gebhart/patrepeval huggingface dataset:
Lipolysis of LDL with phospholipase A2 alters the expression of selected apoB-100 epitopes and the interaction of LDL with cells (1988)

To assess the effects of perturbing the surface of low density lipoprotein (LDL) on the conformation of apoB-100, LDL (d 1.030-1.050 g/ml) isolated from normal subjects were treated with phospholipase A2 (PL-A2) for 0.5 to 15 min. The resulting P-LDL and concurrent control LDL (C-LDL) incubated without PL-A2 were isolated by gel permeation chromatography. Approximately 50% of LDL-phosphatidylcholine was hydrolyzed in 2 min and approximately 85% in 5 min. Lysophosphatidylcholine compounds (LPC) and free fatty acids (FFA) accumulated during lipolysis but most of the LPC and all of FFA could be removed by adding FFA-free albumin to the lipolysis mixtures. Immunoreactivities of P-LDL and C-LDL were evaluated in competitive radioimmunoassays, using a library of anti-human LDL monoclonal antibodies directed against the major regions of apoB-100 (the T4, T3, and T2 thrombin fragments). One epitope defined by monoclonal antibody 465B6C3 and localized near the carboxyl end of the apoB-100 molecule became less immunoreactive (ED 50s increased); three other epitopes on the T2 fragment near the LDL receptor recognition site and four epitopes localized towards the middle (T3) and amino terminal (T4) regions did not change. Altered immunoreactivities were not related to LPC and FFA contents. Thus, the conformation of apoB-100 was selectively altered by phospholipolysis. The interactions of P-LDL with cultured fibroblasts were grossly altered: P-LDL were bound nonspecifically to fibroblasts of both normal and homozygous familial hypercholesterolemic subjects and P-LDL were not degraded. LPC and FFA retained in LDL did not explain these alterations, nor did changes of epitope expression near the LDL receptor recognition site. It is likely that the apoB-100 aberrant cell interaction is due to loss of surface phospholipids and "uncovering" of core lipids that react nonspecifically with cell surface components.
ATRP of Methacrylates Utilizing CuIIX2/L and Copper Wire (2010)

Methacrylate monomers were successfully polymerized by ATRP utilizing copper wire as an in situ reducing agent at near-ambient temperatures (35 °C). Well-controlled polymerizations were demonstrated with both PMDETA and dNbpy ligands. Polymerization rates, when conducted with PMDETA, were dependent on the surface area of Cu0. Upon reduction of the copper deactivator concentration (i.e., CuIIBr2), polymerizations would only occur in the presence of excess ligand, whereas polymerization rates were independent of [CuIIBr2]. Proper selection of initiator and copper halide improved polymerization control with PMDETA. dNbpy was found to be an excellent ligand for MMA, resulting in polymerization systems with controlled behavior, predetermined molecular weights, narrow molecular weight distributions (Mw/Mn ≤ 1.2), and near-quantitative initiation. The versatility of dNbpy was demonstrated by polymerization of a wide range of methacrylates, synthesis of polymethacrylates with molecular weights up to 80 000, and efficient chain extension of a PMMA macroinitiator.
Selecting Receptive Fields in Deep Networks (2024)

Recent deep learning and unsupervised feature learning systems that learn from unlabeled data have achieved high performance in benchmarks by using extremely large architectures with many features (hidden units) at each layer. Unfortunately, for such large architectures the number of parameters can grow quadratically in the width of the network, thus necessitating hand-coded “local receptive fields ” that limit the number of connections from lower level features to higher ones (e.g., based on spatial locality). In this paper we propose a fast method to choose these connections that may be incorporated into a wide variety of unsupervised training methods. Specifically, we choose local receptive fields that group together those low-level features that are most similar to each other according to a pairwise similarity metric. This approach allows us to harness the advantages of local receptive fields (such as improved scalability, and reduced data requirements) when we do not know how to specify such receptive fields by hand or where our unsupervised training algorithm has no obvious generalization to a topographic setting. We produce results showing how this method allows us to use even simple unsupervised training algorithms to train successful multi-layered networks that achieve state-of-the-art results on CIFAR and STL datasets: 82.0 % and 60.1 % accuracy, respectively. 1
The Acidic Repetitive Domain of the Magnetospirillum gryphiswaldense MamJ Protein Displays Hypervariability but Is Not Required for Magnetosome Chain Assembly (2007)

