gebhart/patrepeval huggingface dataset:
Enhanced translation and increased turnover of c-myc proteins occur during differentiation of murine erythroleukemia cells. (1990)

To determine whether regulation of c-myc proteins occurs during the differentiation of murine erythroleukemia cells, we examined c-myc protein synthesis and accumulation throughout dimethyl sulfoxide (DMSO)- or hypoxanthine-induced differentiation. c-myc protein expression exhibited an overall biphasic reduction, with an initial concomitant decrease in c-myc RNA, protein synthesis, and protein accumulation early during the commitment phase. However, as the mRNA and protein levels recovered, c-myc protein synthesis levels dissociated from the levels of c-myc mRNA and protein accumulation. This dissociation appears to result from unusual translational and posttranslational regulation during differentiation. Translational enhancement was suggested by the observation that relatively high levels of c-myc proteins were synthesized from relatively moderate levels of c-myc RNA. This translational enhancement was not observed with c-myb. Under certain culture conditions, we also observed a change in the relative synthesis ratio of the two independently initiated c-myc proteins. Posttranslational regulation was evidenced by a dramatic postcommitment decrease in the accumulated c-myc protein levels despite relatively high levels of c-myc protein synthesis. This decrease corresponded with a twofold increase in the turnover of c-myc proteins. The consequence of this regulation was that the most substantial decrease in c-myc protein accumulation occurred during the postcommitment phase of differentiation. This result supports the hypothesis that the reduction in c-myc at relatively late times is most important for completion of murine erythroleukemia cell terminal differentiation.
Microwave-assisted acid hydrolysis of proteins combined with liquid chromatography MALDI MS/MS for protein identification (2005)

Simple and efficient digestion of proteins, particularly hydrophobic membrane proteins, is of significance for comprehensive proteome analysis using the bottom-up approach. We report a microwave-assisted acid hydrolysis (MAAH) method for rapid protein degradation for peptide mass mapping and tandem mass spectrometric analysis of peptides for protein identification. It uses 25% trifluoroacetic acid (TFA) aqueous solution to dissolve or suspend proteins, followed by microwave irradiation for 10 min. This detergent-free method generates peptide mixtures that can be directly analyzed by liquid chromatography (LC) matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) without the need of extensive sample cleanup. LC-MALDI MS/MS analysis of the hydrolysate from 5 microg of a model transmembrane protein, bacteriorhodopsin, resulted in almost complete sequence coverage by the peptides detected, including the identification of two posttranslational modification sites. Cleavage of peptide bonds inside all seven transmembrane domains took place, generating peptides of sizes amenable to MS/MS to determine possible sequence errors or modifications within these domains. Cleavage specificity, such as glycine residue cleavage, was observed. Terminal peptides were found to be present in relatively high abundance in the hydrolysate, particularly when low concentrations of proteins were used for MAAH. It was shown that these peptides could still be detected from MAAH of bacteriorhodopsin at a protein concentration of 1 ng/microl or 37 fmol/microl. To evaluate the general applicability of this method, it was applied to identify proteins from a membrane protein enriched fraction of cell lysates of human breast cancer cell line MCF7. With one-dimensional LC-MALDI MS/MS, a total of 119 proteins, including 41 membrane-associated or membrane proteins containing one to 12 transmembrane domains, were identified by MS/MS database searching based on matches of at least two peptides to a protein.
Modeling of Precipitation Phase Boundaries in Mixed Surfactant Systems Using an Improved Counterion Binding Model (2012)

