gebhart/patrepeval huggingface dataset:
Pseudo-Prolines as a Molecular Hinge:  Reversible Induction ofcisAmide Bonds into Peptide Backbones (1997)

Serine, threonine-derived (4S)-oxazolidine-4-carboxylic acid, and cysteine-derived (4R)-thiazolidinecarboxylic acid, denoted pseudo-proline (Xaa[ΨR1,R2pro]), serve as structure disrupting, solubilizing building blocks in peptide synthesis. Variation of the 2-C substituents within the heterocyclic system results in different physicochemical and conformational properties. NMR studies of a series of pseudo-proline (ΨPro)-containing peptides reveal a pronounced effect of the 2-C substituents upon the cis to trans ratio of the adjacent amide bond in solution. 2-C unsubstituted systems show a preference similar to that of the proline residue for the trans form, whereas 2,2-dimethylated derivatives adopt the cis amide conformation in high content. For 2-monosubstituted ΨPro, the cis−trans distribution depends on the 2-C chirality. For the 2-(S)-diastereoisomer, both forms are similarly populated in solution, whereas the 2-(R)-epimer adopts preferentially the trans form. The results are supported by conformational energy calculations and suggest that, by tailoring the degree of substitution, pseudo-prolines may serve as a temporary proline mimetic or as a hinge in peptide backbones.
Lipase-Catalyzed Synthesis of a Pure Macrocyclic Polyester from Dimethyl Terephthalate and Diethylene Glycol (2002)

The polymerization of dimethyl terephthalate and diethylene glycol by enzymic catalysis in toluene is described. The potential pi-pi interactions of the aromatic rings together with the relative flexibility of the diol segment have been regarded as synergy factors responsible for the formation of a pure cyclic compound. The so-called C2 macrocycle was characterized by (1)H and (13)C NMR, size-exclusion chromatography, differential scanning calorimetry, mass spectrometry, and X-ray diffraction on powder. Structurally speaking, it is made of two repeating units. The substitution of the central oxygen atom of the diol by -CH(2)- or -S- as well as the presence of ortho-substituents (-NH(2) or -NO(2)) on the phthalate were expected to disrupt the stacking of the phenyl groups more or less.
IR laser polarimetry: breaking limits of FTIR polarimetry for thin film studies (2021)

Advances in polarimetric techniques are of high interest in multiple scientific fields. Polarimetry characterizes optical and material properties such as anisotropy and structure, which relate to physical, chemical and functional properties of materials used in optoelectronic, polymer, plasmonic, bio-related and pharmaceutical applications. Laser-based infrared (IR) spectroscopic methods beyond classical Fourier-transform infrared (FTIR) spectroscopy enable previously impossible polarimetric investigations from macroscopic to nanoscopic length scales. This contribution focuses on new polarimetry techniques for detailed analyses of structural and material properties of thin films and surfaces. Specifically, we show applications of two laboratory-based instruments that employ tunable quantum cascade lasers (QCLs) from Daylight Solutions as brilliant light sources. Regarding far-field IR spectroscopic measurements, a novel laser ellipsometer (built in cooperation with Sentech Instruments) simultaneously measures spectral amplitude and phase information via single-shot detection of four different polarization states. The device reaches temporal resolutions in the &mu;s to ms range at high spectral (&lt; 0.5 cm<sup>−1</sup> ) and lateral resolutions (&le; 125&mu;m). At the nanoscale, photothermal atomic force microscopy (AFM)-IR (Anasys, Bruker), based on a QCL and a polarizing unit, enables polarimetry with lateral resolutions of a few 10 nm.
Medically Induced Euthyroid Hypothyroxinemia May Extend Survival in Compassionate Need Cancer Patients: An Observational Study (2014)

Although this is an uncontrolled observational experience with frank limitations, compassionate medical induction of hypothyroxinemia should be considered for patients with advanced cancers to whom other avenues of treatment are closed.
Relative Price Variability and Inflation in a Fixed Price Regime (2011)

