gebhart/patrepeval huggingface dataset:
Hybridoma cell lines secreting monoclonal antibodies to mouse H-2 and Ia antigens. (1980)

Hybridoma cell lines secreting antibodies to mouse H-2 or Ia antigens have been generated by fusing mouse immune lymphocytes with appropriate myeloma lines. Among the 11 established clones reported here, nine produce anti-H-2 antibodies and two produce anti-Ia antibodies. The specificities and cross-reactions of these monoclonal antibodies have been studied in detail. One hybridoma antibody reacted only to Kk antigens without any detectable cross-reactions, thus suggesting reaction to a private specificity of the Kk molecule. All other anti-H-2 hybridoma antibodies appeared to detect public specificities as defined either by reactions with products of more than one H-2 locus or with different alleles at one or more loci. The two anti-Ia antibodies both reacted with I-E/C products, but exhibited different cross-reactivity patterns. Strain distribution analyses so far indicate that the public specificities detected by these monoclonal antibodies are considerably different from those that had been established by traditional serology. Since public specificities defined by the hybridoma antibodies must by definition represent cross-reactions, these findings may have important implications relating to the structure and evolution of MHC gene products.
The impact of ion-host interactions on the 5d-to-4f spectra of lanthanide rare earth ions (1985)

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1985.
Statistical reduction of EEG data (2002)

Analyzing multi-channel EEG can be a daunting chore due to the volume of information that must be examined. For this reason, it is often more productive to reduce the data set by limiting the analysis to certain features or by selecting a subset of the data according to a certain criteria. One traditional method is to use frequency domain techniques to focus upon certain aspects of the data. However, when the frequency domain is used to analyze EEG data, the temporal domain features are lost. In this paper we examine an alternative method of data reduction and channel grouping using a statistical approach which retains time information.
Bumetanide and furosemide inhibited vascular endothelial cell proliferation (1994)

In this study, we examined the role of the bumetanide-sensitive Na+/K+/Cl-cotransport in the mitogenic signal of vascular endothelial cell proliferation. The activity of the Na+/K+/Cl- cotransport is dramatically decreased in quiescent subconfluent cells, as compared to subconfluent cells growing in the presence of FGF. The Na+/K+/Cl- cotransport activity of quiescent subconfluent cultures deprived of FGF decreased to 6%, whereas that of quiescent cells grown to confluency was reduced to only 33% of the activity of subconfluent cells growing in the presence of FGF. The basal low activity of Na+/K+/Cl- cotransport in the quiescent subconfluent vascular endothelial cells was dramatically stimulated by FGF. In order to explore the role of the Na+/K+/Cl- cotransport in the mitogenic signal of the endothelial cells, the effect of two specific inhibitors of the cotransport -furosemide and -bumetanide was tested on cell proliferation induced by FGF. Bumetanide and furosemide inhibited synchronized cell proliferation measured by direct counting of cells and by DNA synthesis. Inhibition by furosemide and bumetanide was reversible; removal of these compounds completely released the cells to proliferate. These results indicate that the effect of these drugs is specific and is not due to an indirect toxic effect. This study clearly demonstrates that the FGF-induced activation of the Na+/K+/Cl- cotransport plays a role in the mitogenic signal pathway of vascular endothelial cells.
Newly emerging roles for prostaglandin E2 regulation of hematopoiesis and hematopoietic stem cell engraftment (2010)

PGE2 has a new role in HSC homing and survival, as well as short-term-HSC engraftment. PGE2 is currently being tested in clinical trials as a potential therapy to enhance HSC engraftment following a transplantation procedure.
"In vitro" and multicolor phenotypic characterization of cell subpopulations identified in fresh human adipose tissue stromal vascular fraction and in the derived mesenchymal stem cells (2007)

The SVF is not a homogeneous cell population, and its final composition could be influenced both by the flow cytometric technique analysis and the SVF extraction steps. The CFU-F frequency in the SVF was 1/4880, a value about seven times greater than the data reported for bone marrow. The antigenic profile of AT-MSC was comparable with bone-marrow derived MSC. AT-MSC were able to differentiate along the osteogenic adipogenic and chondrogenic lineages. The data here reported, further contribute to the characterization of SVF, a tissue providing an alternative as a source of MSC for clinical applications.
Regularization approach to inductive genetic programming (2001)

