gebhart/patrepeval huggingface dataset:
What should a wildebeest say? Interactive nature films for high school classrooms (1997)

Nature documentaries play an important role in high school biology classrooms, yet they deliver a passive and biased account of the behavior of organisms. To engage students in more active problem solving around behavioral topics, we created an interactive video system called Animal Landlord. Part of a week-long curriculum designed to introduce concepts in behavioral ecology, Animal Landlord presents film clips of the Serengeti lion hunting its prey. Students select and annotate video frames with explanations of their significance to the hunt, compare annotations across films, and ultimately genera!ize a qualitative model of predation behaviors. This paper discusses the motivations for changing the nature of documentary use in the classroom, the ways in which we change the form of traditional narration for pedagogical purposes, and the interactivity that emerges in the social context of the classroom.
Isolation and native characterization of cysteine-rich collagens from bovine placental tissues and uterus and their relationship to types IV and V collagens (1982)

A simplified procedure for the fractionation and purification of different collagen types from various tissues is described which is particularly efficient in separating type-V from type-IV collagen, and high-mol.-wt. (HMW) aggregates from 7 S collagen. Uterus and maternal villi contain 2 forms of type-V collagen - [alpha 1(V)]2 alpha 2(V) and [alpha 1(V) alpha 2(V) alpha 3(V) - which have been separated on DEAE-cellulose. Uterus however appears to be the richest source of both HMW aggregates and the [alpha 1(V) alpha 2(V) alpha 3(V)] collagen, and a probable relationship between these collagens is discussed.
Crystalline Two‐Dimensional DNA‐Origami Arrays (2010)

DNA-Origami im großen Stil: Eine doppellagige DNA-Origamikachel mit zwei orthogonalen Domänen bildete durch Selbstorganisation hoch reguläre 2D-DNA-Anordnungen mit Kantenlängen von 2–3 μm (siehe Schema und AFM-Bild). Diese Größe dürfte vermutlich ausreichen, um Bottom-up-Methoden der Mustererzeugung mit Top-down-Ansätzen zu verknüpfen. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Restricted Distribution of the Butyrate Kinase Pathway among Butyrate-Producing Bacteria from the Human Colon (2004)

The final steps in butyrate synthesis by anaerobic bacteria can occur via butyrate kinase and phosphotransbutyrylase or via butyryl-coenzyme A (CoA):acetate CoA-transferase. Degenerate PCR and enzymatic assays were used to assess the presence of butyrate kinase among 38 anaerobic butyrate-producing bacterial isolates from human feces that represent three different clostridial clusters (IV, XIVa, and XVI). Only four strains were found to possess detectable butyrate kinase activity. These were also the only strains to give PCR products (verifiable by sequencing) with degenerate primer pairs designed within the butyrate kinase gene or between the linked butyrate kinase/phosphotransbutyrylase genes. Further analysis of the butyrate kinase/phosphotransbutyrylase genes of one isolate, L2-50, revealed similar organization to that described previously from different groups of clostridia, along with differences in flanking sequences and phylogenetic relationships. Butyryl-CoA:acetate CoA-transferase activity was detected in all 38 strains examined, suggesting that it, rather than butyrate kinase, provides the dominant route for butyrate formation in the human colonic ecosystem that contains a constantly high concentration of acetate.
Chlorophyll Breakdown in Senescent Arabidopsis Leaves. Characterization of Chlorophyll Catabolites and of Chlorophyll Catabolic Enzymes Involved in the Degreening Reaction (2005)

During senescence, chlorophyll (chl) is metabolized to colorless nonfluorescent chl catabolites (NCCs). A central reaction of the breakdown pathway is the ring cleavage of pheophorbide (pheide) a to a primary fluorescent chl catabolite. Two enzymes catalyze this reaction, pheide a oxygenase (PAO) and red chl catabolite reductase. Five NCCs and three fluorescent chl catabolites (FCCs) accumulated during dark-induced chl breakdown in Arabidopsis (Arabidopsis thaliana). Three of these NCCs and one FCC (primary fluorescent chl catabolite-1) were identical to known catabolites from canola (Brassica napus). The presence in Arabidopsis of two modified FCCs supports the hypothesis that modifications, as present in NCCs, occur at the level of FCC. Chl degradation in Arabidopsis correlated with the accumulation of FCCs and NCCs, as well as with an increase in PAO activity. This increase was due to an up-regulation of Pao gene expression. In contrast, red chl catabolite reductase is not regulated during leaf development and senescence. A pao1 knockout mutant was identified and analyzed. The mutant showed an age- and light-dependent cell death phenotype on leaves and in flowers caused by the accumulation of photoreactive pheide a. In the dark, pao1 exhibited a stay-green phenotype. The key role of PAO in chl breakdown is discussed.
An approach to rapid protein crystallization using nanodroplets (2002)

