gebhart/patrepeval huggingface dataset:
Segmentation of myocardium using velocity field constrained front propagation (2003)

We present a velocity-constrained front propagation approach for myocardium segmentation from magnetic resonance intensity image (MRI) and its matching phase contrast velocity (PCV) images. Our curve evolution criterion is dependent on the prior probability distribution of the myocardial boundary and the conditional boundary probability distribution, which is constructed from the MRI intensity gradient, the PCV magnitude, and the local phase coherence of the PCV direction. A two-step boundary finding strategy is employed to facilitate the computation. For the first image frame, a gradient-only fast marching/level set step is used to approach the boundary, and a narrowband is formed around the curve. The initial boundary is then refined using the full information from priors and all three image sources. For the other frames, the resulting contours from the previous frames are used as the initialization contours, and only refinement step is needed. Experiment results from canine MRI sequence are presented, and are compared to results from gradient-only segmentation.
Spectral analysis of speech by linear prediction (1973)

The autocorrelation method of linear prediction is formulated in the time, autocorrelation, and spectral domains. The analysis is shown to be that of approximating the short-time signal power spectrum by an all-pole spectrum. The method is compared with other methods of spectral analysis such as analysis-by-synthesis and cepstral smoothing. It is shown that this method can be regarded as another method of analysis-by-synthesis where a number of poles is specified, with the advantages of noniterative computation and an error measure which leads to a better spectral envelope fit for an all-pole spectrum. Compared to spectral analysis by cepstral smoothing in conjunction with the chirp z transform (CZT), this method is expected to give a better spectral envelope fit (for an all-pole spectrum) and to be less sensitive to the effects of high pitch on the spectrum. The normalized minimum error is defined and its possible usefulness as a voicing detector is discussed.
LSMR: An Iterative Algorithm for Sparse Least-Squares Problems (2011)

An iterative method LSMR is presented for solving linear systems $Ax=b$ and least-squares problems $\min \|Ax-b\|_2$, with A being sparse or a fast linear operator. LSMR is based on the Golub–Kahan bidiagonalization process. It is analytically equivalent to the MINRES method applied to the normal equation $A^T\! Ax = A^T\! b$, so that the quantities $\|A^T\! r_k\|$ are monotonically decreasing (where $r_k = b - Ax_k$ is the residual for the current iterate $x_k$). We observe in practice that $\|r_k\|$ also decreases monotonically, so that compared to LSQR (for which only $\|r_k\|$ is monotonic) it is safer to terminate LSMR early. We also report some experiments with reorthogonalization.
Efficient Semitransparent Solar Cells with High NIR Responsiveness Enabled by a Small‐Bandgap Electron Acceptor (2017)

Inspired by the remarkable promotion of power conversion efficiency (PCE), commercial applications of organic photovoltaics (OPVs) can be foreseen in near future. One of the most promising applications is semitransparent (ST) solar cells that can be utilized in value-added applications such as energy-harvesting windows. However, the single-junction STOPVs utilizing fullerene acceptors show relatively low PCEs of 4%-6% due to the limited sunlight absorption because it is a dilemma that more photons need to be harvested in UV-vis-near-infrared (NIR) region to generate high photocurrent, which leads to the significant reduction of device transparency. This study describes the development of a new small-bandgap electron-acceptor material ATT-2, which shows a strong NIR absorption between 600 and 940 nm with an E<sub>g</sub><sup>opt</sup> of 1.32 eV. By combining with PTB7-Th, the as-cast OPVs yield PCEs of up to 9.58% with a fill factor of 0.63, an open-circuit voltage of 0.73 V, and a very high short-circuit current of 20.75 mA cm<sup>-2</sup> . Owing to the favorable complementary absorption of low-bangap PTB7-Th and small-bandgap ATT-2 in NIR region, the proof-of-concept STOPVs show the highest PCE of 7.7% so far reported for single-junction STOPVs with a high transparency of 37%.
Human Nerve Growth Factor Protects Common Marmosets against Autoimmune Encephalomyelitis by Switching the Balance of T Helper Cell Type 1 and 2 Cytokines within the Central Nervous System (2000)

