gebhart/patrepeval huggingface dataset:
Selection of a monoclonal antibody reactive with a high-molecular-weight glycoprotein circulating in the body fluid of gastrointestinal cancer patients. (1988)

The monoclonal antibody NCC-CO-450 (IgM kappa) was selected by screening of reactivity with high-molecular-weight antigens (Mr greater than 10(6] isolated from ascitic fluid of a colon cancer patient. This antibody detected heterogeneous but predominantly high-molecular-weight antigens in 4 of 6 ascitic fluid samples from gastrointestinal cancer patients by immunoblotting analysis. A sandwich radioimmunoassay was developed in order to examine the serum level of this antigen, and the cutoff value was defined as the mean plus 2 SD of values obtained with sera from normal donors. While 97% (93 of 96) of sera had a negative antigen value in normal donors, 56% (14 of 25) of patients with colorectal carcinoma and 40% (8 of 20) of patients with gastric carcinoma showed a positive antigen value. The distribution of the antigen in sera of patients with various cancers did not show any correlation with the distribution of carcinoembryonic antigen or CA 19-9. From immunohistochemical and biochemical analyses, NCC-CO-450 antigen was characterized as a mucin-like glycoprotein abundant in normal colonic epithelium as well as in carcinomas of the colon, stomach, and pancreas. The immunohistochemical reactivity of NCC-CO-450 was distinct from that of other monoclonal antibodies reported to be useful for serological diagnosis. The epitope recognized by NCC-CO-450 is considered to be an O-linked carbohydrate chain without terminal sialic acid but is different from the known carbohydrate chains, i.e., Lea, Lex, LeY, Tn, sialyl-Lea, and sialyl sugar chain defined by NCC-ST-439 in a competitive binding inhibition assay of monoclonal antibodies. This newly defined antigen is a good example of a normal antigen shed from cancer cells that can be used successfully as a serum tumor marker.
Modulation of Neuronal Migration by NMDA Receptors (1993)

The N-methyl-D-aspartate (NMDA) subtype of the glutamate receptor is essential for neuronal differentiation and establishment or elimination of synapses in a developing brain. The activity of the NMDA receptor has now been shown to also regulate the migration of granule cells in slice preparations of the developing mouse cerebellum. First, blockade of NMDA receptors by specific antagonists resulted in the curtailment of cell migration. Second, enhancement of NMDA receptor activity by the removal of magnesium or by the application of glycine increased the rate of cell movement. Third, increase of endogenous extracellular glutamate by inhibition of its uptake accelerated the rate of cell migration. These results suggest that NMDA receptors may play an early role in the regulation of calcium-dependent cell migration before neurons reach their targets and form synaptic contacts.
Isolation and characterisation of plant defensins from seeds of Asteraceae, Fabaceae, Hippocastanaceae and Saxifragaceae (1995)

From seeds of Aesculus hippocastanum, Clitoria ternatea, Dahlia merckii and Heuchera sanguinea five antifungal proteins were isolated and shown to be homologous to plant defensins previously characterised from radish seeds and gamma-thionins from Poaceae seeds. Based on the spectrum of their antimicrobial activity and the morphological distortions they induce on fungi the peptides can be divided into two classes. The peptides did not inhibit any of three different alpha-amylases.
Isolation, Co-Crystallization and Structure-Based Characterization of Anabaenopeptins as Highly Potent Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (TAFIa) (2016)

Mature thrombin activatable fibrinolysis inhibitor (TAFIa) is a carboxypeptidase that stabilizes fibrin clots by removing C-terminal arginines and lysines from partially degraded fibrin. Inhibition of TAFIa stimulates the degradation of fibrin clots and may help to prevent thrombosis. Applying a lead finding approach based on literature-mining, we discovered that anabaenopeptins, cyclic peptides produced by cyanobacteria, were potent inhibitors of TAFIa with IC50 values as low as 1.5 nM. We describe the isolation and structure elucidation of 20 anabaenopeptins, including 13 novel congeners, as well as their pronounced structure-activity relationships (SAR) with respect to inhibition of TAFIa. Crystal structures of the anabaenopeptins B, C and F bound to the surrogate protease carboxypeptidase B revealed the binding modes of these large (~850 Da) compounds in detail and explained the observed SAR, i.e. the strong dependence of the potency on a basic (Arg, Lys) exocyclic residue that addressed the S1' binding pocket, and a broad tolerance towards substitutions in the pentacyclic ring that acted as a plug of the active site.
A Study of Deterministic Pilot Allocation for Sparse Channel Estimation in OFDM Systems (2012)

