gebhart/patrepeval huggingface dataset:
Virus Isolation From and Identification of HTLV-III/LAV-Producing Cells in Brain Tissue From a Patient With AIDS (1986)

Primary cultures from a brain biopsy specimen of a human T-cell lymphotropic virus type III/lymphadenopathy-associated virus (HTLV-III/LAV) seropositive patient with progressive dementia contained small numbers of monocytoid cells and showed reverse transcriptase activity that persisted for as long as 100 days. Electron microscopy of these cells revealed the presence of HTLV-III/LAV virions. Subcultured cells removed from primary cultures by trypsinization were nonspecific esterase negative and did not express virus or show evidence of HTLV-III/LAV proviral sequences, while those remaining in the original flasks were nonspecific esterase positive and continued to produce virus. Virus from primary cultures was transmitted to peripheral blood-derived monocyte-macrophages and T cells. Virus production in T-cell cultures was transient while the monocyte-macrophages, like the primary cultures, produced virus for at least 120 days. Infection of several brain-derived cells with this and another HTLV-III/LAV isolate failed to demonstrate virus replication. These results indicate that the HTLV-III/LAV-infected cells recovered from the brain of this patient are cells of the mononuclear phagocyte series.
Growth factors and their receptors in pancreatic cancer (2000)

Pancreatic cancer has an incidence of approximately 8 to 10 cases per 100,000 citizens in Western industrialized countries, and the incidence has been increasing throughout the last decades. Insensitivity to antigrowth and apoptotic signals as well as self-sufficiency in growth signals are hallmarks of malignant growth. Pancreatic cancers often exhibit alterations in growth inhibitory pathways such as Smad4 mutations and Smad6 and Smad7 overexpression, and evade apoptosis through p53 mutations and aberrant expression of apoptosis regulating genes. In addition, in pancreatic cancer a variety of growth factors are expressed at increased levels. For example, the concomitant presence of the EGF-receptor and its ligands EGF, TGF-alpha, and/or amphiregulin is associated with enhanced tumor aggressiveness and shorter survival periods following tumor resection. Furthermore, a number of other growth factors and their receptors, such as fibroblast growth factors, nerve growth factor, platelet-derived growth factors, and insulin-like growth factors and their respective receptors are expressed at increased levels in pancreatic cancer and are thought to contribute to its malignant phenotype. Taken together, the disturbance of growth inhibitory and apoptotic pathways and the abundance of growth promoting factors give pancreatic cancer cells a distinct growth advantage which clinically results in rapid tumor progression and poor survival prognosis.
The Effects of Contact Lens Deformation on Tear Film Pressure and Thickness During Motion of the Lens Towards the Eye (1983)

An analysis is made of the motion of a contact lens normal to the eye through a tear film. The eye is modeled as a rigid sphere and the lens as a deformable spherical cap. Graphs of pressure distribution and tear film thickness variations are obtained. It is found that the pressures are very markedly reduced and film thicknesses increased by decreasing the modulus of the lens materials.
Cell-Permeable Peptide Nucleic Acid Designed to Bind to the 5‘-Untranslated Region of E-cadherin Transcript Induces Potent and Sequence-Specific Antisense Effects (2006)

Establishing a general and effective method for regulating gene expression in mammalian systems is important for many aspects of biological and biomedical research. Herein we report the antisense activities of a cell-permeable, guanidine-based peptide nucleic acid (PNA) called GPNA. We show that a GPNA oligomer designed to bind to the transcriptional start-site of human E-cadherin gene induces potent and sequence-specific antisense effects and is less toxic to the cells than the corresponding PNA-polyarginine conjugate. GPNA confers its silencing effect by blocking protein translation. The findings reported in this study provide a molecular framework for designing the next generation cell-permeable nucleic acid mimics for regulating gene expression in live cells and intact organisms.
Pleckstrin homology (PH) domains in signal transducton (1994)