Multiple sclerosis is a demyelinating disorder of the central nervous system (CNS), in which an immune attack directed against myelin constituents causes myelin destruction and death of oligodendrocytes, the myelin-producing cells. Here, the efficacy of nerve growth factor (NGF), a growth factor for neurons and oligodendrocytes, in promoting myelin repair was evaluated using the demyelinating model of experimental allergic encephalomyelitis (EAE) in the common marmoset. Surprisingly, we found that NGF delayed the onset of clinical EAE and, pathologically, prevented the full development of EAE lesions. We demonstrate by immunocytochemistry that NGF exerts its antiinflammatory effect by downregulating the production of interferon gamma by T cells infiltrating the CNS, and upregulating the production of interleukin 10 by glial cells in both inflammatory lesions of EAE and normal-appearing CNS white matter. Thus, NGF, currently under investigation in human clinical trials as a neuronal trophic factor, may be an attractive candidate for therapy of autoimmune demyelinating disorders.
Toward Multimodal Image-to-Image Translation (2017)

Many image-to-image translation problems are ambiguous, as a single input image may correspond to multiple possible outputs. In this work, we aim to model a \emph{distribution} of possible outputs in a conditional generative modeling setting. The ambiguity of the mapping is distilled in a low-dimensional latent vector, which can be randomly sampled at test time. A generator learns to map the given input, combined with this latent code, to the output. We explicitly encourage the connection between output and the latent code to be invertible. This helps prevent a many-to-one mapping from the latent code to the output during training, also known as the problem of mode collapse, and produces more diverse results. We explore several variants of this approach by employing different training objectives, network architectures, and methods of injecting the latent code. Our proposed method encourages bijective consistency between the latent encoding and output modes. We present a systematic comparison of our method and other variants on both perceptual realism and diversity.
Protection by Immunoglobulin Dual-Affinity Retargeting Antibodies against Dengue Virus (2013)

Dengue viruses are the most common arthropod-transmitted viral infection, with an estimated 390 million human infections annually and ∼3.6 billion people at risk. Currently, there are no approved vaccines or therapeutics available to control the global dengue virus disease burden. In this study, we demonstrate the binding, neutralizing activity, and therapeutic capacity of a novel bispecific dual-affinity retargeting molecule (DART) that limits infection of all four serotypes of dengue virus.
Socioeconomic Factors and Cancer Incidence Among Blacks and Whites (1991)

Findings from previous studies suggest that differences in socioeconomic status may be responsible for some, if not all, of the elevated incidence of cancer among blacks as compared with whites. Using incidence data from the National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER) Program, we tested this hypothesis by correlating black and white cancer incidence rates in three US metropolitan areas between 1978 and 1982 with data from the 1980 census on socioeconomic status within individual census tracts. The study analyzed data on the incidence of cancer at all sites combined (greater than 100 cancer sites) and at seven major sites separately. As in other studies, income and educational levels served as surrogates for socioeconomic status. The present study also used census-tract data on population density as a surrogate factor. Each of these measures of socioeconomic status was analyzed independently. Before correlation with census-tract data, age-adjusted data on cancer incidence showed statistically significant elevated risks among blacks for cancer at all sites combined and at four of the seven separate sites; whites showed an elevated risk for cancer at two sites. Cancer at only one site, the colon, showed no significant association with race. When age-adjusted incidence data were correlated with socioeconomic status, the comparative black-white risks changed: Whites showed an elevated risk of cancer at all sites combined and at three of the seven separate sites; blacks maintained their elevated risk at three sites. These findings suggest that the disproportionate distribution of blacks at lower socioeconomic levels accounts for much of the excess cancer burden among blacks. They also suggest that for both blacks and whites unidentified racial factors, which may be either cultural or genetic and which are not closely linked to socioeconomic status, may play a role in the incidence of some cancers.
Engineering Dental Pulp‐like Tissue in Vitro (1996)

