gebhart/patrepeval huggingface dataset:
A tumor-immune mathematical model of CD4+ T helper cell dependent tumor regression by oncogene inactivation (2013)

Understanding the complex dynamics between the tumor cells and the host immune system will be key to improved therapeutic strategies against cancer. We propose an ODE-based mathematical model of both the tumor and immune system and how they respond to inactivation of the driving oncogene. Our model supports experimental results showing that cellular senescence of tumor cells is dependent on CD4+ T helper cells, leading to relapse of tumors in immunocompromised hosts.
An observational study for detection and quantification of interferon- γ in sweat toward inflammation monitoring (2022)

This work demonstrates the quantification and detection of interferon- γ (IFN-γ), a key inflammatory biomarker in sweat using a flexible, nanoporous sweat sensor. IFN-γ is a pro-inflammatory cytokine released during the innate and adaptive response to enable antibacterial/antiviral immunity to an infection. Further, IFN-γ is critical marker to combat cancer through anti-tumor and pro-apoptotic mechanism. Therefore, real-time, continuous monitoring of pro-inflammatory cytokines can aid clinicians in active feedback on the administered therapeutic regimen. However, conventional blood-based laboratory methods are not feasible for continuous monitoring while sweat-based monitoring allows to continuously track the biomarker level in a point-of-need setting. This work demonstrates a sweat sensor device for rapid and accurate detection of IFN-γ in human sweat with less than 10% of variation. Highly sensitive and selective detection of IFN-γ with a limit of detection of 1 pg/mL and dynamic range of 1–512 pg/mL using impedance spectroscopy. The sensor demonstrated minimal to no signal response to non-specific cytokines. The performance of sweat sensor was further validated by comparing to state-of-art reference method and a Pearson's correlation of r > 0.95 was achieved in an observational study comprising of human subject samples confirming the reliability of the sweat sensor to report sweat IFN-γ levels. The promising findings from this work demonstrate the viability of utilizing the detection of IFN-γ in sweat for several inflammatory diseases such as cancer. Detection of IFN-γ in sweat will be pivotal in monitoring and aiding physicians in administering precision treatment strategies for patients diagnosed with cancer through continuous monitoring of immune status.
Solvatochromism and linear solvation energy relationship of diol- and proline-functionalized azo dyes using the Kamlet–Taft and Catalán solvent parameter sets (2008)

New donor–acceptor-substituted azo dyes, such as 2-({4-[(E)-(2,4-dinitrophenyl)diazenyl]-2-nitrophenyl}amino)propane-1,3-diol, (2S)-1-{4-[(E)-(2,4-dinitrophenyl)diazenyl]-2-nitrophenyl}-pyrrolidine-2-carboxylic acid and methyl-(2S)-1-{4-[(E)-(2,4-dinitrophenyl)diazenyl]-2-nitrophenyl}pyrrolidine-2-carboxylate have been obtained in a single step by nucleophilic aromatic substitution of (E)-1-(2,4-dinitrophenyl)-2-(4-fluoro-3-nitrophenyl)diazene with 2-aminopropane-1,3-diol, (S)-proline and (S)-proline methyl ester hydrochloride. The solvatochromism of the diol- and (S)-proline-methyl-ester-containing azo dye was studied and analysed using the empirical Kamlet–Taft and Catalán solvent parameter set. The dyes undergo a reversible protonation–deprotonation equilibrium in a concentration range of 5–12 M hydrochloric acid. The UV/Vis absorption spectra show a bathochromic shift with increasing acid strength of the medium.
The Secreted Form of Respiratory Syncytial Virus G Glycoprotein Helps the Virus Evade Antibody-Mediated Restriction of Replication by Acting as an Antigen Decoy and through Effects on Fc Receptor-Bearing Leukocytes (2008)

