gebhart/patrepeval huggingface dataset:
Cartoon Corner (1998)

“Cartoon Corner” is designed to include cartoons that can be used to highlight mathematics in an interesting way. The questions accompanying the cartoons can be used as a large- or small-group activity, as homework, or as an extracredit assignment. Students might want to create their own mathematicsrelated cartoons that demonstrate in a humorous way how mathematics is used and misused. Readers are encouraged to submit three copies of cartoons and classroom-tested questions, doublespaced, for review by the editor of this section. The cartoons must include the date and the newspaper syndicate that holds the copyright.
Cellular Uptake and Ultrastructural Localization Underlie the Pro-apoptotic Activity of a Hydrocarbon-stapled BIM BH3 Peptide (2015)

Hydrocarbon stapling has been applied to restore and stabilize the α-helical structure of bioactive peptides for biochemical, structural, cellular, and in vivo studies. The peptide sequence, in addition to the composition and location of the installed staple, can dramatically influence the properties of stapled peptides. As a result, constructs that appear similar can have distinct functions and utilities. Here, we perform a side-by-side comparison of stapled peptides modeled after the pro-apoptotic BIM BH3 helix to highlight these principles. We confirm that replacing a salt-bridge with an i, i + 4 hydrocarbon staple does not impair target binding affinity and instead can yield a biologically and pharmacologically enhanced α-helical peptide ligand. Importantly, we demonstrate by electron microscopy that the pro-apoptotic activity of a stapled BIM BH3 helix correlates with its capacity to achieve cellular uptake without membrane disruption and accumulate at the organellar site of mechanistic activity.
Role of telomerase in cellular proliferation and cancer (1999)

Telomerase is a cellular reverse transcriptase that helps to provide genomic stability in highly proliferative normal, immortal, and tumor cells by maintaining the integrity of the chromosome ends, the telomeres. The activity of telomerase is associated with the majority of malignant human cancers. Telomerase or another mechanism for telomere maintenance is required for continuous tumor cell proliferation. Telomerase-positive cells that exit the cell cycle via quiescence downregulate telomerase through a transcriptional repression pathway. In the case of cell cycle exit via terminal differentiation, proteolysis of telomerase may also be involved. In response to mitogenic or growth factor signaling, telomerase-competent quiescent cells reenter the cell cycle and express telomerase activity independent of DNA synthesis. Under normal growth conditions, inhibition of telomerase activity in tumor-derived cells results in continued cell division coupled with telomere shortening, eventually followed by cellular senescence or death. Thus, repression of telomerase activity may be a novel adjuvant therapy for the treatment of human cancer and detection of telomerase activity may be important for cancer diagnostics.
Shape indexing using approximate nearest-neighbour search in high-dimensional spaces (2002)

Shape indexing is a way of making rapid associations between features detected in an image and object models that could have produced them. When model databases are large, the use of high-dimensional features is critical, due to the improved level of discrimination they can provide. Unfortunately, finding the nearest neighbour to a query point rapidly becomes inefficient as the dimensionality of the feature space increases. Past indexing methods have used hash tables for hypothesis recovery, but only in low-dimensional situations. In this paper we show that a new variant of the k-d tree search algorithm makes indexing in higher-dimensional spaces practical. This Best Bin First, or BBF search is an approximate algorithm which finds the nearest neighbour for a large fraction of the queries, and a very close neighbour in the remaining cases. The technique has been integrated into a fully developed recognition system, which is able to detect complex objects in real, cluttered scenes in just a few seconds.
Functional interactions between smooth muscle myosin light chain kinase and calmodulin (1982)

