gebhart/patrepeval huggingface dataset:
Molecular basis for the transfer of nicotinamide adenine dinucleotide among dehydrogenases (1985)

NADH is transferred directly from one dehydrogenase enzyme site to another without intervention of the aqueous solvent whenever the two dehydrogenases are of opposite chiral specificity as regards the C4 H of NADH which is transferred in the catalyzed reduction reaction. When both enzymes catalyze the transfer of hydrogen from the same face of the nicotinamide ring, direct enzyme-enzyme transfer of NADH is not possible [Srivastava, D. K., & Bernhard, S. A. (1984) Biochemistry 23, 4538-4545; Srivastava, D. K., & Bernhard, S. A. (1985) Biochemistry (preceding paper in this issue)]. Utilizing an advanced computer graphics facility, and the known three-dimensional coordinates for three dehydrogenases, we have investigated the feasibility of various aspects of the direct transfer of dinucleotide from the site of one enzyme to the site of the other. The facile passage of the coenzyme through the first enzyme site requires an open protein conformation, characteristic of the apoenzyme rather than the holoenzyme structure. Since two dehydrogenases of the same chirality bind coenzyme in the same conformation, the direct transfer of coenzyme from one site to the other is impossible due to the restriction in molecular rotation of the coenzyme in the path of transfer from one binding site to the other; therefore, coenzyme can only be transferred from one dehydrogenase site to another site via the intermediate dissociation of coenzyme into the aqueous milieu. In contrast, when an A dehydrogenase and a B dehydrogenase are juxtaposed, it is stereochemically feasible to transfer the nicotinamide ring from its specific binding site in one enzyme to the site in the other.(ABSTRACT TRUNCATED AT 250 WORDS)
Molecular Characterization of a Functional cDNA Encoding the Rat Substance P Receptor (1990)

Substance P is a member of the tachykinin peptide family and participates in the regulation of diverse biological processes. The polymerase chain reaction and conventional library screening were used to isolate a complementary DNA (cDNA) encoding the rat substance P receptor from brain and submandibular gland. By homology analysis, this receptor belongs to the G protein-coupled receptor superfamily. The receptor cDNA was expressed in a mammalian cell line and the ligand binding properties of the encoded receptor were pharmacologically defined by Scatchard analysis and tachykinin peptide displacement as those of a substance P receptor. The distribution of the messenger RNA for this receptor is highest in urinary bladder, submandibular gland, striatum, and spinal cord, which is consistent with the known distribution of substance P receptor binding sites. Thus, this receptor appears to mediate the primary actions of substance P in various brain regions and peripheral tissues.
Biological Significance of a Human Enterovirus B-Specific RNA Element in the 3′ Nontranslated Region (2002)

The secondary structures predicted for the enteroviral 3' nontranslated region (3'NTR) all seem to indicate a conformation consisting of two (X and Y) hairpin structures. The higher-order RNA structure of the 3'NTR appears to exist as an intramolecular kissing interaction between the loops of these two hairpin structures. The enterovirus B-like subgroup possesses an additional stem-loop structure, domain Z, which is not present in the poliovirus-like enteroviruses. It has been suggested that the Z domain originated from a burst of short sequence repetitions (E. V. Pilipenko, S. V. Maslova, A. N. Sinyakov, and V. I. Agol, Nucleic Acids Res. 20:1739-1745, 1992). However, no functional features have yet been ascribed to this enterovirus B-like-specific RNA element in the 3'NTR. In this study, we tested the functional characteristics and biological significance of domain Z. A mutant of the cardiovirulent coxsackievirus group B3 strain Nancy which completely lacked the Z domain and which therefore acquired enterovirus C-like secondary structures exhibited a wild-type growth phenotype, as determined by single-cycle growth analysis with BGM cells. This result proves that the Z domain is virtually dispensable for viral growth in tissue cultures. Partial distortion of the Z domain structure resulted in a disabled virus with reduced growth kinetics, probably due to alternative conformations of the overall structure of the domain. Infection of mice showed that the recombinant coxsackievirus group B3 mutant which completely lacked the Z domain was less virulent. Pancreatic tissues from mice infected with wild-type virus and recombinant virus were equally affected. However, the heart tissue from mice infected with the recombinant virus showed only slight signs of myocarditis. These results suggest that the enterovirus B-like-specific Z domain plays a role in coxsackievirus-induced pathogenesis.
A Peptide That Mimics the C-terminal Sequence of SNAP-25 Inhibits Secretory Vesicle Docking in Chromaffin Cells (1997)