Magnetotactic bacteria navigate along the earth's magnetic field using chains of magnetosomes, which are intracellular organelles comprising membrane-enclosed magnetite crystals. The assembly of highly ordered magnetosome chains is under genetic control and involves several specific proteins. Based on genetic and cryo-electron tomography studies, a model was recently proposed in which the acidic MamJ magnetosome protein attaches magnetosome vesicles to the actin-like cytoskeletal filament formed by MamK, thereby preventing magnetosome chains from collapsing. However, the exact functions as well as the mode of interaction between MamK and MamJ are unknown. Here, we demonstrate that several functional MamJ variants from Magnetospirillum gryphiswaldense and other magnetotactic bacteria share an acidic and repetitive central domain, which displays an unusual intra- and interspecies sequence polymorphism, probably caused by homologous recombination between identical copies of Glu- and Pro-rich repeats. Surprisingly, mamJ mutant alleles in which the central domain was deleted retained their potential to restore chain formation in a DeltamamJ mutant, suggesting that the acidic domain is not essential for MamJ's function. Results of two-hybrid experiments indicate that MamJ physically interacts with MamK, and two distinct sequence regions within MamJ were shown to be involved in binding to MamK. Mutant variants of MamJ lacking either of the binding domains were unable to functionally complement the DeltamamJ mutant. In addition, two-hybrid experiments suggest both MamK-binding domains of MamJ confer oligomerization of MamJ. In summary, our data reveal domains required for the functions of the MamJ protein in chain assembly and maintenance and provide the first experimental indications for a direct interaction between MamJ and the cytoskeletal filament protein MamK.
RNase-L-dependent Destabilization of Interferon-induced mRNAs (2000)

The 2–5A system is an interferon-regulated RNA degradation pathway with antiviral, growth-inhibitory, and pro-apoptotic activities. RNase-L mediates the antiviral activity through the degradation of viral RNAs, and the anticellular effects of the 2–5A system are thought to be similarly mediated through the degradation of cellular transcripts. However, specific RNase-L-regulated cellular RNAs have not been identified. To isolate candidate RNase-L substrates, differential display was used to identify mRNAs that exhibited increased expression in RNase-L-deficient N1E-115 cells as compared with RNase-L-transfected cells. A novel interferon-stimulated gene encoding a 43-kDa ubiquitin-specific protease, designated ISG43, was identified in this screen. ISG43 expression is induced by interferon and negatively regulated by RNase-L. ISG43 induction is a primary response to interferon treatment and requires a functional JAK/STAT signaling pathway. The kinetics of ISG43 induction were identical in wild type and RNase-L knock-out fibroblasts; however, the decline in ISG43 mRNA following interferon treatment was markedly attenuated in RNase-L knock-out fibroblasts. The delayed shut-off kinetics of ISG43 mRNA corresponded to an increase in its half-life in RNase-L-deficient cells. ISG15 mRNA also displayed RNase-L-dependent regulation. These findings identify a novel role for the 2–5A system in the attenuation of the interferon response.
Integrated data from 2 randomized, double‐blind, placebo‐controlled, phase 3 trials of active cellular immunotherapy with sipuleucel‐T in advanced prostate cancer (2009)

The integrated results of D9901 and D9902A demonstrate a survival benefit for patients treated with sipuleucel-T compared with those treated with placebo. The generally modest toxicity profile, coupled with the survival benefit, suggests a favorable risk-benefit ratio for sipuleucel-T in patients with advanced prostate cancer.
Modifying Effect of Selenium on Catalytic Reactivity of Transition Metals (1989)

