gebhart/patrepeval huggingface dataset:
Transforming growth factor-? signaling in cancer (2001)

Transforming growth factor (TGF-beta) is a multifunctional polypeptide implicated in the regulation of a variety of cellular processes including growth, differentiation, apoptosis, adhesion, and motility. Abnormal activation or inhibition of these TGF-beta regulated processes is implicated in many diseases, including cancer. Cancers can develop through selective exploitation of defects in TGF-beta signaling that occur at several different levels in the pathway. The TGF-beta signal transduction cascade is initiated when TGF-beta binds to transmembrane receptors. The TGF-beta receptors then phosphorylate and activate Smad proteins, which transduce the signal from the cytoplasm to the nucleus. In the nucleus, Smads can bind directly to DNA and cooperate with other transcription factors to induce transcription of TGF-beta target genes. Mutations in target genes, Smads, or the TGF-beta receptor are associated with certain human cancers.
Advances in the delivery of RNA therapeutics: from concept to clinical reality (2017)

The rapid expansion of the available genomic data continues to greatly impact biomedical science and medicine. Fulfilling the clinical potential of genetic discoveries requires the development of therapeutics that can specifically modulate the expression of disease-relevant genes. RNA-based drugs, including short interfering RNAs and antisense oligonucleotides, are particularly promising examples of this newer class of biologics. For over two decades, researchers have been trying to overcome major challenges for utilizing such RNAs in a therapeutic context, including intracellular delivery, stability, and immune response activation. This research is finally beginning to bear fruit as the first RNA drugs gain FDA approval and more advance to the final phases of clinical trials. Furthermore, the recent advent of CRISPR, an RNA-guided gene-editing technology, as well as new strides in the delivery of messenger RNA transcribed in vitro, have triggered a major expansion of the RNA-therapeutics field. In this review, we discuss the challenges for clinical translation of RNA-based therapeutics, with an emphasis on recent advances in delivery technologies, and present an overview of the applications of RNA-based drugs for modulation of gene/protein expression and genome editing that are currently being investigated both in the laboratory as well as in the clinic.
Elastomeric Origami: Programmable Paper‐Elastomer Composites as Pneumatic Actuators (2012)

Abstract The development of soft pneumatic actuators based on composites consisting of elastomers with embedded sheet or fiber structures (e.g., paper or fabric) that are flexible but not extensible is described. On pneumatic inflation, these actuators move anisotropically, based on the motions accessible by their composite structures. They are inexpensive, simple to fabricate, light in weight, and easy to actuate. This class of structure is versatile: the same principles of design lead to actuators that respond to pressurization with a wide range of motions (bending, extension, contraction, twisting, and others). Paper, when used to introduce anisotropy into elastomers, can be readily folded into 3D structures following the principles of origami; these folded structures increase the stiffness and anisotropy of the elastomeric actuators, while being light in weight. These soft actuators can manipulate objects with moderate performance; for example, they can lift loads up to 120 times their weight. They can also be combined with other components, for example, electrical components, to increase their functionality.
Enantioselective Conjugate Borylation (2010)

Learn your ABCs! The asymmetric borylation in conjugate fashion has rapidly progressed in recent years if not months (see scheme, pin=pinacolato, TM=transition metal). This Highlight summarizes these breathtaking developments, including a mechanistic analysis. An outlook onto a future asymmetric organocatalysis is presented as well.
Human CD14+ leukocytes acquire the phenotype and function of antigen-presenting dendritic cells when cultured in GM-CSF and IL-4 (1996)