Excitation-secretion uncoupling peptides (ESUPs) are inhibitors of Ca2+-dependent exocytosis in neural and endocrine cells. Their mechanism of action, however, remains elusive. We report that ESUP-A, a 20-mer peptide patterned after the C terminus of SNAP-25 (synaptosomal associated protein of 25 kDa) and containing the cleavage sequence for botulinum neurotoxin A (BoNT A), abrogates the slow, ATP-dependent component of the exocytotic pathway, without affecting the fast, ATP-independent, Ca2+-mediated fusion event. Ultrastructural analysis indicates that ESUP-A induces a drastic accumulation of dense-core vesicles near the plasma membrane, mimicking the effect of BoNT A. Together, these findings argue in favor of the notion that ESUP-A inhibits ATP-primed exocytosis by blocking vesicle docking. Identification of blocking peptides which mimic sequences that bind to complementary partner domains on interacting proteins of the exocytotic machinery provides new pharmacological tools to dissect the molecular and mechanistic details of neurosecretion. Our findings may assist in developing ESUPs as substitute drugs to BoNTs for the treatment of spasmodic disorders.
Combined prophylactic and therapeutic intranasal vaccination against human papillomavirus type-16 using different adeno-associated virus serotype vectors (2009)

Our results show that rAAV5 and rAAV9 vectors are promising candidates for a non-invasive nasal vaccination strategy.
Discovery of Small Molecule RIP1 Kinase Inhibitors for the Treatment of Pathologies Associated with Necroptosis (2013)

Potent inhibitors of RIP1 kinase from three distinct series, 1-aminoisoquinolines, pyrrolo[2,3-b]pyridines, and furo[2,3-d]pyrimidines, all of the type II class recognizing a DLG-out inactive conformation, were identified from screening of our in-house kinase focused sets. An exemplar from the furo[2,3-d]pyrimidine series showed a dose proportional response in protection from hypothermia in a mouse model of TNFα induced lethal shock.
Synthesizing transformations for locality enhancement of imperfectly-nested loop nests (2014)

We present an approach for synthesizing transformations to enhance locality in imperfectly-nested loops. The key idea is to embed the iteration space of every statement in a loop nest into a special iteration space called the product space. The product space can be viewed as a perfectly-nested loop nest, so embedding generalizes techniques like code sinking and loop fusion that are used in ad hoc ways in current compilers to produce perfectly-nested loops from imperfectly-nested ones. In contrast to these ad hoc techniques however, our embeddings are chosen carefully to enhance locality. The product space is then transformed further to enhance locality, after which fully permutable loops are tiled, and code is generated. We evaluate the effectiveness of this approach for dense numerical linear algebra benchmarks, relaxation codes, and the tomcatv code from the SPEC benchmarks.
Rapid multi-layer PCB prototyping (2002)

Testing PCB designs using prototypes has always been an integral part of any serious research and development effort. However, due to two changes in the PCB industry, many design engineers are finding that traditional prototyping methods are either (1) too slow or (2) unable to produce the level of sophistication required for today's highly competitive electronics market. As a result, many designers are turning to a revolutionary new rapid prototyping system manufactured by a small high tech firm in West Lebanon, NH. This new technology gives engineers the unprecedented power to produce high quality multi-layer PCBs in less than a day.
Neratinib: an oral, irreversible dual EGFR/HER2 inhibitor for breast and non-small cell lung cancer (2009)

Both preclinical and human studies have shown that neratinib has promising activity in both advanced breast cancer and NSCLC with an acceptable safety profile. The data support its continued clinical development.
Cathelicidins, multifunctional peptides of the innate immunity (2003)

