gebhart/patrepeval huggingface dataset:
Early stages of LDL oxidation: apolipoprotein B structural changes monitored by infrared spectroscopy (2001)

Changes in the conformation of apoliprotein B-100 in the early stages of copper-mediated low density lipoprotein oxidation have been monitored by infrared spectroscopy. During the lag phase no variation in structure is observed, indicating that copper binding to the protein does not significantly affect its structure. In the propagation phase, while hydroperoxides are formed but the protein is not modified, no changes in secondary structure are observed, but the thermal profile of the band corresponding to alpha-helix is displaced in frequency, indicating changes in tertiary structure associated with this conformation but not with beta-sheet components. When aldehyde formation starts, a decrease of approximately 3% in the area of bands corresponding to alpha-helix and beta-sheet is produced, concomitantly with an increase in beta-turns and unordered structure. The two bands corresponding to beta-turns vary as well under these conditions, indicating changes in these structures. Also at this stage the thermal profile shows variations in frequency for the bands corresponding to both alpha-helix and beta-sheet. The results are consistent with the hypothesis that as soon as the polyunsaturated fatty acids from the particle core are modified, this change is reflected at the surface, in the alpha-helical components contacting the monolayer.
Identification of a novel endogenous memory facilitating cyclic dipeptide cyclo‐prolylglycine in rat brain (1996)

Using high-performance liquid chromatography, gas-chromatography and chromato-mass spectrometry methods a novel endogenous cyclic dipeptide cyclo-prolylglycine was identified in rat brain. Its content according to gas chromatography is 2.8 +/- 0.3 nmol/g wet brain. Synthetic cyclo-prolylglycine has demonstrated antiamnesic activity in the passive avoidance test in rats at a dose of 0.1 mg/kg i.p. Cyclic dipeptide cyclo-prolylglycine seems to be a memory facilitating substance and its presence in rat brain suggests the existence of a new mechanism of memory regulation.
Inhibition of squamous cell carcinoma angiogenesis by direct interaction of retinoic acid with endothelial cells. (1996)

Retinoic acid (RA) is a multifunctional drug that is particularly effective at preventing the development of multiple primary oral squamous cell carcinomas. A portion of this activity is due to the inhibition of tumor angiogenesis. It has been thought that RA influences tumor angiogenesis only via its interactions with the tumor cells themselves. Here, we test the hypothesis that the drug can also block neovascularization by directly inhibiting the angiogenic activity of normal endothelial cells. Clinically achievable doses of RA rapidly caused large- and small-vessel endothelial cells to become refractory to stimulation of migration either by tumor-conditioned media or purified angiogenic factors (a-fibroblast growth factor (aFGF), bFGF, vascular endothelial GF, platelet-derived GF, TGF beta-1, and IL-8). However, RA had little effect on their proliferation. Inhibition of migration was complete within 3 hours and was reversed 36 hours after drug removal. The migration of human oral keratinocytes was not sensitive to RA, whereas the migration of fibroblasts and vascular smooth muscle cells was inhibited. To determine if systemic RA affected neovascularization, rats were given 1 mg/kg/day of all-trans RA and their angiogenic potential was tested by implanting pellets of tumor-conditioned media into their avascular corneas. This treatment rendered the rats unable to mount a neovascular response in their corneas. These data demonstrate that RA directly affects endothelial cells, rapidly and reversibly inhibiting their ability to migrate toward a variety of stimuli in vitro and halting the formation of new vessels in vivo. These direct effects on vascular cells seem likely to contribute to the success of RA as a chemopreventive agent for oral squamous cell carcinoma.
Changes in Na+ Channel Currents of Rat Dorsal Root Ganglion Neurons Following Axotomy and Axotomy-Induced Autotomy (2002)

Section of rat sciatic nerve (axotomy) increases the excitability of neurons in the L(4)-L(5) dorsal root ganglia (DRG). These changes are more pronounced in animals that exhibit a self-mutilatory behavior known as autotomy. We used whole cell recording to examine changes in the tetrodotoxin-sensitive (TTX-S) and the tetrodotoxin-resistant (TTX-R) components of sodium channel currents (I(Na)) that may contribute to axotomy-induced increases in excitability. Cells were initially divided on the basis of size into "large," "medium," and "small" groups. TTX-S I(Na) predominated in "large" cells, whereas TTX-R I(Na) predominated in some, but not all "small cells." "Small" cells were therefore subdivided into "small-slow" cells, which predominantly exhibited TTX-R I(Na) and "small fast" cells that exhibited more TTX-S I(Na). In contrast to results obtained in other laboratories, where slightly different experimental procedures were used, we found that axotomy increased TTX-R and/or TTX-S I(Na) and slowed inactivation. The effects were greatest in "small-slow" cells and least in "large" cells. The changes promoted by axotomy were expressed more clearly in animals that exhibited autotomy. Also, the presence of autotomy correlated with a shift in the properties of I(Na) in "large" rather than "small-slow," putative nociceptive cells. These trends parallel previous observations on axotomy-induced increases in excitability, spike height, and spike width that are also greatest in "small" cells and least in "large" cells. In addition, the presence of autotomy correlates with an increase in excitability of "large" rather than "small" cells. Increases in TTX-R and TTX-S I(Na) thus coincide with axotomy-induced increases in excitability and alterations in spike shape across the whole population of sensory neurons. Injury-induced changes of this type are likely associated with the onset of chronic pain in humans.
A 3D fully convolutional neural network and a random walker to segment the esophagus in CT (2017)

