gebhart/patrepeval huggingface dataset:
Modular and orthogonal synthesis of hybrid polymers and networks (2015)

Biomaterials scientists strive to develop polymeric materials with distinct chemical make-up, complex molecular architectures, robust mechanical properties and defined biological functions by drawing inspirations from biological systems. Salient features of biological designs include (1) repetitive presentation of basic motifs; and (2) efficient integration of diverse building blocks. Thus, an appealing approach to biomaterials synthesis is to combine synthetic and natural building blocks in a modular fashion employing novel chemical methods. Over the past decade, orthogonal chemistries have become powerful enabling tools for the modular synthesis of advanced biomaterials. These reactions require building blocks with complementary functionalities, occur under mild conditions in the presence of biological molecules and living cells and proceed with high yield and exceptional selectivity. These chemistries have facilitated the construction of complex polymers and networks in a step-growth fashion, allowing facile modulation of materials properties by simple variations of the building blocks. In this review, we first summarize features of several types of orthogonal chemistries. We then discuss recent progress in the synthesis of step growth linear polymers, dendrimers and networks that find application in drug delivery, 3D cell culture and tissue engineering. Overall, orthogonal reactions and modulular synthesis have not only minimized the steps needed for the desired chemical transformations but also maximized the diversity and functionality of the final products. The modular nature of the design, combined with the potential synergistic effect of the hybrid system, will likely result in novel hydrogel matrices with robust structures and defined functions.
Chlamydia psittaci— Reemergence of a Forgotten Pathogen (1986)

The genus chlamydia consists of two species, psittaci and trachomatis. C. psittaci attracted attention during a pandemic in 1929–1930, when it was shown to cause psittacosis ("parrot fever," from the Greek word psittakos, "parrot").1 Exotic birds are not the only source of human infections, however. C. psittaci has been recovered from more than 130 avian species and is also an important pathogen among domestic mammals. Psittacosis is an occupational hazard to workers in the poultry industry.Psittacosis is considered to be exclusively a zoonosis; person-to-person transmission can occur but is rare. Some cases of psittacosis involve no known avian . . .
Self-Assembling, Cystine-Derived, Fused Nanotubes Based on Spirane Architecture:  Design, Synthesis, and Crystal Structure of Cystinospiranes (2001)

A novel family of cystine-based spirobicyclic peptides (cystinospiranes) has been synthesized by a single-step procedure involving condensation of pentaerythritol-derived tetrachloride with either the simple L-cystine dimethyl ester or its C,C'-extended bispeptides leading to a variety of 19-membered spirobicyclic peptides or its N,N'-extended bispeptides affording the ring-expanded 25-membered cystinospiranes. The design is flexible with respect to the ring size that can be adjusted depending upon the length of the N,N'-extended cystine bispeptide, and the choice of an amino acid, as illustrated here with the preparation of a large number of cystinospiranes containing a wide variety of amino acids. X-ray crystal structure of the parent spirane (5a) revealed nanotube formation by vertical stacking of relatively flat spirobicyclic molecules through contiguous NH- - -O==C hydrogen bonding. The fused pair of parallel nanotubes is open-ended, hollow, and extends to infinity. Crystallographic parameters are the following: C(33)H(52)N(4)O(16)S(4), space group C2, a = 42.181(3) A, b = 5.1165(7) A, c = 11.8687(9) A, beta = 106.23(1) degrees.
Conversion of glycerol to the valuable intermediates acrolein and allyl alcohol in the presence of heterogeneous catalysts (2010)