Cathelicidins comprise a family of mammalian proteins containing a C-terminal cationic antimicrobial domain that becomes active after being freed from the N-terminal cathelin portion of the holoprotein. Many other members of this family have been identified since the first cathelicidin sequences were reported 10 years ago. The mature peptides generally show a wide spectrum of antimicrobial activity and, more recently, some of them have also been found to exert other biological activities. The human cathelicidin peptide LL-37 is chemotactic for neutrophils, monocytes, mast cells, and T cells; induces degranulation of mast cells; alters transcriptional responses in macrophages; stimulates wound vascularization and re-epithelialization of healing skin. The porcine PR-39 has also been involved in a variety of processes, including promotion of wound repair, induction of angiogenesis, neutrophils chemotaxis, and inhibition of the phagocyte NADPH oxidase activity, whereas the bovine BMAP-28 induces apoptosis in transformed cell lines and activated lymphocytes and may thus help with clearance of unwanted cells at inflammation sites. These multiple actions provide evidence for active participation of cathelicidin peptides in the regulation of the antimicrobial host defenses.
Assessment of vagal activity during transcutaneous vagus nerve stimulation in mice (2008)

Department of Medicine III, Martin-Luther-University Halle-Wittenberg, Klinikum Kröllwitz, Ernst-Grube-Strasse, Halle/Saale, Germany
The Upregulation of p27Kip1 by Rapamycin Results in G1 Arrest in Exponentially Growing T-Cell Lines (1998)

An immunosuppressant Rapamycin (Rap) has been reported to cause G1 arrest by inhibiting p70 S6 kinase and G1 cyclin/cdks kinase activities when added to quiescent cells with mitogens. However, antiproliferative effects of Rap on exponentially growing cells have been poorly investigated. We examined the intracellular events after the treatment of Rap in exponentially growing T cells and found that Rap upregulated a cdks inhibitor, p27Kip1 at both mRNA and protein levels in Rap-sensitive cells. Antiproliferative effect of Rap was mainly ascribed to the inhibition of cyclin E/cdk2 kinase activity through the formation of cyclin E/cdk2-p27Kip1 complex rather than inhibition of p70 S6 kinase activity. Furthermore, we showed that Rap-sensitive cells with elevated p27Kip1 expression lost sensitivity to Rap when antisense p27Kip1 was introduced, which indicates that the basal level of p27Kip1 is one of the limiting factors that determine the sensitivity to Rap in already cycling cells. These data suggest the presence of a putative threshold level of p27Kip1 at late G1 phase in already cycling cells. Rap may cause G1 arrest by upregulating the amount of p27Kip1 beyond the threshold in some Rap-sensitive cells that are exponentially growing.
Human Growth: A Practitioner’s Guide (1995)

A continuing problem for anthropologists is how to respond to the well-intentioned, nevertheless naive, question, "… and what do you do for a living?" My usual response these days is, "I pinch children." This rejoinder rivets the questioner in place while I explain that I measure the height, weight, and body composition (this is where the "pinching" of skinfolds comes into play) of school children and youth in Guatemala and in the United States. Most people even stay long enough to hear that I do this in order to evaluate the quality of the social, economic, and political environment of these two countries.
Influence of resinous monomers on the differentiation in vitro of human pulp cells into odontoblasts (2002)

Odontoblasts are highly differentiated postmitotic cells, which under pathological conditions such as carious lesions and dental injuries may degenerate and be replaced by other pulp cells. A recent work showed that this physiological event can be reproduced in an in vitro assay system. The purpose of the present study was to evaluate the effects of resinous monomers on odontoblast differentiation in vitro. Pulp cores from extracted human third molars were cultured with beta-glycerophosphate (2 mM) and used to evaluate the effects of TEGDMA, HEMA, UDMA, and Bis-GMA on the differentiation of pulp fibroblasts into odontoblasts. The effect of the monomers was studied by evaluating the expression of several odontoblast specific genes. In the absence of monomers, mineral nodule formation was observed. Pulp cells contributing to the nodule formation synthesized type I collagen, osteonectin, and dentin sialoprotein (DSP). In addition, Fourier transform infrared microspectroscopy showed that the mineral and organic composition of the nodules were characteristic of dentin. When the monomers were added at nontoxic concentrations, the effects of HEMA and Bis-GMA were more evident than that of TEGDMA and UDMA on collagen 1, osteonectin, and DSP expression. However, all monomers significantly decreased DSP expression and completely inhibited the mineral nodule formation.
Multimodal MRI Neuroimaging Biomarkers for Cognitive Normal Adults, Amnestic Mild Cognitive Impairment, and Alzheimer's Disease (2011)