An approach that enables up to a two order of magnitude reduction in the amount of protein required and a tenfold reduction in the amount of time required for vapor-diffusion protein crystallization is reported. A prototype high-throughput automated system was used for the production of diffraction-quality crystals for a variety of proteins from a screen of 480 conditions using drop volumes as small as 20 nL. This approach results in a significant reduction in the time and cost of protein structure determination, and allows for larger and more efficient screens of crystallization parameter space. The ability to produce diffraction-quality crystals rapidly with minimal quantities of protein enables high-throughput efforts in structural genomics and structure-based drug discovery.
Learning program behavior profiles for intrusion detection (1999)

Profiling the behavior of programs can be a useful reference for detecting potential intrusions against systems. This paper presents three anomaly detection techniques for profiling program behavior that evolve from memorization to generalization. The goal of monitoring program behavior is to be able to detect potential intrusions by noting irregularities in program behavior. The techniques start from a simple equality matching algorithm for determining anomalous behavior, and evolve to a feed-forward backpropagation neural network for learning program behavior, and finally to an Elman network for recognizing recurrent features in program execution traces. In order to detect future attacks against systems, intrusion detection systems must be able to generalize from past observed behavior. The goal of this research is to employ machine learning techniques that can generalize from past observed behavior to the problem of intrusion detection. The performance of these systems is compared by testing them with data provided by the DARPA Intrusion Detection Evaluation program.
Systemic Acquired Resistance and Induced Systemic Resistance in Conventional Agriculture (2004)

Plants possess a range of defenses that can be actively expressed in response to pathogens and parasites of various scales, ranging from microscopic viruses to insect herbivores. The timing of these defense responses is critical and can be the difference between being able to cope or succumbing to the challenge of a pathogen or parasite. Systemic acquired resistance (SAR) and induced systemic resistance (ISR) are two forms of induced resistance; in both SAR and ISR, plant defenses are preconditioned by prior infection or treatment that results in resistance (or tolerance) against subsequent challenge by a pathogen or parasite. Great strides have been made over the past 20 yr in understanding the physiological and biochemical basis of SAR and ISR. Much of this knowledge is due to the identification of a number of chemical and biological elicitors, some of which are commercially available for use in conventional agriculture. However, the effectiveness of these elicitors to induce SAR and ISR as a practical means to control various plant diseases is just being realized. In this review, we first briefly summarize the fundamentals of ISR and SAR, for which a number of critical reviews already exist. We then examine the efficacy of SAR and ISR in published field‐based studies. We place special emphasis on the benefits, drawbacks, and future considerations for the improved use of chemical and biological elicitors of induced resistance in conventional agriculture; this includes the potential to exploit genetic variability within populations of crop species to improve the utility of SAR and ISR in the field.
Structural Basis of Small-Molecule Aggregate Induced Inhibition of a Protein–Protein Interaction (2017)

A prevalent observation in high-throughput screening and drug discovery programs is the inhibition of protein function by small-molecule compound aggregation. Here, we present the X-ray structural description of aggregation-based inhibition of a protein-protein interaction involving tumor necrosis factor α (TNFα). An ordered conglomerate of an aggregating small-molecule inhibitor (JNJ525) induces a quaternary structure switch of TNFα that inhibits the protein-protein interaction between TNFα and TNFα receptors. SPD-304 may employ a similar mechanism of inhibition.
Nociceptive Neuropeptide Increases and Periorbital Allodynia in a Model of Traumatic Brain Injury (2012)

