gebhart/patrepeval huggingface dataset:
Implications and concepts of polyamine‐nucleic acid interactions (1991)

Modeling, x-ray diffraction, and solution studies have contributed to the understanding of interactions between polyamines and nucleic acids. Polyamines stabilize a variety of unusual DNA structures and conformations in vitro, including both the left-handed Z and the right-handed A DNA. In addition, polyamines condense DNA and may be important in bending specific sequences. Investigations into the mechanisms of these effects provide support for both specific and nonspecific interactions between polyamines and DNA. Although exact relationships between the binding of polyamines and conformational changes in nucleic acids are still being clarified, polyamines remain important candidates for regulators of DNA conformation in vivo.
Mannan binding protein in sera positive for rheumatoid factor (1997)

Low levels of mannan binding protein (MBP) may protect against rheumatoid arthritis and other inflammatory conditions associated with agalactosyl IgG. MBP concentrations were measured in 99 sera found to be positive for rheumatoid factor, at least 41 of which were from patients with rheumatoid arthritis, and the values compared to the data from 352 controls. MBP was undetectable in similar proportions of patients' and control sera (4.0 and 4.3%, respectively), and low values generally were similarly distributed in the two groups. Overall, however, the patient values were distorted upwards relative to controls, consistent with an acute-phase response. These findings do not refute the proposed role for MBP-agalactosyl IgG-mediated complement activation in the pathogenesis of rheumatoid arthritis, but certainly provide no support for that hypothesis.
Expression of the c-myb proto-oncogene in bovine vascular smooth muscle cells. (1992)

Previously we have shown that bovine vascular smooth muscle cells (SMCs) express c-myb mRNA (Reilly, C. F., Kindy, M. S., Brown, K. E., Rosenberg, R. D., and Sonenshein, G. E. (1989) J. Biol. Chem. 264, 6990-6995). Here we have characterized changes in the low level of c-myb mRNA expressed in quiescent serum-deprived subconfluent SMCs upon entry into the cell cycle. After serum stimulation, levels of c-myb mRNA increased 3-4-fold during late G1 and remained at this level during S phase. A 1.5-kilobase partial c-myb cDNA clone, isolated from a bovine SMC library, was partially sequenced and found to be 89 and 85% homologous to the human and murine c-myb genes, respectively. Using bovine and murine c-myb clones, no change in the rate of c-myb gene transcription or mRNA stability was detected during the cell cycle. Thus, the regulation of changes in c-myb mRNA levels in SMCs appears distinct from mechanisms seen in hematopoietic or fibroblastic cells. Vectors containing myb binding sites linked to the thymidine kinase promoter and the chloramphenicol acetyltransferase reporter gene were transiently transfected into SMC cultures. KHK-CAT-dAX, which contains nine concatenated myb binding sites, exhibited 7-fold more activity than the parental dAX-TK-CAT vector in exponentially growing SMCs. The levels of chloramphenicol acetyltransferase activity in exponentially growing cells were approximately 2-fold higher than in cells that had been serum deprived for 24 h and were entering quiescence. Thus SMCs produce a functional c-myb protein that can activate transcription from a heterologous promoter. Furthermore, introduction of antisense c-myb oligonucleotides to quiescent serum-deprived SMC cultures severely inhibited entry of cells into S phase upon serum addition. Thus, expression of the c-myb oncogene plays an important role in cell cycle progression of SMCs.
A Role for Thymic Stromal Lymphopoietin in CD4+ T Cell Development (2004)

Thymic stromal lymphopoietin (TSLP) signals via a receptor comprising the interleukin (IL)-7 receptor alpha chain and a distinctive subunit, TSLP receptor (TSLPR), which is most related to the common cytokine receptor gamma chain, gamma(c). We have generated TSLPR knockout (KO) mice and found that although these mice had normal lymphocyte numbers, gamma(c)/TSLPR double KO mice had a greater lymphoid defect than gamma(c) KO mice. This indicates that TSLP contributes to lymphoid development and accounts for some of the residual lymphoid development in gamma(c) KO mice and presumably in patients with X-linked severe combined immunodeficiency. Injection of TSLP into gamma(c) KO mice induced the expansion of T and B cells. Moreover, sublethally irradiated TSLPR KO mice showed weaker recovery of lymphocyte populations than wild-type (WT) littermates, even when neutralizing anti-IL-7 antibodies were injected. Interestingly, TSLP preferentially stimulated the proliferation and survival of CD4(+) single positive thymocytes and peripheral T cells in vitro. Additionally, CD4(+) T cells from TSLPR KO mice expanded less efficiently than WT CD4(+) T cells in irradiated hosts, and TSLP preferentially expanded CD4(+) T cells both in vitro and in vivo. Thus, as compared with other known cytokines, TSLP is distinctive in exhibiting a lineage preference for the expansion and survival of CD4(+) T cells.
Involvement of Sigma-1 Receptors in the Antidepressant-like Effects of Dextromethorphan (2014)

