gebhart/patrepeval huggingface dataset:
On Biblical Typology and the Interpretation of Literature (1969)

A RECURRING PHENOMENON Of literary scholarship is discovery of a concept which, though well known to writers of past and extremely (though often subtly) influential in their work, became, with passage of time, no longer part of intellectual milieu of present. A classic example of such a discovery is A. O. Lovejoy's work on the Great Chain of Being, a concept so important for understanding Shakespeare and Milton that it is now part of every teacher's lectures on those poets (and others), no matter whether teacher holds the Great Chain of
Relative critical sets in RR(N) and applications to image analysis (1998)

Geometric structure of pixel intensity functions can be used to identify the “shape” features of objects and figures in three dimensional greyscale images, such as MRI and CAT images. Such geometric descriptions provide tools for tackling medical imaging problems, including the segmentation and registration problems. Pizer and Eberly defined a shape skeleton, called the core, for greyscale images by applying a ridge construction to a medialness function that is directly derived from the greyscale image. 
The d-dimensional (height) ridges of a function f∈C∞U , for U⊂Rn , generalize the idea of local maxima of f. They are a special type of d-dimensional relative critical set, and fit into a ridge-valley-connector set that conveys important geometric information about f. The objective of this dissertation is to present a classification of the local generic geometric properties of d-dimensional ridges, relative critical sets, and ridge-valley-connector sets. These results will then be used to classify the local generic properties of Pizer and Eberly's 1- and 2-dimensional shape skeleton for three dimensional greyscale images. 
The Thom transversality theorem (and modified versions) will yield our genericity results once we identify submanifolds of jet space that define properties of d-dimensional relative critical sets. These submanifolds are defined using three auxiliary maps on an open dense subset U0⊂U , whose complement contains points at which H(f), the Hessian of f, has a repeated eigenvalue. 
To understand how repeated eigenvalues affect the geometric structure of the d-dimensional relative critical sets, we stratify the space of n × n symmetric matrices according to corank and eigenvalue multiplicity. This along with universal properties of the d-dimensional relative critical sets on U0 allow us to determine how a d-dimensional relative critical set ends and is continued by another d-dimensional relative critical set. 
Extending the classification to the space of medial functions involves expressing the medial construction as a local differential operator on the space of solutions to the heat equation. By showing the image of this operator is transverse to the submanifolds identified in the previous work, a modified version of the Thom transversality theorem yields the classification of local generic properties of Pizer and Eberly's shape skeleta.
An end-to-end approach to segmentation in medical images with CNN and posterior-CRF (2021)

Conditional Random Fields (CRFs) are often used to improve the output of an initial segmentation model, such as a convolutional neural network (CNN). Conventional CRF approaches in medical imaging use manually defined features, such as intensity to improve appearance similarity or location to improve spatial coherence. These features work well for some tasks, but can fail for others. For example, in medical image segmentation applications where different anatomical structures can have similar intensity values, an intensity-based CRF may produce incorrect results. As an alternative, we propose Posterior-CRF, an end-to-end segmentation method that uses CNN-learned features in a CRF and optimizes the CRF and CNN parameters concurrently. We validate our method on three medical image segmentation tasks: aorta and pulmonary artery segmentation in non-contrast CT, white matter hyperintensities segmentation in multi-modal MRI, and ischemic stroke lesion segmentation in multi-modal MRI. We compare this with the state-of-the-art CNN-CRF methods. In all applications, our proposed method outperforms the existing methods in terms of Dice coefficient, average volume difference, and lesion-wise F1 score.
Characterization of reaction enthalpy and kinetics in a microscale flow platform (2020)

We report an isothermal flow calorimeter for characterization of reaction enthalpy and kinetics.
Ageing-associated small RNA cargo of extracellular vesicles (2023)