A diverse array of molecules involved in signal transduction have recently been recognised as containing a new homology domain, the pleckstrin homology (PH) domain. These include kinases (both serine/threonine and tyrosine specific), all currently known mammalian phospholipase Cs, GTPases, GTPase-activating proteins, GTPase-exchange factors, "adapter" proteins, cytoskeletal proteins, and kinase substrates. This has sparked a new surge of research into elucidating its structure and function. The NMR solution structure of the PH domains of beta-spectrin and pleckstrin (the N-terminal domain) both display a core consisting of seven anti-parallel beta-sheet strands. The carboxy terminus is folded into a long alpha-helix. The molecule is electrostatically polarised and contains a pocket which may be involved in the binding of a ligand. The PH domains overall topological relatedness to the retinoid binding protein family of molecules would suggest a lipid ligand could bind to this pocket. The prime function of the PH domain still remains to be elucidated. However, it has been shown to be important in signal transduction, most probably by mediating protein-protein interactions. An extended PH domain of the beta-adrenergic receptor kinase (beta ARK), as well as that of several other molecules, can bind to beta gamma subunits of the heterotrimeric G-proteins. The possibility that the PH domain, which is found in so many signalling molecules, being generally involved in beta gamma binding is provocative of implicating these proteins in G-protein signal transduction.(ABSTRACT TRUNCATED AT 250 WORDS)
Abstract 671: CD38-specific engineered toxin body: Therapeutic potential for multiple myeloma (2014)

Abstract Multiple myeloma is a malignancy of plasma cells that accounts for 10% of all hematological cancers. Current treatments for multiple myeloma include immunomodulatory agents, protease inhibitors and chemotherapies and, while these therapies are often initially effective, most patients experience relapse. New therapeutics are urgently required. CD38 is a transmembrane glycoprotein absent on most resting leukocytes but expressed on lymphoid malignancies, including multiple myeloma and lymphoma, making it an attractive target for directed therapy. Recent clinical trials with antibodies to CD38 have shown promise in multiple myeloma. While these antibodies rely on the recruitment of an immune response for cytotoxicity, we have developed an engineered toxin body (ETB) comprising a CD38 binding scFv and a de-immunogenized form of Shiga-like Toxin A (MT-4001) capable of specifically recognizing and directly killing CD38 expressing cells. Our results show that MT-4001 is a promising targeted therapeutic agent against CD38 positive cancer cells and is currently under further development. Citation Format: Sangeetha Rajagopalan, Brigitte Brieschke, Garrett L. Robinson, Jennifer Erdman, William Null, Jack P. Higgins, Erin K. Willert. CD38-specific engineered toxin body: Therapeutic potential for multiple myeloma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 671. doi:10.1158/1538-7445.AM2014-671
Increasingly frequent diagnosis of acute gastrointestinal graft-versus-host disease after allogeneic hematopoietic cell transplantation (2004)

The reported incidence of grades II to IV acute graft-versus-host disease (GVHD) after hematopoietic cell transplantation with HLA-identical sibling donors has increased considerably during the past 15 to 20 years at our center. The purpose of this study was to evaluate the potential reasons for this change. We reviewed organ stages and overall grades of GVHD for 2220 patients who received a first marrow or peripheral blood cell transplant from an HLA-identical sibling or an HLA-allele-matched unrelated donor with the use of a posttransplantation immunosuppressive regimen that included both methotrexate and cyclosporine between 1985 and 2001. The most striking change was an increased incidence of stage 1 gut involvement from 10% to 20% before 1992 to 50% to 60% since 1992, both with related and unrelated donors. This change increased the incidence of grade II GVHD with sibling donors, such that the overall incidence of grade II to IV GVHD is now 60% to 70%. Among patients with chronic myeloid leukemia in chronic phase, the increasingly frequent diagnosis of acute GVHD since 1992 has not been associated with decreased survival. A high diagnostic sensitivity and increased awareness that gut GVHD can occur without skin involvement account for the increased incidence of acute GVHD at our center.
Recombinant Plasma Gelsolin Diminishes the Acute Inflammatory Response to Hyperoxia in Mice (2002)

These data imply that i) gelsolin depletion contributes to the pathogenesis of oxygen toxicity and ii) repletion of gelsolin can partially abrogate the resultant exudative response.
Respiratory rate derived from principal component analysis of single lead electrocardiogram (2008)