Injury or infection of adult dental pulp often necessitates root canal therapy. This terminates dentin formation and subsequent tooth maturation. In addition, the synthetic materials currently utilized to replace lost tooth structure are not capable of completely replacing the function of the lost tissue, and often fail over time. This report describes a technique to engineer new pulp-like tissues utilizing cultured cells and synthetic extracellular matrices. Fibroblasts were obtained from human adult dental pulps and multiplied in culture. These cells were subsequently seeded onto synthetic matrices fabricated from fibers (approximately 15 microns in diameter) of polyglycolic acid (PGA). The pulp-derived fibroblasts adhered to the fibers, proliferated, and formed a new tissue over 60 days in culture with a cellularity similar to that of native pulp. These tissues may find application in the regeneration of oral tissues and may provide novel systems in which to study the biocompatibility of materials and chemicals used in dentistry.
Positional Proteomics at the N-Terminus as a Means of Proteome Simplification (2011)

One strategy to reduce complexity in proteome analysis is through rational reduction of the proteolytic peptides that constitute the analyte for mass spectrometric analysis. Methods for selective isolation of C- and N-terminal peptides have been developed. In this chapter, we outline the context and variety of methods for selective isolation of N-terminal peptides and detail one method based on negative selection through differential removal of internal peptides.
Topology Optimization of an Automotive Tailor-Welded Blank Door (2014)

Bidirectional evolutionary structural optimization (BESO) method has been successfully applied for a wide range of topology optimization problems. In this paper, the BESO method is further extended to the optimal design of an automotive tailor-welded blank (TWB) door with multiple thicknesses. Different from the traditional topology optimization for solid-void designs, topology optimization of the TWB door needs to identify the weld lines which joint sheets with different thicknesses. The finite element (FE) model of the automotive door assembly is established and verified by a series of stiffness experiments. Then, the proposed optimization procedure is applied to the optimization of the automotive TWB indoor panel for the optimal thickness layout and weld lines locations. Numerical results give guidelines for the lightweight design of TWB components to some extent.
Generation and phenotypic analysis of sigma receptor type I (σ1) knockout mice (2003)

Sigma (sigma) sites are a type of nonopiate receptor whose role has been associated with several behaviours, including anxiety, depression, analgesia, learning processes and psychosis. Although there are several known sigma receptor types, only the type I receptor (sigma 1) has been cloned. To uncover the in vivo relevance of sigma-receptors, we have generated knockout mice for sigma 1. Despite the broad expression pattern found for the sigma 1-gene, homozygous mutant mice are viable, fertile and do not display any overt phenotype, compared with their wild-type litter-mates, in mixed genetic backgrounds. However, a significant decrease in the hypermotility response has been measured in knockout mice upon challenge with (+)SKF-10 047, in agreement with the involvement of sigma 1-receptors in the induction of psychostimulant actions. The activity of sigma 2-receptors seems to be unaffected in sigma 1-mutant mice. These knockout mice could contribute to better understand the in vivo role of sigma-receptors.
Serum cachectin/tumor necrosis factor in critically ill patients with burns correlates with infection and mortality. (1990)

Serum cachectin/tumor necrosis factor (TNF), a cytokine implicated in the pathogenesis of septic shock, may appear in the circulation during serious infection, but the frequency of detection of elevated serum levels during protracted critical burn injury is unknown. Serial serum samples taken from 43 critically ill patients with burns with and without sepsis were analyzed for TNF using an enzyme-linked immunosorbent assay (ELISA). TNF was detectable (greater than 34 picograms per milliliter) at one or more time points in 69 per cent of the patients with sepsis versus 33 per cent of those without sepsis, in 71 per cent of the patients who died versus only 31 per cent of the survivors and in only one healthy normal control patient (n = 21). The frequency of the appearance of TNF correlated with both infection and mortality rate. Moreover, all three patients with TNF levels greater than 540 picograms per milliliter died. Neither the size of the burn nor injury from inhalation correlated with detection of TNF. A subset of 16 patients was studied longitudinally from admission until resolution of injury and these data demonstrate that TNF appears transiently and repetitively in the circulation of patients during infection and protracted critical burn injury. Also, serum cortisol levels were significantly higher during sepsis and death in the absence of serum TNF, compared with sepsis and death with detectable cachectin, suggesting that cortisol may interact with the production or detection of this cytokine during ongoing infection and lethal injury. In this study, we have demonstrated that serum TNF is detectable with greater frequency and in higher concentration in patients with sepsis and in those who ultimately succumb to the burn injury, that serum TNF appears transiently and repetitively in the circulation during injury and that higher serum cortisol levels are correlated with the absence of serum TNF during sepsis and lethal injury.
Synthetic Peptides: A User's Guide (2002)