Calmodulin (CaM) binding by turkey gizzard myosin light chain kinase (MLCK) causes subtle changes in the fluorescence emission and polarization excitation spectra of the enzyme. Fluorescence experiments using 9-anthroyl-choline (9AC), which competes with ATP in binding, demonstrate mutually stabilizing interactions between the CaM and ATP binding sites corresponding to delta G = -0.6 to -0.7 kcal/mol. Fluorescence titrations in the presence of 9AC or 5,5'-bis[8-(phenylamino)-1-naphthalenesulfonate] confirm the stoichiometry of 1 mol of CaM/MLCK. Phosphorylation of MLCK has no effect on either the protein fluorescence or the binding of ATP and 9AC. The dissociation constant for the MLCL-CaM complex is increased approximately 500-fold on phosphorylation. Values of Kd for the phosphorylated enzyme range from 0.5 to 1.1 microM in 0.2 N KCl, pH 7.3, 25 degrees C. We showed competition between MLCK and other CaM binding proteins and peptides by using both fluorescence and catalytic activity measurements. Competition for CaM occurs with ACTH, beta-endorphin, substance P, glucagon, poly(L-arginine), myelin basic protein, troponin I, and histone H2A. Phosphorylation of the last three proteins by the adenosine cyclic 3',5'-phosphate dependent protein kinase diminishes their ability to compete. Phosphorylation of MLCK by the protein kinase gives 0.95 +/- 0.04 and 2.2 +/- 0.4 mol of incorporated 32P in the presence and absence of CaM, respectively. These stoichiometries agree with those recently reported [Conti, M. A. & Adelstein, R. S. (1981) J. Biol. Chem. 256, 3178].
Results on weighted stepanov-like pseudo periodic functions and applications (2016)

In this article, we first established some new results on composition of weighted Stepanov-like pseudo periodic function of class $r$ under a uniform continuity condition with respect to $L^p$ norm. And then, we proved the existence and uniqueness of weighted pseudo periodic solutions to a semi-linear functional differential equation with finite delay under Stepanov-like nonlinear term.
KDR/Flk-1 is a major regulator of vascular endothelial growth factor-induced tumor development and angiogenesis in murine hepatocellular carcinoma cells (1999)

Vascular endothelial growth factor (VEGF), which is one of the most potent angiogenic factors, has been shown to play a pivotal role in tumor angiogenesis, including hepatocellular carcinoma (HCC). The effects of VEGF are mediated mainly through two distinct receptors, flt-1 and KDR/Flk-1. It has been suggested that KDR/Flk-1 plays an important role in tumor development. However, the role of KDR/Flk-1 in HCC has not been examined. We previously reported that VEGF tightly regulated murine HCC development, based on the results of a study using a retroviral tetracycline-regulated (Retro-Tet) gene expression system. This system allows VEGF gene expression to be manipulated in vivo by providing tetracycline in the drinking water. In the present study, we combined the KDR/Flk-1-specific neutralizing monoclonal antibody (KDR/Flk-1mAb) and the Retro-Tet system to elucidate the role of KDR/Flk-1 in VEGF-induced tumor development and angiogenesis in a murine HCC experimental model. In a xenograft study, tumor augmentation induced by VEGF overexpression was almost abolished by means of KDR/Flk-1mAb treatment, with accompanying inhibition of angiogenesis, KDR/Flk-1 autophosphorylation, but not interference of flt-1 activation. This inhibitory effect was achieved even on established tumors and regardless of whether the tumor size was small or large. On the contrary, KDR/Flk-1mAb treatment significantly increased the apoptosis in the tumor. With orthotopic transplantation, KDR/Flk-1mAb also inhibited HCC development in the liver. These results suggest that KDR/Flk-1 is a major regulator of VEGF-mediated HCC development and angiogenesis not only at the initial stage, but also after the tumor has fully developed.
A Modified Infrared Spectrometer with High Time Resolution and Its Application for Investigating Fast Conformational Changes of the GTPase Ras (2014)

Time-resolved infrared spectroscopy is a valuable tool for the investigation of proteins and protein interactions. The investigation of many biological processes is possible by means of caged compounds, which set free biologically active substances upon light activation. Some caged compounds could provide sub-nanosecond time resolution, e.g., para-hydroxyphenacyl-guanosine 5'-triphosphate (GTP) forms GTP in picoseconds. However, the time resolution in single shot experiments with rapid-scan Fourier transform infrared (FT-IR) spectrometers is limited to about 10 ms. Here we use an infrared diode laser instead of the conventional globar and achieve a time resolution of 100 ns. This allows for the time-resolved measurement of the fast Ras(off) to Ras(on) conformational change at room temperature. We quantified the activation parameters for this reaction and found that the free energy of activation for this reaction is mainly enthalpic. Investigation of the same reaction in the presence of the Ras binding domain of the effector Raf (RafRBD) reveals a four orders of magnitude faster reaction, indicating that Ras·RafRBD complex formation directly induces the conformational change. Recent developments of broadly tunable quantum cascade lasers will further improve time resolution and usability of the setup. The reported 100 ns time resolution is the best achieved for a non-repetitive experiment so far.
Biostimulation of Wound Healing in Vivo by a Helium-Neon Laser (1987)