The combination of granulocyte-macrophage colony stimulating factor (GM-CSF) and interleukin-4 (IL-4) induces the growth of antigen-presenting cells (APC) from adherent peripheral blood leukocytes. These cells have been characterized as dendritic cells (DC), yet many questions exist regarding their relationship to other DC populations and the nature of their progenitors. To address these issues, we utilized a combination of immunomagnetic depletion, cell sorting, and cell culture to isolate four distinct APC populations; macrophages expressing high levels of CD14 (CD14bright macrophages), DC produced by culturing adherent cells in GM-CSF and IL-4 (cultured DC), and two different subsets of fresh DC that express low levels of CD14 (CD14dim DC). Each population exhibited a unique morphology and a unique profile of cell surface markers. In contrast to macrophages,all three DC populations expressed the DC marker CD83, as well as highlevels of MHC molecules and the costimulatory molecules B7-1 (CD80) and B7-2 (CD86). In addition. all three DC populations presented soluble tetanus toxin antigen and stimulated T cell proliferation to levels far superior to that of macrophages. Blocking studies demonstrated a costimulatory role for B7-1, B7-2, and CD40 in antigen presentation, although B7-2 expression was the single most important factor. To identify the progenitors of cultured DC, we sorted the adherent fraction of PBMC into discrete subpopulations prior to exposure to GM-CSF and IL-4. DC activity derived entirely from CD14+ precursors and was equally demonstrable using either the CD14dim or CD14bright subsets. Although these DC precursors lost expression of CD14 in culture, they maintained most of their other myeloid features. We conclude that human CD14+ leukocytes acquire the phenotype and function of DC when cultured in GM-CSF and IL-4.
A new method for the selective isolation of phosphoserine‐containing peptides (1987)

Meyer et al. [(1986) FEBS Lett 204, 61-66] have shown that phosphoserine can be converted to S-ethylcysteine by beta-elimination and addition of ethanethiol. I have utilised this modification to develop a rapid method for the selective purification of phosphoserine-containing peptides from complex mixtures. Changing phosphoserine to S-ethylcysteine increases the hydrophobicity of a peptide, altering its mobility during reverse-phase chromatography. The number of S-ethylcysteine residues in a peptide can be quantified at the picomolar level, following acid hydrolysis and conversion to the phenylthiocarbamyl derivative. The procedure may be particularly powerful for the analysis of peptides that are phosphorylated at multiple sites in vivo.
HIV-1 env DNA vaccine administered to rhesus monkeys elicits MHC class II-restricted CD4+ T helper cells that secrete IFN-gamma and TNF-alpha (1997)

The Th cell response elicited by an HIV-1 env plasmid DNA vaccine was assessed in rhesus monkeys by isolation of gp120-specific, MHC class II-restricted CD4+ T cell lines from PBL of vaccinated animals. The Env-specific CD4+ T cell lines recognized epitopes located in the second hypervariable region and in the carboxyl terminus of HIV-1 gp120. These cell lines proliferated in response to APC in the presence of recombinant gp120, as well as to APC expressing virally encoded Env. All of the CD4+ T cell lines responded to Env peptide by secreting IFN-gamma and TNF-alpha without appreciable IL-4 production. Recombinant gp120 stimulation of PBL from these vaccinated monkeys elicited the secretion of a similar profile of cytokines. Demonstration of a nucleotide vaccine eliciting a Th1-like immune response is consistent with the well documented ability of naked DNA vaccines to induce durable CD8+ CTL responses.
Efficacy and Tolerability of Cancer Pain Management with Controlled-release Oxycodone Tablets in Opioid-naive Cancer Pain Patients, Starting with 5 mg Tablets (2004)

The results suggest that controlled-release oxycodone tablets offered stable and adequate pain control within a short period of time in most Japanese cancer patients who have not been taking opioid analgesics, and could be effectively titrated against pain from a starting dose of 5 mg every 12 h. This indicates that a lower strength controlled-release oxycodone formulation may make it possible to start and titrate the dose more appropriately and carefully in patients who are sensitive to opioid analgesics.
Melanin Pigmentation in Mammalian Skin and Its Hormonal Regulation (2004)

Cutaneous melanin pigment plays a critical role in camouflage, mimicry, social communication, and protection against harmful effects of solar radiation. Melanogenesis is under complex regulatory control by multiple agents interacting via pathways activated by receptor-dependent and -independent mechanisms, in hormonal, auto-, para-, or intracrine fashion. Because of the multidirectional nature and heterogeneous character of the melanogenesis modifying agents, its controlling factors are not organized into simple linear sequences, but they interphase instead in a multidimensional network, with extensive functional overlapping with connections arranged both in series and in parallel. The most important positive regulator of melanogenesis is the MC1 receptor with its ligands melanocortins and ACTH, whereas among the negative regulators agouti protein stands out, determining intensity of melanogenesis and also the type of melanin synthesized. Within the context of the skin as a stress organ, melanogenic activity serves as a unique molecular sensor and transducer of noxious signals and as regulator of local homeostasis. In keeping with these multiple roles, melanogenesis is controlled by a highly structured system, active since early embryogenesis and capable of superselective functional regulation that may reach down to the cellular level represented by single melanocytes. Indeed, the significance of melanogenesis extends beyond the mere assignment of a color trait.
5-Methylcytosine-DNA glycosylase activity is present in a cloned G/T mismatch DNA glycosylase associated with the chicken embryo DNA demethylation complex (2000)

