gebhart/patrepeval huggingface dataset:
The Arabidopsis DIMINUTO/DWARF1 Gene Encodes a Protein Involved in Steroid Synthesis (1998)

We have identified the function of the Arabidopsis DIMINUTO/DWARF1 (DIM/DWF1) gene by analyzing the dim mutant, a severe dwarf with greatly reduced fertility. Both the mutant phenotype and gene expression could be rescued by the addition of exogenous brassinolide. Analysis of endogenous sterols demonstrated that dim accumulates 24-methylenecholesterol but is deficient in campesterol, an early precursor of brassinolide. In addition, we show that dim is deficient in brassinosteroids as well. Feeding experiments using deuterium-labeled 24-methylenecholesterol and 24-methyldesmosterol confirmed that DIM/DWF1 is involved in both the isomerization and reduction of the Delta24(28) bond. This conversion is not required in cholesterol biosynthesis in animals but is a key step in the biosynthesis of plant sterols. Transient expression of a green fluorescent protein-DIM/DWF1 fusion protein and biochemical experiments showed that DIM/DWF1 is an integral membrane protein that most probably is associated with the endoplasmic reticulum.
Mechanism of action of rituximab (2002)

Rituximab, the humanized chimeric anti-CD20 monoclonal antibody, represents a powerful tool for treating B-cell malignancies and is licensed for the treatment of relapsed or chemorefractory low-grade or follicular non-Hodgkin's lymphoma (NHL). It has a unique mode of action and can induce killing of CD20+ cells via multiple mechanisms. The direct effects of rituximab include complement-mediated cytotoxicity and antibody-dependent cell-mediated cytotoxicity, and the indirect effects include structural changes, apoptosis, and sensitization of cancer cells to chemotherapy. In vitro studies have made a significant contribution to the understanding of these mechanisms of action and have led to the development of innovative and effective treatment strategies to optimize patient response. The most significant of these strategies is the combination of rituximab and CHOP chemotherapy (cyclophosphamide, doxorubicin, vincristine and prednisone), which is proving a highly effective combination in the treatment of NHL. However, all patients do not respond equally well to rituximab, and in vitro studies have identified a possible mechanism of resistance involving the anti-complement inhibitors CD55 and CD59. Neutralizing antibodies to CD55 and CD59 can overcome resistance to rituximab-mediated complement-mediated cytotoxicity in vitro. This paper overviews our understanding of the mechanisms of action of rituximab and identifies how this knowledge could be applied in a clinical setting to maximize response in both sensitive and resistant patients.
Advanced mobile phone service (1980)

The advanced mobile phone service (AMPS) system, an FM cellular radio system in the final stages of development, is described. A brief description of the system is followed by a discussion of the control algorithms which are basic to its operation. Finally, a status report is presented on the Chicago developmental system (an operational cellular system) and the cellular test bed in Newark, NJ (a field laboratory used to evaluate the radio performance of FM cellular systems with cells as small as 1.4-mi radius).
Leukemia inhibitory factor and interleukin‐11 promote maturation of murine and human megakaryocytes in vitro (1992)

The growth-promoting activities of optimally stimulating concentrations of leukemia inhibitory factor (LIF) and interleukin-11 (IL-11), a stromal cell-derived cytokine, on megakaryocytes in liquid marrow cultures were compared to interleukin-6 (IL-6), a known megakaryocytes maturation factor. Maximally stimulating concentrations of LIF (25 ng/ml), IL-11 (10 ng/ml), or IL-6 alone (10 ng/ml) promoted an 81, 157, and 153% increase, respectively, in acetylcholinesterase (AchE) activity in murine serum-free cultures compared with controls (n = 5). In combination with 25 U/ml murine interleukin-3 (IL-3), LIF, IL-6, and IL-11 showed increases, respectively, of 35%, 49%, and 174% in AchE activity compared with IL-3 alone (n = 4). Flow cytometric analysis of 4-day-old cultures showed that LIF alone had minimal effect on megakaryocytic ploidy, whereas IL-11 and IL-6 alone markedly augmented high ploidy cells. Enumeration of cells stained for AchE showed that IL-11 increased the numbers of Mks in comparison to LIF, IL-6 or controls by up to 59%. Moreover, a twofold increment in Mk number was noted when IL-11 was used in combination with IL-3 (compared with either IL-3 alone of IL-3+IL-6). Flow cytometric ploidy analysis of 8-day-old human liquid marrow cultures showed that either LIF, IL-11, or IL-6 alone markedly augmented the percentage of 32N cells compared with cultures containing only human IL-3. The data suggest that LIF and IL-11 promote murine and human Mk maturation in vitro, although the effect of IL-11 exceeds that of LIF in mice. Despite the comparable influence of IL-11 and IL-6 on Mk ploidy, IL-11 has the additional characteristic of enhancing the number of Mks, particularly in combination with IL-3.
Growth and partial differentiation of presumptive human cardiac myoblasts in culture. (1989)