We study the relation between inflation rate and relative price variability using data of prices on 23 disaggregated food items since 1960 to 2003 in Chile. The behavior of inflation rate is quite variable in that country during that time span and more interestingly, there are periods of time in which prices were determined (fixed) by the economic authorities. We find consistent evidence that a larger inflation rate causes a larger relative price variability and this effect is much larger in periods in which prices were fixed. We interpret that result as firms over-reacting to inflation when setting their relative prices if they assume that it is unlikely to reset their prices in the near future. That result holds even if we follow different econometric approaches and it holds for all the food products considered.
Factors that influence quality and yield of circulating-free DNA: A systematic review of the methodology literature (2018)

This is the first systematic review of methodological factors that influence recovery and quantification of cfDNA, enabling recommendations to be made that will support standardization of methodological approaches towards development of blood-based cancer tests.
Cutting Edge: Scavenging of Inflammatory CC Chemokines by the Promiscuous Putatively Silent Chemokine Receptor D6 (2003)

In an effort to define the actual function of the promiscuous putatively silent chemokine receptor D6, transfectants were generated in different cell types. Engagement of D6 by inflammatory CC chemokines elicited no calcium response nor chemotaxis, but resulted in efficient agonist internalization and degradation. Also in lymphatic endothelium, where this receptor is expressed in vivo, D6 did not elicit cellular responses other than ligand internalization and degradation. In particular, no evidence was obtained for D6-mediated transcytosis of chemokines in the apical-to-basal or basal-to-apical directions. These results indicate that D6 acts as an inflammatory chemokine scavenging nonactivatory decoy receptors and suggest that in lymphatic vessels D6 may function as a gatekeeper for inflammatory CC chemokines, by clearing them and preventing excessive diffusion via afferent lymphatics to lymph nodes.
Postnatal Administration of Allopregnanolone Modifies Glutamate Release but Not BDNF Content in Striatum Samples of Rats Prenatally Exposed to Ethanol (2015)

Ethanol consumption during pregnancy may induce profound changes in fetal CNS development. We postulate that some of the effects of ethanol on striatal glutamatergic transmission and neurotrophin expression could be modulated by allopregnanolone, a neurosteroid modulator of GABAA receptor activity. We describe the acute pharmacological effect of allopregnanolone (65 μg/kg, s.c.) administered to juvenile male rats (day 21 of age) on the corticostriatal glutamatergic pathway, in both control and prenatally ethanol-exposed rats (two ip injections of 2.9 g/kg in 24% v/v saline solution on gestational day 8). Prenatal ethanol administration decreased the K(+)-induced release of glutamate regarding the control group. Interestingly, this effect was reverted by allopregnanolone. Regarding BDNF, allopregnanolone decreases the content of this neurotrophic factor in the striatum of control groups. However, both ethanol alone and ethanol plus allopregnanolone treated animals did not show any change regarding control values. We suggest that prenatal ethanol exposure may produce an alteration of GABAA receptors which blocks the GABA agonist-like effect of allopregnanolone on rapid glutamate release, thus disturbing normal neural transmission. Furthermore, the reciprocal interactions found between GABAergic neurosteroids and BDNF could underlie mechanisms operating during the neuronal plasticity of fetal development.
Chemosensitization of Androgen-Independent Prostate Cancer with Neutral Endopeptidase (2004)

These results suggest that NEP enzyme activity contributes to anticancer drug-induced PC cell apoptosis dependent on PKCdelta-mediated mitochondrial events. More importantly, the combination of NEP with anticancer drugs may be a promising therapeutic modality because rNEP is able to augment chemosensitivity in androgen-independent PC with minimal toxicity in normal tissues.
Exploring the relationship between network competence, network capability and firm performance : a resource-based perspective in an emerging economy (2009)

Growing interest in business-to-business networks and the demonstrated linkage between firm performance and collaborative efforts within these networks fuels the continued search for a greater understanding of what is needed to manage firms in complex business constellations. Key components of managing in networks, and the focus of this study, are the competencies and capabilities required at the firm level in order to engage in meaningful network relationships to enhance performance. Adopting the resource-based view (RBV) of a firm, an attempt is made to validate measures of network competence and network capability under South African conditions. Secondly, this study considers the relationship between network competence, network capability and subjective measures of firm performance. The analysis is based on data collected using a multi-informant mail survey of 219 business managers in South Africa. Factor analysis and structural equation modelling were utilised to test a conceptual model based on contemporary literature. Our results suggest significant relationships between network competence and network capability, and between network capabilities and firm performance, but not between network competence and firm performance. In addition to providing greater clarity on the relationships depicted in the model, the study also contributes to the rich debate on network management challenges.
Estradiol-17 beta and mu-opioid peptides rapidly hyperpolarize GnRH neurons: a cellular mechanism of negative feedback? (1995)