In this letter, we investigate the deterministic pilot allocation for sparse channel estimation in OFDM systems. Based on the rule of minimizing the coherence of the DFT submatrix, we derive that the pilot design according to the cyclic different set (CDS) is optimal. However, the CDS only exists for some specific number of OFDM subcarriers. For those cases where the CDS is unavailable, we propose a scheme using discrete stochastic approximation to obtain a near-optimal pilot pattern. Simulation results demonstrate that our scheme is much faster convergent and more efficient than the exhaustive search; and it has been shown that substantial improvement for channel estimation can be achieved.
XPS Characterization of the Surface Oxide Film of 316L Stainless Steel Samples that were Located in Quasi-Biological Environments (2002)

The purpose of this study was to characterize the surface oxide films on 316L austenitic stainless steel located in various environments to estimate the reconstruction of the film in human body. Five kinds of specimens were prepared according to the following methods: polished in deionized water, autoclaved, immersed in Hanks’ solution, immersed in cell culture medium, and incubated with cultured cells. X-ray photoelectron spectroscopy (XPS) was performed to estimate the compositions of the surface oxide film and substrate and the thickness of the film. Surface oxide film on 316L steel after polished in water consists of iron and chromium oxides containing small amount of nickel, molybdenum, and manganese oxides. The surface oxide contained a large amount of OH−. Calcium phosphate was formed on/in the film after immersion in the Hanks’ solution and medium and incubated with the cells. Sulfate is adsorbed by the surface oxide film and reduced to sulfite and/or sulfate in cell culture medium and with culturing cells. The results in this study suggest that nickel and manganese are depleted in the oxide film and the surface oxide changes into iron and chromium oxides containing a small amount of molybdenum oxide in human body.
An incremental learning technique for detecting driving behaviors using collected EV big data (2015)

This paper presents an expansible machine learning approach applying the EV big data as the human sensor to extract driving behaviors and driving modes. A pattern recognition approach is proposed to model the driving pattern according to the energy consumption of an EV. The growing hierarchical self-organizing maps (GHSOM) is applied to learn driver's behaviors gradually in the offline process, and the clustered neurons are used as the training sets for implementing online classifiers based on support vector machine (SVM). This proposed framework would facilitate the understanding of driver's behaviors and help drivers overcome range anxiety.
Antigen-Specific Immune Responses and Clinical Outcome After Vaccination With Glioma-Associated Antigen Peptides and Polyinosinic-Polycytidylic Acid Stabilized by Lysine and Carboxymethylcellulose in Children With Newly Diagnosed Malignant Brainstem and Nonbrainstem Gliomas (2014)

GAA peptide vaccination in children with gliomas is generally well tolerated and has preliminary evidence of immunologic and clinical responses. Careful monitoring and management of pseudoprogression is essential.
Joint Object and Part Segmentation Using Deep Learned Potentials (2015)

Segmenting semantic objects from images and parsing them into their respective semantic parts are fundamental steps towards detailed object understanding in computer vision. In this paper, we propose a joint solution that tackles semantic object and part segmentation simultaneously, in which higher object-level context is provided to guide part segmentation, and more detailed part-level localization is utilized to refine object segmentation. Specifically, we first introduce the concept of semantic compositional parts (SCP) in which similar semantic parts are grouped and shared among different objects. A two-stream fully convolutional network (FCN) is then trained to provide the SCP and object potentials at each pixel. At the same time, a compact set of segments can also be obtained from the SCP predictions of the network. Given the potentials and the generated segments, in order to explore long-range context, we finally construct an efficient fully connected conditional random field (FCRF) to jointly predict the final object and part labels. Extensive evaluation on three different datasets shows that our approach can mutually enhance the performance of object and part segmentation, and outperforms the current state-of-the-art on both tasks.
On Internet Traffic Classification: A Two-Phased Machine Learning Approach (2016)

