gebhart/patrepeval huggingface dataset:
Bioaccessibility of β-Carotene, Lutein, and Lycopene from Fruits and Vegetables (2006)

Epidemiological studies have consistently demonstrated that there is an association between carotenoid-rich food intakes with a low incidence in chronic diseases. Nevertheless, there is not an association between the intake of total dietary carotenoids and chronic health incidence in the European population, probably because of different carotenoid food sources and bioavailability. The objective of this study was to evaluate the small and large intestine bioaccessibilities of major dietary carotenoids from fruits and vegetables in a common diet. A bioaccessibility model that includes enzymatic digestion and in vitro colonic fermentation was employed. Lutein presented greater small intestine bioaccessibility (79%) than beta-carotene (27%) or lycopene (40%). With regard to large intestine bioaccessibility, similar amounts of lycopene and beta-carotene were released from the food matrix (57%), whereas small amounts of lutein (17%) were released. These results suggest that 91% of the beta-carotene, lutein, and lycopene contained in fruits and vegetables is available in the gut during the entire digestion process. Colonic fermentation is shown to be important for carotenoid availability in the gut.
Negative pressure wound therapy as postoperative dressing in below knee amputation stump closure of patients with chronic venous insufficiency. (2011)

This experience suggests that early, short-term application of NPWT may be a valuable adjunct in BKA stump closure. ﻿﻿﻿.
Molecular and immunohistochemical diagnosis of Francisella noatunensis subsp. orientalis from formalin-fixed, paraffin-embedded tissues (2012)

Members of the genus Francisella (viz., F. noatunensis subsp. orientalis [Fno] and F. noatunensis subsp. noatunensis) have been described as causative agents of chronic granulomatous and pyogranulomatous lesions in wild and cultured fish species. In the present study, 68 archived formalin-fixed, paraffin-embedded (FFPE) tissues from several fish species, collected at different geographical locations from 2000 to 2011, were analyzed using a real-time polymerase chain reaction assay for the detection of the Fno intracellular growth loci C (iglC) gene and by immunohistochemistry for the demonstration of Fno antigens. The results revealed a high correlation between these 2 diagnostic techniques validating their use for the diagnosis of Fno infection in archived FFPE tissues and confirming the presence of Fno in fish species from the Cari y years of the present century.
Chromatic and high-frequency cVEP-based BCI paradigm (2015)

We present results of an approach to a code-modulated visual evoked potential (cVEP) based brain-computer interface (BCI) paradigm using four high-frequency flashing stimuli. To generate higher frequency stimulation compared to the state-of-the-art cVEP-based BCIs, we propose to use the light-emitting diodes (LEDs) driven from a small micro-controller board hardware generator designed by our team. The high-frequency and green-blue chromatic flashing stimuli are used in the study in order to minimize a danger of a photosensitive epilepsy (PSE). We compare the the green-blue chromatic cVEP-based BCI accuracies with the conventional white-black flicker based interface. The high-frequency cVEP responses are identified using a canonical correlation analysis (CCA) method.
B-Myc:  N-Terminal Recognition of Myc Binding Proteins (2006)

B-Myc is an endogenous, N-terminal homologue of transcription factor c-Myc that lacks the C-terminal DNA binding and protein dimerization domain of c-Myc. Clinical mutations in the c-Myc N-terminal region, and the subsequent misregulation of Myc, are implicated in the development of numerous human cancers. Myc functions to both activate and repress transcription by associating with multiple binding partners. We investigated the structural and dynamical properties of B-Myc, free or associated with the transactivation inhibitor, MM-1, and the activator, TBP, using NMR spectroscopy. B-Myc has no persistent tertiary structure, yet regions corresponding to Myc homology boxes 1 and 2 (MBI and MBII, respectively) have molten globule-like characteristics. B-Myc binds to MM-1 in a specific manner without becoming highly structured. The local regions of B-Myc involved in binding differ for MM-1 and TBP, and regions not identified by mutagenesis are found to be involved in MM-1 binding. The results provide new insights into Myc N-terminal protein-protein interactions. We propose a model for Myc regulation through differential involvement of MBI and MBII in the binding of Myc interacting proteins.
Molecular analysis of the structure and function of plant myosins. (1996)