Dextromethorphan is an antitussive with a high margin of safety that has been hypothesized to display rapid-acting antidepressant activity based on pharmacodynamic similarities to the N-methyl-D-aspartate (NMDA) receptor antagonist ketamine. In addition to binding to NMDA receptors, dextromethorphan binds to sigma-1 (σ1) receptors, which are believed to be protein targets for a potential new class of antidepressant medications. The purpose of this study was to determine whether dextromethorphan elicits antidepressant-like effects and the involvement of σ1 receptors in mediating its antidepressant-like actions. The antidepressant-like effects of dextromethorphan were assessed in male, Swiss Webster mice using the forced swim test. Next, σ1 receptor antagonists (BD1063 and BD1047) were evaluated in conjunction with dextromethorphan to determine the involvement of σ receptors in its antidepressant-like effects. Quinidine, a cytochrome P450 (CYP) 2D6 inhibitor, was also evaluated in conjunction with dextromethorphan to increase the bioavailability of dextromethorphan and reduce exposure to additional metabolites. Finally, saturation binding assays were performed to assess the manner in which dextromethorphan interacts at the σ1 receptor. Our results revealed dextromethorphan displays antidepressant-like effects in the forced swim test that can be attenuated by pretreatment with σ1 receptor antagonists, with BD1063 causing a shift to the right in the dextromethorphan dose response curve. Concomitant administration of quinidine potentiated the antidepressant-like effects of dextromethorphan. Saturation binding assays revealed that a Ki concentration of dextromethorphan reduces both the Kd and the Bmax of [(3)H](+)-pentazocine binding to σ1 receptors. Taken together, these data suggest that dextromethorphan exerts some of its antidepressant actions through σ1 receptors.
Distinctive ribonucleic acid patterns of human rotavirus subgroups 1 and 2 (1981)

The ribonucleic acid migration patterns of 7 subgroup 1 and 16 subgroup 2 human rotaviruses recovered from four geographic areas were compared. The subgroup 1 ribonucleic acid patterns had strikingly slower-moving segments 10 and 11, suggesting a correlation between the ribonucleic acid pattern and the subgroup specificity.
Mapping of the p53 and mdm-2 interaction domains. (1993)

The 90-kDa cellular protein encoded by the mouse mdm-2 oncogene binds to the p53 protein in vivo and inhibits its transactivation function (J. Momand, G. P. Zambetti, D. C. Olson, D. George, and A. J. Levine, Cell 69:1237-1245, 1992). cDNA clones encoding the human homolog of the mdm-2 protein (also called hdm-2) were isolated from a HeLa cell cDNA library. A series of monoclonal antibodies have been generated against human mdm-2 protein, and the epitopes recognized by these antibodies have been mapped. By construction of a series of deletion mutants, the region of the mdm-2 protein that is critical for complex formation with the p53 protein has been mapped to the N-terminal portion of the human mdm-2 protein. Interestingly, a monoclonal antibody with an epitope located in this same region failed to immunoprecipitate the mdm-2-p53 complex and appeared to recognize only free mdm-2 protein. The domain of the p53 protein that is sufficient for interaction with human mdm-2 protein has been mapped to the N-terminal 52 amino acid residues of the p53 protein. This region contains the transactivation domain of p53, suggesting that mdm-2 may inhibit p53 function by disrupting its interaction with the general transcription machinery.
Oligonucleotide labeling methods 3. Direct labeling of oligonucleotides employing a novel, non-nucleosidic, 2-aminobutyl-1,3-propanediol backbone (1992)