Abstract Anionic surfactants, commonly used in household products and the detergency industry, tend to precipitate with divalent counterions in hard water. The unsightly soap scum thus formed also removes the surfactant from the cleaning action. The current research has improved prediction of the precipitation phase boundary for mixtures of surfactants in hard water in two ways: firstly, an accurate value of the solubility product ( K SP ) has been determined for the calcium salt of 4‐octylbenzene sulfonate, and accurate temperature dependent K SP values have been determined for the calcium salts of dodecyl sulfate and decyl sulfate; secondly, improvements in prediction of the precipitation phase boundary have been achieved using an improved model. The K SP values of the decyl sulfate and dodecyl sulfate salts strongly increase with increasing temperature, with the shorter chain surfactant having significantly higher K SP than its longer chain analogue. At 30 °C the K SP of the 4‐octylbenzenesulfonate salt is similar to that of the dodecyl sulfate salt, perhaps due to the similarity in the length of their hydrocarbon tails. A recent counterion binding model proposed by our research group and micellization models have been used to model the precipitation phase boundaries for both single anionic surfactant and binary mixed anionic surfactant systems, improving thermodynamic modeling of the precipitation phase boundary of single and binary mixed anionic surfactant systems. In particular, the improved model of counterion binding has allowed the model to predict the phase boundary accurately over a range of temperatures.
Postsynthetic diazeniumdiolate formation and NO release from MOFs (2010)

Two different metal–organic frameworks (MOFs) have been modified with nitric oxide (NO) through covalent postsynthetic modification (PSM) to form diazeniumdiolate-functionalized and releasing MOFs.
Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals (1997)

A new Caenorhabditis elegans homeobox gene, ceh-25, is described that belongs to the TALE superclass of atypical homeodomains, which are characterized by three extra residues between helix 1 and helix 2. ORF and PCR analysis revealed a novel type of alternative splicing within the homeobox. The alternative splicing occurs such that two different homeodomains can be generated, which differ in their first 25 amino acids. ceh-25 is an orthologue of the vertebrate Meis genes and it shares a new conserved domain of 130 amino acids with them. A thorough analysis of all TALE homeobox genes was performed and a new classification is presented. Four TALE classes are identified in animals: PBC, MEIS, TGIF and IRO (Iroquois); two types in fungi: the mating type genes (M-ATYP) and the CUP genes; and two types in plants: KNOX and BEL. The IRO class has a new conserved motif downstream of the homeodomain. For the KNOX class, a conserved domain, the KNOX domain, was defined upstream of the homeodomain. Comparison of the KNOX domain and the MEIS domain shows significant sequence similarity revealing the existence of an archetypal group of homeobox genes that encode two associated conserved domains. Thus TALE homeobox genes were already present in the common ancestor of plants, fungi and animals and represent a branch distinct from the typical homeobox genes.
Snapshot imaging spectropolarimeter (2002)

We present and analyze a technique for snapshot imaging spectropolarimetry. The technique involves the combination of channeled spectropolarimetry with computed tomography imaging spectrometry (CTIS). Channeled spectropolarimetry uses sideband modulation to encode the spectral dependence of all four Stokes parameters in a single spectrum. CTIS is a snapshot imaging spectrometry method in which a computer-generated holographic disperser is employed to acquire dispersed images of the target scene, and both spatial and spectral information is reconstructed using the mathematics of computed tomography. The combination of these techniques provides the basis for a snapshot imaging complete Stokes spectropolarimeter that can be implemented with no moving parts. We review design considerations for the spectropolarimeter and present preliminary simulation results.
Atomistic simulation of water and salt transport in the reverse osmosis membrane FT-30 (1998)

Atomistic computer simulations of water and salt (NaCl) transport in the polyamide discriminating layer of the reverse osmosis membrane FT-30 are reported. We find that water transport occurs by a “jump” diffusion process, similar to the diffusion of simple, dissolved gas molecules in amorphous polymer glasses. As expected, lower water mobilities are observed at higher polymer densities. Cross-linking in the polymer matrix leads to an increase in density, which results in a decrease in water mobility, in accordance with experiment. We also observe a lower mobility for Cl− in the hydrated polymer, relative to Na+, which we attribute in part to the larger number of polar groups on the polymer chain that participate in solvating the anion. That the anion limits salt transport in our model FT-30 structures is consistent with experimental observations. Finally, although we find that the presence of salt reduces water mobility in the polyamide, in accordance with experiments; contrary to previous views, this effect is not related to a change in polymer density. Based on estimates of the salt partition coefficient and the diffusion coefficient of salt in the membrane, we conclude that high salt rejection in FT-30 is due in large part to the large difference in water and salt mobilities within the polyamide discriminating layer.
AMD3100, a Potent and Specific Antagonist of the Stromal Cell-Derived Factor-1 Chemokine Receptor CXCR4, Inhibits Autoimmune Joint Inflammation in IFN-γ Receptor-Deficient Mice (2001)