Abstract Sodium selenite increased the catalytic reactivity of the metal salts (MoCl5, FeCl2, SnCl2, HgCl2, CuCl2, PbCl2 and AsCl3) and decreased that of the metal salts (NaAuCl4, AgCl, BiCl3, CoCl2, NiCl2, PdCl2, and Na2PtCl6) in the reduction of nitrobenzene to N-phenylhydroxylamine and/or aniline with sodium borohydride in water.
The Expression of Interleukin-6 in the Pregnant Rat Corpus Luteum and Its Regulation by Progesterone and Glucocorticoid* (1998)

Interleukin (IL)-6, a multifunctional cytokine originally described as a T cell-derived factor, is also produced by different cell types, and it influences a wide variety of physiological and pathophysiological processes. Recent studies further suggest that IL-6 has a role in down-regulating hormone production by endocrine organs and can negatively affect the steroidogenic capacity of both ovaries and testes. Thus, the aims of this investigation were to examine whether IL-6 plays a role in luteolysis and, more specifically, to determine whether luteal cells express the IL-6 gene, whether this expression is developmentally and hormonally regulated in pregnancy, and whether the corpus luteum could be a target for IL-6 action. Using semiquantitative RT-PCR, messenger RNA (mRNA) encoding both components of the IL-6 receptor [the ligand-binding subunit (IL-6 R) and the IL-6 R-associated signal transducer (gp130)] were found to be highly expressed in corpora lutea throughout pregnancy. In contrast, IL-6 mRNA expression was barely detectable from day 4 through the end of pregnancy, whereas a sharp and abrupt expression of IL-6 mRNA occurred immediately after parturition. Although the corpus luteum does not express IL-6 mRNA during most of pregnancy, it could be induced to express this gene with an in vivo injection of the bacterial endotoxin, lipopolysaccharide. In addition, when corpora lutea from day-15 pregnant rats were isolated and maintained in culture, IL-6 mRNA that was undetectable at 0 h increased in a time-related manner and reached significant levels after 4 h of incubation, followed by a similar increase in IL-6 protein secreted in the culture media. Isolation of the small and large luteal cells by elutriation indicated that both cell populations can secrete IL-6 in culture. The apparent ability of luteal cells to spontaneously express IL-6 in vitro, together with the lack of IL-6 expression during most of pregnancy, led us to examine whether the IL-6 gene is silenced throughout pregnancy by luteotropic hormones. Corpora lutea from day-15 pregnant rats were cultured in the presence of different doses of progesterone; the synthetic glucocorticoid, dexamethasone; 17beta-estradiol; and PRL. Progesterone and dexamethasone markedly inhibited IL-6 mRNA expression, whereas 17beta-estradiol had a minimal inhibitory effect, and PRL did not affect IL-6 mRNA expression. In summary, results of this investigation have revealed that the rat corpus luteum expresses the IL-6 receptor system and that luteal cells are able to secrete IL-6. However, IL-6 gene expression is silenced during most of pregnancy, probably by the high levels of progesterone locally produced in the corpus luteum. The salient finding that progesterone and glucocorticoid strongly inhibit the expression of IL-6 in the corpus luteum suggests that one important luteotropic role of progesterone and glucocorticoids could be to prevent the expression of IL-6, which might have a deleterious effect on luteal function.
Development of a robust framework for an outdoor mobile manipulation UAV (2016)

There is a growing interest to autonomously collect or manipulate objects in remote or unknown environments, such as mountains, gullies, bush-land, or rough terrain. There are several limitations of conventional methods using manned or remotely controlled aircraft. The capability of small Unmanned Aerial Vehicles (UAV) used in parallel with robotic manipulators could overcome some of these limitations. By enabling the autonomous exploration of both naturally hazardous environments, or areas which are biologically, chemically, or radioactively contaminated, it is possible to collect samples and data from such environments without directly exposing personnel to such risks. This paper covers the design, integration, and initial testing of a framework for outdoor mobile manipulation UAV. The framework is designed to allow further integration and testing of complex control theories, with the capability to operate outdoors in unknown environments. The results obtained act as a reference for the effectiveness of the integrated sensors and low-level control methods used for the preliminary testing, as well as identifying the key technologies needed for the development of an outdoor capable system.
FASTUS: A System for Extracting Information from Natural-Language Text (1992)