Precise delineation of organs at risk (OAR) is a crucial task in radiotherapy treatment planning, which aims at delivering high dose to the tumour while sparing healthy tissues. In recent years algorithms showed high performance and the possibility to automate this task for many OAR. However, for some OAR precise delineation remains challenging. The esophagus with a versatile shape and poor contrast is among these structures. To tackle these issues we propose a 3D fully (convolutional neural network (CNN) driven random walk (RW) approach to automatically segment the esophagus on CT. First, a soft probability map is generated by the CNN. Then an active contour model (ACM) is fitted on the probability map to get a first estimation of the center line. The outputs of the CNN and ACM are then used in addition to CT Hounsfield values to drive the RW. Evaluation and training was done on 50 CTs with peer reviewed esophagus contours. Results were assessed regarding spatial overlap and shape similarities. The generated contours showed a mean Dice coefficient of 0.76, an average symmetric square distance of 1.36 mm and an average Hausdorff distance of 11.68 compared to the reference. These figures translate into a very good agreement with the reference contours and an increase in accuracy compared to other methods. We show that by employing a CNN accurate estimations of esophagus location can be obtained and refined by a post processing RW step. One of the main advantages compared to previous methods is that our network performs convolutions in a 3D manner, fully exploiting the 3D spatial context and performing an efficient and precise volume-wise prediction. The whole segmentation process is fully automatic and yields esophagus delineations in very good agreement with the used gold standard, showing that it can compete with previously published methods.
Perceiving spatial relationships in computer-generated images (1992)

The sources of visual information that must be present to correctly interpret spatial relations in images, the relative importance of different visual information sources with regard to metric judgments of spatial relations in images, and the ways that the task in which the images are used affect the visual information's usefulness are discussed. Cue theory, which states that the visual system computes the distances of objects in the environment based on information from the posture of the eyes and from the patterns of light projected onto the retinas by the environment, is presented. Three experiments in which the influence of pictorial cues on perceived spatial relations in computer-generated images was assessed are discussed. Each experiment examined the accuracy with which subjects matched the position, orientation, and size of a test object with a standard by interactively translating, rotating, and scaling the test object.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Microsatellite alterations plasma DNA of primary breast cancer patients. (2000)

The aim of this study was to analyze plasma DNA from primary and metastatic breast cancer cases for tumor-specific alterations and to compare these findings with immunocytochemistry and estimation of cytokeratin 19 (CK19) mRNA for detection of micrometastases. DNA was extracted from plasma, lymphocytes, and microdissected tumor tissue sections obtained from 71 patients with breast cancer and 9 controls. DNA samples were analyzed for loss of heterozygosity (LOH) and/or microsatellite instability (MI) by PCR with two polymorphic markers (DM-1 and D16S400). Reverse transcription-quantitative PCR (QPCR) and immunocytochemistry were used for detection of CK19 mRNA and protein. Breast cancer plasma DNA displayed frequent LOH (31.3%) and MI (11.6%) supported by the same alteration in microdissected tumor DNA. Most notably, 10 of the 39 patients with primary breast cancer showed LOH (n = 6) or MI (n = 4). We compared plasma tumor DNA, plasma and bone marrow QPCR, and blood and bone marrow immunocytochemistry in 32 of the patients with primary cancer. Of these, only one patient had immunocytochemically detectable carcinoma cells in the blood, and three showed abnormally high levels of plasma CK19 mRNA. All four of these patients had plasma DNA alterations. We then compared bone marrow findings: of the 10 primary breast cancers that showed LOH or MI, 6 had elevated CK19 mRNA and 5 had immunocytochemically positive cells. Tumor DNA is readily detectable in plasma of primary and metastatic breast cancer patients, and plasma DNA alterations (LOH and MI) reflect those seen in the tumor. The application of microsatellite analyses to plasma DNA may be useful in assessing tumor burden in breast cancer patients, particularly when combined with QPCR, and is preferable for patients with breast cancer, for whom sequential bone marrow aspiration is undesirable.
Bardoxolone Methyl in Type 2 Diabetes and Stage 4 Chronic Kidney Disease (2013)