Control of the HPG axis involves a rapid (30 min) inhibition of LH (GnRH) release by E2. The time course of this effect is faster than expected for a purely transcriptional mechanism of E2 action. To elucidate the mechanism of E2 action, intracellular recordings in TTX were performed in guinea pig hypothalamic GnRH neurons. These neurons were directly hyperpolarized by both the mu-opioid agonist, DAMGO (Tyr-D-Ala-Gly-MePhe-Gly-ol, 9 mV) and the GABAB agonist, baclofen (18 mV) by opening K+ channels. Schild analysis with naloxone (Ke = 2.4 nM) confirmed that mu-opioid receptors mediated the effect of DAMGO. E2 also directly hyperpolarized GnRH neurons by opening K+ channels. Coupled with previous work showing a rapid effect of E2 to alter mu-opioid potency (1), a model is presented in which E2 rapidly inhibits GnRH neurons through parallel, possibly synergistic pathways.
Structure and development of a benthic marine microbial mat (1985)

Vertically stratified microbial communities of phototrophic bacteria in the upper intertidal zones of the North Sea island of Mellum were investigated. Growth and population dynamics of the cyanobacterial mat were followed over three successive years. It was concluded that the initial colonization of the sandy sediments was by the cyanobacterium Oscillatoria. In well-established mats, however, the dominant organism was Microcoleus chthonoplastes. The observed succession of cyanobacteria during mat development is correlated with nitrogen fixation. Nitrogen fixation is necessary in this low-nutrient environment to ensure colonization by mat-constructing cyanobacteria. Under certain conditions, a red layer of purple sulfur bacteria developed underneath the cyanobacterial mat in which Chromatium and Thiocapsa spp. dominated, but Thiopedia and Ectothiorhodospira spp. have also been observed. Measurements of light penetrating the cyanobacterial mat indicated that sufficient light is available for the photosynthetic growth of purple sulfur bacteria. Profiles of oxygen, sulfide and redox potential within the microbial mat were measured using microelectrodes. Maximum oxygen concentrations, measured at a depth of 0.7 mm, reached levels more than twice the normal air saturation. Dissolved sulfide was not detected by the microelectrodes. Determination of acid-distilled sulfide, however, revealed appreciable amounts of bound sulfide in the mat. Redox profiles measured in the mat led to the conclusion that the upper 10 mm of the sedimentary sequence is in a relatively oxidized state.
Activated Protein C Resistance and Inherited Thrombosis (1995)

Journal Article Activated Protein C Resistance and Inherited Thrombosis Get access George M. Rodgers, MD, PhD George M. Rodgers, MD, PhD Departments of Pathology and Medicine Veterans Affairs and University of Utah Medical Centers Salt Lake City, Utah and Associated Regional and University Pathologists Search for other works by this author on: Oxford Academic Google Scholar American Journal of Clinical Pathology, Volume 103, Issue 3, 1 March 1995, Pages 261–262, https://doi.org/10.1093/ajcp/103.3.261 Published: 01 March 1995
Scattering optics of foam (2001)

The multiple scattering of light by aqueous foams is systematically studied as a function of wavelength, bubble size, and liquid fraction. Results are analyzed in terms of the transport mean free path of the photons and an extrapolation length ratio for the diffuse photon concentration field. The wavelength dependence is minimal and may be attributed entirely to the wavelength dependence of the refractive index of water rather than thin-film interference effects. The transport mean free path is found to be proportional to the bubble diameter and the reciprocal of the square root of liquid fraction. The extrapolation length ratio varies almost linearly with liquid fraction between the values for water-glass-air and air-glass-air interfaces.
Effects of Promyelocytic Leukemia Protein on Virus-Host Balance (2002)