Respiratory syncytial virus (RSV) readily infects and reinfects during infancy and throughout life, despite maternal antibodies and immunity from prior infection and without the need for significant antigenic change. RSV has two neutralization antigens, the F and G virion glycoproteins. G is expressed in both membrane-bound (mG) and secreted (sG) forms. We investigated whether sG might act as a decoy for neutralizing antibodies by comparing the in vitro neutralization of wild-type (wt) RSV versus recombinant mG RSV expressing only mG. wt RSV indeed was less susceptible than mG RSV to monovalent G-specific and polyvalent RSV-specific antibodies, whereas susceptibility to F-specific antibodies was equivalent. This difference disappeared when the virus preparations were purified to remove sG. Thus, sG appears to function as a neutralization decoy. We evaluated this effect in vivo in mice by comparing the effects of passively transferred antibodies on the pulmonary replication of wt RSV versus mG RSV. Again, wt RSV was less sensitive than mG RSV to G-specific and RSV-specific antibodies; however, a similar difference was also observed with F-specific antibodies. This confirmed that sG helps wt RSV evade the antibody-dependent restriction of replication but indicated that in mice, it is not acting primarily as a decoy for G-specific antibodies, perhaps because sG is produced in insufficient quantities in this poorly permissive animal. Rather, we found that the greater sensitivity of mG versus wt RSV to the antiviral effect of passively transferred RSV antibodies required the presence of inflammatory cells in the lung and was Fc gamma receptor dependent. Thus, sG helps RSV escape the antibody-dependent restriction of replication via effects as an antigen decoy and as a modulator of leukocytes bearing Fc gamma receptors.
Exploring Oxidation of Half-Sandwich Rhodium Complexes: Oxygen Atom Insertion into the Rhodium–Carbon Bond of κ2-Coordinated 2-Phenylpyridine (2014)

The reactions of oxygen atom transfer reagents with Rh(Cp*) complexes, each with a bidentate ligand and an accessible coordination site, are described (Cp* = η5-pentamethylcyclopentadienyl). When [Rh(Cp*)(phpy)(NCArF)][B(ArF)4] (1, phpy = 2-phenylene-κC1′-pyridine-κN, NCArF = 3,5-bis(trifluoromethyl)benzonitrile, B(ArF)4 = tetrakis[3,5-bis(trifluoromethyl)phenyl]borate) was treated with the soluble oxygen atom transfer reagent 2-tert-butylsulfonyliodosylbenzene (sPhIO), oxygen atom insertion into the rhodium–carbon bond of coordinated phpy was observed. This resulted in the formation of a κ2 2-(2-pyridyl)phenoxide ligand. Following insertion to form a new bidentate ligand, a second equivalent of sPhIO, acting as a neutral, two-electron donor ligand, coordinated to the rhodium center through the iodosyl oxygen. Over time, the sPhIO ligand dissociates and dimerization occurs to generate a phenoxide-bridged dinuclear species. The 2-(2-pyridyl)phenoxide ligand could be protonated and cleaved from the mononuclear rhodium-(sPhIO) adduct by treating with a carboxylic acid (pivalic acid) at room temperature. In addition, when rhodium complex 1 was treated with excess phpy (14 equiv), hydrogen peroxide, and acetic acid, 5 equiv of 2-(2-pyridyl)phenol formed. Deactivation of the organometallic species, probably due to oxidative degradation of Cp*, severely limited this catalysis.
Characterization of germanium site distribution in zeolite ITQ-7 by photoluminescence. (2001)

Zeolite ITQ-7 containing germanium emits luminescence upon excitation at the wavelength of the absorption maxima; control experiments with amorphous GeO2 and all-silica zeolites indicate that the emission is attributable to Ge atoms occupying framework positions; the emission decays on the nanosecond time scale and it fits to variable proportions of three exponential kinetics, this being compatible with the presence of three families of Ge atoms in the solid.
Dynamic Control of the Bionic Handling Assistant (2016)

In the previous decade, multiple approaches for kinematic controllers of continuum manipulators were successfully developed. However, for fast and exact motions of continuum robots that are hardly seen so far, dynamic controllers are necessary-especially for spatial manipulators with multiple sections. Therefore, a dynamic controller in actuator space is developed that both exploits input constraints and decouples the actuators in order to provide a good and intuitive dynamic behavior of the manipulator. Having a pneumatically actuated manipulator with multiple actuators, this can be achieved using a cascaded control approach with a centralized actuator length controller and an underlying decoupled pneumatic controller. For both the outer multiple-input multiple-output (MIMO) controller and the inner single-input single-output (SISO) controllers, model-based controllers are developed based on suitable models using feedback linearization and a combination of feedforward control and linear PD-controllers. The resulting actuator controller can be used for tracking optimized trajectories in actuator space and also for possible extensions towards direct tool center point feedback.
Carbon monoxide can prevent acute lung injury observed after ischemia reperfusion of the lower extremities (2005)