Autoimmune collagen-induced arthritis (CIA) in IFN-gammaR-deficient DBA/1 mice was shown to be reduced in severity by treatment with the bicyclam derivative AMD3100, a specific antagonist of the interaction between the chemokine stromal cell-derived factor-1 (SDF-1) and its receptor CXCR4. The beneficial effect of the CXCR4 antagonist was demonstrable when treatment was initiated between the time of immunization and appearance of the first symptoms. Treatment also reduced the delayed-type hypersensitivity response to the autoantigen, collagen type II. These observations are indicative of an action on a late event in the pathogenesis, such as chemokine-mediated attraction of leukocytes toward joint tissues. The notion of SDF-1 involvement was further supported by the observation that exogenous SDF-1 injected in periarthritic tissue elicited an inflammatory response that could be inhibited by AMD3100. The majority of leukocytes harvested from inflamed joints of mice with CIA were found to be Mac-1(+) and CXCR4(+), and AMD3100 was demonstrated to interfere specifically with chemotaxis and Ca(2+) mobilization induced in vitro by SDF-1 on Mac-1(+)/CXCR4(+) splenocytes. We conclude that SDF-1 plays a central role in the pathogenesis of murine CIA, by attracting Mac-1(+)/CXCR4(+) cells to the inflamed joints.
Invasion by Salmonella typhimurium is affected by the direction of flagellar rotation (1992)

When grown aerobically, Salmonella typhimurium exhibits a low level of entry into tissue culture cells. We have isolated an S. typhimurium Tn10 mutant which, when grown under aerobic conditions, efficiently invades HEp-2 cells. Sequencing of S. typhimurium DNA adjacent to the site of the Tn10 element showed that the insertion disrupted transcription of the aspartate receptor gene, tar. Polar effects of the transposon on downstream genes also eliminated chemotaxis. Isogenic nonchemotactic (Che-), as well as nonmotile (Mot-) and nonflagellated (Fla-), S. typhimurium strains were examined for their ability to invade HEp-2 cells. "Smooth" swimming Che- mutants (cheA, cheW, cheR, and cheY) were found to possess increased invasiveness for cultured mammalian cells. In contrast, a "tumbly" cheB mutant and Mot- (flagellated) strain were found to have decreased levels of tissue culture invasiveness. A Fla- strain was found to be as invasive as the wild-type strain if centrifugation was used to facilitate contact with the monolayer surface. In addition, the observed hyperinvasiveness of the smooth swimming tar::Tn10 mutant was suppressed when the strain was paralyzed by the introduction of a mot or fla mutation. A murine infection model was used to demonstrate that the mutant invasive phenotypes were also observed in vivo. These data are most consistent with the idea that the rotation and physical orientation of flagella around the bacteria affect the ability of salmonellae to enter host cells.
The molecular basis of eukaryotic transcription (2007)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Comparison of Tilmicosin and Cephapirin as Therapeutics for Staphylococcus aureus Mastitis at Dry-off (1999)

Forty-four cows (26 Jerseys and 18 Holsteins) that had at least 1 mammary quarter that was naturally (n = 12) or experimentally (n = 84) infected with Staphylococcus aureus were allotted to three treatment groups of approximately equal number at the end of lactation. Cows were dried off by abrupt cessation of milking, and dry cow therapy was administered as an intramammary infusion of cephapirin benzathine at 10 ml per quarter, an intramammary infusion of tilmicosin (solution containing 300 mg/ml) at 5 ml per quarter, or a subcutaneous injection of tilmicosin at 5 mg/kg of body weight on the day of drying off and another injection 4 d later. Mammary secretions were monitored during the dry period and postpartum for antimicrobial residues, intramammary infection (IMI) status, and somatic cell counts. Results demonstrated the following percentage cures for IMI caused by Staph. aureus at 28 d postcalving based on individual mammary quarters: cephapirin benzathine, 78.1%; tilmicosin infused, 74.2%; and tilmicosin injected, 9.1%. During the first 4 wk after drying off, the mean concentration of tilmicosin in mammary secretions from cows infused with the antibiotic remained approximately 10-fold higher than that in secretions from cows injected with the antibiotic (3.43 vs. 0.32 ppm), and, by the time of calving, concentrations for cows treated with both methods were below the dilution limit of the assay (< 0.1 ppm). Results demonstrated that intramammary infusion of tilmicosin was equally as effective as cephapirin benzathine in curing IMI caused by Staph. aureus at drying off; however, the subcutaneous injection of tilmicosin at the dose used was not effective as a dry cow therapeutic against Staph. aureus.
Microinjection of the Catalytic Subunit of cAMP-dependent Protein Kinase Induces Expression of the c-fos Gene (1988)