This paper presents an approach to regularization of inductive genetic programming tuned for learning polynomials. The objective is to achieve optimal evolutionary performance when searching high-order multivariate polynomials represented as tree structures. We show how to improve the genetic programming of polynomials by balancing its statistical bias with its variance. Bias reduction is achieved by employing a set of basis polynomials in the tree nodes for better agreement with the examples. Since this often leads to over-fitting, such tendencies are counteracted by decreasing the variance through regularization of the fitness function. We demonstrate that this balance facilitates the search as well as enables discovery of parsimonious, accurate, and predictive polynomials. The experimental results given show that this regularization approach outperforms traditional genetic programming on benchmark data mining and practical time-series prediction tasks.
Self-stabilized magnetic colloids: Ultrafine Co particles in polymers (1996)

Self-stabilized magnetic colloids consist of magnetic particles dispersed in an appropriate matrix. Fixing the particles in a stabilizing matrix has the advantage of preventing particle agglomeration, increasing resistance to oxidation, and allowing control over the interparticle spacing and particle size. We describe the chemical synthesis of cobalt nanoparticles in a polystyrene/triphenylphosphine polymer matrix. Depending on the synthesis parameters, magnetic properties of the as-synthesized nanocomposites range from superparamagnetic to ferromagnetic with coercivities on the order of 130 Oe. Solvent choice and polymer crosslinking significantly affect the magnetic properties. Annealing in vacuum produces coercivities of up to 600 Oe and remanence ratios of up to 0.4. Measurement of the isothermal remanence magnetization and dc demagnetization indicate the presence of both magnetizing and demagnetizing interactions, in contrast to particles synthesized without the polymer, which show no evidence for magnetizing interactions. The zero-field-cooled temperature-dependent magnetization displays a cusp, while the field-cooled magnetization increases monotonically below the cusp temperature. Glassy behavior is observed for temperatures below the cusp, although the mechanism producing this behavior is not yet understood.
Fourier transform infrared spectroscopy of follicular fluids from large and small antral follicles (2000)

Fourier transform infrared spectroscopy (FTIR) was used to obtain 'biochemical fingerprints' for the constitution of follicular fluids from large and small antral luteinized follicles (n = 54 pairs). All samples gave reproducible characteristic biological infrared absorption spectra, with recognizable amide I protein vibrations and acyl vibrations from fatty acids. Discriminant function analysis of the first derivative FTIR spectra, together with hierarchical cluster analysis used to construct a dendrogram, showed fluid from large follicles formed a homogeneous closely related cluster, whilst that from small follicles was distinct from the large, and heterogeneous in nature. The large follicle fluids showed closer biochemical similarity to each other than to the corresponding fluid taken from small matched follicles. An artificial neural network was trained and following validation with an independent test set, successfully distinguished follicular fluids from large and small follicles. The sex steroid concentrations in the fluids from large and small follicles were significantly different. These results show that fluid from large follicles is distinct in biochemical nature from that from small follicles, but the degree of homogeneity implies size-specific changes take place. These may have consequences for the developmental potential of the oocyte.
Intravenous administration of phosphorylated acid alpha-glucosidase leads to uptake of enzyme in heart and skeletal muscle of mice. (1991)

The lysosomal storage disorder glycogenosis type II is caused by acid alpha-glucosidase deficiency. In this study we have investigated the possible applicability of mannose 6-phosphate receptor-mediated enzyme replacement therapy to correct the enzyme deficiency in the most affected tissues. Bovine testes acid alpha-glucosidase containing phosphorylated mannose residues was intravenously administered to mice and found to be taken up by heart (70% increase of activity) and skeletal muscle (43% increase); the major target organs. The uptake of nonphosphorylated human placenta acid alpha-glucosidase by heart and skeletal muscle appeared to be significantly less efficient, whereas uptake of dephosphorylated bovine testes enzyme was not detectable. The phosphorylated bovine testes acid alpha-glucosidase remained present in mouse skeletal muscle up to 9-15 d after administration, with a half-life of 2-4 d. Besides being measured in skeletal muscle and heart, uptake of phosphorylated bovine testes and nonphosphorylated human placenta acid alpha-glucosidase was measured in several other organs, but not in brain. The increase of acid alpha-glucosidase activity was highest in liver and spleen. We concluded that application of mannose 6-phosphate receptor-mediated enzyme replacement therapy may offer new perspectives for treatment of glycogenesis type II.
An Interesting Synthetic Application of S-Alkyl (Aryl)bis(alkylsulfanyl)thioacetates: General Procedure for the Preparation of (±)-α-Arylpropionic Acids (2002)