Boutros, Cherif N. MD; Zegdi, Rachid MD; Lila, Nermine VD; Combillau, Michele MD; Fornes, Paul MD; Carpentier, Alain MD; Fabiani, Jean Noel MD Author Information
Electronic structure of tetracoordinate transition-metal complexes. 5. Comparative theoretical ab initio/Hartree-Fock-Slater and ultraviolet-photoelectron spectroscopic studies of building blocks for low-dimensional conductors. Dibenzo[b,i][1,4,8,11]tetraazacyclotetradecine complexes of nickel(II) and palladium(II) (1992)

The electronic structure of the Ni and Pd complexes of the title ligand have been studied by an integrated experimental He I/He II photoelectron spectroscopic as well as theoretical ab initio pseudopotential and first-principles local exchange DV-Xa approach. Theoretical calculations have provided a complete assignment of photoelectron spectra as well as useful information on the peculiarities of the valence electronic system that, in turn, is of relevance in understanding the properties of low-dimensional, partially oxidized, [M(TAA)e], systems. Furthermore, similarities and differences between the present complexes and partially oxidized metallophthalocyanines are discussed in terms of the nature of the HOMO and of twisting motion effects upon the valence bandwidths. The present results argue that the charge transport in tetraazaannulene molecular conductors occurs via bands that are predominantly ligand pi-electron in character, and that twisting motions (librations) scarcely affect the resistivity.
Information Theory (2016)

The information theory as formulated primarily through the research work at the Bell Laboratories by a number of researchers, of whom Claude Shannon is the prominent example, led to the development of digital telecommunications and the information and communications technology (ICT) people are familiar with today. This chapter describes information content measurement, source information generation rate and entropy. It also explains principles of source coding and link budget calculation. Link budget calculations are very important in system design. They may be used to determine the distance over which communications can be made, or calculate the amount of necessary power that yields a desired receiver signal to noise ratio (SNR). Link budget analysis can be used to calculate the maximum possible transmission rate on the link, or channel capacity. Maximum transmission rate calculation uses the second of Shannon's contribution to the field of information theory, namely channel capacity.
Abstract 2014: An estrogen receptor - centered network for probing anti-estrogen drug resistance with siRNA screening technology (2010)

Abstract De novo and acquired drug resistance pose significant problems for the effective treatment of estrogen-receptor (ER) positive breast cancers. We hypothesized that changes in the action of proteins interacting with core components of the estrogen response machinery may be responsible for such resistance, and that inhibition of these proteins may modulate response to hormonal therapies. To test this idea, we created a 631 gene network using ERα (ESR1), ERβ (ESR2), estrogen related receptors α (ESRRA) and γ (ESRRG), and aromatase as seed genes. The addition of genes to the network was selectively based on connectedness to the 5 seed genes. We used a set of bioinformatic resources including protein-protein interactions (PPIs), protein complexes, canonical pathways and estrogen responsive genes, to generate candidates for insertion into this network. An siRNA library has been developed from these 631 genes, for use in screening of breast cancer cell lines. Our primary goal is to identify networks of candidate genes involved in resistance to estrogen pathway-targeted drugs, corresponding to genes that reduce cell viability specifically in the presence of the hormonal therapies fulvestrant and tamoxifen. We have used MCF7/LCC1 cells (tamoxifen sensitive/fulvestrant sensitive), MCF7/LCC2 (tamoxifen resistant/fulvestrant sensitive) and MCF7/LCC9 (tamoxifen resistant/ fulvestrant resistant) cell lines as syngeneic models with varying drug resistance profiles for these experiments. In addition, we are identifying genes that differentially affect the intrinsic viability of these cell lines, and thus should illuminate the mechanism of their resistance to hormonal therapies. Our goal is to elucidate a network of regulators of anti-estrogen resistance. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2014.
Class IV alcohol/retinol dehydrogenase localization in epidermal basal layer: Potential site of retinoic acid synthesis during skin development (1997)