Among patients with type 2 diabetes mellitus and stage 4 chronic kidney disease, bardoxolone methyl did not reduce the risk of ESRD or death from cardiovascular causes. A higher rate of cardiovascular events with bardoxolone methyl than with placebo prompted termination of the trial. (Funded by Reata Pharmaceuticals; BEACON ClinicalTrials.gov number, NCT01351675.).
Focusing Gain Model of Time-Reversed Signals in Dense Multipath Channels (2012)

The time reversal (TR) technique consists of transmitting in the channel a signal filtered by the time-reversed channel impulse response. To assess the performance of a TR system using impulse radio ultrawideband signals, one interesting parameter is the focusing gain defined as the ratio of the maxima in the time waveforms of the received signal with and without the time-reversal operation. We propose a heuristic approach to get an approximate analytical expression for the distribution function of this gain, as a function of the channel delay spread normalized to the pulse width and assuming a dense multipath environment. Predicted results are compared to experimental values obtained in reverberating chambers.
Correction for EPI distortions using multi-echo gradient-echo imaging (1999)

A novel and effective technique is described for distortion correction in echo planar imaging (EPI) utilizing the field maps derived from multi-echo gradient-echo images. The distortions from different off-resonance related factors such as field inhomogeneity, eddy current effect, radiofrequency pulse frequency offset, and chemical shift effect can be simultaneously reduced to a great extent. With the proposed post-processing algorithm of multi-channel modulation, distortions may be corrected without unwrapping the phase discontinuities in the derived field map, a process that usually restricts the application of other field map-based correction methods. Results from phantom and animal experiments at 4.7 T demonstrate the efficiency of the method in reducing the geometrical distortions in gradient-echo EPI.
Shape analogies (2002)

This sketch presents "Shape Analogies," a method for learning line styles from examples. With this approach, an artist or end-user simply draws in the desired style; the system analyzes the drawings and generates new imagery in the same style. For example, to design an outline style for a nervous character, one may draw a jittery stroke; to design an outline style for a robot, one may draw a very rigid style with many sharp angles.
BET Inhibition Induces Apoptosis in Aggressive B-Cell Lymphoma via Epigenetic Regulation of BCL-2 Family Members (2016)

Targeting BET bromodomain proteins using small molecules is an emerging anticancer strategy with clinical evaluation of at least six inhibitors now underway. Although MYC downregulation was initially proposed as a key mechanistic property of BET inhibitors, recent evidence suggests that additional antitumor activities are important. Using the Eμ-Myc model of B-cell lymphoma, we demonstrate that BET inhibition with JQ1 is a potent inducer of p53-independent apoptosis that occurs in the absence of effects on Myc gene expression. JQ1 skews the expression of proapoptotic (Bim) and antiapoptotic (BCL-2/BCL-xL) BCL-2 family members to directly engage the mitochondrial apoptotic pathway. Consistent with this, Bim knockout or Bcl-2 overexpression inhibited apoptosis induction by JQ1. We identified lymphomas that were either intrinsically resistant to JQ1-mediated death or acquired resistance following in vivo exposure. Strikingly, in both instances BCL-2 was strongly upregulated and was concomitant with activation of RAS pathways. Eμ-Myc lymphomas engineered to express activated Nras upregulated BCL-2 and acquired a JQ1 resistance phenotype. These studies provide important information on mechanisms of apoptosis induction and resistance to BET-inhibition, while providing further rationale for the translation of BET inhibitors in aggressive B-cell lymphomas. Mol Cancer Ther; 15(9); 2030-41. ©2016 AACR.
Chemical Changes in Tobacco during Flue-Curing (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical Changes in Tobacco during Flue-CuringC. W. Bacon, Raymond Wenger, and J. F. BullockCite this: Ind. Eng. Chem. 1952, 44, 2, 292–296Publication Date (Print):February 1, 1952Publication History Published online1 May 2002Published inissue 1 February 1952https://pubs.acs.org/doi/10.1021/ie50506a021https://doi.org/10.1021/ie50506a021research-articleACS PublicationsRequest reuse permissionsArticle Views250Altmetric-Citations22LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
From the director’s chair (2005)

The Department of Health publication Commissioning a Patient Led NHS spells out a new future for PCTs and SHAs. PCTS are going to become larger bodies which will focus on commissioning and no longer provide services. SHAs will cover larger areas than they currently do. However there is no clarity yet as to what their functions will be.
Metastatic cutaneous squamous cell carcinoma of the head and neck (2009)