A cell culture model for human cardiac myogenesis is introduced. Human fetal myocardial cells were dissociated enzymatically, and cultured in a mitogen-rich medium that promoted the growth of presumptive cardiac myoblasts. Strains of human cardiac myoblasts were generated from different anatomical regions of the fetal heart. The cells could be cultured for at least 30 generations, or frozen and recovered for later use. Differentiation was induced by culturing the cardiac myoblasts in a mitogen-poor medium. Differentiation of cardiac myoblasts was marked primarily by transcriptional activation of the atrial natriuretic factor (ANF) gene. Evidence is presented that posttranscriptional processing of ANF transcripts is affected by the anatomical origin of the cardiac myoblasts and the presence of cocultured neuronal cells. Cardiac myoblasts induced to differentiate in culture synthesized only low levels of sarcomeric myosin and cardiac alpha-actin, suggesting that differentiation of these cells progresses through two phases: an initial, noncontractile phase that is represented by the differentiating cultured cells; and a later contractile phase, in which myofibrillar assembly is accentuated and modulated by secondary signals from the cardiac milieu.
Widespread optogenetic expression in macaque cortex obtained with MR-guided, convection enhanced delivery (CED) of AAV vector to the thalamus (2017)

MR-guided CED infusion into thalamus provides a simplified approach to transduce large cortical areas by thalamo-cortico-thalamic projections in primate brain.
Endogenous Control and Task Representation: An fMRI Study in Algebraic Problem-solving (2008)

The roles of prefrontal and anterior cingulate cortices have been widely studied, yet little is known on how they interact to enable complex cognitive abilities. We investigated this issue in a complex yet well-defined symbolic paradigm: algebraic problem solving. In our experimental problems, the demands for retrieving arithmetic facts and maintaining intermediate problem representations were manipulated separately. An analysis of functional brain images acquired while participants were solving the problems confirmed that prefrontal regions were affected by the retrieval of arithmetic facts, but only scarcely by the need to manipulate intermediate forms of the equations, hinting at a specific role in memory retrieval. Hemodynamic activity in the dorsal cingulate, on the contrary, increased monotonically as more information processing steps had to be taken, independent of their nature. This pattern was essentially mimicked in the caudate nucleus, suggesting a related functional role in the control of cognitive actions. We also implemented a computational model within the Adaptive Control of Thought-Rational (ACT-R) cognitive architecture, which was able to reproduce both the behavioral data and the time course of the hemodynamic activity in a number of relevant regions of interest. Therefore, imaging results and computer simulation provide evidence that symbolic cognition can be explained by the functional interaction of medial structures supporting control and serial execution, and prefrontal cortices engaged in the on-line retrieval of specific relevant information.
Proteolytic Peptide Mapping (2004)

Analysis of intact proteins is hampered by the fact that even when using high-resolution techniques, like electrospray mass spectrometry, you will only be able to tell whether the protein has the expected mass. If you find a deviation from the expected you will, in most cases, be left wondering where (and perhaps what) the difference is. These observations are compounded when using low-resolution techniques like gel filtration or sodium dodecyl sulfate (SDS) gel electrophoresis. Although 2D gel electrophoresis is able to show a single charge difference, in the absence of additional information you are still left wondering where and what the differences are.
STING Specifies IRF3 Phosphorylation by TBK1 in the Cytosolic DNA Signaling Pathway (2012)