Previous work on murine models and humans demonstrated global as well as tissue-specific molecular ageing trajectories of RNAs. Extracellular vesicles (EVs) are membrane vesicles mediating the horizontal transfer of genetic information between different tissues. We sequenced small regulatory RNAs (sncRNAs) in two mouse plasma fractions at five time points across the lifespan from 2-18 months: (1) sncRNAs that are free-circulating (fc-RNA) and (2) sncRNAs bound outside or inside EVs (EV-RNA). Different sncRNA classes exhibit unique ageing patterns that vary between the fcRNA and EV-RNA fractions. While tRNAs showed the highest correlation with ageing in both fractions, rRNAs exhibited inverse correlation trajectories between the EV- and fc-fractions. For miRNAs, the EV-RNA fraction was exceptionally strongly associated with ageing, especially the miR-29 family in adipose tissues. Sequencing of sncRNAs and coding genes in fat tissue of an independent cohort of aged mice up to 27 months highlighted the pivotal role of miR-29a-3p and miR-29b-3p in ageing-related gene regulation that we validated in a third cohort by RT-qPCR.
Perfluoroalkylated Phospholipids as Surfactants and Co-Surfactants for Injectable Fluorocarbon Emulsions (1992)

Highly fluorinated phospholipids were investigated as sole surfactant, and as co-surfactant with egg yolk phospholipids (EYP), in the formulation of 50% and 100% w/v perfluorodecalin emulsions. The surfactant's capability to stabilize such emulsions improves with the length of the perfluoroalklylated tail and with the increase of its relative weight in the hydrophobic chain. As sole surfactant, 2, which has the longest fluorinated tail has the highest efficacy. As co-surfactant with EYP, a strong stabilizing effect is found when the total hydrophobic chain length is adjusted to the EYP membrane's thickness, which is the case of 1. Dispersions of the F-phospholipids do not modify cell growth and viability and show no hemolytic activity on human red blood cells at concentrations in the 60-100g/L range. Acute toxicity tests in mice indicate - i.v. DL50 greater than 2.75 g/Kg body wt.
Tumor-Specific Immune Response: Current In Vitro Analyses May Not Reflect the In Vivo Immune Status (1998)

Although our knowledge and understanding of tumor-specific cytotoxic T lymphocytes (CTL) have expanded considerably, the long-term work needed to assay CTL has precluded their analysis in large numbers of patients. Moreover, in vitro culture steps may introduce major biases. New approaches to identify tumor-specific CTL clones would be helpful. As a means to describe the in situ immune status by T-cell repertoire analysis, we developed the Immunoscope approach, a PCR-based method that allows us to determine the spectra of CDR3 lengths of the TCR chains displayed by complex populations of T cells. We review here some of our data about melanoma. Tumor-infiltrating lymphocytes of a melanoma patient were analyzed by different means and melanoma-specific T-cell clones were derived. Two categories of tumor-specific CD8+ CTL clones were derived from the infiltrate of a tumor-proximal invaded lymph node. The majority of T-cell clones specifically lyse the autologous tumor cell lines and predominantly recognize the HLA-A2/MART-1(27-35) peptide complex. The in vivo representativity of such CTL was assessed by the immunoscope technology. Among three MART-1-specific clones, none was detectable in situ. The other kind of tumor-specific CD8+ CTL did not lyse autologous melanoma cell lines but lysed the "fresh" autologous tumor cells in a MHC class I dependent manner. The immunoscope approach revealed that one of the latter was detectable in situ among tumor-infiltrating lymphocytes although not among PBMC. These data indicate that melanoma-specific lymphocytes that could not have been selected through conventional screening procedures may be important in tumor rejection. Our results suggest that a better characterization of tumor-specific immune responses will be important for the optimization of specific immunotherapy strategies and the long-term follow-up of patients.
Lymphatic‐to‐blood vessel transition in adult microvascular networks: A discovery made possible by a top‐down approach to biomimetic model development (2019)

Our results reveal the ability for lymphatic vessels to transition into blood vessels in adult microvascular networks and discover a new paradigm for investigating lymphatic/blood endothelial cell dynamics during microvascular remodeling.
Combined use of T2‐weighted MRI and T1‐weighted dynamic contrast–enhanced MRI in the automated analysis of breast lesions (2011)