: Patients who underwent surgery and received adjuvant radiotherapy had a better outcome compared with patients who underwent surgery alone. Patients who had moderate- or high-risk ITEM scores, usually because of extranodal spread and involved excision margins, had a poor outcome. The authors recommend considering these patients for inclusion in adjuvant chemoradiotherapy trials. Cancer 2009. (c) 2009 American Cancer Society.
Sterically Hindered Group IVA Organometallics. Preparation and Properties of Certain Neopentyltins1 (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSterically Hindered Group IVA Organometallics. Preparation and Properties of Certain Neopentyltins1Hans Zimmer, I. Hechenbleikner, Otto A. Homberg, and Mitchell DanzikCite this: J. Org. Chem. 1964, 29, 9, 2632–2636Publication Date (Print):September 1, 1964Publication History Published online1 May 2002Published inissue 1 September 1964https://pubs.acs.org/doi/10.1021/jo01032a038https://doi.org/10.1021/jo01032a038research-articleACS PublicationsRequest reuse permissionsArticle Views138Altmetric-Citations20LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Effect of deglycosylation on the binding and immunoreactivity of human thyroxine-binding globulin. (1979)

Thyroxine-binding globulin (TBG), prepared from human serum by an improved purification method, was treated with a mixture of neuraminidase, beta-galactosidase, alpha-mannosidase, and beta-N-aectylglucosaminidase, which resulted in the removal of approximately 86% of saccharides. Purification by thyroxine-Sepharose affinity chromatography gave a homogeneous protein as shown by equilibrium sedimentation and sodium dodecylsulfate-polyacrylamide gel electrophoresis. Amino acid and NH2-terminal sequence analysis indicated that the protein moiety was intact. Deglycosylation had no effect on the stoichiometry of the binding of L-thyroxine as shown by tryptophanyl fluorescence quenching and equilibrium dialysis at pH 8.6 and 25 degrees C. However, the affinity constant for L-thyroxine was reduced from 1.6 X 10(9) M-1 to 0.58 X 10(9) M-1. Analysis of radioimmunoassay data revealed that deglycosylation resulted in a slight decrease of the affinity constant for anti-TBG antibody from 3.9 X 10(10) M-1 to 1.8 X 10(10) M-1. These results suggest that the polypeptide moiety, rather than the heterosaccharides, contains the antigenic determinants. Removal of the majority of the heterosaccharides of TBG has only a minor effect on its immunoreactivity and on the binding of thyroid hormone.
An experimental comparison of min-cut/max- flow algorithms for energy minimization in vision (2004)

After [15], [31], [19], [8], [25], [5], minimum cut/maximum flow algorithms on graphs emerged as an increasingly useful tool for exact or approximate energy minimization in low-level vision. The combinatorial optimization literature provides many min-cut/max-flow algorithms with different polynomial time complexity. Their practical efficiency, however, has to date been studied mainly outside the scope of computer vision. The goal of this paper is to provide an experimental comparison of the efficiency of min-cut/max flow algorithms for applications in vision. We compare the running times of several standard algorithms, as well as a new algorithm that we have recently developed. The algorithms we study include both Goldberg-Tarjan style "push-relabel" methods and algorithms based on Ford-Fulkerson style "augmenting paths." We benchmark these algorithms on a number of typical graphs in the contexts of image restoration, stereo, and segmentation. In many cases, our new algorithm works several times faster than any of the other methods, making near real-time performance possible. An implementation of our max-flow/min-cut algorithm is available upon request for research purposes.
Transcription of genes encoding iron and heme acquisition proteins of Haemophilus influenzae during acute otitis media (1997)

Unencapsulated Haemophilus influenzae is the second most common etiologic agent of otitis media in children. H. influenzae requires heme for aerobic growth in vitro and is able to utilize hemoglobin and complexes of heme-hemopexin, heme-albumin, and hemoglobin-haptoglobin and ferritransferrin as sources of iron and heme in vitro. Several of the acquisition mechanisms have been characterized and been shown to be heme repressible in vitro. However, little is known about the expression of heme and/or iron acquisition mechanisms during infections in the middle ear. This study was performed to determine if the genes encoding heme and iron acquisition proteins are transcribed during in vivo growth and to compare these findings with those for samples grown in vitro. Reverse transcriptase PCR (RT-PCR) was used to analyze total RNA fractions derived from in vitro- and in vivo-grown H. influenzae. Genes encoding the transferrin-binding proteins TbpA and TbpB, the 100-kDa hemopexin-binding protein HxuA, and the hemoglobin-binding protein HgpA were transcribed during otitis media. Twelve middle ear fluid samples were analyzed by blind RT-PCR to determine the transcriptional status of these genes in H. influenzae during otitis media. Five isolates had transcripts corresponding to tbpA, tbpB, and hxuA. The presence of hgpA transcripts was variable, depending on the presence of hgpA in the genome of the H. influenzae isolate. Samples without H. influenzae gene transcripts contained other etiologic agents commonly causing otitis media. These data demonstrate that H. influenzae iron and/or heme acquisition genes are transcribed during otitis media and suggest that the microenvironment during acute otitis media starves H. influenzae of heme.