Novel CE-phosphoramidite (7a-e) and CPG (8a, c, d, e) reagents have been prepared from a unique 2-aminobutyl-1,3-propanediol backbone. The reagents have been used to directly label oligonucleotides with fluorescein, acridine, and biotin via automated DNA synthesis. The versatile 2-aminobutyl-1,3-propanediol backbone allows for labeling at any position (5', internal, and 3') during solid phase oligonucleotide synthesis. Multiple labels can be achieved by repetitive coupling cycles. Furthermore, the 3-carbon atom internucleotide phosphate distance is retained when inserted internally. Using this method, individual oligonucleotides possessing two and three different reporter molecules have been prepared.
Human peripheral blood eosinophils express stem cell factor (2001)

Stem cell factor (SCF) or c-Kit ligand is a cytokine associated with the differentiation, survival, and activation of mast cells. Eosinophils have pleiotropic functions in several diseases and, together with mast cells, are key cells in allergy. Mast cell-eosinophil interactions can take place during the late and chronic phases of allergy. It was, therefore, investigated whether eosinophils can produce SCF and consequently influence mast cells. Human peripheral blood eosinophils variably expressed mRNA for the soluble and uncleaved forms of SCF (reverse transcription-polymerase chain reaction) and produced the 18.5-kd protein backbone of SCF (Western blot analysis). After overnight incubation in medium, eosinophils also produced SCF of higher molecular weight (42-45 kd) that might represent its glycosylated forms. Eosinophils expressed cytoplasmic SCF that colocalized with major basic protein (confocal laser microscopy). Freshly isolated eosinophils contained 8.9 +/- 1.7 pg SCF/10(6) (mean +/- SEM; enzyme-linked immunosorbent assay). Although overnight incubation of the eosinophils in either culture medium or in phorbol 12-myristate 13-acetate-calcium ionophore did not cause the secretion of SCF, the addition of chymase induced SCF release. In summary, it was demonstrated that human peripheral blood eosinophils are a source of SCF. These results may contribute to a better understanding of the interactions between eosinophils and mast cells in allergic inflammation.
Long‐term Results of Radiofrequency Rhizotomy in the Treatment of Cluster Headache (1995)

Although the primary treatment of chronic cluster headache is medical, surgical treatment is sometimes used. The authors reviewed the charts of seven patients (ages 36 to 68 years) with chronic cluster headache to identify who responded best to percutaneous stereotactic radiofrequency rhizotomy after medical treatment failed. All patients had immediate pain relief after surgery. At follow-up (median 5 years, range 2 to 20 years), two patients remained pain-free 7 and 20 years later (excellent results); three patients had mild pain recurrence that was well controlled on medications (good results) 6 to 12 months after surgery; and two patients had major pain recurrence 4 days and 2 months after surgery (poor results). Six patients had relief of vasomotor symptoms. One patient had transient diplopia and keratitis without permanent sequelae. Both patients with excellent results had preoperative major pain around the eye; both patients with poor results had major pain around the temple, ear, and cheek; and the three patients with good results had pain equally severe in the eye, temple, and cheek. There was no association between patient age or sex, pain duration, preoperative response to lidocaine blockade, or previous surgery with pain relief. No differences occurred in pain relief between patients with dense hypalgesia and patients with analgesia. The authors conclude that (1) some patients with chronic cluster headache treated by percutaneous stereotactic radiofrequency rhizotomy achieve long-term pain relief, and (2) surgery on the trigeminovascular system alone may not cure the condition in patients with major pain around the temple, ear, and cheek.
A comparative analysis of the molecular genetic processes in the pathogenesis of psoriasis and Crohn’s disease (2009)

A comparative bioinformatics analysis of the molecular genetic processes in the pathogenesis of multifactorial diseases—psoriasis and Crohn’s disease—was performed using the results of microarray experiments deposited with the GEO DataSets database. A number of genes and molecular genetic processes common to both pathologies were found. The involvement of several transcription factors, including AP-1 transcription factors, in the pathogeneses of both psoriasis and Crohn’s disease was postulated.
New routes for the synthesis of pyrrolo-[3,2-d]- and -[2,3-d]-pyrimidine systems starting from a common pyrrole derivative (1978)

New routes for the synthesis of pyrrolo-[3,2-d]- and -[2,3-d]-pyrimidines from a common 2,3-dicarboxypyrrole derivative are described. The common starting material, 3-ethoxycarbonyl-2-carboxy-4-methylpyrrole (1) is conveniently functionalized to give 2- or 3-azidocarbonylpyrroles (4), (17), and (22) which on Curtius rearrangement followed by treatment with ammonia or amines give the pyrrolylurea (6a) or its derivatives (6b–d), or (23). These, in basic medium cyclise to 7-methylpyrrolo[3,2-d]pyrimidine-2,4-diones (7a), its 3-substituted derivatives (7b–d), or to 5-methylpyrrolo[2,3-d]pyrimidine-2,4-diones (19).
Gene transfer method for transient gene expression, stable transformation, and cotransformation of suspension cell cultures. (1985)