Myosin is a protein that can convert the chemical energy in ATP into mechanical energy. In plants, myosin is thought to function in actin-associated processes like cytoplasmic streaming and directed vesicle transport. My thesis project has utilized a reverse genetics approach in order to study the structure and function of plant myosin. To analyze the structure and complexity of plant myosin, four different Arabidopsis myosin cDNA clones were isolated and sequenced. Sequence analysis of these cDNA clones and three additional genomic PCR products indicated that Arabidopsis possesses a large myosin gene family that is composed of at least three distinct classes based on the overall structure of the predicted proteins (two novel classes and one previously-identified class; class V). The expression of these myosins was analyzed by Northern blotting and RNA in situ hybridization. Northern blot analysis indicated that the four Arabidopsis myosins were differentially expressed in a variety of plant organs. RNA in situ hybridization of floral tissue sections indicated that the MYA1 and MYA3 genes were expressed in a developmentally regulated manner in distinct cells of the sepals and anther filaments. In leaves, the MYA1 and MYA3 genes were expressed in the mature trichomes, where they may function in the cytoplasmic streaming that has been visualized in these large, unicellular structures. In whole seedlings, the MYA1 gene was found to be expressed throughout the expanded cotyledons (with the exception of the vascular tissue). To investigate the function of plant myosin, transgenic plants were generated that contained constructs designed to either repress or overexpress/ectopically express the Arabidopsis MYA1 myosin. The expression of the MYA1 gene in the different transgenic lines was found to be indistinguishable from wild type, even in plants expressing high levels of MYA1 antisense RNA. These results suggest that the expression of the MYA1 gene is tightly regulated or that changes in MYA1 expression are detrimental to Arabidopsis.
An absolute test for axicon surfaces (2011)

We present a method for absolute testing of axicon surfaces in a null test setup. The absolute test exploits the symmetry of axicons, which allows us to introduce a shift of the surface under test in both the axial and rotational directions while still maintaining the null test condition. With two shifts of the surface under test and four measurements, the interferometer and null optics error can be removed. The absolute surface local deviation can be obtained by wavefront reconstruction with a double-side spiral-path direct integration method. A simulation of the method, including typical systematic as well as statistical errors as input, is presented to estimate the error propagation. Experimental absolute test results of a 90° axicon surface are given.
Line Tunable Ultraviolet Laser (2005)

An ultraviolet laser is demonstrated using a dual wavelength Nd:YAG oscillator, sum frequency and second harmonic process.Synchronous pulses at 1.052 and 1.319 micrometers are amplified, mixed and subsequently doubled, producing pulses at 0.293 micrometers.
Real-Time Fiber-Optic Casing Imager (2010)

Summary During the last several years, significant progress has been made in the use of fiber-optic technology for well and reservoir surveillance. While most effort in this field appears to be concentrated on the development of fiber-optic-based meters for temperature, pressure, and flow, comparably few publications have been made to date about the use of fiber-optic technology for monitoring deformations of well tubulars and casings. In this article, we report on recent advances in our development of a real-time fiber-optic-based casing imager. This device is designed for continuous, high-resolution monitoring of the shape of casings or well tubulars and, therefore, enables the determination of strain imposed on the well. Small-scale and full-casing-sized laboratory tests have demonstrated that the latest generation of this system is sufficiently sensitive to detect casing deformations of less than 10°/100 ft and covers compressive and tensile axial-strain ranges from less than 0.1 to 10%. We will discuss the background technology, measurement sensitivity and strain-response characterization, as well as the scaleup work that has been performed to date. Our article also includes an overview of field-test results and illustrates how real-time deformation monitoring could form a significant component of reservoir-surveillance strategies.
Supplementary Figure S3. from Decreased Serum Thrombospondin-1 Levels in Pancreatic Cancer Patients Up to 24 Months Prior to Clinical Diagnosis: Association with Diabetes Mellitus (2023)

&lt;p&gt;Detection of CA1-9 by ELISA in (A) individual time to diagnosis groups and (B) diagnosed samples and controls.&lt;/p&gt;
A maximum-flow formulation of the N-camera stereo correspondence problem (2002)