Cytosolic double-stranded DNA (dsDNA) stimulates the production of type I interferon (IFN) through the endoplasmic reticulum (ER)-resident adaptor protein STING (stimulator of IFN genes), which activates the transcription factor interferon regulatory factor 3 (IRF3); however, how STING activates IRF3 is unclear. Here, we showed that STING stimulates phosphorylation of IRF3 by the kinase TBK1 (TANK-binding kinase 1) in an in vitro reconstitution system. With this system, we identified a carboxyl-terminal region of STING that was both necessary and sufficient to activate TBK1 and stimulate the phosphorylation of IRF3. We also found that STING interacted with both TBK1 and IRF3 and that mutations in STING that selectively disrupted its binding to IRF3 abrogated phosphorylation of IRF3 without impairing the activation of TBK1. These results suggest that STING functions as a scaffold protein to specify and promote the phosphorylation of IRF3 by TBK1. This scaffolding function of STING (and possibly of other adaptor proteins) may explain why IRF3 is activated in only a subset of signaling pathways that activate TBK1.
A transform domain classified vector quantizer for image coding (1992)

An image-coding technique, in which the discrete cosine transform (DCT) is combined with a classified vector quantization (CVQ), is presented. A DCT-transformed input block is classified according to the perceptual feature, partitioned into several smaller vectors, and then vector quantized. An efficient edge-oriented classifier employing the DCT coefficients as feature for classification is used to maintain the edge integrity in the reconstructed image. Based on a smaller geometric mean vector variance, a partition scheme in which 2-D DCT coefficients are divided into several smaller size vectors is also investigated. Because the distortion rate function (DRF) used is essential for the bit allocation algorithm to perform well, attempts have been made to modify the asymptotic DRF to estimate the performance of real VQs at low bit rates, and the modification is shown to be in good agreement with experimental results. Simulation results indicate that a good visual quality of the coded image in the range of 0.4 approximately 0.7 b/pixel is obtained.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Synthesis of 3’,5’-cyclic diguanylic acid (cdiGMP) Using 1-(4-chlorophenyl)-4-ethoxypiperidin-4-yl as a Protecting Group for 2’-hydroxy Functions of Ribonucleosides (2007)

We herein report a convenient synthesis of 3',5'-cyclic diguanylic acid via the modified H-phosphonate approach. The 1-(4-chlorophenyl)-4-ethoxypiperidin-4-yl (Cpep) group was used as protecting group for the 2'-hydroxy functions of ribonucleosides. Complete unblocking of the fully protected 3',5'-cyclic diguanylic acid gave cdiGMP as a homogeneous compound in an excellent yield.
High Frequency of Coexistent Mutations of PIK3CA and PTEN Genes in Endometrial Carcinoma (2005)

The phosphatidylinositol 3'-kinase (PI3K) pathway is activated in many human cancers. In addition to inactivation of the PTEN tumor suppressor gene, mutations or amplifications of the catalytic subunit alpha of PI3K (PIK3CA) have been reported. However, the coexistence of mutations in these two genes seems exceedingly rare. As PTEN mutations occur at high frequency in endometrial carcinoma, we screened 66 primary endometrial carcinomas for mutations in the helical and catalytic domains of PIK3CA. We identified a total of 24 (36%) mutations in this gene and coexistence of PIK3CA/PTEN mutations at high frequency (26%). PIK3CA mutations were more common in tumors with PTEN mutations (17 of 37, 46%) compared with those without PTEN mutations (7 of 29, 24%). Array comparative genomic hybridization detected 3q24-qter amplification, which covers the PIK3CA gene (3q26.3), in one of nine tumors. Knocking down PTEN expression in the HEC-1B cell line, which possesses both K-Ras and PIK3CA mutations, further enhances phosphorylation of Akt (Ser473), indicating that double mutation of PIK3CA and PTEN has an additive effect on PI3K activation. Our data suggest that the PI3K pathway is extensively activated in endometrial carcinomas, and that combination of PIK3CA/PTEN alterations might play an important role in development of these tumors.
On enantiomorph-polarity estimation (1983)

The behaviour of Rogers's η parameter for enantiomorph-polarity estimation is examined theoretically and experimentally on simulated intensity data for seven well-assorted compounds. An alternative parameter x, based on incoherent scattering from twin components related by a centre of symmetry, is also considered. It is found that both parameters are very well adapted to implementation in a least-squares program and converge well. The η parameter can give false and over-precise indications of chirality-polarity for structures which are nearly centrosymmetric, whereas the x parameter does not have this fault and converges more rapidly than η.
Chemical generation of bispecific antibodies (2010)