Clinical observations have suggested that low-energy lasers might stimulate wound healing. To understand the mechanism of the biostimulation, we previously examined the effects of low-energy lasers on collagen production by human skin fibroblasts and reported an increase of collagen synthesis in vitro. To examine the effects of low-energy lasers in vivo, hairless mice were experimentally wounded, sutured, and subjected to laser irradiation by a helium-neon laser with a power output of 1.56 mW and an energy fluence of 1.22 Joules/cm2. Experimental wounds were subjected to laser treatment every other day for 2 months; control wounds remained untreated. Specimens from the wounds were then examined for histological findings, tensile strength, and total collagen content. Results demonstrated a considerable improvement in the tensile strength of the laser-irradiated wounds at 1 and 2 weeks. Furthermore, the total collagen content was significantly increased at 2 months when compared with control wounds. These results suggest a beneficial effect of the helium-neon laser on wound healing in vivo.
Mesothelin overexpression promotes autocrine IL-6/sIL-6R trans-signaling to stimulate pancreatic cancer cell proliferation (2011)

Mesothelin (MSLN) overexpression in pancreatic cancer (PC) leads to enhanced cell survival/proliferation and tumor progression. After screening for a number of growth factors/cytokines, we found that the MSLN expression correlated closely with interleukin (IL)-6 in human PC specimens and cell lines. Stably overexpressing MSLN in different PC cell lines (MIA-MSLN and Panc1-MSLN) led to higher IL-6 production. Silencing MSLN by small interfering RNA (siRNA) significantly reduced IL-6 levels. Blocking the observed constitutive activation of nuclear factor-kappaB (NF-κB) with IKK inhibitor wedelolactone in MIA-MSLN cells also reduced IL-6. Silencing IL-6 by siRNA reduced cell proliferation, cell cycle progression and induced apoptosis with significant decrease of c-myc/bcl-2. Interestingly, recombinant IL-6-induced proliferation of MIA-MSLN cells but not MIA-V cells. Although messenger RNA/protein levels of IL-6R did not vary, soluble IL-6R (sIL-6R) was significantly elevated in MIA-MSLN and was reduced by treatment with the TACE/ADAM17 inhibitor TAPI-1, indicating intramembrane IL-6R cleavage and IL-6 trans-signaling may be operative in MIA-MSLN cells. Blocking the IL-6/sIL-6R axis using sIL-6R antibody abrogated basal proliferation/survival as well as recombinant human IL-6-induced cell proliferation. Our data suggest that MSLN-activated NF-κB induces elevated IL-6 expression, which acts as a growth factor to support PC cell survival/proliferation through a novel auto/paracrine IL-6/sIL-6R trans-signaling. In addition, using a panel of PC cells with varying MSLN/IL-6 expressions, we showed that MSLN/IL-6 axis is a major survival axis in PC supporting tumor cell growth under anchorage-dependent and independent conditions. The close correlation between MSLN and IL-6 provides a new rationale for combination therapy for effective control of MSLN-overexpressing PCs.
Efficacy and safety of etravirine at week 96 in treatment-experienced HIV type-1-infected patients in the DUET-1 and DUET-2 trials (2010)

Etravirine, in combination with an antiretroviral background regimen, provided durable virological and immunological responses with no new safety concerns in treatment-experienced patients over 96 weeks in the DUET trials.
Radio-and chemotoxicity in mice during hypothermia. (2002)