This paper describes a new algorithm for solving the N-camera stereo correspondence problem by transforming it into a maximum-flow problem. Once solved, the minimum-cut associated to the maximum-flow yields a disparity surface for the whole image at once. This global approach to stereo analysis provides a more accurate and coherent depth map than the traditional line-by-line stereo. Moreover, the optimality of the depth surface is guaranteed and can be shown to be a generalization of the dynamic programming approach that is widely used in standard stereo. Results show improved depth estimation as well as better handling of depth discontinuities. While the worst case running time is O(n/sup 2/d/sup 2/log(nd)), the observed average running time is O(n/sup 1.2/ d/sup 1.3/) for an image size of n pixels and depth resolution d.
Stormram 2: A MRI-compatible robotic system for breast biopsy (2016)

A novel MRI-compatible 5 DOF needle manipulator driven by custom pneumatic linear stepper motors has been developed. The robot's frame measures 185x160x100mm, making it small enough to fit inside the bore of the scanner together with the patient. It also has sufficient speed, force and dexterity to manipulate the needle towards a chosen target in a soft breast phantom.
385 Evidence for Stratification of Rumen Wall Microbial Communities Revealed By 16S rRNA Based Amplicon Sequencing. (2018)

Rumen microbes have been characterized as two distinct groups; feed-associated and luminal microbes and epithelial rumen wall microbes. The rumen wall environment has been relatively understudied regarding microbial taxonomy and function. Rumen microbial fermentations provide key metabolic products for the host such as short chain fatty acids, which are absorbed through rumen epithelial tissues. Rumen wall microorganisms are thus positioned in a prime location to interact with the host, possibly assisting in nutrient exchange across the rumen wall, barrier function and signaling to the host. In addition, the rumen content naturally stratifies based on particle size and density. This stratification is always present, and shifts from large, dry forages nearer to the dorsal portion of the rumen (mat) to the liquid phase in the ventral section of the rumen. Constant interaction with the stratification of the rumen contents led us to hypothesize that the rumen wall microbial communities organize in a similar stratified manner mirroring the stratification of the rumen content, adapting to the different nutrient conditions. Five fistulated, milking Holstein cows of similar age and management conditions were sampled for this project. Three different rumen epithelial biopsies were taken through the fistula, corresponding to the stratification of the rumen content: one aligned with the dorsal portion of the mat (A), another ten centimeters ventral to the first (B) and the last 10 centimeters ventral to the second site (C). We sampled each of these cows twice to gain insight into the temporal stability of the rumen wall microbial populations. DNA was extracted using the Qiagen Powerlyzer Powersoil kit and used for 16S rRNA gene Illumina MiSeq sequencing. Sequences were clustered into operational taxonomic units (OTU) based on a 97% similarity cutoff using MOTHUR. After quality control, 1,079,735 reads remained for 30 samples which were clustered into 3,520 OTUs with 10 or more reads. 96% of the reads were bacterial, whereas 4% affiliated to Archaea. Statistical analysis revealed that among the 20 most abundant OTUs, phylotypes classified as Prevotella, Brachymonas, Fibrobacter, and Suttonella were significantly more abundant at the sample site A compared to C. On a whole community level, Analysis of molecular variance (AMOVA) revealed differences between groups A and C, although not statistically significant (P=0.07). Initial data from this project reveal first evidence that a stratification of rumen wall microbes is present in dairy cattle. Currently, additional rumen wall samples are being sequenced to provide a larger dataset for more robust statistical analyses.
ConsDock: A new program for the consensus analysis of protein–ligand interactions (2002)