Reported here is a new procedure for the synthesis of α-arylpropionic acids 1 in the racemic form, starting from derivatives of aromatic carboxylic acids 2 (i.e., esters), via 1-aryl-2,2,2-tris(alkylsulfanyl)ethanones 4-6, S-alkyl (aryl)bis(alkylsulfanyl)thioacetates 7-9, S-alkyl α-aryl-α-(alkylsulfanyl)thiopropionates 10-12 and S-alkyl α-arylthiopropionates 13-15. Each stage takes place easily and yields are always high.
Dexmedetomidine versus Propofol Sedation Reduces Delirium after Cardiac Surgery (2015)

When compared with propofol, dexmedetomidine sedation reduced incidence, delayed onset, and shortened duration of POD in elderly patients after cardiac surgery. The absolute risk reduction for POD was 14%, with a number needed to treat of 7.1.
Stress proteins and regulation of microglial amyloid-β phagocytosis (2004)

Recent studies have indicated that prolonged dysfunction and/or stress in the endoplasmic reticulum (ER) may contribute to pathogenesis and neurodegeneration. The disorder caused by misfolding and aggregation of proteins has been referred to as conformational disease, including Alzheimer's disease (AD). AD is characterized by the accumulation of extracellular amyloid-beta1-42 (A beta 42) fibrils with reactive microglia. Understanding the balance of production and clearance of A beta 42 is the key to elucidating amyloid plaque homeostasis. We have recently found that microglial phagocytosis of A beta 42 may be essentially driven by dynamic reorganization of the actin cytoskeleton through the pathway of WAVE and Rac1. In addition, an extracellular stress protein, such as Hsp90, enhances A beta 42 phagocytosis. HMGB1 inhibits microglial phagocytosis of A beta 42, and it binds A beta 42 and stabilizes the oligomerization. These results suggest that microglial clearance of A beta 42 may be another option for investigations in the search for a therapeutic strategy for AD, in addition to the study of production and degradation of A beta 42.
cDNA-based functional domains of a calnexin-like melanosomal protein, p90. (1993)

We have recently identified a gene encoding a calnexin-like protein (p90) by the immunoscreening of a human melanoma cDNA library, using a rabbit anti-human melanosomal antibody. This p90 protein was highly expressed by human melanocytes and associated with melanosomal membrane and endoplasmic reticulum. In this study we report the computer analysis of the predicted amino acid sequence of this calnexin-like melanosomal protein. We found that p90 is a membrane-bound protein whose large N-terminal domain is located within the melanosomal compartment; its shorter C-terminal is exposed to the cytosol and separated by a short transmembrane region. This p90 protein was found to have consensus sequences of a Ca(2+)-binding loop and a protein kinase C phosphorylation site at the N-terminal domain. The C-terminal domain, on the other hand, contained sequences of a casein kinase II phosphorylation site and two protein kinase A phosphorylation sites. Such functional motifs could provide signal transduction across the melanosomal membrane, the reception of melanogenic protein via carriers at the melanosomal membrane and the translocation of melanosomes in the melanocyte.
Synthetic glycopeptides and glycoproteins as tools for biology (2004)

Investigations into the roles of protein glycosylation have revealed functions such as modulating protein structure and localization, cell-cell recognition, and signaling in multicellular systems. However, detailed studies of these events are hampered by the heterogeneous nature of biosynthetic glycoproteins that typically exist in numerous glycoforms. Research into protein glycosylation, therefore, has benefited from homogeneous, structurally-defined glycoproteins obtained by chemical synthesis. This tutorial review focuses on recent applications of homogeneous synthetic glycopeptides and glycoproteins for studies of structure and function. In addition, the future of synthetic glycopeptides and glycoproteins as therapeutics is discussed.
Applications of magnetic nanoparticles in biomedicine (2003)