Injury to the somatosensory cortex results in persistent periorbital allodynia and increases in brainstem nociceptive neuropeptides. Findings suggest that persistent allodynia and increased neuropeptides are maintained by mechanisms other than activation of macrophage/microglia or astrocyte in the injured somatosensory cortex.
Dihydroartemisinin Enhances Apo2L/TRAIL-Mediated Apoptosis in Pancreatic Cancer Cells via ROS-Mediated Up-Regulation of Death Receptor 5 (2012)

Background: Dihydroartemisinin (DHA), a semi-synthetic derivative of artemisinin, has recently shown antitumor activity in various cancer cells. Apo2 ligand or tumor necrosis factor-related apoptosis-inducing ligand (Apo2L/TRAIL) is regarded as a promising anticancer agent, but chemoresistance affects its efficacy as a treatment strategy. Apoptosis induced by the combination of DHA and Apo2L/TRAIL has not been well documented, and the mechanisms involved remain unclear.
Increased Ischemic Tissue Survival through Targeting Thrombospondin‐1 (2007)

Tissue survival requires sustained perfusion. Ischemia secondary to surgery or trauma can limit soft tissue survival, resulting in tissue necrosis and delayed wound healing. Therapeutic interventions to increase soft tissue perfusion have to date met with limited success. The bioactive gas nitric oxide (NO), which is produced by vascular endothelial cells constitutively, can rapidly dilate arteries and increase tissue perfusion. However, under ischemic conditions endogenous NO is insufficient to prevent tissue necrosis. We recently discovered that endogenous thrombospondin‐1 (TSP1) is a potent antagonist of NO‐induced vasodilation. TSP1 released by activated platelets and produced by vascular cells potently blocks NO driven relaxation of vascular smooth muscle cells at the level of soluble guanylate cyclase via its receptor CD47. In the absence of TSP1 or CD47, survival of ischemic injury is dramatically increased. We are investigating therapeutic approaches to target TSP1 or CD47 to increase wound healing under conditions of ischemia.
Effect of Fish Oil on Heart Rate in Humans (2005)

In randomized controlled trials in humans, fish oil reduces HR, particularly in those with higher baseline HR or longer treatment duration. These findings provide firm evidence that fish oil consumption directly or indirectly affects cardiac electrophysiology in humans. Potential mechanisms such as effects on the sinus node, ventricular efficiency, or autonomic function deserve further investigation.
Cloning and expression of a cDNA coding for the anticoagulant hirudin from the bloodsucking leech, Hirudo medicinalis. (1986)

Cloned cDNAs have been isolated that encode a variant of hirudin, a potent thrombin inhibitor that is secreted by the salivary glands of the medicinal leech, Hirudo medicinalis. This variant probably corresponds to a form that has been purified from leech heads but differs in amino acid sequence from the hirudin purified from whole leeches. There are at least three hirudin transcripts detectable in leech RNAs that are different in size, site of synthesis, inducibility by starvation, and relationship to hirudin activity. The new hirudin variant predicted by the cDNA and the heterodisperse transcription products suggest a hirudin protein family. The hirudin cDNA was expressed in Escherichia coli under the control of the bacteriophage lambda PL promoter. The recombinant product is biologically active, inhibiting the cleavage by thrombin of fibrinogen and a synthetic tripeptide substrate.
Oligogalacturonides and chitosan activate plant defensive genes through the octadecanoid pathway. (1995)

Jasmonic acid, synthesized from linolenic acid (the octadecanoid pathway), has been proposed to be part of a signal transduction pathway that mediates the induction of defensive genes in plants in response to oligouronide and polypeptide signals generated by insect and pathogen attacks. We report here that the induction of proteinase inhibitor accumulation in tomato leaves by plant-derived oligogalacturonides and fungal-derived chitosan oligosaccharides is severely reduced by two inhibitors (salicylic acid and diethyldi-thiocarbamic acid) of the octadecanoid pathway, supporting a role for the pathway in signaling by oligosaccharides. Jasmonic acid levels in leaves of tomato plants increased several fold within 2 hr after supplying the polypeptide systemin, oligogalacturonides, or chitosan to the plants through their cut stems, as expected if they utilize the octadecanoid pathway. The time course of jasmonic acid accumulation in tomato leaves in response to wounding was consistent with its proposed role in signaling proteinase inhibitor mRNA and protein synthesis. The cumulative evidence supports a model for the activation of defensive genes in plants in response to insect and pathogen attacks in which various elicitors generated at the attack sites activate the octadecanoid pathway via different recognition events to induce the expression of defensive genes in local and distal tissues of the plants.
Collisional fragmentation of glycopeptides by electrospray ionization LC/MS and LC/MS/MS: methods for selective detection of glycopeptides in protein digests (1993)