Vitamin A (retinol) plays a signaling role in the development of skin and other epithelial tissues. This is accomplished by a two-step metabolic pathway in which the rate-limiting step is oxidation of retinol to retinal, followed by oxidation of retinal to retinoic acid, which serves as the active ligand to activate nuclear retinoic acid receptors. Previous studies in mouse skin have shown that retinol oxidation is catalyzed by a cytosolic retinol dehydrogenase that may be a member of the alcohol dehydrogenase (ADH) enzyme family. Analysis of the ADH family has shown that class IV ADH is the most efficient isozyme for retinol oxidation but that other isozymes can catalyze this reaction. Here we have examined mouse skin for the expression of genes encoding class I ADH and class IV ADH, the only ADH isozymes in this species able to function as retinol dehydrogenases in vitro. In situ hybridization analysis of mouse skin revealed that class I ADH mRNA was absent, whereas class IV ADH mRNA was abundant and localized in the epidermal basal layer, providing evidence that the skin retinol dehydrogenase previously identified was class IV ADH. Immunohistochemical studies indicated that class I ADH protein was absent in the mouse skin, but class IV ADH protein was detected primarily in the basal layer of the epidermis, with less detection in the spinous layer and no detection in the cornified layer. This apparent down-regulation of class IV ADH expression during keratinocyte terminal differentiation provides evidence that the basal layer of the epidermis may be the primary site of local retinoic acid synthesis needed for retinoid signaling in the skin.
CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere (2015)

Inheritance of each chromosome depends upon its centromere. A histone H3 variant, centromere protein A (CENP-A), is essential for epigenetically marking centromere location. We find that CENP-A is quantitatively retained at the centromere upon which it is initially assembled. CENP-C binds to CENP-A nucleosomes and is a prime candidate to stabilize centromeric chromatin. Using purified components, we find that CENP-C reshapes the octameric histone core of CENP-A nucleosomes, rigidifies both surface and internal nucleosome structure, and modulates terminal DNA to match the loose wrap that is found on native CENP-A nucleosomes at functional human centromeres. Thus, CENP-C affects nucleosome shape and dynamics in a manner analogous to allosteric regulation of enzymes. CENP-C depletion leads to rapid removal of CENP-A from centromeres, indicating their collaboration in maintaining centromere identity.
Ab Initio Structure Determination of Vaterite by Automated Electron Diffraction (2012)

"This is a mineral about which there has been much discussion" is a typical statement about vaterite in older standard textbooks of inorganic chemistry. This polymorph of CaCO(3) was first mentioned by H. Vater in 1897, plays key roles in weathering and biomineralization processes, but occurs only in the form of nanosized crystals, unsuitable for structure determination. Its structure could now be solved by automated electron diffraction tomography from 50 nm sized nanocrystals.
Large Hierarchies from ApproximateRSymmetries (2009)

We show that hierarchically small vacuum expectation values of the superpotential in supersymmetric theories can be a consequence of an approximate R symmetry. We briefly discuss the role of such small constants in moduli stabilization and understanding the huge hierarchy between the Planck and electroweak scales.
Comparison between NIR and UV-Sensitized Radical and Cationic Reactivity of Iodonium Salts Comprising Anions with Different Coordination Behavior (2017)

Substituted diaryliodonium salts bearing weak coordinating anions ([(CF3SO2)3C]-; [(CF3SO2)2N]-; [PF6]-; [PF3(C2F5)3]-; [PF3(n-C4F9)3]-) were tested regarding their efficiency as radical initiator to initiate radical polymerization according to a sensitized mechanism. A NIR LED emitting at 790 nm was applied to initiate sensitized polymerization applying the polymethine S2265 as sensitizer. Change of the sensitizer resulting in spectral overlap with emission of UV-LED emitting at 395 nm complimented the experiments to understand the behavior of these iodonium salts under different exposure conditions. Furthermore, formation of protons was quantitatively probed by Rhodamine B lactone showing that UV sensitization resulted in a significant higher yield compared to NIR-sensitized photopolymerization. Surprisingly, the iodonium salt bearing the [(CF3SO2)3C]--anion exhibited a good performance in both radical photopolymerization and photoinduced formation of protons. Thioxanthon (ITX) served as sensitizer for all UV-LED experiments.
Activation of Cartilage-Derived Morphogenetic Protein-1 in Torn Rotator Cuff (2002)