Protein-based virtual screening of chemical libraries is a powerful technique for identifying new molecules that may interact with a macromolecular target of interest. Because of docking and scoring limitations, it is more difficult to apply as a lead optimization method because it requires that the docking/scoring tool is able to propose as few solutions as possible and all of them with a very good accuracy for both the protein-bound orientation and the conformation of the ligand. In the present study, we present a consensus docking approach (ConsDock) that takes advantage of three widely used docking tools (Dock, FlexX, and Gold). The consensus analysis of all possible poses generated by several docking tools is performed sequentially in four steps: (i) hierarchical clustering of all poses generated by a docking tool into families represented by a leader; (ii) definition of all consensus pairs from leaders generated by different docking programs; (iii) clustering of consensus pairs into classes, represented by a mean structure; and (iv) ranking the different means starting from the most populated class of consensus pairs. When applied to a test set of 100 protein–ligand complexes from the Protein Data Bank, ConsDock significantly outperforms single docking with respect to the docking accuracy of the top-ranked pose. In 60% of the cases investigated here, ConsDock was able to rank as top solution a pose within 2 Å RMSD of the X-ray structure. It can be applied as a postprocessing filter to either single- or multiple-docking programs to prioritize three-dimensional guided lead optimization from the most likely docking solution. Proteins 2002;47:521–533. © 2002 Wiley-Liss, Inc.
Reference Values for the Marx Activity Rating Scale in a Young Athletic Population (2015)

Assessing activity as a patient-reported outcome after knee ligament injury is important, and reference values for these instruments need to account for the influence of prior injury and sex.
CNN-IETS (2017)

Information Extraction by Text Segmentation (IETS) aims at segmenting text inputs to extract implicit data values contained in them.The state-of-art IETS approaches mainly rely on machine learning techniques, either supervised or unsupervised.However, while the supervised approaches require a large labelled training data, the performance of the unsupervised ones could be unstable on different data sets.To overcome their weaknesses, this paper introduces CNN-IETS, a novel unsupervised probabilistic approach that takes the advantages of pre-existing data and a Convolution Neural Network (CNN)-based probabilistic classification model. While using the CNN model can ease the burden of selecting high-quality features in associating text segments with attributes of a given domain, the pre-existing data as a domain knowledge base can provide training data with a comprehensive list of features for building the CNN model.Given an input text, we do initial segmentation (according to the occurrences of these words in the knowledge base) to generate text segments for CNN classification with probabilities. Then, based on the probabilistic CNN classification results, we work on finding the most probable labelling way to the whole input text.As a complementary, a bidirectional sequencing model learned on-demand from test data is finally deployed to do further adjustment to some problematic labelled segments.Our experimental study conducted on several real data collections shows that CNN-IETS improves the extraction quality of state-of-art approaches by more than 10%.
Na+-Dependent High-Affinity Glutamate Transport in Macrophages (2000)

Excessive accumulation of glutamate in the CNS leads to excitotoxic neuronal damage. However, glutamate clearance is essentially mediated by astrocytes through Na+-dependent high-affinity glutamate transporters (excitatory amino acid transporters (EAATs)). Nevertheless, EAAT function was recently shown to be developmentally restricted in astrocytes and undetectable in mature astrocytes. This suggests a need for other cell types for clearing glutamate in the brain. As blood monocytes infiltrate the CNS in traumatic or inflammatory conditions, we addressed the question of whether macrophages expressed EAATs and were involved in glutamate clearance. We found that macrophages derived from human blood monocytes express both the cystine/glutamate antiporter and EAATs. Kinetic parameters were similar to those determined for neonatal astrocytes and embryonic neurons. Freshly sorted tissue macrophages did not possess EAATs, whereas cultured human spleen macrophages and cultured neonatal murine microglia did. Moreover, blood monocytes did not transport glutamate, but their stimulation with TNF-alpha led to functional transport. This suggests that the acquisition of these transporters by macrophages could be under the control of inflammatory molecules. Also, monocyte-derived macrophages overcame glutamate toxicity in neuron cultures by clearing this molecule. This suggests that brain-infiltrated macrophages and resident microglia may acquire EAATs and, along with astrocytes, regulate extracellular glutamate concentration. Moreover, we showed that EAATs are involved in the regulation of glutathione synthesis by providing intracellular glutamate. These observations thus offer new insight into the role of macrophages in excitotoxicity and in their response to oxidative stress.
Le syndrome psoriasis avec ses comorbidités. (2014)