Mass spectrometric methods of glycopeptide-specific detection in liquid chromatography/electrospray mass spectrometry (LC/ESMS) of glycoprotein digests are explored using a variety of glycopeptide models and then applied to soluble complement receptor type I, a 240-kDa glycoprotein containing 25 potential sites of N-glycosylation. The most specific method, requiring a triple quadrupole, involves monitoring of sugar oxonium fragment ions during precursor-ion scan ESMS/MS. Signals derived from nonglycosylated peptides are virtually eliminated, resulting in a total-ion current chromatographic trace of only the glycopeptides present in the digest. The corresponding mass spectra yield molecular weight and glycopeptide microheterogeneity information. An alternative and complementary approach that we term collisional-excitation scanning also involves fragmentation of glycopeptides to sugar oxonium ion fragments but does not involve any mass-selection process, permitting the experiment to be performed on a single quadrupole instrument. The resulting total ion chromatogram is similar to the UV chromatogram (215 nm), but a selected-ion chromatogram for carbohydrate-specific ions such as the N-acetylhexosamine oxonium ion (m/z 204) produces a glycopeptide-specific trace. Although there can sometimes be peptide interferences in the spectra of the indicated glycopeptide-containing chromatographic peaks, this latter approach permits peptide mapping to be performed on the same data set that also indicates the location of glycopeptides in the chromatogram. Both methods are suitable for detection of glycopeptides with all common classes of oligosaccharides in either N- or O-linkage to the peptide.
Inhibition of bovine lens leucine aminopeptidase by bestatin: number of binding sites and slow binding of this inhibitor (1993)

Aminopeptidases catalyze the hydrolysis of amino acid residues from the amino terminus of peptide substrates. Their activity has been implicated in myriad fundamental biochemical and physiological processes, and alterations in aminopeptidase activity have been correlated with a variety of pathologies. Nevertheless, information about this group of proteases is less well developed. Bovine lens leucine aminopeptidase (blLAP) can be considered prototypical of many enzymes in this family of peptidases. It shows common features of (1) requiring divalent metal ions for activity, (2) having a relatively large size, and (3) having slow, relatively tight binding of bestatin, a transition-state analog of the substrate PheLeu. Bovine lens LAP is the only bestatin-inhibitable aminopeptidase for which structural and mechanistic data are available. However, full exploitation of these data required knowledge of the number of inhibitor molecules bound per subunit. Independent direct binding experiments and kinetic determinations indicate that one bestatin is bound per subunit in blLAP. Ki and Ki* for formation of the initial and final complexes are approximately 1.1 x 10(-7) and 1.3 x 10(-9) M, respectively. The mode of binding is slow and competitive. The t1/2 for formation and deformation of the final enzyme-inhibitor complex is approximately 30 and 22 min, respectively, with 10(-8) M bestatin. To perform these measures, a new assay using physiological peptides (LeuGlyGly) as substrate was adapted. Taken together with prior NMR, photoaffinity labeling, and crystallographic data, these binding data allow us to propose a mechanism of the blLAP-catalyzed hydrolysis of peptides.
Calcitonin gene‐related peptide levels during nitric oxide‐induced headache in patients with chronic tension‐type headache (2001)