Traffic classification utilizing flow measurement enables operators to perform essential network management. Flow accounting methods such as NetFlow are, however, considered inadequate for classification requiring additional packet-level information, host behaviour analysis, and specialized hardware limiting their practical adoption. This paper aims to overcome these challenges by proposing two-phased machine learning classification mechanism with NetFlow as input. The individual flow classes are derived per application through<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:mi>k</mml:mi></mml:mrow></mml:math>-means and are further used to train a C5.0 decision tree classifier. As part of validation, the initial unsupervised phase used flow records of fifteen popular Internet applications that were collected and independently subjected to<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mrow><mml:mi>k</mml:mi></mml:mrow></mml:math>-means clustering to determine unique flow classes generated per application. The derived flow classes were afterwards used to train and test a supervised C5.0 based decision tree. The resulting classifier reported an average accuracy of 92.37% on approximately 3.4 million test cases increasing to 96.67% with adaptive boosting. The classifier specificity factor which accounted for differentiating content specific from supplementary flows ranged between 98.37% and 99.57%. Furthermore, the computational performance and accuracy of the proposed methodology in comparison with similar machine learning techniques lead us to recommend its extension to other applications in achieving highly granular real-time traffic classification.
Identification of endothelial cell genes by combined database mining and microarray analysis (2003)

Vascular endothelial cells maintain the interface between the systemic circulation and soft tissues and mediate critical processes such as inflammation in a vascular bed-selective fashion. To expand our understanding of the genetic pathways that underlie these specific functions, we have focused on the identification of novel genes that are differentially expressed in all endothelial cells, as well as restricted groups of this cell type. Virtual subtraction was conducted employing gene expression data deposited in public databases and 384 genes identified. These genes were spotted on custom microarrays, along with 288 genes identified through subtraction cloning from TGF-beta-stimulated endothelial cells. Arrays were evaluated with RNA samples representing endothelial cells cultured from four vascular sources and five non-endothelial cell types. These studies identified 64 pan-endothelial markers that were differentially expressed with at least a threefold difference (range 3- to 55-fold). In addition, differences in gene expression profiles among endothelial cells from different vascular beds were identified. Validation of these findings was performed by RNA blot expression studies, and a number of the novel genes were shown to be expressed under angiogenic conditions in the developing mouse embryo. The combined tools of database mining and transcriptional profiling thus provide expanded knowledge of endothelial cell gene expression and endothelial cell biology.
Segmentation and quantification of retinal lesions in age-related macular degeneration using polarization-sensitive optical coherence tomography (2010)

We present polarization-sensitive optical coherence tomography (PS-OCT) for quantitative assessment of retinal pathologies in age-related macular degeneration (AMD). On the basis of the polarization scrambling characteristics of the retinal pigment epithelium, novel segmentation algorithms were developed that allow one to segment pathologic features such as drusen and atrophic zones in dry AMD as well as to determine their dimensions. Results from measurements in the eyes of AMD patients prove the ability of PS-OCT for quantitative imaging based on the retinal features polarizing properties. Repeatability measurements were performed in retinas diagnosed with drusen and geographic atrophy in order to evaluate the performance of the described methods. PS-OCT appears as a promising imaging modality for three-dimensional retinal imaging and ranging with additional contrast based on the structures' tissue-inherent polarization properties.
Experimental test of scaling of mixing by chaotic advection in droplets moving through microfluidic channels (2003)

This letter describes an experimental test of a simple argument that predicts the scaling of chaotic mixing in a droplet moving through a winding microfluidic channel. Previously, scaling arguments for chaotic mixing have been described for a flow that reduces striation length by stretching, folding, and reorienting the fluid in a manner similar to that of the baker's transformation. The experimentally observed flow patterns within droplets (or plugs) resembled the baker's transformation. Therefore, the ideas described in the literature could be applied to mixing in droplets to obtain the scaling argument for the dependence of the mixing time, t~(aw/U)log(Pe), where w [m] is the cross-sectional dimension of the microchannel, a is the dimensionless length of the plug measured relative to w, U [m s(-1)] is the flow velocity, Pe is the Péclet number (Pe=wU/D), and D [m(2)s(-1)] is the diffusion coefficient of the reagent being mixed. Experiments were performed to confirm the scaling argument by varying the parameters w, U, and D. Under favorable conditions, submillisecond mixing has been demonstrated in this system.
An Assay for the Quantitation of Photofrin in Tissues and Fluids (1997)