Localization and expression of cartilage-derived morphogenetic protein-1 in tissues of torn rotator cuff tendons were examined by in situ hybridization and immunohistochemical analysis. Histologic findings of torn rotator cuff tendons showed that active cells synthesizing the alpha-1 chain of collagen Type I messenger ribonucleic acid were localized predominantly in the torn edge and in the bursa side rather than in the joint side, and scarcely localized in a site distant from the torn edge. Cartilage-derived morphogenetic protein-1 had a similar distribution as the alpha-1 chain of collagen Type I. The current findings provide the first observational evidence that cartilage-derived morphogenetic protein-1 was activated specifically at the site of the torn rotator cuff tendon. The current findings suggest that the cells in the torn rotator cuffs are capable of synthesizing cartilage-derived morphogenetic protein-1, one of the known essential factors for tendon formation.
Dielectrophoretic manipulation of finite sized species and the importance of the quadrupolar contribution (2004)

Dielectrophoresis (DEP) is the movement of polarizable species in a nonuniform electric field. DEP is used to attract (positive DEP) to or repel from (negative DEP) regions of high field intensity and is useful for manipulating species, including biological species. Current theoretical and numerical approaches used to predict the response to DEP forces assume that the target species is a point particle; however, in practice, the target species is of finite size, e.g., macromolecules, spores and assay beads. To elucidate the importance of target species size effects, higher order terms in the DEP force multipole expansion must be considered [Electrophoresis 23, 1973 (2002)]]. In this paper, we used the method of Green's function to derive and explore the importance of the quadrupolar contribution to the DEP forces acting on finite-sized species produced by a planar, interdigitated array of electrodes. Based on the analysis, it was found, for example, that at a fixed height of 20 mum in an interdigitated DEP array with an electrode width and spacing of 20 mum energized by a 10 Vp p, 1.0 MHz ac signal, the quadrupolar contribution to the total DEP force was 5% for a latex bead with 4.2 mum in radius and 10% for the one with 6 mum in radius. For a fixed, fractional quadrupolar contribution, beta , both the exact calculation and the scaling estimate elucidate that the critical size of particle increase linearly with the electrode width (and spacing) at a fixed height, while the critical particle radius increases with a square-root dependence on the width height above the electrode in the electrode array.
Olefin Polymerization (1999)

A family of zirconocene, yttrocene, and scandocene complexes have been prepared utilizing an easily modified doubly bridged ligand array, (1,2-SiMe2)2{η5-C5H2-4-R}{η5-C5H-3,5-CHMe2)2}, developed in our laboratories. Variations in ligand array substitution and metal center provide complexes that exhibit a range of stereoselectivities and activities in α-olefin polymerizations. A series of Cs- and C1- symmetric metallocenes have been utilized for the preparation of polypropylene and polypentene under various polymerization conditions. Analysis of the resulting polymer microstructures has provided valuable information about the factors that dictate syndiospecificity, as well as common error forming mechanisms for these systems.
Simplification of the genetic code: restricted diversity of genetically encoded amino acids (2012)

At earlier stages in the evolution of the universal genetic code, fewer than 20 amino acids were considered to be used. Although this notion is supported by a wide range of data, the actual existence and function of the genetic codes with a limited set of canonical amino acids have not been addressed experimentally, in contrast to the successful development of the expanded codes. Here, we constructed artificial genetic codes involving a reduced alphabet. In one of the codes, a tRNAAla variant with the Trp anticodon reassigns alanine to an unassigned UGG codon in the Escherichia coli S30 cell-free translation system lacking tryptophan. We confirmed that the efficiency and accuracy of protein synthesis by this Trp-lacking code were comparable to those by the universal genetic code, by an amino acid composition analysis, green fluorescent protein fluorescence measurements and the crystal structure determination. We also showed that another code, in which UGU/UGC codons are assigned to Ser, synthesizes an active enzyme. This method will provide not only new insights into primordial genetic codes, but also an essential protein engineering tool for the assessment of the early stages of protein evolution and for the improvement of pharmaceuticals.