The attractiveness of crude oil as a feed stock for the chemical industry decreases with its scarcity and its correlated increasing price. Simultaneously, environmental issues as global warming underlines the necessity of alternative feed stocks and benign processes. The production of diesel fuel from plant oils is considered as a solution to these problems. However, the transesterification process for bio-diesel production leads to larger amounts of glycerol as a by product. The overproduced bio-diesel glycerol did not only suppress its price to very low levels but also loaded extra costs on the bio-diesel producers in terms of storage. Therefore there is great interest to use glycerol as starting material for its transformation in highly valuable intermediates for the chemical industry. Acrolein is an important intermediate in the organic industrial chemistry. Refined acrolein is used especially for the production of methionin. Much larger quantities are needed for the production of acrylic acid which is the monomer of poly acrylic acid. Poly acrylic acid is used as super absorbent mainly in diapers and hygienic pads. Currently acrolein is produced from propylene, which is originated from crude oil. Allyl alcohol is another intermediate with increasing application areas. It is used for the production of epichlorohydrine and 1-4 butane diol. Allyl alcohol is also currently produced from crude oil based materials. The subject of the present work is the heterogeneously catalyzed continious conversion of glycerol to the mentioned valuable intermediates; acrolein and ally alcohol. Shifting the source of carbon for the production of these chemicals from propylene to glycerol would not only encourage bio-diesel producers by enabling commercial possibilities for their by-product, but it would also avoid using crude oil in the production of acrolein and allyl alcohol. By that, acrolein, allyl alcohol and mentioned sequent chemicals would be biomass based and a CO2-neutral production would be provided. The development of suitable catalysts, screening of these catalysts under different experimental conditions, as well as investigation of the reaction routes, the side products and relationships between the properties of the catalyst and their performance in particular on the acrolein formation represent the scope of this work. The following achievements represent the core and the key findings of the present work. The surface acidity/basicity of the catalyst was found to be crucial for its performance in terms of acrolein yield. These catalyst properties could be manipulated by several measures. The catalyst system, WO3/TiO2, was revealed to be very suitable for the dehydration of glycerol to acrolein, outperforming the known catalysts in the literature up to date. The direct conversion of glycerol to allyl alcohol was discovered. The direct production of allyl alcohol from glycerol represents a novel and benign process.
Use of Agrobacterium expressing green fluorescent protein to evaluate colonization of sonication-assisted Agrobacterium-mediated transformation-treated soybean cotyledons (2000)

Colonization and infection of soybean cotyledons by Agrobacterium tumefaciens and subsequent elimination of bacteria from cotyledons were monitored using bacteria expressing green fluorescent protein (GFP). GFP provided a quick, non-destructive method to evaluate, in real time, Agrobacterium colonization of cotyledon surfaces as well as infection of internal cells. GFP was first detected 7 h following inoculation of the cotyledon. By 36 h, GFP expression was very intense, and was limited to the adaxial surface of the cotyledon. Expression of GFP also served as a useful indicator of successful elimination of the bacterium from plant tissue following antibiotic treatment.
Reducing the Complexity of Quasi-ML Detectors for MIMO Systems Through Simplified Branch Metric and Accumulated Branch Metric Based Detection (2013)

A detection scheme built on a combination of a simplified branch metric based search and refined calculation is proposed in this work to reduce the computational complexity of the quasi-maximum-likelihood (QML) detectors, such as the QR-decomposition combined with M-algorithm (QRD-M), list sequential sphere decoder (LISS) and list sphere decoding (LSD), for multiple-input multiple-output (MIMO) multiplexing systems, while maintaining similar performance to the original methods. More specifically, the proposed method utilizes a multiplication-free accumulated branch metric to first identify the potential candidates with significantly reduced search complexity. The optimal solution is then determined by the standard squared Euclidean distance metric from the initial candidates. The key idea of the proposed method lies in the fact that the best candidate identified by the simplified branch metric coincides with that of which is based on the conventional one with a high probability for a properly designed parameter. Numerical results demonstrates that the QRD-M detector using the proposed method achieves significantly better performance than the conventional one with comparable (or even less) computational complexity.
Glycogen Synthase Kinase 3β Is a Natural Activator of Mitogen-activated Protein Kinase/Extracellular Signal-regulated Kinase Kinase Kinase 1 (MEKK1) (2003)