Changes in the concentration of cAMP have been shown to regulate cell shape (Porter et al. 1974) and metabolism (Schacter et al. 1984) and have been implicated in the inhibition of cell growth (Otten et ai. 1972), although it is now believed that a sustained increase in the cellular level of cAMP constitutes a growth-promoting signal in mammalian (Rozengurt 1986) and yeast (Matsumoto et al. 1985) ceils. In Escherichia coli, the expression of genes encoding enzymes involved in sugar catabolism is activated following binding of cAMP to a catabolite gene-activator protein (cap) and subsequent binding of the complex to specific DNA sequences of cAMP-regulated genes (de Crombrugghe et al. 1984). In
Compression of 3D Point Clouds Using a Region-Adaptive Hierarchical Transform (2016)

In free-viewpoint video, there is a recent trend to represent scene objects as solids rather than using multiple depth maps. Point clouds have been used in computer graphics for a long time, and with the recent possibility of real-time capturing and rendering, point clouds have been favored over meshes in order to save computation. Each point in the cloud is associated with its 3D position and its color. We devise a method to compress the colors in point clouds, which is based on a hierarchical transform and arithmetic coding. The transform is a hierarchical sub-band transform that resembles an adaptive variation of a Haar wavelet. The arithmetic encoding of the coefficients assumes Laplace distributions, one per sub-band. The Laplace parameter for each distribution is transmitted to the decoder using a custom method. The geometry of the point cloud is encoded using the well-established octtree scanning. Results show that the proposed solution performs comparably with the current state-of-the-art, while being much more computationally efficient. We believe this paper represents the state of the art in intra-frame compression of point clouds for real-time 3D video.
MrBUMP: a smooth operator for structure determination by molecular replacement (2007)

The PHENIX project [1] is an international effort to automate macromolecular crystal structure determination by developing new and improved algorithms, and by taking full advantage of current hardware and software development technology. The structure refinement module of PHENIX is the phenix.refine program. After about four years of intense development, phenix.refine includes most state-of-the-art procedures, including TLS, simulated annealing, NCS, twin refinement, maximum likelihood targets, etc. phenix.refine is embedded in the higher-level PHENIX wizards integrating model building and refinement. Under active development are alternative model parameterizations to reduce the number of refinable parameters (e.g. in torsion angle space). This is expected to stabilize refinement at lower resolutions and to increase the radius of convergence. We will present the latest results of this ongoing work.
Automatic Detection of Aortic Valve Opening Using Seismocardiography in Healthy Individuals (2018)

Accurate detection of fiducial points in a seismocardiogram (SCG) is a challenging research problem for its clinical application. In this paper, an automated method for detecting aortic valve opening (AO) instants using the dorso-ventral component of the SCG signal is proposed. This method does not require electrocardiogram (ECG) as a reference signal. After preprocessing the SCG, multiscale wavelet decomposition is carried out to get signal components in different wavelet subbands. The subbands having possible AO peaks are selected by a newly proposed dominant-multiscale-kurtosis- and dominant-multiscale-central-frequency-based criterion. The signal is reconstructed using selected subbands, and it is emphasized using the weights derived from the proposed relative squared dominant multiscale kurtosis. The Shannon energy followed by autocorrelation coefficients is computed for systole envelope construction. Finally, AO peaks are detected by a Gaussian-derivative-filtering-based scheme. The robustness of the proposed method is tested using clean and noisy SCG signals from the combined measurement of ECG, breathing, and SCG database. Evaluation results show that the method can achieve an average sensitivity of 94%, a prediction rate of 90%, and a detection accuracy of 86% approximately over 4585 analyzed beats.
A Candidate Gene Study of Obstructive Sleep Apnea in European Americans and African Americans (2010)