A multiparametric computer-aided diagnosis scheme that combines information from T1-weighted dynamic contrast-enhanced (DCE)-MRI and T2-weighted MRI was investigated using a database of 110 malignant and 86 benign breast lesions. Automatic lesion segmentation was performed, and three categories of lesion features (geometric, T1-weighted DCE, and T2-weighted) were automatically extracted. Stepwise feature selection was performed considering only geometric features, only T1-weighted DCE features, only T2-weighted features, and all features. Features were merged with Bayesian artificial neural networks, and diagnostic performance was evaluated by ROC analysis. With leave-one-lesion-out cross-validation, an area under the ROC curve value of 0.77±0.03 was achieved with T2-weighted-only features, indicating high diagnostic value of information in T2-weighted images. Area under the ROC curve values of 0.79±0.03 and 0.80 ± 0.03 were obtained for geometric-only features and T1-weighted DCE-only features, respectively. When all features were considered, an area under the ROC curve value of 0.85±0.03 was achieved. We observed P values of 0.006, 0.023, and 0.0014 between the geometric-only, T1-weighted DCE-only, and T2-weighted-only features and all features conditions, respectively. When ranked, the P values satisfied the Holm-Bonferroni multiple-comparison test; thus, the improvement of multiparametric computer-aided diagnosis was statistically significant. A computer-aided diagnosis scheme that combines information from T1-weighted DCE and T2-weighted MRI may be advantageous over conventional T1-weighted DCE-MRI computer-aided diagnosis.
A combinatorial multicomponent plug mixer for systems chemistry. (2008)

We report the construction and testing of a combinatorial multicomponent plug mixer (CMPM) chip that generates a large number of mix ratios. The CMPM chip has been designed to study ribonucleotide reductase (RNR) protein-protein/protein-ligand interaction networks. The 4-component chip is capable of 5400 different combinations in a 30 plug cycle. CMPM chips were tested producing fluorescent dye and dihydrofolate reductase NADPH/MX mixtures with plug lengths of 2 mm.
Interleukin 18 and IL-18 BP response to Sars-CoV-2 virus infection (2022)

The immune response to the SARS-CoV-2 infection is crucial to the patient outcome. IL-18 is involved in the lymphocyte response to the disease and it is well established its important role in the complex developing of the host response to viral infection. This study aims at the analysis of the concentrations of IL-18, IL-18BP, INF-γ at the onset of the SARS-CoV-2 infection. The serum levels of measured interleukins were obtained through enzyme-linked immunosorbent assay. Furthermore, the free fraction of IL-18 was numerically evaluated. The enrolled patients were divided in two severity groups according to a threshold value of 300 for the ratio of arterial partial pressure of oxygen and fraction of inspired oxygen fraction and according to the parenchymal involvement as evaluated by computerized tomography at the admittance. In the group of patients with a more severe disease, a significant increase of the IL-18, INF-γ and IL-18BP levels have been observed, whereas the free IL-18 component values were almost constant. The results confirm that, at the onset of the disease, the host response keep the inflammatory cytokines in an equilibrium and support the hypothesis to adopt the IL-18BP modulation as a possible and effective therapeutic approach.
Association of Intestinal Granulomas with Smoking, Phenotype, and Serology in Chinese Patients with Crohn's Disease (2006)

Intestinal granulomas in the setting of CD may be helpful in determining phenotypic subtypes of CD, but is unhelpful in predicting disease severity. Smoking impairs the formation of granulomas in CD.
Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study (2018)

Habitual fiber consumption and MVPA behaviors help explain the differential abundance of specific microbial taxa and overall gut microbial diversity differences in first-year college students.
Entubulization Repair of Severed Cavernous Nerves in the Rat Resulting in Return of Erectile Function (1992)