Glycogen synthase kinase 3beta (GSK3 beta) is implicated in many biological events, including embryonic development, cell differentiation, apoptosis, and insulin response. GSK3 beta has now been shown to induce activation of the mitogen-activated protein kinase kinase kinase MEKK1 and thereby to promote signaling by the stress-activated protein kinase pathway. GSK3 beta-binding protein blocked the activation of MEKK1 by GSK3 beta in human embryonic kidney 293 (HEK293) cells. Furthermore, co-immunoprecipitation analysis revealed a physical association between endogenous GSK3 beta and MEKK1 in HEK293 cells. Overexpression of axin1, a GSK3 beta-regulated scaffolding protein, did not affect the physical interaction between GSK3 beta and MEKK1 in transfected HEK293 cells. Exposure of cells to insulin inhibited the activation of MEKK1 by GSK3 beta, and this inhibitory effect of insulin was abolished by the phosphatidylinositol 3-kinase inhibitor wortmannin. Furthermore, MEKK1 activity under either basal or UV- or tumor necrosis factor alpha-stimulated conditions was reduced in embryonic fibroblasts derived from GSK3 beta knockout mice compared with that in such cells from wild-type mice. Ectopic expression of GSK3 beta increased both basal and tumor necrosis factor alpha-stimulated activities of MEKK1 in GSK3 beta(-/-) cells. Together, these observations suggest that GSK3 beta functions as a natural activator of MEKK1.
S100β Stimulates Inducible Nitric Oxide Synthase Activity and mRNA Levels in Rat Cortical Astrocytes (1996)

The glia-derived, neurotrophic protein S100 beta has been implicated in development and maintenance of the nervous system. However, S100 beta has also been postulated to play a role in mechanisms of neuropathology, because of its specific localization and selective overexpression in Alzheimer's disease. To begin to address the question of whether S100 beta can induce potentially toxic signaling pathways, we examined the effects of the protein on nitric oxide synthase (NOS) activity in cultures of rat cortical astrocytes. S100 beta treatment of astrocytes induced a time- and dose-dependent increase in accumulation of the NO metabolite, nitrite, in the conditioned medium. The S100 beta- stimulated nitrite production was blocked by cycloheximide and by the NOS inhibitor N-nitro-L-arginine methylester, but not by the inactive D-isomer of the inhibitor. Direct measurement of NOS enzymatic activity in cell extracts and analysis of NOS mRNA levels showed that the NOS activated by S100 beta addition is the calcium-independent, inducible isoform. Furthermore, the specificity of the effects of S100 beta on activation of NOS was demonstrated by the inability of S100 alpha and calmodulin to induce an increase in nitrite levels. Our data indicate that S100 beta can induce a potent activation of inducible NOS in astrocytes, an observation that might have relevance to the role of S100 beta in neuropathology.
Mutational Analysis of Terminal Deoxynucleotidyltransferase- Mediated N-Nucleotide Addition in V(D)J Recombination (2004)

The addition of nontemplated (N) nucleotides to coding ends in V(D)J recombination is the result of the action of a unique DNA polymerase, TdT. Although N-nucleotide addition by TdT plays a critical role in the generation of a diverse repertoire of Ag receptor genes, the mechanism by which TdT acts remains unclear. We conducted a structure-function analysis of the murine TdT protein to determine the roles of individual structural motifs that have been implicated in protein-protein and protein-DNA interactions important for TdT function in vivo. This analysis demonstrates that the N-terminal portion of TdT, including the BRCA-1 C-terminal (BRCT) domain, is not required for TdT activity, although the BRCT domain clearly contributes quantitatively to N-nucleotide addition activity. The second helix-hairpin-helix domain of TdT, but not the first, is required for activity. Deletional analysis also suggested that the entire C-terminal region of TdT is necessary for N-nucleotide addition in vivo. The long isoform of TdT was found to reduce N-nucleotide addition by the short form of TdT, but did not increase nucleotide deletion from coding ends in either human or rodent nonlymphoid cells. We consider these results in light of the recently reported structure of the catalytic region of TdT.
Deep Learning for Production Main Controlling Factors Analysis of Tight Oil (2018)