Bispecific antibodies (BsAbs) are regarded as promising therapeutic agents due to their ability to simultaneously bind two different antigens. Several bispecific modalities have been developed, but their utility is limited due to problems with stability and manufacturing complexity. Here we report a versatile technology, based on a scaffold antibody and pharmacophore peptide heterodimers, that enables rapid generation and chemical optimization of bispecific antibodies, which are termed bispecific CovX-Bodies. Two different peptides are joined together using a branched azetidinone linker and fused to the scaffold antibody under mild conditions in a site-specific manner. Whereas the pharmacophores are responsible for functional activities, the antibody scaffold imparts long half-life and Ig-like distribution. The pharmacophores can be chemically optimized or replaced with other pharmacophores to generate optimized or unique bispecific antibodies. As a prototype, we developed a bispecific antibody that binds both vascular endothelial growth factor (VEGF) and angiopoietin-2 (Ang2) simultaneously, inhibits their function, shows efficacy in tumor xenograft studies, and greatly augments the antitumor effects of standard chemotherapy. This unique antiangiogenic bispecific antibody is in phase-1 clinical trials.
Photoinduced Intramolecular Charge Transfer in an Electronically Modified Flavin Derivative: Roseoflavin (2014)

The photophysical properties of a push-pull flavin derivative, roseoflavin (RoF), are investigated in different surroundings at the molecular level, with focus on intramolecular charge transfer (ICT). Time-dependent density functional theory (TD-DFT, CAM-B3LYP functional) and DFT-based multireference configuration interaction (DFT/MRCI) are used to compute excited-state energies and one-electron properties of a truncated RoF model, roseolumiflavin (RoLF). Solvent effects are taken into account implicitly by the conductor-like polarizable continuum model and explicitly through a microsolvation scheme. In the gas phase, the calculations predict no crossing between the lowest locally excited (LE) and charge-transfer (CT) states upon twisting the dimethylamine donor group relative to the plane of the isoalloxazine acceptor moiety, whereas this crossing is found to be facile in solution (i.e., in water or benzene). Crossing of the LE and CT states facilitates ICT, which is the main cause of the fluorescence quenching and dual fluorescence character experimentally observed for roseoflavin in solution. The barrier for the ICT process is computed to be lower in water than in benzene, consistent with the enhanced ICT rates observed in more polar solvents. We present a detailed study of the molecular mechanism of the photoinduced ICT process in RoLF. For a typical donor-acceptor chromophore, three such mechanisms are discussed in the literature, which differ in the alignment of the donor and acceptor planes, namely, planar ICT (PICT), perpendicular-twisted ICT (TICT), and wagging ICT (WICT). Our theoretical results suggest that the TICT mechanism is favored in RoLF.
Human Neural Stem and Progenitor Cells: In Vitro and In Vivo Properties, and Potential for Gene Therapy and Cell Replacement in the CNS (2001)

The generation of unlimited quantities of neural stem and/or progenitor cells derived from the human brain holds great interest for basic and applied neuroscience. In this article we critically review the origins and recent developments of procedures developed for the expansion, perpetuation, identification, and isolation of human neural precursors, as well as their attributes. Factors influencing their in vitro properties, both under division and after differentiation conditions, are evaluated, with the aim of identifying properties common to the different culture systems reported. This analysis suggests that different culture procedures result in cells with different properties, or even in different cells being isolated. With respect to in vivo performance, present evidence obtained in rodents indicate that cultured human neural precursors, in general, are endowed with excellent integrative properties. Differentiation of the implanted cells, in particular in the case of adult recipients, seems not to be complete, and functionality still needs to be demonstrated. In relation to gene transfer and therapy, aspects currently underexplored, initial data support the view that human neural stem and progenitor cells may serve a role as a platform cell for the delivery of bioactive substances to the diseased CNS. Although a large deal of basic research remains to be done, available data illustrate the enormous potential that human neural precursors isolated, expanded, and characterized in vitro hold for therapeutic applications. In spite of this potential, maintaining a critical view on many unresolved questions will surely help to drive this research field to a good end, that is, the development of real therapies for diseases of the human nervous system.
Phase I study of inotuzumab ozogamicin (CMC‐544) in Japanese patients with follicular lymphoma pretreated with rituximab‐based therapy (2010)