Abstract : FASTUS is a system for extracting information from free text in English, and potentially other languages as well, for entry into a database, and potentially for other applications. It works essentially as a cascaded, nondeterministic finite state automaton. There are four steps in the operation of FASTUS. In Step (1) sentences are scanned for certain trigger words to determine whether further processing should be done. In Step (2) noun groups, verb groups, and prepositions and some other particles are recognized. The input to Step (3) is the sequence of phrases recognized in Step (2); patterns of interest are identified in Step (3) and corresponding incident structures are built up. In Step (4) incident structures that derive from the same incident are identified and merged, and these are used in generating database entries. FASTUS is an order of magnitude faster than any comparable system; it can process a news report in an average of less than eleven seconds. This translates directly into fast development time. In the three and a half weeks between its first use and the MUC-4 evaluation in May 1992, we were able to build up its domain knowledge to a point where it was among the leaders in the evaluation.
Measurement of intracompartmental pressure: a comparison of the slit catheter, side-ported needle, and simple needle. (1993)

An experimental model of acute compartment syndrome involving the anterolateral compartment of the hindlimb in dogs was used to compare three methods of measurement of intracompartmental pressure: the simple-needle technique, use of the slit catheter, and use of the side-ported needle. No statistical difference was found between the values obtained with the slit catheter and those obtained with the side-ported needle; the mean difference was 1.4 millimeters of mercury throughout the range of compartment pressures that were measured. The side-ported needle appeared to be as accurate as the slit catheter for the measurement of compartment pressures (p = 0.355, 1-beta = 0.9). The values obtained with use of the simple needle were consistently higher than those obtained with the other two methods (p < 0.001): an average of 18.3 millimeters of mercury higher than the values measured with the slit catheter and 19.3 millimeters of mercury higher than those measured with the side-ported needle. Clinically, the side-ported needle or the slit catheter can be used to obtain accurate measurements of compartment pressure. Use of the simple 18-gauge needle is not recommended for this purpose.
One-Dimensional Gas Concentration Profiles Within a Burning Cigarette During a Puff (1975)

Abstract A technique for axial concentration measurements of several gas phase components of cigarette smoke during a two-second puff has been described. Gas concentration profiles constructed from these measurements were used to determine the axial order of the reactions which determine these concentrations. A one-dimensional model combustion reaction profile and a one-dimensional model coal temperature profile were presented. The diffusivities of several combustion gases through cigarette paper were calculated from the concentration data using the Owens-Reynolds model for the isothermal diffusion of gases through cigarette paper.
Trans-splicing as a possible molecular mechanism for the multiple isotype expression of the immunoglobulin gene. (1991)

We analyzed the molecular mechanism for the immunoglobulin (Ig) multiple isotype expression using a transgenic mouse (TG.SA) model system. Though most of the endogenous mu chain expression was excluded by the expression of the human rearranged mu transgene in the TG.SA mouse, a significant portion of splenic B lymphocytes could express the transgenic human IgM and endogenous mouse IgG simultaneously after stimulation with lipopolysaccharide and interleukin 4. The fluorescence-activated cell sorter-purified population of the human IgM+/mouse IgG+ cells expressed mRNA that consisted of properly spliced sequences of the transgenic VHDJH and the endogenous mouse C gamma genes (trans-mRNA), together with the transgenic human mu mRNA and germline transcripts of the mouse C gamma gene, without apparent rearrangement of the transgene. We also found that a lymphoma tumor, derived from the cross between the TG.SA mouse and another transgenic mouse carrying Ig H chain enhancer-driven c-myc oncogene, expressed about equal levels of the trans-mRNA and the transgenic mu mRNA without DNA rearrangement in either the transgene or the endogenous mouse switch region. These findings strongly support our previous proposal that the trans-splicing can account for the multiple isotype expression in this transgenic model and also suggest that novel molecular mechanism(s) might be involved in this reaction.
Conformational and Linear B-Cell Epitopes of Asp f 2, a Major Allergen ofAspergillus fumigatus, Bind Differently to Immunoglobulin E Antibody in the Sera of Allergic Bronchopulmonary Aspergillosis Patients (1999)