It has been proposed that nitric oxide (NO) induced headache in primary headaches may be associated with release of calcitonin gene-related peptide (CGRP). In the present study we aimed to investigate plasma levels of CGRP during headache induced by the NO donor glyceryl trinitrate (GTN) in 16 patients with chronic tension-type headache and 16 healthy controls. The subjects were randomly allocated to receive 0.5 microg/kg/min GTN or placebo over 20 min on two headache-free days. Blood samples were collected at baseline, 10, 20 and 60 min after start of infusion. Both patients and controls developed significantly stronger immediate headache on the GTN day than on the placebo day and the headache was significantly more pronounced in patients than in controls. There was no difference between the area under the CGRP curve (AUCCGRP) on GTN vs. placebo day in either patients (P=0.65) or controls (P=0.48). The AUCCGRP recorded on the GTN day did not differ between patients and controls (P=0.36). Both in patients and controls, CGRP levels changed significantly over time, on both the GTN and placebo days (P < 0.05). The present study indicates that NO-induced immediate headache is not associated with release of CGRP.
Lipopolysaccharide‐induced cytokine production in human monocytes: Role of tyrosine phosphorylation in transmembrane signal transduction (1994)

The signal transduction events that follow the binding of lipopolysaccharide (LPS) to the macrophage cell surface are not well defined. In the current studies LPS was found to induce alterations in phosphorylation of monocyte proteins on tyrosine. Herbimycin A and genistein, inhibitors of tyrosine kinases, markedly attenuated LPS-induced tumor necrosis factor-alpha (TNF-alpha) and interleukin-6 (IL-6) protein and mRNA production. Reciprocally, the tyrosine phosphatase inhibitor sodium orthovanadate enhanced LPS-induced production of TNF-alpha. LPS induced a concentration-dependent increase in tyrosine phosphorylation of several proteins, which paralleled and preceded the onset of LPS-induced TNF-alpha production. LPS stimulation had different but reproducible effects on three members of the src family of tyrosine kinases. Both Hck and Lyn kinase activity increased before the onset of TNF-alpha production, consistent with their participation in the observed LPS-induced tyrosine phosphoprotein accumulation. In contrast, Yes kinase activity was not affected. These observations were made at concentrations of LPS that required serum rich in LPS-binding protein and the monocyte surface antigen CD14 for TNF-alpha production. These data indicate that tyrosine kinases and phosphatases are involved in the signal transduction cascade by which LPS induces production of TNF-alpha and IL-6 by human monocytes, and suggest that Lyn and Hck are candidate participants in this process.
Characterization of high molecular weight FK-506 binding activities reveals a novel FK-506-binding protein as well as a protein complex. (1992)

The immunoregulant FK-506 potently inhibits particular calcium-associated signal transduction events that occur early during T-lymphocyte activation and during IgE receptor-mediated exocytosis in mast cells. FK-506 binds to a growing family of receptors termed FK-506-binding proteins (FKBPs), the most abundant being a 12-kDa cytosolic receptor, FKBP12. To date, there is no formal evidence proving that FKBP12 is the sole receptor mediating the immunosuppressive effects or toxic side effects of FK-506. Using gel filtration chromatography as an assay for novel FK-506-binding proteins, we identified FK-506 binding activities in extracts prepared from calf brain and from JURKAT cells. Both of these new activities comigrated with apparent molecular masses of 110 kDa. However, further characterization of both binding activities revealed that the two are not identical. The 110-kDa activity observed in brain extracts appears to be the FKBP12.FK-506.calcineurin (CaN) complex previously reported (Liu, J., Farmer, J., Lane, W., Friedman, J., Weissman, I., and Schreiber, S. (1991) Cell 66, 807-815) while the 110 kDa activity observed in JURKAT cells is a novel FK-506-binding protein. Our characterization of the FKBP12.FK-506.CaN complex reveals a dependence upon calmodulin (CaM) for formation of the complex and demonstrates that the peptidyl-prolyl cis-trans isomerase (PPIase) activity of FKBP12 is not required for binding of FKBP12.FK-506 to CaN or for inhibition of CaN phosphatase activity. The novel FK-506-binding protein in JURKAT cells has been purified to homogeneity, migrates with an apparent mass of 51 kDa on denaturing gels, and has been termed FKBP51. Like FKBP12, FKBP51 has PPIase activity, but, unlike FKBP12.FK-506, FKBP51.FK-506 does not complex with or inhibit the phosphatase activity of, CaN. These results indicate that complex formation with CaN may not be a general property of the FKBPs. Peptide sequencing reveals that FKBP51 may be similar, if not identical, to hsp56, a component of non-transformed steroid receptors.