Inotuzumab ozogamicin (CMC-544), an antibody-targeted chemotherapeutic agent composed of an anti-CD22 antibody conjugated to calicheamicin, a potent cytotoxic antibiotic, specifically targets the CD22 antigen present in >90% of B-lymphoid malignancies, rendering it useful for treating patients with B-cell non-Hodgkin lymphoma (B-NHL). This phase I study evaluated the safety, tolerability, efficacy, and pharmacokinetics of inotuzumab ozogamicin in Japanese patients. Eligible patients had relapsed or refractory CD22-positive B-NHL without major organ dysfunction. Inotuzumab ozogamicin was administered intravenously once every 28 days (dose escalation: 1.3 and 1.8 mg/m(2)). All 13 patients had follicular lymphoma, were previously treated with > or =1 rituximab-alone or rituximab-containing chemotherapy, and were enrolled into two dose cohorts (1.3 mg/m(2), three patients; 1.8 mg/m(2), 10 patients). No patient had dose-limiting toxicities, and the maximum tolerated dose, previously determined in non-Japanese patients (1.8 mg/m(2)), was confirmed. Drug-related adverse events (AEs) included thrombocytopenia (100%), leukopenia (92%), lymphopenia (85%), neutropenia (85%), elevated AST (85%), anorexia (85%), and nausea (77%). Grade 3/4 drug-related AEs in > or =15% patients were thrombocytopenia (54%), lymphopenia (31%), neutropenia (31%), and leukopenia (15%). The AUC and C(max) of inotuzumab ozogamicin increased dose-dependently with pharmacokinetic profiles similar to non-Japanese. Seven patients had complete response (CR, 54%) including unconfirmed CR, four patients had partial response (31%), and two patients had stable disease (15%). The overall response rate was 85% (11/13). Inotuzumab ozogamicin was well tolerated at doses up to 1.8 mg/m(2) and showed preliminary evidence of activity in relapsed or refractory follicular lymphoma pretreated with rituximab-containing therapy, warranting further investigations. This trial was registered in ClinicalTrials.gov (NCT00717925).
Predictive Value of Microtubule Associated Proteins Tau and Stathmin in Patients With Nonmuscle Invasive Bladder Cancer Receiving Adjuvant Intravesical Taxane Therapy (2011)

Assessment of tau and stathmin protein expression should be considered to select patients before intravesical taxane based chemotherapy for nonmuscle invasive, bacillus Calmette-Guérin refractory bladder cancer since those who have tumors with low tau/stathmin protein expression show a better response to therapy.
Analysis of Murine CD8+T-Cell Clones Specific for the Dengue Virus NS3 Protein: Flavivirus Cross-Reactivity and Influence of Infecting Serotype (1999)

Serotype-cross-reactive dengue virus-specific cytotoxic T lymphocytes (CTL) induced during a primary dengue virus infection are thought to play a role in the immunopathogenesis of dengue hemorrhagic fever (DHF) during a secondary dengue virus infection. Although there is no animal model of DHF, we previously reported that murine dengue virus-specific CTL responses are qualitatively similar to human dengue virus-specific CTL responses. We used BALB/c mice to study the specificity of the CTL response to an immunodominant epitope on the dengue virus NS3 protein. We mapped the minimal H-2Kd-restricted CTL epitope to residues 298 to 306 of the dengue type 2 virus NS3 protein. In short-term T-cell lines and clones, the predominant CD8(+) CTL to this epitope in mice immunized with dengue type 2 virus or vaccinia virus expressing the dengue type 4 virus NS3 protein were cross-reactive with dengue type 2 or type 4 virus, while broadly serotype-cross-reactive CTL were a minority population. In dengue type 3 virus-immunized mice, the predominant CTL response to this epitope was broadly serotype cross-reactive. All of the dengue virus-specific CTL clones studied also recognized the homologous NS3 sequences of one or more closely related flaviviruses, such as Kunjin virus. The critical contact residues for the CTL clones with different specificities were mapped with peptides having single amino acid substitutions. These data demonstrate that primary dengue virus infection induces a complex population of flavivirus-cross-reactive NS3-specific CTL clones in mice and suggest that CTL responses are influenced by the viral serotype. These findings suggest an additional mechanism by which the order of sequential flavivirus infections may influence disease manifestations.