The cellular promyelocytic leukemia protein (PML) associates with the proteins of several viruses and in some cases reduces viral propagation in cell culture. To examine the role of PML in vivo, we compared immune responses and virus loads of PML-deficient and control mice infected with lymphocytic choriomeningitis virus (LCMV) and vesicular stomatitis virus (VSV). PML(-/-) mice exhibited accelerated primary footpad swelling reactions to very-low-dose LCMV, higher swelling peaks upon high-dose inoculation, and higher viral loads in the early phase of systemic LCMV infection. T-cell-mediated hepatitis and consequent mortality upon infection with a hepatotropic LCMV strain required 10- to 100-times-lower inocula despite normal cytotoxic T-lymphocyte reactivity in PML(-/-) mice. Furthermore, PML deficiency rendered mice 10 times more susceptible to lethal immunopathology upon intracerebral LCMV inoculation. Accordingly, 10-times-lower VSV inocula elicited specific neutralizing-antibody responses, a replication-based effect not observed with inactivated virus or after immunization with recombinant VSV glycoprotein. These in vivo observations corroborated our results showing more virus production in PML(-/-) fibroblasts. Thus, PML is a contributor to innate immunity, defining host susceptibility to viral infections and to immunopathology.
SET8 induces epithelial-mesenchymal transition and enhances prostate cancer cell metastasis by cooperating with ZEB1 (2015)

Mounting evidence suggested that histone H4K20-specific methyltransferase SET8 is required to maintain the malignant phenotype of various cancer types; however, the role of SET8 in mediating tumor metastasis in prostate cancer (PCa) has remained elusive. The present study demonstrated that small interfering RNA-mediated knockdown of SET8 inhibited the invasive potential of the PCa cell line PC-3 in vitro. Knockdown of SET8 reduced sphere formation, downregulated E-cadherin and α-catenin, and upregulated N-cadherin and vimentin expression in CaP cells, while upregulation of SET8 expression with a recombinant plasmid had the opposite effect. Furthermore, SET8 was shown to be physically associated with the epithelial-mesenchymal transition (EMT) inducer zinc finger E-box-binding homeobox 1 (ZEB1) in PCa cell lines. Chromatin immunoprecipitation suggested that SET8 binds to the promoter of cell adhesion molecule E-cadherin and vimentin. Luciferase reporter assays suggested that E-cadherin and vimentin are direct targets of SET8; furthermore, loss- and gain-of function studies of SET8 and ZEB1 indicated that suppression of downstream E-cadherin and activation of vimentin are important mechanisms by which SET8 and ZEB1 cooperatively trigger metastasis. Furthermore, SET8-induced methylated H4K20 was indicated to exert a dual function in ZEB1-regulated gene expression. In conclusion, the present study revealed that SET8 and ZEB1 are functionally interdependent in promoting the EMT and enhancing the invasive potential of PCa cells in vitro.
Rewiring the RNAs of influenza virus to prevent reassortment (2009)

Influenza viruses contain segmented, negative-strand RNA genomes. Genome segmentation facilitates reassortment between different influenza virus strains infecting the same cell. This phenomenon results in the rapid exchange of RNA segments. In this study, we have developed a method to prevent the free reassortment of influenza A virus RNAs by rewiring their packaging signals. Specific packaging signals for individual influenza virus RNA segments are located in the 5' and 3' noncoding regions as well as in the terminal regions of the ORF of an RNA segment. By putting the nonstructural protein (NS)-specific packaging sequences onto the ORF of the hemagglutinin (HA) gene and mutating the packaging regions in the ORF of the HA, we created a chimeric HA segment with the packaging identity of an NS gene. By the same strategy, we made an NS gene with the packaging identity of an HA segment. This rewired virus had the packaging signals for all eight influenza virus RNAs, but it lost the ability to independently reassort its HA or NS gene. A similar approach can be applied to the other influenza A virus segments to diminish their ability to form reassortant viruses.
First-Principles Study of Chemical Stability of the Lithium Oxide Garnets Li7La3M2O12 (M = Zr, Sn, or Hf) (2014)