Chelation of the bare and hydrated iron(II) cation by quercetin has been investigated at the DF/B3LYP level in the gas phase. Several complexed species arising from neutral and anionic forms of the ligand have been taken into account. Both 1:1 and 1:2 metal/flavonoid stoichiometries have been considered. Results indicate that among the potential sites of chelation present on quercetin, the oxygen atoms belonging to the 3-hydroxy and 4-oxo, and to the 5-hydroxy and 4-oxo groups, are the preferred ones. Time-dependent density functional theory (TDDFT) calculations, used to reproduce the electronic UV-vis spectra of isolated quercetin and its complexes with Fe2+, were also performed in methanol and dimethylsulfoxide.
Wandering spleen in a young girl with Gaucher disease. (2001)

1. Hackman RC, Wolford JL, Gleaves CA, Myerson D, Beauchamp MD, Meyers JD, McDonald GB. Recognition and rapid diagnosis of upper gastrointestenal cytomegalovirus infection in marrow transplant recipients. A comparison of seven virologic methods. Transplantation 1994;57:231±7. 2. Zipeto D, Mrris S, Hong C. Human cytomegalovirus (CMV) DNA in plasma reflects quantity of CMV DNA present in leukocytes. J Clin Microbiol 1995;33:2607±11. 3. Oderda G, Cinti S, Cangiotti AM, Forni M, Ansaldi N. Increased tight junction width in two children with Menetrier's disease. J Pediatr Gastroenterol Nutr 1990;11:123±7.
Spi-1/PU.1 Transgenic Mice Develop Multistep Erythroleukemias (1996)

Insertional mutagenesis of the spi-1 gene is associated with the emergence of malignant proerythroblasts during Friend virus-induced acute erythroleukemia. To determine the role of spi-1/PU.1 in the genesis of leukemia, we generated spi-1 transgenic mice. In one founder line the transgene was overexpressed as an unexpected-size transcript in various mouse tissues. Homozygous transgenic animals gave rise to live-born offspring, but 50% of the animals developed a multistep erythroleukemia within 1.5 to 6 months of birth whereas the remainder survived without evidence of disease. At the onset of the disease, mice became severely anemic. Their hematopoietic tissues were massively invaded with nontumorigenic proerythroblasts that express a high level of Spi-1 protein. These transgenic proerythroblasts are partially blocked in differentiation and strictly dependent on erythropoietin for their proliferation both in vivo and in vitro. A complete but transient regression of the disease was observed after erythrocyte transfusion, suggesting that the constitutive expression of spi-1 is related to the block of the differentiation of erythroid precursors. At relapse, erythropoietin-independent malignant proerythroblasts arose. Growth factor autonomy could be partially explained by the autocrine secretion of erythropoietin; however, other genetic events appear to be necessary to confer the full malignant phenotype. These results reveal that overexpression of spi-1 is essential for malignant erythropoiesis and does not alter other hematopoietic lineages.
Oxidized Cellulose Binding to Allergens with a Carbohydrate-Binding Module Attenuates Allergic Reactions (2010)

Grass and mite allergens are of the main causes of allergy and asthma. A carbohydrate-binding module (CBM) represents a common motif to groups I (β-expansin) and II/III (expansin-like) grass allergens and is suggested to mediate allergen-IgE binding. House dust mite group II allergen (Der p 2 and Der f 2) structures bear strong similarity to expansin's CBM, suggesting their ability to bind carbohydrates. Thus, this study proposes the design of a carbohydrate-based treatment in which allergen binding to carbohydrate particles will promote allergen airway clearance and prevent allergic reactions. The aim of the study was to identify a polysaccharide with high allergen-binding capacities and to explore its ability to prevent allergy. Oxidized cellulose (OC) demonstrated allergen-binding capacities toward grass and mite allergens that surpassed those of any other polysaccharide examined in this study. Furthermore, inhalant preparations of OC microparticles attenuated allergic lung inflammation in rye grass-sensitized Brown Norway rats and OVA-sensitized BALB/c mice. Fluorescently labeled OC efficiently cleared from the mouse airways and body organs. Moreover, long-term administration of OC inhalant to Wistar rats did not result in toxicity. In conclusion, many allergens, such as grass and dust mite, contain a common CBM motif. OC demonstrates a strong and relatively specific allergen-binding capacity to CBM-containing allergens. OC's ability to attenuate allergic inflammation, together with its documented safety record, forms a firm basis for its application as an alternative treatment for prevention and relief of allergy and asthma.