Multimodal magnetic resonance imaging (MRI) techniques have been developed to noninvasively measure structural, metabolic, hemodynamic and functional changes of the brain. These advantages have made MRI an important tool to investigate neurodegenerative disorders, including diagnosis, disease progression monitoring, and treatment efficacy evaluation. This paper discusses recent findings of the multimodal MRI in the context of surrogate biomarkers for identifying the risk for AD in normal cognitive (NC) adults, brain anatomical and functional alterations in amnestic mild cognitive impairment (aMCI), and Alzheimer's disease (AD) patients. Further developments of these techniques and the establishment of promising neuroimaging biomarkers will enhance our ability to diagnose aMCI and AD in their early stages and improve the assessment of therapeutic efficacy in these diseases in future clinical trials.
Towards molecular farming in the future: transient protein expression in plants (1999)

Molecular farming in plants can be achieved by stable or transient expression of a recombinant protein. Transient expression of recombinant proteins in plants can rapidly provide large amounts of the proteins for detailed characterization. It is fast, flexible and can be carried out at field scale using viral vectors, but it lacks the increases in production volume that can be achieved easily with stable transgenic crops. This review article focuses on discussing the applications of transient expression using viral vectors, biolistic methods or agroinfiltration.
MAP kinase pathways activated by stress: The p38 MAPK pathway (2000)

A stress-activated serine/threonine protein kinase, p38 mitogen-activated protein kinase (p38 MAPK), belongs to the MAP kinase superfamily. Diverse extracellular stimuli, including ultraviolet light, irradiation, heat shock, high osmotic stress, proinflammatory cytokines and certain mitogens, trigger a stress-regulated protein kinase cascade culminating in activation of p38 MAPK through phosphorylation on a TGY motif within the kinase activation loop. p38 MAPK appears to play a major role in apoptosis, cytokine production, transcriptional regulation, and cytoskeletal reorganization, and has been causally implicated in sepsis, ischemic heart disease, arthritis, human immunodeficiency virus infection, and Alzheimer's disease. The availability of specific inhibitors helps to clarify the role that p38 MAPK plays in these processes, and may ultimately offer therapeutic benefit for certain critically ill patients.
Regeneration of PAPS for the Enzymatic Synthesis of Sulfated Oligosaccharides (2000)

This paper describes the study of 3'-phosphoadenosine-5'-phosphosulfate (PAPS) regeneration from 3'-phosphoadenosine-5'-phosphate (PAP) for use in practical syntheses of carbohydrate sulfates which are catalyzed by sulfotransferases. Among the regeneration systems, the one with recombinant aryl sulfotransferase proved to be the most practical. This regeneration system was coupled with a sulfotransferase-catalyzed reaction, using a recombinant Nod factor sulfotransferase, for the synthesis of various oligosaccharide sulfates that were further glycosylated using glycosyltransferases.
Electrical Resistivity of Composites (1990)

Percolation and Bruggeman's effective media theories, as they apply to the electrical conductivity of composites, are reviewed, and a general effective media (GEM) equation, which combines most aspects of both percolation and effective media theories, is introduced. It is then shown that the GEM equation quantitatively fits electrical resistivity (conductivity) as a function of the volume fraction data for binary composites. The parameters used to fit the experimental data are the electrical resistivities of the two phases, the percolation threshold for the lower resistivity phase (ô c ), and an exponent t. Preliminary work, showing how the GEM equation can be used to model the piezoresistivity of composites by postulating that ô c is a function of the independent variable, is also presented.
Processing efficiency of immobilized non‐growing bacteria: Biocatalytic modeling and experimental analysis (1999)

Abstract Modeling methods used to optimize the biocatalytic efficiency of freely suspended cells have been applied to non‐growing microbial cells entrapped within a macro‐porous carrier. The catalytic rate, which is dependent on cell concentration inside the biocatalyst beads, coincided with catalytic parameters for freely suspended cells. Immobilized non‐growing cell systems could be optimized utilizing the characteristics of freely suspended cells without requiring extensive experimentation to define catalytic behaviour inside the biocatalyst. A dynamic diffusion–reaction model was developed and validated using experimental data for thiodiglycol degradation by Alcaligenes xylosoxidans subsp. xylosoxidans immobilized within macro‐porous poly(vinyl alcohol) cryogel in a completely mixed batch bioreactor.
Dual Regulation of SIRPα Phosphorylation by Integrins and CD47 (2007)

