

Abstract The frequency and functional activity of pathogen-specific T cells reflect the effectiveness of immune responses. We have developed an assay to measure the frequency and efficacy of antigen-specific CD8 T cells. The assay measures changes of intracellular Ca2+ in real time by fluorescent microscopy in individual CD8 T cells, which are immobilized on a glass surface to form a monolayer enabling the cells to present cognate peptides to each other. The T cells were labeled with Ca2+ dependent fluorophore, and intracellular fluorescence in the cells was analyzed before and after stimulation with specific antigenic peptides. Subtraction of the fluorescent intensity measured prior and after the stimulation revealed responding T cells and the kinetics of intracellular Ca2+ accumulation. The proposed assay permits comparison of the same cell before and after stimulation providing a significant increase in the sensitivity and utility of the assay. We found that as little as 3–5 responding T cells among 1×104 CD8 T cells could be reliably detected and that as much as 100 T cells with different specificities could be identified in a single round of analysis. We utilized the assay to characterize the frequency and quality of human cytomegalovirus-specific CD8 T cells from peripheral blood of healthy donors and patients who underwent haploidentical stem cell transplantation. The data revealed potential diagnostic and prognostic values of the proposed assay.
Pneumococcal surface protein A (PspA) family distribution among clinical isolates from adults over 50 years of age collected in seven countries (2006)

The pneumococcal surface protein PspA, a cell-wall-associated surface protein, is a promising component for pneumococcal vaccines. In this study, the distribution of the PspA family was determined in a panel of invasive and clinically important pneumococcal isolates from adults over 50 years of age, collected between 1995 and 2002. One thousand eight hundred and forty-seven recent isolates from invasive pneumococcal disease were obtained from seven Western countries, together with clinical data. An ELISA-based serological method was standardized in order to determine the PspA family and clade distribution. Molecular tests were used when isolates were non-typable by ELISA (PspA family typing by PCR). Only 42 (2.3 %) isolates were non-typable by ELISA and PspA family typing by PCR was performed. Finally, 3 isolates were considered as non-pneumococcal and 1844 were classified as follows: 749 (40.6 %) were PspA family 1, 1078 (58.5 %) were PspA family 2, 13 (0.7 %) were PspA family 1 and 2 and 4 (0.2 %) remained non-typable. The cross-reactivity of antibodies to PspAs of different clades was confirmed. In conclusion, inclusion of PspA family 1 and family 2 in future pneumococcal vaccines would ensure broad coverage of pneumococcal strains infecting people over 50 years of age.
A polymerase chain reaction-enzyme-linked immunosorbent assay method for detecting human papillomavirus in cervical carcinomas and high-grade cervical cancer precursors (1995)

The PCR-ELISA-based HPV detection provides the potential for an automated, rapid, and sensitive test for cervical cancer and high-grade cervical lesions.
Computer Aided Detection for Pulmonary Embolism Challenge (CAD-PE) (2020)

Rationale: Computer aided detection (CAD) algorithms for Pulmonary Embolism (PE) algorithms have been shown to increase radiologists' sensitivity with a small increase in specificity. However, CAD for PE has not been adopted into clinical practice, likely because of the high number of false positives current CAD software produces. Objective: To generate a database of annotated computed tomography pulmonary angiographies, use it to compare the sensitivity and false positive rate of current algorithms and to develop new methods that improve such metrics. Methods: 91 Computed tomography pulmonary angiography scans were annotated by at least one radiologist by segmenting all pulmonary emboli visible on the study. 20 annotated CTPAs were open to the public in the form of a medical image analysis challenge. 20 more were kept for evaluation purposes. 51 were made available post-challenge. 8 submissions, 6 of them novel, were evaluated on the 20 evaluation CTPAs. Performance was measured as per embolus sensitivity vs. false positives per scan curve. Results: The best algorithms achieved a per-embolus sensitivity of 75% at 2 false positives per scan (fps) or of 70% at 1 fps, outperforming the state of the art. Deep learning approaches outperformed traditional machine learning ones, and their performance improved with the number of training cases. Significance: Through this work and challenge we have improved the state-of-the art of computer aided detection algorithms for pulmonary embolism. An open database and an evaluation benchmark for such algorithms have been generated, easing the development of further improvements. Implications on clinical practice will need further research.
Reduced field of view single‐shot spiral perfusion imaging (2017)

Purpose To develop a single‐shot spiral perfusion pulse sequence with outer‐volume suppression (OVS) to achieve whole‐heart coverage with a short temporal footprint of 10 ms per slice location. Methods A highly accelerated single‐shot variable density spiral pulse sequence with an integrated OVS module for reduced field of view (rFOV) perfusion imaging with 2 mm spatial resolution was developed and evaluated in simulations, phantom experiments and in clinical patients with (n = 8) or without (n = 8) OVS. Images were reconstructed by block low‐rank sparsity with motion guidance (BLOSM) and graded by two cardiologists on a 5‐point scale (1, excellent; 5, poor). Results Simulation and phantom results showed that OVS effectively suppressed the signal outside the desired field of view (FOV). Clinical patient data demonstrated high quality perfusion images with rFOV. The average image quality scores of full FOV cases and rFOV cases were 3.1 ± 0.64 and 2.3 ± 0.46, respectively, ( P = 0.02) from cardiologist 1 and 2.5 ± 0.54 and 1.8 ± 0.47, respectively, ( P = 0.04) from cardiologist 2, showing superior image quality for the rFOV images compared with the full FOV images. Conclusion A single‐shot spiral perfusion sequence that uses OVS and BLOSM performs perfusion imaging with a very short temporal footprint per image supporting whole‐heart coverage with good image quality. Magn Reson Med 79:208–216, 2018. © 2017 International Society for Magnetic Resonance in Medicine.