We used principal component analysis to derive the respiratory rate from single lead ECGs. In this algorithm the respiratory induced beat-to-beat variability of the ECG is described by the coefficients of the principal components. Subjects were asked to breathe at different rates and naturally while respiration and ECG were recorded. Breathing rate, determined by Fourier analysis, was compared for the ECG derived respiration obtained by principal component analysis and the recorded respiratory signal. Across the different breathing patterns the mean absolute differences between reference respiratory rate and ECG respiratory rate were 0.2 breaths per minute (bpm) or less. In all cases the respiratory rate was accurately determined from respiratory surrogates derived from principal component analysis of the single lead ECGs.
RNA‐Mediated Gene Assembly from DNA Arrays (2012)

Gene Genie: RNA-mediated gene assembly is possible in a single day from oligonucleotide sequences on a DNA array. A T7 promoter is appended to each surface-bound oligonucleotide and many RNA copies of each are then produced with T7 RNA polymerase (see Figure). These RNA molecules self-assemble into the desired full-length transcript by hybridization and ligation, which is then converted into double-stranded DNA by reverse transcriptase polymerase chain reaction.
Preparation ofN-Monoalkyl andO-Acyl Derivatives of Allosamidin, and Their Chitinase Inhibitory Activities (1993)

Journal Article Preparation of N-Monoalkyl and O-Acyl Derivatives of Allosamidin, and Their Chitinase Inhibitory Activities Get access Masayoshi Kinoshita, Masayoshi Kinoshita Department of Biotechnology, Faculty of Engineering, Osaka University, 2-1 Yamada-oka, Suita-shi, Osaka 565, Japan Search for other works by this author on: Oxford Academic Google Scholar Shohei Sakuda, Shohei Sakuda Department of Biotechnology, Faculty of Engineering, Osaka University, 2-1 Yamada-oka, Suita-shi, Osaka 565, Japan Search for other works by this author on: Oxford Academic Google Scholar Yasuhiro Yamada Yasuhiro Yamada Department of Biotechnology, Faculty of Engineering, Osaka University, 2-1 Yamada-oka, Suita-shi, Osaka 565, Japan Corresponding author. Search for other works by this author on: Oxford Academic Google Scholar Bioscience, Biotechnology, and Biochemistry, Volume 57, Issue 10, 1 January 1993, Pages 1699–1703, https://doi.org/10.1271/bbb.57.1699 Published: 01 January 1993 Article history Published: 01 January 1993 Received: 14 April 1993
Potential thrombolysis under selective infusion of autologous plasmin(AP) solution. (1989)

Thrombolytic therapy with plasminogen activators, urokinase (UK) and streptokinase (SK), can produce serious complications such as systemic bleeding. We have developed an autologous plasmin (AP) solution as a new potential thrombolytic agent and evaluated its efficacy in animal experiments. The AP solution was prepared by the addition of UK to autologous plasma separated by centrifugation (4 degrees C, 3,000 rpm, 10 min). The plasmin activity in the AP solution was measured by the plasminogen-free fibrin plate method and spectrophotometric assay with the chromogenic substrate S-2251. In animal experiments, the femoral artery of anesthetized mongrel dogs (n = 20) was constricted by ligation (1 mm in diameter) and a fibrin clot was embolized into this site. Either AP solution (n = 8), UK solution (n = 6) or saline (n = 6) was selectively infused for 3 min. Prior to the infusion, a temporary flow obstruction was made by inflation of a balloon tip catheter located proximal to the embolized site. The thrombolytic effect was sequentially observed with an ultrasound flow meter for up to 60 min. The total dose of UK was 120,000 IU in both AP and UK solutions. The results showed that the plasmin activity of AP solution was maintained up to 90 min at 22 degrees C with an additional dose of more than 6,000 IU/ml of UK. In animal experiments, a restoration of the flow was observed more frequently with the AP solution than the UK solution within 15 min of the infusion (p less than 0.01). Thus, a high thrombolytic efficacy was observed with a selective infusion of rich, activated plasmin (AP) solution. This treatment could be applied as a new approach for arterial thrombolysis.
An unsupervised model for text message normalization (2009)