A method for determining the concentration of Photofrin in tissues and biological fluids was developed. The procedure is based on the dissolution of biological material with Solvable, a commercially available tissue solubilizer, followed by porphyrin-specific fluorescence detection and measurement. It was found necessary to use a quadratic standard curve for the estimation of unknown Photofrin concentrations. While this method is limited to compounds that are stable in strong base, it has the advantages of being sensitive, rapid and low cost.
Improving the binding affinity of an antibody using molecular modeling and site‐directed mutagenesis (1998)

Activated Factor X releases F1.2, a 271-amino acid peptide, from the amino terminus of prothrombin during blood coagulation. A nine-amino acid peptide, C9 (DSDRAIEGR), corresponding to the carboxyl terminus of F1.2 was synthesized and used to produce a monoclonal antibody, TA1 (K(D)) 1.22 x 10(-6) M). To model the TA1 antibody, we entered the sequence information of the cloned TA1 Fv into the antibody modeling program, ABM, which combines homology methods, conformational search procedures, and energy screening and has proved to be a reliable and reproducible antibody modeling method. Using a novel protein fusion procedure, we expressed the C9 peptide fused to the carboxyl terminus of the PENI repressor protein from Bacillus licheniformis in Escherichia coli. We constructed fusion proteins containing alanine substitutions for each amino acid in the C9 epitope. Binding studies, using the C9 alanine mutants and TA1, and spatial constraints predicted by the modeled TA1 binding cleft enabled us to establish a plausible conformation for C9 complexed with TA1. Furthermore, based on binding results of conservative amino acid substitutions in C9 and mutations in the antibody, we were able to refine the complex model and identify antibody mutations that would improve binding affinity.
DNA Sequencing Based on Intrinsic Molecular Charges (2006)

Ladungszunahme: Markierungsfreie DNA-Sequenzierung gelingt über den Nachweis der intrinsischen Molekülladung mithilfe eines Feldeffekttransistors (siehe Bild). Oligonucleotidsonden werden auf der Oberfläche des Si3N4-Gatters immobilisiert und mit der passenden Ziel-DNA hybridisiert. Die Änderung der Ladungsdichte am Si3N4/SiO2-Gatter, die durch jede Einzelbasenverlängerung ausgelöst wird, bewirkt eine Verschiebung der Grenzspannung. VG=Gatterspannung.
Inhibition of Postsynaptic PKC or CaMKII Blocks Induction But Not Expression of LTP (1989)

Long-term potentiation (LTP) of synaptic transmission is a widely studied cellular example of synaptic plasticity. However, the identity, localization, and interplay among the biochemical signals underlying LTP remain unclear. Intracellular microelectrodes have been used to record synaptic potentials and deliver protein kinase inhibitors to postsynaptic CA1 pyramidal cells. Induction of LTP is blocked by intracellular delivery of H-7, a general protein kinase inhibitor, or PKC(19-31), a selective protein kinase C (PKC) inhibitor, or CaMKII(273-302), a selective inhibitor of the multifunctional Ca2+-calmodulin-dependent protein kinase (CaMKII). After its establishment, LTP appears unresponsive to postsynaptic H-7, although it remains sensitive to externally applied H-7. Thus both postsynaptic PKC and CaMKII are required for the induction of LTP and a presynaptic protein kinase appears to be necessary for the expression of LTP.
Vaccines containing purified GM2 ganglioside elicit GM2 antibodies in melanoma patients. (1987)