Asp f 2 is a major Aspergillus fumigatus allergen involved in allergic bronchopulmonary aspergillosis. Knowledge of the B-cell epitopes may contribute to the understanding of immunoregulation and immunodiagnosis. To elucidate the immunoglobulin E (IgE) binding epitopes in the linear sequence of Asp f 2, we synthesized decamer peptides spanning the whole molecule of Asp f 2 on derivatized cellulose membranes and evaluated IgE binding in ABPA patient and control sera. Peptides three to five amino acids long were synthesized based on amino acid sequences within the IgE binding regions and evaluated for the specificity of epitope antibody interactions. Nine IgE binding regions were recognized in this protein of 268 amino acid residues. Of the nine epitopes, seven (ATQRRQI, RKYFG, HWR, YTTRR, DHFAD, ALEAYA, and THEGGQ) are present in the hydrophilic regions of Asp f 2. Immunologic evaluation of the three recombinant fragments, Asp f 2A encompassing the N-terminal epitope region, Asp f 2B without N- and C-terminal regions of the protein, and Asp f 2C representing C-terminal epitopes, revealed that either the N- or C-terminal region of the protein is essential for the correct folding and conformation for IgE antibody binding.
Neuromodulation of evoked muscle potentials induced by epidural spinal-cord stimulation in paralyzed individuals (2013)

Epidural stimulation (ES) of the lumbosacral spinal cord has been used to facilitate standing and voluntary movement after clinically motor-complete spinal-cord injury. It seems of importance to examine how the epidurally evoked potentials are modulated in the spinal circuitry and projected to various motor pools. We hypothesized that chronically implanted electrode arrays over the lumbosacral spinal cord can be used to assess functionally spinal circuitry linked to specific motor pools. The purpose of this study was to investigate the functional and topographic organization of compound evoked potentials induced by the stimulation. Three individuals with complete motor paralysis of the lower limbs participated in the study. The evoked potentials to epidural spinal stimulation were investigated after surgery in a supine position and in one participant, during both supine and standing, with body weight load of 60%. The stimulation was delivered with intensity from 0.5 to 10 V at a frequency of 2 Hz. Recruitment curves of evoked potentials in knee and ankle muscles were collected at three localized and two wide-field stimulation configurations. Epidural electrical stimulation of rostral and caudal areas of lumbar spinal cord resulted in a selective topographical recruitment of proximal and distal leg muscles, as revealed by both magnitude and thresholds of the evoked potentials. ES activated both afferent and efferent pathways. The components of neural pathways that can mediate motor-evoked potentials were highly dependent on the stimulation parameters and sensory conditions, suggesting a weight-bearing-induced reorganization of the spinal circuitries.
Cancer and Thrombosis (1994)

Thrombosis is the most frequent complication and the second cause of death in patients with overt malignant disease. Increasing evidence suggests that thrombotic episodes may also precede the diagnosis of cancer by months or years thus representing a potential marker for occult malignancy. Recently, emphasis has been given to the potential risk of cancer therapy (both surgery and chemotherapy) in enhancing the risk for thromboembolic disease. Post-operative deep vein thrombosis is indeed more frequent in patients operated for malignant diseases than for other disorders. On the other hand, both chemotherapy and hormone therapy are associated with an increased thrombotic risk, which can be prevented by low-dose oral anticoagulation. Possible contributory causes for thromboembolic disease in cancer include the capacity of tumor cells and their products to interact with platelets, clotting and fibrinolytic systems, as well as their interactions with endothelial cells and tumor-associated macrophages. Cytokine release, acute phase reaction and neovascularization may contribute, in cancer patient, to in vivo clotting activation, which is well documented by several plasmatic markers of an hypercoagulable state. Last but not least, a direct pathogenetic role of clotting activation in the progression of malignancy has been repeatedly proposed on the basis of pharmacological studies with anticoagulant/fibrinolytic drugs in experimental animals and selected clinical malignancies, as well as, lately, in genetically modified animal models (e.g. mice transgenic for PAI-1).