We previously have shown that DNA demethylation by chicken embryo 5-methylcytosine DNA glycosylase (5-MCDG) needs both RNA and proteins. One of these proteins is a RNA helicase. Further peptides were sequenced, and three of them are identical to the mammalian G/T mismatch DNA glycosylase. A 3,233-bp cDNA coding for the chicken homologue of human G/T mismatch DNA glycosylase was isolated and sequenced. The derived amino acid sequence (408 aa) shows 80% identity with the human G/T mismatch DNA glycosylase, and both the C and N-terminal parts have about 50% identity. As for the highly purified chicken embryo DNA demethylation complex the recombinant protein expressed in Escherichia coli has both G/T mismatch and 5-MCDG activities. The recombinant protein has the same substrate specificity as the chicken embryo 5-MCDG where hemimethylated DNA is a better substrate than symmetrically methylated CpGs. The activity ratio of G/T mismatch and 5-MCDG is about 30:1 for the recombinant protein expressed in E. coli and 3:1 for the purified enzyme from chicken embryos. The incubation of a recombinant CpG-rich RNA isolated from the purified DNA demethylation complex with the recombinant enzyme strongly inhibits G/T mismatch glycosylase while slightly stimulating the activity of 5-MCDG. Deletion mutations indicate that G/T mismatch and 5-MCDG activities share the same areas of the N- and C-terminal parts of the protein. In reconstitution experiments RNA helicase in the presence of recombinant RNA and ATP potentiates the activity of 5-MCDG.
The Importance of Adjuvant Formulation in the Development of a Tuberculosis Vaccine (2012)

An effective protein-based vaccine for tuberculosis will require a safe and effective adjuvant. There are few adjuvants in approved human vaccines, including alum and the oil-in-water-based emulsions MF59 (Novartis Vaccines and Diagnostics), AS03 and AS04 (GlaxoSmithKline Biologics), AF03 (Sanofi), and liposomes (Crucell). When used with pure, defined proteins, both alum and emulsion adjuvants are effective at inducing primarily humoral responses. One of the newest adjuvants in approved products is AS04, which combines monophosphoryl lipid A, a TLR-4 agonist, with alum. In this study, we compared two adjuvants: a stable oil-in-water emulsion (SE) and a stable oil-in-water emulsion incorporating glucopyranosyl lipid adjuvant, a synthetic TLR-4 agonist (GLA-SE), each together with a recombinant protein, ID93. Both the emulsion SE and GLA-SE adjuvants induce potent cellular responses in combination with ID93 in mice. ID93/SE induced Th2-biased immune responses, whereas ID93/GLA-SE induced multifunctional CD4(+) Th1 cell responses (IFN-γ, TNF-α, and IL-2). The ID93/GLA-SE vaccine candidate induced significant protection in mice and guinea pigs, whereas no protection was observed with ID93/SE, as assessed by reductions in bacterial burden, survival, and pathology. These results highlight the importance of properly formulating subunit vaccines with effective adjuvants for use against tuberculosis.
Cloning and expression of a neuronal calcium channel beta subunit (1993)

Although pharmacological and electrophysiological studies have demonstrated the existence of multiple types of voltage-dependent calcium channels in neuronal tissue, the subunit composition of these channels is not well known. Here, we report the cloning and expression of a new rat brain beta subunit (beta 4). Northern blot analysis indicates that beta 4 mRNA is expressed almost exclusively in neuronal tissues, with the highest levels being found in the cerebellum. Coexpression studies indicate that rat beta 4 can interact with rabbit cardiac muscle alpha 1, rabbit skeletal muscle alpha 1, and calcium channels endogenous to Xenopus oocytes. beta 4 modulation of alpha 1 activity is similar to the modulation induced by beta 1, beta 2, or beta 3. The most striking effect of beta subunits is their ability to increase functional alpha 1 activity, which can be measured as either increased dihydropyridine binding to membranes from transfected COS cells or increased calcium channel activity in Xenopus oocytes.
Function-based indexing for object-oriented databases (1994)