Cell phone text messaging users express themselves briefly and colloquially using a variety of creative forms. We analyze a sample of creative, non-standard text message word forms to determine frequent word formation processes in texting language. Drawing on these observations, we construct an unsupervised noisy-channel model for text message normalization. On a test set of 303 text message forms that differ from their standard form, our model achieves 59% accuracy, which is on par with the best supervised results reported on this dataset.
IL-9 Production by Regulatory T Cells Recruits Mast Cells That Are Essential for Regulatory T Cell-Induced Immune Suppression (2010)

Both mast cells (MCs) and regulatory T cells (Tregs) have gained attention as immunosuppressive cell populations. To investigate a possible interaction, we used the Th1- and Th17-dependent model of nephrotoxic serum nephritis (NTS), in which both MCs and Tregs have been shown to play a protective role. Transfer of wild-type (wt) Tregs into wt recipients almost completely prevents development of NTS and leads to a profound increase of MCs in the renal draining lymph nodes (LNs). By contrast, transfer of wt Tregs into animals deficient in MCs, which are characterized by an exaggerated susceptibility to NTS, no longer exhibited protective effects. Blocking the pleiotropic cytokine IL-9, known to be involved in MC recruitment and proliferation, by means of a mAb in mice receiving Tregs abrogated protection from NTS. Moreover, transfer of IL-9-deficient Tregs also failed to protect from NTS. In the absence of Treg-derived IL-9, MCs fail to accumulate in the LNs, despite the fact that IL-9 deficiency does not alter the general suppressive activity of Tregs. In summary, to our knowledge, we provide the first direct in vivo evidence that the nephroprotective, anti-inflammatory effects of Tregs critically depend on IL-9-mediated attraction of MCs into kidney-draining LNs.
Characterization of strain HY99, a novel microorganism capable of aerobic and anaerobic degradation of aniline (2000)

We have characterized a novel microorganism, strain HY99, which is capable of aerobic and anaerobic degradation of aniline. Strain HY99 was found to aerobically metabolize aniline via catechol and 2-hydroxymuconic semialdehyde intermediates, and to transform aniline via p-aminobenzoate in anaerobic environments. Physiological and biochemical tests revealed that strain HY99 was most similar to Delftia acidovorans, but unlike D. acidovorans, strain HY99 was able to metabolize aniline under anaerobic conditions linked with nitrate reduction. Phylogenetic analysis based on 16S rDNA sequencing also revealed that strain HY99 was closely related to D. acidovorans, with 96% overall similarity.
Single-Colony Derived Strains of Human Marrow Stromal Fibroblasts Form Bone After Transplantation In Vivo (1997)

Populations of marrow stromal fibroblasts (MSFs) can differentiate into functional osteoblasts and form bone in vivo. It is not known, however, what proportion of MSF precursor cells, colony forming units-fibroblast (CFU-Fs), have osteogenic potential. In the present study, analysis of bone formation in vivo by single-colony derived strains of human marrow stromal fibroblasts (HMSFs) has been performed for the first time. Each strain originated from an individual CFU-F and underwent four passages in vitro prior to subcutaneous implantation into immunodeficient mice within vehicles containing hydroxyapatite-tricalcium phosphate ceramic. Multicolony derived HMSF strains were also transplanted to serve as positive controls. After 8 weeks, abundant bone formation was found in the transplants of all multicolony derived HMSF strains, whereas 20 out of 34 (58.8%) single-colony derived strains from four donors formed bone. Immunostaining with antibody directed against human osteonectin and in situ hybridization for human-specific alu sequences demonstrated that cells forming new bone were of human origin and were vital for at least 45 weeks post-transplantation. Both the incidence of bone-forming colonies and the extent of bone formation by single-colony derived HMSF strains were increased by cultivation with dexamethasone and ascorbic acid phosphate. Other factors, including type of transplantation vehicle, morphology, size, and structure of the original HMSF colonies showed no obvious correlation with the incidence or extent of bone formation. Hematopoietic tissue within the newly formed bone was developed in the transplants exhibiting exuberant bone formation. These results provide evidence that individual human CFU-Fs have osteogenic potential and yet differ from each other with respect to their osteogenic capacity.
Structure of REC2, a recombinational repair gene of Ustilago maydis, and its function in homologous recombination between plasmid and chromosomal sequences. (1994)