Tight oil production has many controlling factors. The relationship between production and factors is non-linear. It is rather difficult to analyze the main controlling factors. Here, we use deep learning method to analyze the production main controlling factors of tight oil. We acquire a group of 35 tight oil wells in sandstone, carbonate and hybrid 3 lithology types, and randomly split wells into training set (n=28) and validation set (n=7). Well engineering process, source rock, reservoir and completion parameters are training data, and the testing daily production data are target data. A 3 hidden layers Deep Neural Network model is built to be trained by well data. After completion of the training, we generate a group of modified well data by individually increasing single parameter 10% of each well and remaining others unchanged, and input into the model. By calculating the change rate between the predicted production and the actual production, we analyze production main controlling factors of 3 types of tight oil. The results show that the training set correlation between the predicted production and the actual production is 0.97, and the validation set correlation is 0.91. The analysis of main controlling factors shows that brittleness index is an important production controlling factors of all 3 types of tight oil; the other main controlling factors are: porosity and Ro for sandstone tight oil; reservoir thickness and TOC for carbonate tight oil; Porosity, Ro and TOC for hybrid tight oil. Deep learning method has efficient learning ability and have good results in analyzing the production main factors of tight oil.
Protein G: a powerful tool for binding and detection of monoclonal and polyclonal antibodies. (1985)

Protein G is an immunoglobulin (IgG)-binding bacterial cell wall protein recently isolated from group G streptococci. We have investigated the avidity of protein G for various monoclonal and polyclonal Ig of the IgG class, and compared it with the binding properties of protein A, the staphylococcal Fc-binding protein. Radiolabeled Ig were mixed with Sepharose-coupled protein G or protein A, and the amounts of radioactivity bound to the matrix-coupled bacterial proteins were determined. The avidity was found to be greater for protein G than for protein A for all examined Ig. Protein G bound all tested monoclonal IgG from mouse IgG1, IgG2a, and IgG3, and rat IgG2a, IgG2b, and IgG2c. In addition, polyclonal IgG from man, cow, rabbit, goat, rat, and mouse bound to protein G, whereas chicken IgG did not. The binding property of protein G was additionally exploited in the Western blot assay, in which iodine-labeled protein G was used successfully for the detection of a rat monoclonal antibody against ovalbumin, and for the detection of rabbit and goat polyclonal whole antisera against human urinary proteins. In these experimental situations, protein G was found to be a powerful reagent for the detection of IgG, and consequently the antigen against which these antibodies are directed.
Induction of DC-STAMP by Alternative Activation and Downstream Signaling Mechanisms (2007)

dc-stamp expression is regulated differently in osteoclasts and macrophage giant cells. c-Fos and NFATc1, both of which are essential for osteoclast differentiation, are needed for dc-stamp expression and cell-cell fusion in osteoclasts, but both factors are dispensable for giant cell formation by macrophages. Because PU.1 and NF-kappaB are recruited to the dc-stamp promoter after stimulation with GM-CSF + IL-4, dc-stamp transcription is regulated in a cell type-specific manner.
Potentiation of methylglyoxal-bis-guanylhydrazone by alpha-difluoromethylornithine in rat prostate cancer (1984)

The polyamines, putrescine, spermidine, and spermine, are fundamentally related to both normal and neoplastic cell proliferation. The prostate gland and prostatic tumors in man and rodents contain large amounts of polyamines. This suggests that inhibition of polyamine biosynthetic enzymes, ornithine decarboxylase (ODC) and S-adenosyl-methionine decarboxylase (SAMDC) may retard the growth of prostatic cancer. Since alpha-difluoromethylornithine (DFMO) and methylglyoxal-bis-guanylhydrazone (MGBG) are irreversible and competitive inhibitors of ODC and SAMDC, respectively, they were tested as single agents and in combination on a transplantable rapidly growing and hormone-resistant G subline of the Dunning R-3327 rat prostatic adenocarcinoma. Groups of rats bearing tumors were treated with various regimens of DFMO, MGBG, and DFMO plus MGBG, daily for 21 days. Analysis of differences in tumor growth between treatment groups and controls showed DFMO had no antitumor effect but was well tolerated, MGBG retarded growth rate significantly but resulted in drug deaths in over 50% of the animals, and the combination of DFMO and MGBG resulted in rapid decline in tumor growth rates after 5 to 9 days of treatment with reduced toxicity. At 21 days, or death, 38 of 60 (63%) rats had no viable tumor on histologic study, whereas tumor was present in each of the animals in the other groups. Alpha-difluoromethylornithine increased the intracellular uptake of MGBG and potentiated the antigrowth activity of MGBG on a hormone refractory rat prostatic tumor with less toxicity than MGBG alone.
Ethyl 3-bromo-2-hydroxyiminopropanoate, a reagent for the preparation of ethyl esters of α-amino acids (1979)