GM2, GD2, and GD3 gangliosides are expressed on the surface of human melanoma cells and represent potential targets for immunological control of melanoma growth by monoclonal antibodies and active immunization. The immunogenicity of GM2 was investigated by analyzing the humoral immune response of melanoma patients to vaccination with cell lines selected for high GM2 expression and with vaccines containing purified GM2. The whole-cell vaccine and vaccines containing purified GM2 and bacillus Calmette-Guérin (BCG) elicited GM2 antibody in a high proportion of patients, particularly in GM2/BCG-vaccinated patients pretreated with cyclophosphamide and given a GM2/BCG booster immunization. Vaccines containing purified GM2 and Salmonella minnesota R595 as the adjuvant were also effective, but only in patients pretreated with cyclophosphamide. GM2 antibodies in vaccinated patients were of the IgM class and were cytotoxic for GM2-positive targets in the presence of human complement.
Methylation Profile and Amplification of Proto-Oncogenes in Rat Pancreas Induced with Phytoestrogens (1995)

Specific gene hypermethylation has been shown in DNA from neonatal rats exposed to the phytoestrogens, coumestrol, and equol. The pancreas is an organ in which estrogen receptors have been shown to be present. Studies have correlated the development of acute pancreatitis with rising levels of human estrogen binding proteins. Neonatal rats were dosed with 10 or 100 micrograms of coumestrol or equol on postnatal day (PND) 1-10. The animals were sacrificed at Day 15. The pancreas was excised and pancreatic acinar cells isolated for molecular analysis. DNA was isolated from the cells by lysis in TEN-9 buffer supplemented with proteinase K and 0.1% SDS. High molecular weight (HMW) DNA was digested with the methylated DNA specific restriction enzymes, Hpa II and Msp I, for determination of methylation profiles. Both coumestrol and equol at high doses caused hypermethylation of the c-H-ras proto-oncogene. No hypermethylation or hypomethylation was observed in the proto-oncogenes, c-myc or c-fos. Methylation is thought to be an epigenetic mechanism involved in the activation (hypomethylation) or inactivation (hypermethylation) of cellular genes which are known to play a role in carcinogenesis. Epidemiology studies have shown that equol may have anti-carcinogenic effects on some hormone-dependent cancers. Additional studies are needed to further understand the role of phytoestrogens and methylation in relation to pancreatic disorders.
The logic of experience: developing appropriate care through effective collaboration. (1996)

The unique role of the psychiatric nurse has always been to facilitate the psychosocial if not the spiritual healing of the person with mental illness. The manner in which psychiatric nurses exercise this 'psychic healing' function distinguishes them from other nurses. What is controversial about this view is the belief that psychiatric nursing is a spiritual activity. In this paper it is argued that psychiatric nursing is practised in a semi-public context in which patients and nurses re-affirm their need for self-examination as a core element of the life process. It is also argued that psychiatric nursing is a maturing force that educates people in the life process. The concept of 'trephotaxis', or the provision of the necessary conditions for the promotion of growth and development, is introduced as the defining characteristic of a new era. In this era the essential value of life and of nursing is comprehended as part of the flow of life as nurses loss themselves in their relationships with patients. Through this process nurses come to understand the stories they are told by their patients and to appreciate the point of patients' illnesses, and possibly the patients' lives.
Persona: a contextualized and personalized web search (2003)

Recent advances in graph-based search techniques derived from Kleinberg's (1997) work have been impressive. This paper further improves the graph-based search algorithm in two dimensions. Firstly, variants of Kleinberg's techniques do not take into account the semantics of the query string nor of the nodes being searched. As a result, polysemy of query words cannot be resolved. This paper presents an interactive query scheme utilizing the simple Web taxonomy provided by the Open Directory Project to resolve meanings of a user query. Secondly, we extend a recently proposed personalized version of the Kleinberg algorithm (Chang et al., 2000). Simulation results are presented to illustrate the sensitivity of our technique. We outline the implementation of our algorithm in the Persona personalized web search system.
The ILLIAC IV Computer (1968)

Abstract—The structure of ILLIAC IV, a parallel-array computer containing 256 processing elements, is described. Special features include multiarray processing, multiprecision arithmetic, and fast data-routing interconnections. Individual processing elements execute 4×10<R>6</R> instructions per second to yield an effective rate of 109 operations per second.