Mutation in the REC2 gene of Ustilago maydis leads to defects in DNA repair, recombination, and meiosis. Analysis of the primary sequence of the Rec2 protein reveals a region with significant homology to bacterial RecA protein and to the yeast recombination proteins Dmc1, Rad51, and Rad57. This homologous region in the U. maydis Rec2 protein was found to be functionally sensitive to mutation, lending support to the hypothesis that Rec2 has a functional RecA-like domain essential for activity in recombination and repair. Homologous recombination between plasmid and chromosomal DNA sequences is reduced substantially in the rec2 mutant following transformation. The frequency can be restored to a level approaching, but not exceeding, that observed in the wild-type strain if transformation is performed with cells containing multiple copies of REC2.
Microalgal blooms: a global issue with negative impact in Chile. (1998)

Ecological and health problems posed by microalgal blooms (red tides) occurring in the Southern part of Chile are reviewed. Out of the six human illnesses provoked by microalgal toxins, paralytic shellfish poisoning is the most important, because of its high mortality rate and the high levels of phycotoxins found in contaminated molluscs. Saxitoxin and its analogues bind to a receptor in the voltage-gated sodium channel of neural membranes. The most important toxin-producer microalgae are Alexandrium catenella and Dinophysis acuta. Phycotoxins become concentrated by filter-feeding shellfish, like Mytilus chilensis. Highly sensitive methods available for detection of microalgal toxins are analyzed.
Relationships between sequestration, antigenic variation and chronic parasitism in Plasmodium chabaudi chabaudi– a rodent malaria model (1990)

We describe here a rodent malaria model using cloned lines of Plasmodium chabaudi chabaudi in inbred CBA/Ca mice that exhibits both clonal antigenic variation in late stage-specific surface antigens, and deep vascular schizogony in the liver. We show that both these features are modulated by the spleen, and that surface antigen expression is crucially involved in the sequestering phenotype. Surface antigens are variant in chronic infection, and host protective immune responses can distinguish between these variants. Splenectomy abolishes this difference. The acute infection with non-sequestering cloned lines is kinetically indistinguishable from sequestering clones, but parasites unable to express variant sequestration-associated antigen do not form a chronic recrudescing infection. Another clone, able to re-express this antigen in the presence of the spleen, undergoes typical chronic recrudescence. In this model, the biological significance of sequestration-associated variant antigen seems to enable the establishment of chronic infection in the presence of a primed spleen.
Design of Inhibitors of Orotidine Monophosphate Decarboxylase Using Bioisosteric Replacement and Determination of Inhibition Kinetics (2006)

Inhibitors of orotidine monophosphate decarboxylase (ODCase) have applications in RNA viral, parasitic, and other infectious diseases. ODCase catalyzes the decarboxylation of orotidine monophosphate (OMP), producing uridine monophosphate (UMP). Novel inhibitors 6-amino-UMP and 6-cyano-UMP were designed on the basis of the substructure volumes in the substrate OMP and in an inhibitor of ODCase, barbituric acid monophosphate, BMP. A new enzyme assay method using isothermal titration calorimetry (ITC) was developed to investigate the inhibition kinetics of ODCase. The reaction rates were measured by monitoring the heat generated during the decarboxylation reaction of orotidine monophosphate. Kinetic parameters (k(cat) = 21 s(-1) and KM = 5 microM) and the molar enthalpy (DeltaH(app) = 5 kcal/mol) were determined for the decarboxylation of the substrate by ODCase. Competitive inhibition of the enzyme was observed and the inhibition constants (Ki) were determined to be 12.4 microM and 29 microM for 6-aza-UMP and 6-cyano-UMP, respectively. 6-Amino-UMP was found to be among the potent inhibitors of ODCase, having an inhibition constant of 840 nM. We reveal here the first inhibitors of ODCase designed by the principles of bioisosterism and a novel method of using isothermal calorimetry for enzyme inhibition studies.
Amine-Catalyzed Addition of Azide Ion to α,β-Unsaturated Carbonyl Compounds (1999)

[formula: see text] A new protocol for the beta-azidation of alpha,beta-unsaturated carbonyl compounds is described. The method employs tertiary amines as catalysts for azide addition. The azide source is a 1:1 mixture of TMSN3 and AcOH. Tertiary amines, either in solution or bound to a solid support, are efficient catalysts for the reaction.