A new method was developed to study transient gene expression, stable transformation, and cotransformation in suspension cells, such as mouse myeloma and erythroleukemia cells. This method involves attachment of cells to a concanavalin A-coated tissue culture dish, treatment of cells with DEAE-dextran to adsorb plasmid DNA to the attached cells, and finally treatment with a 40% solution of polyethylene glycol to facilitate the uptake of DNA by the cells. Plasmids pSV2cat and pSV2neo were used as markers to optimize the conditions for transient gene expression and stable transformation, respectively, of mouse myeloma and erythroleukemia cells. This method was successfully used to obtain cotransformants of mouse myeloma cells.
Status Epilepticus (2011)

Status epilepticus is a neurological emergency that is commonly encountered by the neurohospitalist. Successful treatment depends upon the recognition of prolonged seizure activity and the acute mobilization of available resources. Pharmacologic treatment regimens have been shown to decrease the time needed for successful control of seizures and have provided for the rapid administration of anticonvulsant medications. Treatment strategies have evolved so that clinicians can administer effective doses of medication by whatever routes of administration are immediately available. Traditional algorithms for the treatment of status epilepticus have used a stepwise approach to the administration of first-, second-, and third-order medications. More recent options have included aggressive anesthetic doses of medications while second-line medications are being titrated.
Changes in indicators of inflammation after eccentric exercise of the elbow flexors (1996)

This study examined muscle swelling and changes in inflammatory markers in the blood following eccentric exercise-induced muscle damage. Subjects (N = 14) who had not been involved in a resistance training program performed 24 maximal eccentric actions of the elbow flexors. Muscle swelling was assessed by measures of the upper arm circumference (CIR), ultrasonography (USG), and magnetic resonance imaging (MRI). Plasma concentrations of interleukin-1 alpha, interleukin-1 beta, interleukin-2, interleukin-6, tumor necrosis factor-alpha, and plasma levels of C-reactive protein, cortisol, and zinc were analyzed. Established indicators of muscle damage (maximal isometric force, range of motion, muscle soreness, and plasma creatine kinase, aspartate aminotransferase, and lactate dehydrogenase activities) were also measured. All measures, including CIR and USG, except for MRI, were assessed immediately before and after and for 5 d post-exercise. MRI was taken at pre- and 1, 3, 6, 10, 23, 31, and 58 d post-exercise. All muscle damage indicators changed significantly after exercise. A large increase in CIR (> 20 mm) was found 4-5 d after exercise, and this coincided with USG, showing an increase in muscle thickness. The echointensity of USG increased with the enlargement of the elbow flexors. MRI displayed enlargement of the biceps brachii and brachialis cross-sectional area that started at 1 d, and lasted until 23 d, post-exercise. The most profound increase in the enlargement and signal intensity of the MRI was found 3 or 6 d after exercise. However, none of the plasma levels of inflammatory makers showed significant muscle swelling, which is indicative of muscle edema, but the inflammatory responses after exercise appear to be different from those accompanying infection or tissue injury.
USING PROBABILISTIC MODELS OF DOCUMENT RETRIEVAL WITHOUT RELEVANCE INFORMATION (1979)

Most probabilistic retrieval models incorporate information about the occurrence of index terms in relevant and non‐relevant documents. In this paper we consider the situation where no relevance information is available, that is, at the start of the search. Based on a probabilistic model, strategies are proposed for the initial search and an intermediate search. Retrieval experiments with the Cranfield collection of 1,400 documents show that this initial search strategy is better than conventional search strategies both in terms of retrieval effectiveness and in terms of the number of queries that retrieve relevant documents. The intermediate search is shown to be a useful substitute for a relevance feedback search. Experiments with queries that do not retrieve relevant documents at high rank positions indicate that a cluster search would be an effective alternative strategy.
Regulation and dysregulation of Epstein–Barr virus latency: Implications for the development of autoimmune diseases (2008)