This candidate gene analysis identified the potential role of genes operating through intermediate disease pathways to influence sleep apnea phenotypes, providing a framework for focusing future replication studies.
Fighting computer crime (1983)

From the Publisher:
A top computer crime expert explains why current computer security methods fall dangerously short of the mark and what we can do to fix them. Based on his 30 years as a cybercrime fighter, during which he interviewed more than 200 perpetrators and their victims, Donn B. Parker provides valuable technical insight about the means cybercriminals employ, as well as penetrating psychological insights into their criminal behavior and motivations.
Phase II Trial of Infusional Fluorouracil, Irinotecan, and Bevacizumab for Metastatic Colorectal Cancer: Efficacy and Circulating Angiogenic Biomarkers Associated With Therapeutic Resistance (2009)

Efficacy and tolerability of FOLFIRI + B appeared favorable to historical controls in this single arm study. Before radiographic progression, there was a shift in balance of CAFs, with a rise in alternate pro-angiogenic cytokines and myeloid recruitment factors in subsets of patients that may represent mechanisms of resistance.
Macrocyclic α-Helical Peptide Drug Discovery (2014)

Macrocyclic α-helical peptides have emerged as a promising new drug class and within the scope of hydrocarbon-stapled peptides such molecules have advanced into the clinic. The overarching concept of designing proteomimetics of an α-helical ‘ligand’ which binds its cognate ‘target’ relative to α-helical interfacing protein-protein interactions has been well-validated and expanded through numerous investigations for a plethora of therapeutic targets oftentimes referred to as “undruggable” with respect to other modalities (e.g., small-molecule or proteins). This chapter highlights the evolution of macrocyclic α-helical peptides in terms of target space, biophysical and computational chemistry, structural diversity and synthesis, drug design and chemical biology. It is noteworthy that hydrocarbon-stapled peptides have successfully risen to the summit of such drug discovery campaigns.
Novel Role for CFTR in Fluid Absorption from the Distal Airspaces of the Lung (2002)

The active absorption of fluid from the airspaces of the lung is important for the resolution of clinical pulmonary edema. Although ENaC channels provide a major route for Na(+) absorption, the route of Cl(-) transport has been unclear. We applied a series of complementary approaches to define the role of Cl(-) transport in fluid clearance in the distal airspaces of the intact mouse lung, using wild-type and cystic fibrosis Delta F508 mice. Initial studies in wild-type mice showed marked inhibition of fluid clearance by Cl(-) channel inhibitors and Cl(-) ion substitution, providing evidence for a transcellular route for Cl(-) transport. In response to cAMP stimulation by isoproterenol, clearance was inhibited by the CFTR inhibitor glibenclamide in both wild-type mice and the normal human lung. Although isoproterenol markedly increased fluid absorption in wild-type mice, there was no effect in Delta F508 mice. Radioisotopic clearance studies done at 23 degrees C (to block active fluid absorption) showed approximately 20% clearance of (22)Na in 30 min both without and with isoproterenol. However, the clearance of (36)Cl was increased by 47% by isoproterenol in wild-type mice but was not changed in Delta F508 mice, providing independent evidence for involvement of CFTR in cAMP-stimulated Cl(-) transport. Further, CFTR played a major role in fluid clearance in a mouse model of acute volume-overload pulmonary edema. After infusion of saline (40% body weight), the lung wet-to-dry weight ratio increased by 28% in wild-type versus 64% in Delta F508 mice. These results provide direct evidence for a functionally important role for CFTR in the distal airspaces of the lung.
Clinical Phenotype of Families with Longevity (2004)

Offspring of centenarians may inherit significantly better health. The authors suggest that a cohort of these subjects and their spouses is ideal to study the phenotype and genotype of longevity and its interaction with the environment.