Erectile dysfunction is a significant complication of radical pelvic surgery in men. Using the rat as an experimental model, we investigated the feasibility of repairing surgically ablated cavernous nerves utilizing silastic tube nerve growth conduits filled with nerve growth enhancing media. Known fertile male Sprague-Dawley rats were randomly divided into four surgical groups consisting of nerve ablation, immediate nerve reconstruction utilizing the entubulization technique (two groups) and control. The nerve ablation group had five mm. sections of the cavernosal nerve excised bilaterally. The entubulization nerve graft group had five mm. sections of the cavernous nerve excised bilaterally, followed by immediate microsurgical reconstruction with a silastic nerve tube conduit filled with either Matrigel and heparin (MA) or Matrigel and heparin plus acidic fibroblast growth factor (MA/aFGF), interposed between the severed cavernous nerve stumps bilaterally. The control group underwent sham operations with the cavernous nerves being exposed only. Erectile function was evaluated at one, two, and four months postoperatively. Return of erectile function was defined as tumescence of the corporal bodies with application of direct electrical stimulation (four volts of five millisecond pulses at 20 Hertz) to the proximal cavernous nerves. The two and four month electrical stimulation studies resulted in tumescence from 50% and 58% of the entubulization nerve reconstructed nerves with MA/aFGF versus 29% and 30% for the MA only group and only 5% and 11% for the ablated group, respectively. We conclude that in this experimental model immediate nerve graft repair utilizing entubulization techniques with the addition of nerve growth enhancing media appears to be a successful method of salvaging erectile function when the cavernous nerves have been divided.
Acromegaly and Pheochromocytoma: A Multiple Endocrine Syndrome Caused by a Plurihormonal Adrenal Medullary Tumor* (1986)

A 42-yr-old man with congestive heart failure and diabetes mellitus was found to have acromegaly and a pheochromocytoma. Serum GH-releasing hormone (GHRH) levels were elevated (2.34 ng/dl; normal, less than 0.02 ng/dl), suggesting that the acromegaly was caused by ectopic secretion of GHRH. Postmortem examination revealed that the right adrenal gland contained a pheochromocytoma in which GHRH was demonstrated by immunohistochemical studies. Gel permeation chromatography combined with the use of two GHRH antisera showed that GHRH-(1-44)-NH2 was a predominant form of the hormone. When the RNA from the tumor was extracted and analyzed by Northern gel blotting, two mRNA species were identified, with transcripts corresponding to 1600 and 780 base pairs. The pituitary gland was enlarged, but no distinct adenoma was found. Diffuse and nodular hyperplasia of somatotrophs in some areas resembling adenoma was identified on histological examination. These findings indicate that GH excess accompanied by somatotroph hyperplasia and acromegaly were secondary to a pheochromocytoma which secreted not only catecholamines but also GHRH.
Layered segmentation and optical flow estimation over time (2012)

Layered models provide a compelling approach for estimating image motion and segmenting moving scenes. Previous methods, however, have failed to capture the structure of complex scenes, provide precise object boundaries, effectively estimate the number of layers in a scene, or robustly determine the depth order of the layers. Furthermore, previous methods have focused on optical flow between pairs of frames rather than longer sequences. We show that image sequences with more frames are needed to resolve ambiguities in depth ordering at occlusion boundaries; temporal layer constancy makes this feasible. Our generative model of image sequences is rich but difficult to optimize with traditional gradient descent methods. We propose a novel discrete approximation of the continuous objective in terms of a sequence of depth-ordered MRFs and extend graph-cut optimization methods with new “moves” that make joint layer segmentation and motion estimation feasible. Our optimizer, which mixes discrete and continuous optimization, automatically determines the number of layers and reasons about their depth ordering. We demonstrate the value of layered models, our optimization strategy, and the use of more than two frames on both the Middlebury optical flow benchmark and the MIT layer segmentation benchmark.
Phosphorus and zinc fertilization effects on dry matter yield and phosphorus and zinc uptake by Crambe (1993)

Abstract Crambe (Crambe abyssinica Hochist.) is an oilseed crop high in euricic acid with industrial applications in production of nylon, plasticizers, and lubricants. Little information is available on crambe response to phosphorus (P) and zinc (Zn) fertilization. This glasshouse study was conducted to evaluate the response of crambe to four rates of P and five rates of Zn fertilizer application to a soil with 10 mg/kg NaHCO3‐extractable P and 0.6 mg/kg DTPA‐extractable Zn. Phosphorus fertilizer, but not Zn fertilizer, increased the dry matter yield of plant tops. Phosphorus response was consistent in both 35‐ and 62‐day‐old plants. Zinc response was most consistent in 35 day‐old plants. Significant interactions were observed between P and Zn for dry matter weight, P:Zn ratio, and Zn uptake at 35 days. No significant interactions were observed at 62 days. Analysis of the data showed a negative correlation coefficient between P or Zn treatment and tissue concentration or uptake for the opposite element. Notes Associate Professor Research Specialist Research Technician
Confidence Estimation for Black Box Automatic Speech Recognition Systems\n Using Lattice Recurrent Neural Networks (2019)