Hypothermia of 28 degrees C induced by chlorpromazine profoundly reduces radiation, doxorubicin-and cisplatin-induced toxicity in mice with males benefiting more than females. The hypothermia itself, not the chlorpromazine, was responsible for these effects. The anti-neoplastic activity was not compromised; rather, it was enhanced, particularly for cisplatin.
A two-dimensional Fourier transform method for the measurement of propagating multimode signals (1991)

A technique for the analysis of propagating multimode signals is presented. The method involves a two-dimensional Fourier transformation of the time history of the waves received at a series of equally spaced positions along the propagation path. The technique has been used to measure the amplitudes and velocities of the Lamb waves propagating in a plate, the output of the transform being presented using an isometric projection which gives a three-dimensional view of the wave-number dispersion curves. The results of numerical and experimental studies to measure the dispersion curves of Lamb waves propagating in 0.5-, 2.0-, and 3.0-mm-thick steel plates are presented. The results are in good agreement with analytical predictions and show the effectiveness of using the two-dimensional Fourier transform (2-D FFT) method to identify and measure the amplitudes of individual Lamb modes.
D-2 Dopamine Receptor-Mediated Inhibition of Adenylate Cyclase Activity in the Intermediate Lobe of the Rat Pituitary Gland Requires Guanosine 5'-Triphosphate (1982)

After treatment with cholera toxin, homogenates of intact intermediate lobe (IL) tissue of rat pituitary gland synthesized more cAMP than did homogenates of untreated IL tissue, and only in the presence of GTP did dopamine or apomorphine diminish the elevated adenylate cyclase activity in homogenates of cholera toxin-treated IL tissue. Furthermore, when tested on cholera toxin-treated IL tissue, 5'-guanylyl imidodiphosphate [Gpp(NH)p] and two other nonhydrolyzable analogs of GTP inhibited adenylate cyclase activity in the absence of either a dopaminergic agonist or GTP; GTP reversed the Gpp(NH)p-induced inhibition of adenylate cyclase activity. Apomorphine, a dopaminergic agonist, abolished the ability of GTP to reverse the inhibition by Gpp(NH)p; this effect of apomorphine was prevented by fluphenazine, a dopaminergic antagonist. Sodium fluoride inhibited adenylate cyclase activity to approximately the same level obtained with GTP and apomorphine. In addition, apomorphine decreased cAMP accumulation and alpha MSH release from dispersed IL cells pretreated with cholera toxin.
2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes (2015)

2-Thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. In particular, the 5-substituted-2-thiouridines (S2Us) present in tRNA play an important role in tuning the translation process through codon-anticodon interactions. The enhanced thermodynamic stability of S2U-containing RNA duplexes and the preferred S2U-A versus S2U-G base pairing are appreciated characteristics of S2U-modified molecular probes. Recently, we have demonstrated that 2-thiouridine (alone or within an RNA chain) is predominantly transformed under oxidative stress conditions to 4-pyrimidinone riboside (H2U) and not to uridine. Due to the important biological functions and various biotechnological applications for sulfur-containing nucleic acids, we compared the thermodynamic stabilities of duplexes containing desulfured products with those of 2-thiouracil-modified RNA and DNA duplexes. Differential scanning calorimetry experiments and theoretical calculations demonstrate that upon 2-thiouracil desulfuration to 4-pyrimidinone, the preferred base pairing of S2U with adenosine is lost, with preferred base pairing with guanosine observed instead. Therefore, biological processes and in vitro assays in which oxidative desulfuration of 2-thiouracil-containing components occurs may be altered. Moreover, we propose that the H2U-G base pair is a suitable model for investigation of the preferred recognition of 3'-G-ending versus A-ending codons by tRNA wobble nucleosides, which may adopt a 4-pyrimidinone-type structural motif.
Antibody-Mediated Renal Allograft Rejection (2007)