Object-oriented databases have been developed to allow applications to store persistent data in the form of objects. As in conventional databases, object-oriented databases need to support queries that allow associative access to data by describing a property of the data of interest. In particular, they should support queries over user-defined sets based on user-defined functions that compute the property of interest. To make such function-based queries run faster, we must support function-based indexes where the keys are these computed properties. Function-based indexes are harder to maintain than indexes in conventional databases because mutations that affect keys can be done without accessing an element of the indexed set.
Bacteriorhodopsin expressed in Schizosaccharomyces pombe pumps protons through the plasma membrane. (1993)

Bacterioopsin (bO) from Halobacterium salinarium ("Halobacterium halobium") has been functionally expressed in a heterologous system, the fission yeast Schizosaccharomyces pombe. Regeneration of bO to bacteriorhodopsin (bR) in S. pombe has been achieved in vivo by addition of the chromophore retinal to the culture medium, as shown for a retinal-negative mutant of H. salinarium (JW5). Western blot analysis revealed that bR is more stable than bO against proteolysis in fission yeast and also in JW5. The light-driven proton pump is expressed in the eukaryotic organism and incorporated into the plasma membrane. Illumination of intact yeast cells leads to acidification of the external medium due to the translocation of H+ from inside to outside of the cell, indicating the same orientation of bR in the yeast plasma membrane as in H. salinarium. The kinetics of proton release into the water phase was observed with the optical pH indicator pyranine. Time-resolved absorbance changes of isolated plasma membrane measured by flash spectroscopy showed rise and decay of the M intermediate during the photocycle similar to those in the homologous system. Photocurrents and photovoltages were recorded with yeast plasma membrane attached to a planar lipid membrane and to a polytetrafluoroethylene (Teflon) film, respectively. Stationary currents measured in the presence of a protonophore showed continuous pumping activity of bR. The action spectrum of the photocurrent and the kinetics of the photovoltage were analyzed and compared with signals obtained from purple membranes. From all these different investigations we conclude that the integral membrane protein bR is correctly folded in vivo into the cytoplasmic membrane of the fission yeast S. pombe.
Increased Susceptibility of Mice Lacking T-bet to Infection with Mycobacterium tuberculosis Correlates with Increased IL-10 and Decreased IFN-γ Production (2005)

A sustained CD4+ Th1-dominated type 1 immune response is required to successfully control Mycobacterium tuberculosis infection. Considerable work has demonstrated that the transcription factor, T-bet, is required for IFN-gamma expression and fundamental to the generation of type 1 immunity in multiple cell types. Mice lacking T-bet are susceptible to virulent M. tuberculosis infection. Susceptibility of T-bet-deficient mice is associated with increased systemic bacterial burden, diminished IFN-gamma production, and the striking accumulation of eosinophilic macrophages and multinucleated giant cells in the lung. Interestingly, T-bet(-/-) mice did not develop a fully polarized Th2 response toward M. tuberculosis, but exhibited selective elevation of IL-10 production. These results indicate that T-bet plays a central role in controlling M. tuberculosis disease progression, in part through the regulation of both IFN-gamma and IL-10.
The challenge problem for automated detection of 101 semantic concepts in multimedia (2006)

We introduce the challenge problem for generic video indexing to gain insight in intermediate steps that affect performance of multimedia analysis methods, while at the same time fostering repeatability of experiments. To arrive at a challenge problem, we provide a general scheme for the systematic examination of automated concept detection methods, by decomposing the generic video indexing problem into 2 unimodal analysis experiments, 2 multimodal analysis experiments, and 1 combined analysis experiment. For each experiment, we evaluate generic video indexing performance on 85 hours of international broadcast news data, from the TRECVID 2005/2006 benchmark, using a lexicon of 101 semantic concepts. By establishing a minimum performance on each experiment, the challenge problem allows for component-based optimization of the generic indexing issue, while simultaneously offering other researchers a reference for comparison during indexing methodology development. To stimulate further investigations in intermediate analysis steps that inuence video indexing performance, the challenge offers to the research community a manually annotated concept lexicon, pre-computed low-level multimedia features, trained classifier models, and five experiments together with baseline performance, which are all available at http://www.mediamill.nl/challenge/.
Diagnosis of Mediterranean Spotted Fever by Indirect Immunofluorescence of Rickettsia conorii in Circulating Endothelial Cells Isolated with Monoclonal Antibody-Coated Immunomagnetic Beads (1992)