Epstein-Barr virus (EBV) is a human herpesvirus hiding in a latent form in memory B cells in the majority of the world population. Although, primary EBV infection is asymptomatic or causes a self-limiting disease, infectious mononucleosis, the virus is associated with a wide variety of neoplasms developing in immunosuppressed or immunodeficient individuals, but also in patients with an apparently intact immune system. In memory B cells, tumor cells, and lymphoblastoid cell lines (LCLs, transformed by EBV in vitro) the expression of the viral genes is highly restricted. There is no virus production (lytic viral replication associated with the expression of all viral genes) in tight latency. The expression of latent viral oncogenes and RNAs is under a strict epigenetic control via DNA methylation and histone modifications that results either in a complete silencing of the EBV genome in memory B cells, or in a cell-type dependent usage of latent promoters in tumor cells, germinal center B cells, and LCLs. Both the latent and lytic EBV proteins are potent immunogens and elicit vigorous B- and T-cell responses. In immunosuppressed and immunodeficient patients, or in individuals with a functional defect of EBV-specific T cells, lytic EBV replication is regularly activated and an increased viral load can be detected in the blood. Enhanced lytic replication results in new infection events and EBV-associated transformation events, and seems to be a risk factor both for malignant transformation and the development of autoimmune diseases. One may speculate that an increased load or altered presentation of a limited set of lytic or latent EBV proteins that cross-react with cellular antigens triggers and perpetuates the pathogenic processes that result in multiple sclerosis, systemic lupus erythematosus (SLE), and rheumatoid arthritis. In addition, in SLE patients EBV may cause defects of B-cell tolerance checkpoints because latent membrane protein 1, an EBV-encoded viral oncoprotein can induce BAFF, a B-cell activating factor that rescues self-reactive B cells and induces a lupus-like autoimmune disease in transgenic mice.
Molecular characterization of a glycosylphosphatidylinositol-linked ADP- ribosyltransferase from lymphocytes (1996)

Mono ADP-ribosyltransferases catalyze the transfer of the ADP-ribose moiety of nicotinamide adenine dinucleotide (NAD) to proteins. It was reported by Wang et al (J Immunol 153:4048, 1994) that incubation of mouse cytotoxic T lymphocytes (CTL) with NAD resulted in the ADP- ribosylation of membrane proteins and inhibition of cell proliferation and cytotoxicity. Treatment of CTL with phosphatidylinositol-specific phospholipase C (PI-PLC) before incubation with NAD prevented the inhibitory effects of NAD on the cells, consistent with the removal of a glycosylphosphatidylinositol (GPI)-anchored ADP-ribosyltransferase on the lymphocyte surface. We have identified and cloned a GPI-linked ADP- ribosyltransferase from Yac-1 mouse T-cell lymphoma cells. The deduced amino acid sequence of the Yac-1 transferase was 70% and 41% identical to those of the rabbit skeletal muscle and chicken heterophil, respectively. It contained three noncontiguous sequences similar to those found in several of the bacterial toxin and vertebrate ADP- ribosyltransferases. Based on crystallography of the bacterial toxins, these regions are believed to form, in part, the catalytic site consistent with a common mechanism for the ADP-ribose transfer reaction. In rat mammary adenocarcinoma (NMU) cells transformed with the Yac-1 transferase cDNA, transferase activity was present on the cell surface and was released into the medium by treatment of cells with PI-PLC. Thus, we have cloned a novel gene that has properties identical to the transferase detected in CTL, and may be involved in the NAD-dependent regulation of proliferation and cytotoxicity.
A novel roll mechanism to increase maneuverability of autonomous underwater vehicles in shallow water (2016)

This paper presents a novel roll mechanism and an efficient control strategy for the roll and pitch of internally actuated autonomous underwater vehicles (AUVs) including most underwater gliders (UGs). The proposed design and approach increases maneuverability which is essential for operating in shallow water or crowded harbors. The design is implemented on Michigan Tech's research UG ROUGHIE (Research Oriented Underwater Glider for Hands-on Investigative Engineering) and the performance is validated. The experimental results demonstrate that ROUGHIE is capable of tight turn radii down to approximately twice the vehicle length in shallow water.
High speed silicon lateral trench detector on SOI substrate (2002)

Lateral trench photodetectors (LTD) on silicon-on-insulator (SOI) have been fabricated using a fully CMOS compatible process. High speed (2.0 GHz), high quantum efficiency (51%), and excellent frequency response characteristics have been achieved at 851 nm with a supply voltage of only 3.3 V.