Signal regulatory protein alpha (SIRPalpha, SHPS-1) is a plasma membrane receptor for CD47 and a key regulator of phagocytosis, growth factor signaling, and migration. Phosphorylation of immunoreceptor tyrosine-based inhibition motifs in its cytoplasmic tail is essential for the functional effects of SIRPalpha, at least in part, because the phosphorylated immunoreceptor tyrosine-based inhibition motifs recruit Src homology 2 domain-containing tyrosine phosphatases. Ligation by CD47 and integrin engagement both have been thought to regulate SIRPalpha phosphorylation. However, their distinct contributions have not been distinguished. Here, we show that the importance of CD47 varies with cell type, since ligation of CD47 is not necessary for SIRPalpha phosphorylation in myeloid cells, whereas it is required in endothelial cells. In contrast, integrin-mediated adhesion is required for SIRPalpha phosphorylation in both cell types. This shows that SIRPalpha phosphorylation is dually regulated and demonstrates a new mechanism for functional cooperation between integrins and the integrin-associated protein CD47.
Characterization and phylogenetic epitope mapping of CD38 ADPR cyclase in the cynomolgus macaque. (2004)

This multi-faceted characterization of CD38 from cynomolgus macaque demonstrates its high genetic and biochemical similarities with human CD38 while the immunological comparison adds new insights into the dominant epitopes of the primate CD38 ectodomain. These results open new prospects for the biomedical and pharmacological investigations of this receptor-enzyme.
Haemostatic safety of a unique recombinant plasmin molecule lacking kringles 2–5 (2010)

We previously demonstrated a significant margin of haemostatic safety for full-length plasmin in comparison with tissue plasminogen activator (t-PA). We now report studies that compare haemostatic safety of full-length plasmin with a novel recombinant plasmin derivative, (Δ K2-5) plasmin, consisting of kringle 1 linked to the serine protease domain of plasmin. Agent was administered intravenously in a randomised, blinded manner in a rabbit model of fibrinolytic haemorrhage. A dose-related decrease in α2-antiplasmin, factor VIII, and fibrinogen followed administration of 1.8, 2.7, 3.7 and 4.6 mg/kg of (Δ K2-5) plasmin, with nadir fibrinogen concentrations of 65%, 40%, 30%, and 0% of initial levels, respectively. Mean primary bleeding time was undisturbed at 1.8 mg/kg (2.2 ± 0.7 minutes), minimally prolonged at 2.7 or 3.7 mg/kg (5 ± 2.9 and 4.4 ± 2.2 minutes), and prolonged at the purposefully toxic 4.6 mg/kg dose (12.8 ± 18.8 minutes). Equimolar amounts of (Δ K2-5) plasmin and full-length plasmin had equal in vitro clot lysis efficacy, but in the bleeding model, (Δ K2-5) plasmin showed better haemostatic competency than full-length plasmin. This safety advantage may be explained by higher residual amounts of plasma fibrinogen in animals given (Δ K2-5) plasmin rather than full-length plasmin. We demonstrate that a unique recombinant plasmin mutant, (Δ K2-5) plasmin, possesses an advantage in hemostatic safety over an equimolar amount of full-length plasmin.
Immune Checkpoint Modulators: An Emerging Antiglioma Armamentarium (2016)

Immune checkpoints have come to the forefront of cancer therapies as a powerful and promising strategy to stimulate antitumor T cell activity. Results from recent preclinical and clinical studies demonstrate how checkpoint inhibition can be utilized to prevent tumor immune evasion and both local and systemic immune suppression. This review encompasses the key immune checkpoints that have been found to play a role in tumorigenesis and, more specifically, gliomagenesis. The review will provide an overview of the existing preclinical and clinical data, antitumor efficacy, and clinical applications for each checkpoint with respect to GBM, as well as a summary of combination therapies with chemotherapy and radiation.