The physical principles underlying some current biomedical applications of magnetic nanoparticles are reviewed. Starting from well-known basic concepts, and drawing on examples from biology and biomedicine, the relevant physics of magnetic materials and their responses to applied magnetic fields are surveyed. The way these properties are controlled and used is illustrated with reference to (i) magnetic separation of labelled cells and other biological entities; (ii) therapeutic drug, gene and radionuclide delivery; (iii) radio frequency methods for the catabolism of tumours via hyperthermia; and (iv) contrast enhancement agents for magnetic resonance imaging applications. Future prospects are also discussed.
Fast approximate string matching in a dictionary (2002)

A successful technique to search large textual databases allowing errors relies on an online search in the vocabulary of the text. To reduce the time of that online search, we index the vocabulary as a metric space. We show that with reasonable space overhead we can improve by a factor of two over the fastest online algorithms, when the tolerated error level is low (which is reasonable in text searching).
Theory of capture rate in polymer translocation (2010)

The translocation of macromolecules through a nanopore requires the impingement of the molecules at the pore followed by threading through the pore. While most of the discussion on the translocation phenomenon focused so far on the threading process, the phenomenology on the frequency of encounters between the polymer and the pore exhibits diverse features in terms of polymer length, solution conditions, driving force, and pore geometry. We derive a general theory for the capture rate of polyelectrolyte molecules and the probability of successful translocation through a nanopore, under an externally imposed electric field. By considering the roles of entropic barrier at the pore entrance and drift of the polyelectrolyte under the electric field, we delineate two regimes: (a) entropic barrier regime and (b) drift regime. In the first regime dominated by the entropic barrier for the polyelectrolyte, the capture rate is an increasing nonlinear function in the electric field and chain length. In the drift regime, where the electric field dwarfs the role of entropic barriers, the capture rate is independent of chain length and linear in electric field. An analytical formula is derived for the crossover behavior between these regimes, and the general results are consistent with various experimentally observed trends.
Increase in bleomycin-detectable iron in ischaemia/reperfusion injury to rat kidneys (1993)

Iron has been shown to be important in ischaemic, immune and toxic forms of tissue injury in various organs. Although it is generally accepted that iron participates in the generation of powerful oxidant species (e.g. hydroxyl radicals) there has not been any direct evidence that iron capable of catalysing free-radical reactions is increased in tissues in these models of injury. In the present study we demonstrate that ischaemia/reperfusion injury to the kidney results in no significant change in total, nonhaem or ferritin iron levels, but there is a marked and specific increase in bleomycin-detectable iron (capable of catalysing free-radical reactions) in the kidney. The increase in bleomycin-detectable iron is observed only after reperfusion but not during the ischaemic period. In a separate study we demonstrate that despite a drastic reduction in the iron content in the kidney, as a result of feeding an iron-deficient diet, there is a similar and a marked increase in the bleomycin-detectable iron in kidneys accompanied by a lack of protection against ischaemia/reperfusion injury.
SET: a pupil detection method using sinusoidal approximation (2015)

Mobile eye-tracking in external environments remains challenging, despite recent advances in eye-tracking software and hardware engineering. Many current methods fail to deal with the vast range of outdoor lighting conditions and the speed at which these can change. This confines experiments to artificial environments where conditions must be tightly controlled. Additionally, the emergence of low-cost eye tracking devices calls for the development of analysis tools that enable non-technical researchers to process the output of their images. We have developed a fast and accurate method (known as "SET") that is suitable even for natural environments with uncontrolled, dynamic and even extreme lighting conditions. We compared the performance of SET with that of two open-source alternatives by processing two collections of eye images: images of natural outdoor scenes with extreme lighting variations ("Natural"); and images of less challenging indoor scenes ("CASIA-Iris-Thousand"). We show that SET excelled in outdoor conditions and was faster, without significant loss of accuracy, indoors. SET offers a low cost eye-tracking solution, delivering high performance even in challenging outdoor environments. It is offered through an open-source MATLAB toolkit as well as a dynamic-link library ("DLL"), which can be imported into many programming languages including C# and Visual Basic in Windows OS (www.eyegoeyetracker.co.uk).
c-FMS inhibitors: a patent review (2011)