Li-oxide garnet-related structures are promising solid-state Li-ion electrolytes in Li-ion batteries. However, garnet-type structures are susceptible to carbonate and hydroxide formation in environments containing gaseous CO2 and H2O. Therefore, in considering garnets for Li-ion conducting applications, chemical stability is an important issue. We examine the chemical stability of Li7La3Zr2O12, Li7La3Sn2O12, and Li7La3Hf2O12 with respect to carbonate and hydroxide formation reactions using density functional theory (DFT) calculations. From these studies, we rank the chemical stability of Li-oxide garnet-related structures against CO2 and H2O. The ranking of these materials by their chemical stability with respect to carbonate and hydroxide formation changes at higher partial pressures of CO2 and H2O.
The molecular biology of cytokines (1998)

Cytokine facts cytokine gene activation and cytokine production cytokine action in vitro properties of cytokines in vivo properties of cytokines cytokines and pathology clinical applications of cytokines and their inhibitors.
Molecular Characterization of KatY (Antigen 5), a Thermoregulated Chromosomally Encoded Catalase-Peroxidase ofYersinia pestis (1999)

The first temperature-dependent proteins (expressed at 37 degrees C, but not 26 degrees C) to be identified in Yersinia pestis were antigens 3 (fraction 1), 4 (pH 6 antigen), and 5 (hereafter termed KatY). Antigens 3 and 4 are now established virulence factors, whereas little is known about KatY, except that it is encoded chromosomally, produced in abundance, possesses modest catalase activity, and is shared by Yersinia pseudotuberculosis, but not Yersinia enterocolitica. We report here an improved chromatographic method (DEAE-cellulose, calcium hydroxylapatite, and Sephadex G-150) that yields enzymatically active KatY (2,423 U/mg of protein). Corresponding mouse monoclonal antibody 1B70.1 detected plasminogen activator-mediated hydrolysis of KatY, and a polyclonal rabbit antiserum raised against outer membranes of Y. pestis was enriched for anti-KatY. A sequenced approximately 16-kb Y. pestis DNA insert of a positive pLG338 clone indicated that katY encodes an 81.4-kDa protein (pI 6.98) containing a leader sequence of 2.6 kDa; the deduced molecular mass and pI of processed KatY were 78.8 kDa and 6. 43, respectively. A minor truncated variant (predicted molecular mass of 53.6 kDa) was also expressed. KatY is similar (39 to 59% identity) to vegetative bacterial catalase-peroxidases (KatG in Escherichia coli) and is closely related to plasmid-encoded KatP of enterohemorrhagic E. coli O157:H7 (75% identity). katY encoded a putative Ca2+-binding site, and its promoter contained three homologues to the consensus recognition sequence of the pCD-encoded transcriptional activator LcrF. rbsA was located upstream of katY, and cybB, cybC, dmsABC, and araD were mapped downstream. These genes are not linked to katG or katP in E. coli.
Radiative properties of strongly driven atoms in the presence of photonic bands and gaps (1993)

We show that the presence of photonic bands and gaps dramatically modifies the properties of single-atom resonance fluorescence. When, for example, photonic gaps suppress radiative emission on one or both of the strong-field resonance fluorescence sidebands, a driven atom is found to emit monochromatic radiation that is insensitive to fluctuations in the driving-field intensity and does not display the photon antibunching that is normally associated with single-atom resonance fluorescence. In such situations the atom’s radiative properties come to resemble those of a perfectly classical dipole.
Spherical navigator echoes for full 3D rigid body motion measurement in MRI (2001)

We developed a 3D spherical navigator (SNAV) echo technique that can measure rigid body motion in all six degrees of freedom simultaneously by sampling a spherical shell in k-space. 3D rotations of an imaged object simply rotate the data on this shell and can be detected by registration of k-space magnitude values. 3D translations add phase shifts to the data on the shell and can be detected with a weighted least-squares fit to the phase differences at corresponding points. MRI pulse sequences were developed to study k-space sampling strategies on such a shell. Data collected with a computer-controlled motion phantom with known rotational and translational motions were used to evaluate the technique. The accuracy and precision of the technique depend on the sampling density. Roughly 2000 sample points were necessary for accurate detection to within the error limits of the motion phantom when using a prototype time-intensive sampling method. This number of samples can be captured in an approximately 27-ms double excitation SNAV pulse sequence with a 3D helical spiral trajectory. Preliminary results with the helical SNAV are encouraging and indicate that accurate motion measurement suitable for retrospective or prospective correction should be feasible with SNAV echoes.