Peptide design considerations principles and practice of solid-phase peptide synthesis evaluation of the finished product applicaitons of synthetic peptides set-up of a core facility. Appendix: services.
Effect of pyruvate on the function of stallion spermatozoa stored for up to 48 hours1 (2002)

Stallion spermatozoa maintain high fertilizing capacity if cooled to 5 degrees C and inseminated within 24 h. However, if spermatozoa are stored for 48 h, fertilizing capacity declines. Therefore, multiple shipments of semen are often required to inseminate mares that remain in estrus for days. Therefore, experiments were designed to determine if adding antioxidants to stallion spermatozoa stored at 5 degrees C for 48 h could maintain motility and fertilizing ability. In the first experiment stallion spermatozoa were incubated in a skim milk (SM) or a skim milk-egg yolk medium in combination with 10 mM pyruvate, 5 mM xanthurenic acid separately or in combination for up to 48 h at 5 degrees C. Spermatozoa incubated in SM for 48 h exhibited higher percentages of motile sperm (57%) than did sperm incubated in skim milk-egg yolk (34%); antioxidant treatment had little effect. In the second experiment, spermatozoa were incubated in SM containing 0, 1, 2, or 5 mM pyruvate. After 24 h of incubation at 5 degrees C, sperm incubated with 1, 2, or 5 mM pyruvate exhibited higher percentages of progressively motile spermatozoa (45%) than control exhibited (26%; P < 0.05). After 48 h, percentages of progressively motile spermatozoa were similar (27, 19, and 30 vs 14, respectively; P > 0.05). However, when incubated at 5 degrees C for 48 h and then incubated an additional 4 h at 25 degrees C, samples containing pyruvate exhibited higher percentages of motile (63 to 80%) and progressively motile (36 to 42%) sperm than did sperm in SM alone (28 and 5%, respectively; P < 0.05). The third experiment attempted to determine the optimal pyruvate concentration to maintain spermatozoal motility. Spermatozoa incubated with 0, 2, 3.5, or 5 mM pyruvate for 48 h at 5 degrees C and then an additional 4 h at 25 degrees C, exhibited similar percentages of progressively motile cells (31, 35, and 28%, respectively) that were higher than control (11%, P < 0.05). The last experiment evaluated the fertilizing potential of cooled spermatozoa. Embryos were recovered from 35, 20, and 30% of mares inseminated with spermatozoa that had been incubated at 5 degrees C, for 24 h in SM, or for 48 h in SM or SM + 2 mM pyruvate, respectively (P > 0.05). These studies indicate that 2 mM pyruvate in SM was beneficial in maintaining spermatozoal motility in 48 h-stored sperm and, although not significant, seemed to help maintain the fertility of 48 h-cooled spermatozoa.
Solubility of xenon in liquid n-alkanols: Thermodynamic functions in simple polar liquids (1984)

Measurements of the Ostwald solubility L(T) as a function of temperature in the range 10.0–50.0 °C are reported for 133Xe gas in 13 liquid normal alcohols: methanol through n-dodecanol, and n-tetradecanol. From the data for each solute–solvent system we find the mole fraction solubility x2(T), and calculate the following thermodynamic functions of solution: chemical potential Δμ○2(T) =−RT ln x2, enthalpy ΔH̄○2, and entropy ΔS̄○2, all based on the mole fraction scale. We also calculate directly from the Ostwald solubility the corresponding quantities based on the number density scale. These quantities are the chemical potential Δμ○ρ2(T) =−RT ln L, enthalpy ΔH○ρ2, and entropy ΔS○ρ2. The solute was chosen as an inert monatomic gas and the solvents were chosen in a polar homologous series in order to construct prototype solute–solvent systems. Solubility results and the associated thermodynamic functions are analyzed and compared with simple models.
The C-terminal loop of the homing endonuclease I-CreI is essential for site recognition, DNA binding and cleavage (2007)