The c-FMS receptor is a hot target for the development of novel regulators of macrophage behavior. Some nice candidates have been developed by a number of groups, and their recent entry into clinical phase testing means that we are now on the cusp of a fuller understanding of the role of these important regulators of the innate and adaptive immune systems in the development of cancer and inflammatory diseases.
Distinct properties of wild‐type and the amyloidogenic human cystatin C variant of hereditary cerebral hemorrhage with amyloidosis, Icelandic type (2001)

Variant human cystatin C (L68Q) is an amyloidogenic protein. It deposits in the cerebral vasculature of Icelandic patients with cerebral amyloid angiopathy, leading to stroke. Wild-type and variant cystatin C are cysteine proteinase inhibitors which form concentration dependent inactive dimers; however, variant cystatin C dimerizes at lower concentrations and has an increased susceptibility to a serine protease. We studied the effect of the L68Q amino acid substitution on cystatin C properties, utilizing full length cystatin C purified in mild conditions from media of cells stably transfected with either the wild-type or variant cystatin C genes. The variant cystatin C forms fibrils in vitro detectable by electron microscopy in conditions in which the wild-type protein forms amorphous aggregates. We also show by circular dichroism, steady-state fluorescence and Fourier-transformed infrared spectroscopy that the amino acid substitution modifies cystatin C structure by destabilizing alpha-helical structures and exposing the tryptophan residue to a more polar environment, yielding a more unfolded molecule. These spectral changes demonstrate that variant cystatin C has a three-dimensional structure different from that of the wild-type protein. The structural differences between variant and wild-type cystatin C account for the susceptibility of the variant protein to unfolding, proteolysis and fibrillogenesis.
Immunogenicity, Including Vitiligo, and Feasibility of Vaccination With AutologousGM-CSF–Transduced Tumor Cells in Metastatic Melanoma Patients (2005)

We conclude that vaccination with GM-CSF-transduced autologous tumor cells has limited toxicity and can enhance T-cell activation against melanocyte differentiation antigens, which can lead to vitiligo. Whether the induction of autoimmune vitiligo may prolong disease-free survival of metastatic melanoma patients who are surgically rendered as having no evidence of disease before vaccination is worthy of further investigation.
Toxicological and pharmacological assessment of AGEN1884, a novel human IgG1 anti-CTLA-4 antibody (2018)

CTLA-4 and CD28 exemplify a co-inhibitory and co-stimulatory signaling axis that dynamically sculpts the interaction of antigen-specific T cells with antigen-presenting cells. Anti-CTLA-4 antibodies enhance tumor-specific immunity through a variety of mechanisms including: blockade of CD80 or CD86 binding to CTLA-4, repressing regulatory T cell function and selective elimination of intratumoral regulatory T cells via an Fcγ receptor-dependent mechanism. AGEN1884 is a novel IgG1 antibody targeting CTLA-4. It potently enhanced antigen-specific T cell responsiveness that could be potentiated in combination with other immunomodulatory antibodies. AGEN1884 was well-tolerated in non-human primates and enhanced vaccine-mediated antigen-specific immunity. AGEN1884 combined effectively with PD-1 blockade to elicit a T cell proliferative response in the periphery. Interestingly, an IgG2 variant of AGEN1884 revealed distinct functional differences that may have implications for optimal dosing regimens in patients. Taken together, the pharmacological properties of AGEN1884 support its clinical investigation as a single therapeutic and combination agent.
Coherent Electric Vibrations in Biological Systems and the Cancer Problem (1978)

The existence of coherent electric vibrations in the 5 x 10/sup 10/-3 x 10/sup 12/ Hz region has now been established experimentally for biologically active microorganisms. It is shown that such vibrations might play a decisive role in the control of growth of tissues and, hence, in the cancer problem.