Alloantibodies to HLA class I or II and other antigens expressed by endothelium cause a variety of effects on renal transplants, ranging from acute to chronic rejection, and even apparent graft acceptance (accommodation). Recognition of these conditions and appropriate therapy requires demonstration of C4d in biopsies, commonly confirmed by tests for circulating alloantibody. Substantial practical experience by pathologists in the interpretation and pitfalls of C4d stains are reviewed along with considerations of the clinical significance and pathologic mechanisms of the different effects of antibody on the endothelium of the renal allograft. Clinical trials will be needed to ascertain the optimal treatment for the newly appreciated conditions chronic humoral rejection and accommodation.
Oligonucleotide-Directed Assembly of Materials:  Defined Oligomers (2001)

A nano-architectural system that has high variability while maintaining component specificity is described. Tetraphenylcyclobutadiene(cyclopentadienyl)cobalt complexes and phenyleneethynylene trimers were synthesized and subsequently modified with oligonucleotides utilizing standard phosphoramidite chemistry. The resulting oligonucleotide modified organics (OMOs) were characterized by UV-vis spectroscopy, fluorescence spectroscopy, and phosphate analysis. Hybridization of these OMOs resulted in a series of self-assembled oligomeric hybrids of varying length and topology. These hybrids were characterized by melting temperature, polyacrylamide gel electrophoresis, and fluorescence spectroscopy. This model system demonstrates the power of DNA to self-assemble modules of interest-independent of the module itself.
Room-temperature operation of a nanoelectromechanical resonator embedded in a phase-locked loop (2005)

We describe the operation of a phase-locked loop (PLL) that tracks the high-frequency electromechanical resonance of a nanoscale beam resonator. The fundamental in-plane flexural resonance of the beam resonator embedded in the PLL is actuated electrostatically and detected optically. PLL operation is demonstrated by locking stably to the resonance frequency of the beam, and by tracking this resonance with high fidelity as the beam is mass loaded. Our analysis reproduces the observed locking behavior. Feedback control schemes for nanoelectromechanical resonators may offer prospects for miniature timekeeping devices and ultrasensitive sensors.
Assessing the Capabilities of a Cased-Hole Reservoir Analysis System in the Gulf of Thailand (2000)

Abstract The option of using a cased-reservoir analysis system as an alternative to traditional open-hole log analysis was tested as a method to reduce drilling rig time. On a series of five wells in the Gulf of Thailand, an integrated pulsed-neutron system that measures Sigma, inelastic spectroscopy, neutron porosity and density was used to drive the cased-hole analysis. The capabilities and accuracy of the cased-hole results were compared to open-hole porosities and water saturations. One concern for cased-hole logging is accuracy in this well-completion environment. These wells are completed as monobores with 2⅞-inch tubing cemented directly into the 6⅛-inch open hole (no well casing). Initially, the pulsed-neutron porosity coefficients for 5½-inch casing were used with reasonable accuracy. To increase the porosity accuracy, the data from this test served as input to an artificial neural network for determining porosity coefficients in this specific borehole environment. The project consisted of 12,099 feet of log data including 30 gas sands, 5 oil sands, and numerous water sands in the five wells. The results of this assessment are shown via log examples over specific intervals. In addition, several cross-plots comparing open-hole data to cased-holed data show the results of this evaluation. Graphs of net pay, net effective porosity, net shale volume, and water saturation are shown for the entire project.
Linking naturally and unnaturally spun silks through the forced reeling of Bombyx mori (2014)

The forced reeling of silkworms offers the potential to produce a spectrum of silk filaments, spun from natural silk dope and subjected to carefully controlled applied processing conditions. Here we demonstrate that the envelope of stress-strain properties for forced reeled silks can encompass both naturally spun cocoon silk and unnaturally processed artificial silk filaments. We use dynamic mechanical thermal analysis (DMTA) to quantify the structural properties of these silks. Using this well-established mechanical spectroscopic technique, we show high variation in the mechanical properties and the associated degree of disordered hydrogen-bonded structures in forced reeled silks. Furthermore, we show that this disorder can be manipulated by a range of processing conditions and even ameliorated under certain parameters, such as annealing under heat and mechanical load. We conclude that the powerful combination of forced reeling silk and DMTA has tied together native/natural and synthetic/unnatural extrusion spinning. The presented techniques therefore have the ability to define the potential of Bombyx-derived proteins for use in fibre-based applications and serve as a roadmap to improve fibre quality via post-processing.