Meganucleases are sequence-specific endonucleases with large cleavage sites that can be used to induce efficient homologous gene targeting in cultured cells and plants. These enzymes open novel perspectives for genome engineering in a wide range of fields, including gene therapy. A new crystal structure of the I-CreI dimer without DNA has allowed the comparison with the DNA-bound protein. The C-terminal loop displays a different conformation, which suggests its implication in DNA binding. A site-directed mutagenesis study in this region demonstrates that whereas the C-terminal helix is negligible for DNA binding, the final C-terminal loop is essential in DNA binding and cleavage. We have identified two regions that comprise the Ser138-Lys139 and Lys142-Thr143 pairs whose double mutation affect DNA binding in vitro and abolish cleavage in vivo. However, the mutation of only one residue in these sites allows DNA binding in vitro and cleavage in vivo. These findings demonstrate that the C-terminal loop of I-CreI endonuclease plays a fundamental role in its catalytic mechanism and suggest this novel site as a region to take into account for engineering new endonucleases with tailored specificity.
Monoclonal antibodies and magnetic microspheres for the depletion of leukaemic cells from bone marrow harvested for autologous transplantation. (1987)

The use of a panel of monoclonal antibodies and anti-mouse immunoglobulin-coated microspheres is described for the depletion of leukaemic blasts from bone marrow. Marrow treated in this way rapidly reconstitutes haemopoietic function after high-dose consolidation chemoradiotherapy. The recovery of cells from bone marrow is similar but not identical to results obtained on removal of neuroblasts from marrow to be used for autologous transplant. This is probably a reflection of the cross-reactivity of 'anti-leukaemic' antibodies with a variety of haemopoietic progenitor cells. The study described here demonstrates the feasibility of using this method to purge leukaemic cells from bone marrow. A much larger randomised study between patients receiving either purged or non-purged bone marrow would be necessary to validate the need to remove small numbers of tumour cells from bone marrow.
Linguistic Features for Quality Estimation (2012)

This paper describes a study on the contribution of linguistically-informed features to the task of quality estimation for machine translation at sentence level. A standard regression algorithm is used to build models using a combination of linguistic and non-linguistic features extracted from the input text and its machine translation. Experiments with English-Spanish translations show that linguistic features, although informative on their own, are not yet able to outperform shallower features based on statistics from the input text, its translation and additional corpora. However, further analysis suggests that linguistic information is actually useful but needs to be carefully combined with other features in order to produce better results. 1
The Lymphocytic Choriomeningitis Virus RING Protein Z Associates with Eukaryotic Initiation Factor 4E and Selectively Represses Translation in a RING-Dependent Manner (2000)

Only a few host cell proteins that associate with arenaviruses have been identified. To date, the arenavirus Z protein associates with the promyelocytic leukemia protein PML and the ribosomal P proteins. The majority of PML is present in nuclear bodies which are translocated to the cytoplasm by infection with the arenavirus, lymphocytic choriomeningitis virus (LCMV). The Z protein is a small zinc-binding RING protein with an unknown function which is required for the viral life cycle. Here, we demonstrate an association between Z and the host cell translation factor, eukaryotic initiation factor 4E (eIF-4E) in infected and transfected cells. Z's association with both ribosomal proteins and this translation factor led us to investigate whether Z could modulate host cell translation. In cell culture, Z selectively represses protein production in an eIF-4E-dependent manner. Specifically, we see reduction in cyclin D1 protein production with no effect on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in cells transfected with Z. Previous reports indicate that cyclin D1 is sensitive to eIF-4E levels, whereas GAPDH is not. Consistent with this, we observe preferential downregulation of cyclin D1 during infection and no effect on GAPDH. Further, no changes in RNA levels were observed for cyclin D1 or GAPDH transcripts. The interaction between eIF-4E and Z may provide a mechanism for slower growth observed in infected cells and a viral strategy for establishing chronic infection.