Rickettsia conorii, an obligate intracellular bacterium that infects vascular endothelial cells, is the etiologic agent of Mediterranean spotted fever (MSF). A new procedure using indirect immunofluorescence was used to directly detect R. conorii in circulating endothelial cells (CEC). CEC were separated from other blood components by using anti-endothelial cell monoclonal antibody-coated magnetic beads. An anti-R. conorii polyclonal rabbit antiserum was used to stain rickettsiae. The entire procedure took 3 h. R. conorii was detected in CEC from 9 of 12 patients ultimately confirmed as having MSF. Among the patients, 5 with R. conorii isolated by centrifugation-shell vial assay were also positive by the new technique. None of 3 patients whose diagnosis was other than MSF had R. conorii detected in CEC. The procedure may be helpful for rapid diagnosis of MSF and may lead to new technical approaches for the diagnosis of infectious diseases caused by intracellular pathogenic microorganisms.
A microprocessor-based digital feeder monitor with high-impedance fault detection (1994)

The high impedance fault detection technology developed at Texas A&M University after more than a decade of research, funded in large part by the Electric Power Research Institute, has been incorporated into a comprehensive monitoring device for overhead distribution feeders. This digital feeder monitor (DFM) uses a high waveform sampling rate for the ac current and voltage inputs in conjunction with a high-performance reduced instruction set (RISC) microprocessor to obtain the frequency response required for arcing fault detection and power quality measurements. Expert system techniques are employed to assure security while maintaining dependability. The DFM is intended to be applied at a distribution substation to monitor one feeder. The DFM is packaged in a non-drawout case which fits the panel cutout for a GE IAC overcurrent relay to facilitate retrofits at the majority of sites were electromechanical overcurrent relays already exist.
Roles of S3 Site Residues of Nattokinase on its Activity and Substrate Specificity (2007)

Nattokinase (Subtilisin NAT, NK) is a bacterial serine protease with high fibrinolytic activity. To probe their roles on protease activity and substrate specificity, three residues of S3 site (Gly(100), Ser(101) and Leu(126)) were mutated by site-directed mutagenesis. Kinetics parameters of 20 mutants were measured using tetrapeptides as substrates, and their fibrinolytic activities were determined by fibrin plate method. Results of mutation analysis showed that Gly(100) and Ser(101) had reverse steric and electrostatic effects. Residues with bulky or positively charged side chains at position 100 decreased the substrate binding and catalytic activity drastically, while residues with the same characters at position 101 could obviously enhance protease and fibrinolytic activity of NK. Mutation of Leu(126) might impair the structure of the active cleft and drastically decreased the activity of NK. Kinetics studies of the mutants showed that S3 residues were crucial to keep protease activity while they moderately affected substrate specificity of NK. The present study provided some original insight into the P3-S3 interaction in NK and other subtilisins, as well as showed successful protein engineering cases to improve NK as a potential therapeutic agent.
Charging megadalton poly(ethylene oxide)s by electrospray ionization. A charge detection mass spectrometry study (2011)

Ions from compounds of megadalton (MDa) molecular weight were produced in an electrospray ionization source from solutions of poly(ethylene oxide) (PEO) samples with average molecular weights ranging from 1,000,000 to 7,000,000 Da. Charge detection mass spectrometry (CDMS) has been used to determine the mass of the MDa PEOs. Simultaneous measurement of the charge and velocity of individual ions allows the mass determination of the ion, after calibration of the instrument with independent samples. In addition to the mass spectra, CDMS generates charge-versus-mass plots, which allow investigation of the charging of electrosprayed ions over a broad range of masses. The experimental charging capacity of MDa PEOs is compared with a simple model based on the affinity of alkali cations for oxygen sites and on the electrostatic potential energy of the charged polymer. The charging capacity of PEOs was also investigated as a function of the concentration of and the type of alkali ions.