T. L. Gilchrist, D. A. Lingham and T. G. Roberts, J. Chem. Soc., Chem. Commun., 1979, 1089 DOI: 10.1039/C39790001089
Multi-qubit compensation sequences (2010)

The Hamiltonian control of n qubits requires precision control of both the strength and timing of interactions. Compensation pulses relax the precision requirements by reducing unknown but systematic errors. Using composite pulse techniques designed for single qubits, we show that systematic errors for n qubit systems can be corrected to arbitrary accuracy given either two non-commuting control Hamiltonians with identical systematic errors or one error-free control Hamiltonian. We also examine composite pulses in the context of quantum computers controlled by two-qubit interactions. For quantum computers based on the XY interaction, single-qubit composite pulse sequences naturally correct systematic errors. For quantum computers based on the Heisenberg or exchange interaction, the composite pulse sequences reduce the logical single-qubit gate errors but increase the errors for logical two-qubit gates.
The Oligopeptide Transport System Is Essential for the Development of Natural Competence inStreptococcus thermophilusStrain LMD-9 (2009)

In gram-positive bacteria, oligopeptide transport systems, called Opp or Ami, play a role in nutrition but are also involved in the internalization of signaling peptides that take part in the functioning of quorum-sensing pathways. Our objective was to reveal functions that are controlled by Ami via quorum-sensing mechanisms in Streptococcus thermophilus, a nonpathogenic bacterium widely used in dairy technology in association with other bacteria. Using a label-free proteomic approach combining one-dimensional electrophoresis with liquid chromatography-tandem mass spectrometry analysis, we compared the proteome of the S. thermophilus LMD-9 to that of a mutant deleted for the subunits C, D, and E of the ami operon. Both strains were grown in a chemically defined medium (CDM) without peptides. We focused our attention on proteins that were no more detected in the ami deletion mutant. In addition to the three subunits of the Ami transporter, 17 proteins fulfilled this criterion and, among them, 7 were similar to proteins that have been identified as essential for transformation in S. pneumoniae. These results led us to find a condition of growth, the early exponential state in CDM, that allows natural transformation in S. thermophilus LMD-9 to turn on spontaneously. Cells were not competent in M17 rich medium. Furthermore, we demonstrated that the Ami transporter controls the triggering of the competence state through the control of the transcription of comX, itself controlling the transcription of late competence genes. We also showed that one of the two oligopeptide-binding proteins of strain LMD-9 plays the predominant role in the control of competence.
Rapid Mobilization Reveals a Highly Engraftable Hematopoietic Stem Cell (2018)

Hematopoietic stem cell transplantation is a potential curative therapy for malignant and nonmalignant diseases. Improving the efficiency of stem cell collection and the quality of the cells acquired can broaden the donor pool and improve patient outcomes. We developed a rapid stem cell mobilization regimen utilizing a unique CXCR2 agonist, GROβ, and the CXCR4 antagonist AMD3100. A single injection of both agents resulted in stem cell mobilization peaking within 15 min that was equivalent in magnitude to a standard multi-day regimen of granulocyte colony-stimulating factor (G-CSF). Mechanistic studies determined that rapid mobilization results from synergistic signaling on neutrophils, resulting in enhanced MMP-9 release, and unexpectedly revealed genetic polymorphisms in MMP-9 that alter activity. This mobilization regimen results in preferential trafficking of stem cells that demonstrate a higher engraftment efficiency than those mobilized by G-CSF. Our studies suggest a potential new strategy for the rapid collection of an improved hematopoietic graft.