Recently, there has been growth in providers of speech transcription services\nenabling others to leverage technology they would not normally be able to use.\nAs a result, speech-enabled solutions have become commonplace. Their success\ncritically relies on the quality, accuracy, and reliability of the underlying\nspeech transcription systems. Those black box systems, however, offer limited\nmeans for quality control as only word sequences are typically available. This\npaper examines this limited resource scenario for confidence estimation, a\nmeasure commonly used to assess transcription reliability. In particular, it\nexplores what other sources of word and sub-word level information available in\nthe transcription process could be used to improve confidence scores. To encode\nall such information this paper extends lattice recurrent neural networks to\nhandle sub-words. Experimental results using the IARPA OpenKWS 2016 evaluation\nsystem show that the use of additional information yields significant gains in\nconfidence estimation accuracy. The implementation for this model can be found\nonline.\n
Foregrounds in the BOOMERANG-LDB data: a preliminary rms analysis (2000)

We present a preliminary analysis of the BOOMERanG LDB maps, focused on foregrounds. BOOMERanG detects dust emission at moderately low galactic latitudes ($b &gt; -20^o$) in bands centered at 90, 150, 240, 410 GHz. At higher Galactic latitudes, we use the BOOMERanG data to set conservative upper limits on the level of contamination at 90 and 150 GHz. We find that the mean square signal correlated with the IRAS/DIRBE dust template is less than 3% of the mean square signal due to CMB anisotropy.
Interpreting Sequences from Mastodon and T. rex (2007)

J. Asara et al. reported that collagen proteins from well-preserved ancient fossil bones from a 160,000- to 600,000-year-old mastodon and a 68-million-year-old T. rex can be extracted and sequenced (“Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry,” 13 April,
The Danish Head and Neck Cancer database (2016)

Half a century of registration of head and neck cancer treatment and outcome has created the basis for understanding and has substantially contributed to improve the treatment of head and neck cancer at both national and international levels.
Tuning-Range Enhancement Through Deterministic Mode Selection in RF Quadrature Oscillators (2015)

Quadrature oscillators (QOs) based on parallel or series coupling mechanisms produce ambiguous phase relationships between the coupled oscillators. Deterministic mode selection is presented and analyzed for a series-coupled LC quadrature oscillator ( LC-QO) and leveraged to increase the tuning range of the QO. Series-coupled LC-QOs have been implemented in a 90-nm CMOS technology. Measured results show a frequency tuning range of 94% for a center frequency of 1.3 GHz, 60% for the oscillator operating at 3.7 GHz, and 52% for the oscillator operating at 4.4 GHz.
Biliverdin, an intermediate in the biosynthesis of plant pigments (1985)

Conference Article| February 01 1985 Biliverdin, an intermediate in the biosynthesis of plant pigments J. ANDREW HOLROYD; J. ANDREW HOLROYD 1Department of Biochemistry, University of Leeds, Leeds LS2 9JT, U.K. Search for other works by this author on: This Site PubMed Google Scholar DAVID I. VERNON; DAVID I. VERNON 1Department of Biochemistry, University of Leeds, Leeds LS2 9JT, U.K. Search for other works by this author on: This Site PubMed Google Scholar STANLEY B. BROWN STANLEY B. BROWN 1Department of Biochemistry, University of Leeds, Leeds LS2 9JT, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1985) 13 (1): 209–210. https://doi.org/10.1042/bst0130209 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation J. ANDREW HOLROYD, DAVID I. VERNON, STANLEY B. BROWN; Biliverdin, an intermediate in the biosynthesis of plant pigments. Biochem Soc Trans 1 February 1985; 13 (1): 209–210. doi: https://doi.org/10.1042/bst0130209 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1985 Biochemical Society1985 Article PDF first page preview Close Modal You do not currently have access to this content.