gebhart/patrepeval huggingface dataset:
Functional Stimuli-Responsive Gels: Hydrogels and Microgels (2018)

One strategy that has gained much attention in the last decades is the understanding and further mimicking of structures and behaviours found in nature, as inspiration to develop materials with additional functionalities. This review presents recent advances in stimuli-responsive gels with emphasis on functional hydrogels and microgels. The first part of the review highlights the high impact of stimuli-responsive hydrogels in materials science. From macro to micro scale, the review also collects the most recent studies on the preparation of hybrid polymeric microgels composed of a nanoparticle (able to respond to external stimuli), encapsulated or grown into a stimuli-responsive matrix (microgel). This combination gave rise to interesting multi-responsive functional microgels and paved a new path for the preparation of multi-stimuli "smart" systems. Finally, special attention is focused on a new generation of functional stimuli-responsive polymer hydrogels able to self-shape (shape-memory) and/or self-repair. This last functionality could be considered as the closing loop for smart polymeric gels.
Transforming growth factor beta isoform 2-specific high affinity binding to native alpha 2-macroglobulin. Chimeras identify a sequence that determines affinity for native but not activated alpha 2-macroglobulin. (1994)

Transforming growth factor beta 2 (TGF-beta 2) is less potent than TGF-beta 1 in some endothelial cell proliferation assays due to the greater tendency of TGF-beta 2 to bind alpha 2-macroglobulin (alpha 2M). Substitution of TGF-beta 1 residues 40-47 into the TGF-beta 2 sequence yields a chimeric molecule that, like TGF-beta 1, expresses activity that is not substantially affected by serum alpha 2M (Burmester, J. K., Qian, S. W., Roberts, A. B., Huang, A., Amatayakul-Chantler, S., Suardet, L., Odartchenko, N., Madri, J. A., and Sporn, M. B. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 8628-8632). In this investigation, we studied the binding of TGF-beta chimeras, which contain TGF-beta 1 residues 40-47, to both major conformations of human alpha 2M under apparent equilibrium conditions. Native alpha 2M, the primary form of this protein in serum, bound TGF-beta 2/beta 1 (40-82) and TGF-beta 2/beta 1 (40-47) with low affinity. The apparent KD values for the two chimeras and native alpha 2M were 310 and 330 nM, respectively. These values were much higher than the KD determined for TGF-beta 2 and native alpha 2M (11 nM) and equivalent to the KD determined for TGF-beta 1 and native alpha 2M. By contrast, both TGF-beta chimeras bound alpha 2M-methylamine, an altered conformation of alpha 2M, with high affinity (16 and 19 nM), which is characteristic of TGF-beta 2 and not TGF-beta 1. Fetal bovine heart endothelial cell DNA synthesis was inhibited to a similar degree by TGF-beta 1, TGF-beta 2, TGF-beta 2/beta 1 (40-82), and TGF-beta 2/beta 1 (40-47) in the presence of dilute (0.2%) fetal bovine serum. When 0.07 microM alpha 2M-methylamine was added, the activities of TGF-beta 2, TGF-beta 2/beta 1 (40-82), and TGF-beta 2/beta 1 (40-47) were significantly counteracted while the activity of TGF-beta 1 was unchanged, as would be predicted by the equilibrium binding analyses. These studies indicate that the TGF-beta structural elements, which mediate binding to native alpha 2M and conformationally transformed alpha 2M, are not equivalent. Residues 40-47 are critical in determining affinity for native alpha 2M but are less important in determining affinity for alpha 2M-methylamine.
Cellular and molecular determinants of all‐ trans retinoic acid sensitivity in breast cancer: Luminal phenotype and RAR α expression (2015)

Forty-two cell lines recapitulating mammary carcinoma heterogeneity were profiled for all-trans retinoic acid (ATRA) sensitivity. Luminal and ER(+) (estrogen-receptor-positive) cell lines are generally sensitive to ATRA, while refractoriness/low sensitivity is associated with a Basal phenotype and HER2 positivity. Indeed, only 2 Basal cell lines (MDA-MB157 and HCC-1599) are highly sensitive to the retinoid. Sensitivity of HCC-1599 cells is confirmed in xenotransplanted mice. Short-term tissue-slice cultures of surgical samples validate the cell-line results and support the concept that a high proportion of Luminal/ER(+) carcinomas are ATRA sensitive, while triple-negative (Basal) and HER2-positive tumors tend to be retinoid resistant. Pathway-oriented analysis of the constitutive gene-expression profiles in the cell lines identifies RARα as the member of the retinoid pathway directly associated with a Luminal phenotype, estrogen positivity and ATRA sensitivity. RARα3 is the major transcript in ATRA-sensitive cells and tumors. Studies in selected cell lines with agonists/antagonists confirm that RARα is the principal mediator of ATRA responsiveness. RARα over-expression sensitizes retinoid-resistant MDA-MB453 cells to ATRA anti-proliferative action. Conversely, silencing of RARα in retinoid-sensitive SKBR3 cells abrogates ATRA responsiveness. All this is paralleled by similar effects on ATRA-dependent inhibition of cell motility, indicating that RARα may mediate also ATRA anti-metastatic effects. We define gene sets of predictive potential which are associated with ATRA sensitivity in breast cancer cell lines and validate them in short-term tissue cultures of Luminal/ER(+) and triple-negative tumors. In these last models, we determine the perturbations in the transcriptomic profiles afforded by ATRA. The study provides fundamental information for the development of retinoid-based therapeutic strategies aimed at the stratified treatment of breast cancer subtypes.
Physics and Technology of Low-Temperature Plasmas (1977)

Plasmatrons and their technical possibilities are considered together with the composition of a plasma, its thermodynamic functions, and the spectral diagnostics of a low-temperature plasma. Thermal and gasdynamic methods of plasma dynamics are examined, giving attention to the determination of the temperature of heavy particles, the measurement of thermal flows, the measurement of the plasma flow rate, and the determination of plasma flow turbulence. High- frequency induction plasmatrons are discussed together with arc plasmatrons, the theory of the plasma at equilibrium, a two-temperature plasma model, aspects of heat transfer in the case of a flow of a low-temperature plasma about a body, and the dynamics of motion and the heating of refractory particles in plasma jets. (IAA)
PREPARATION OF OPHTHALMIC SOLUTIONS WITH SPECIAL REFERENCE TO HYDROGEN ION CONCENTRATION AND TONICITY (1950)

A GREAT deal has been written in the ophthalmologic literature about the importance of the hydrogen ion concentration and the tonicity of ophthalmic therapeutic solutions. Much of the published material is not in a form that is readily usable by the practicing ophthalmologist. We decided to investigate the practical limits of variability of these two factors and to evaluate their importance. Our aim is to present here what we believe to be the best solutions, based on present knowledge, for practical prescribing and feasible compounding of solutions containing most of the frequently used ophthalmic drugs. Recently, Swan<sup>1</sup>summarized the factors known at present which influence the permeability of the cornea by therapeutic agents. He pointed out that the tonicity of the tears, as reported by various workers in terms of the sodium chloride equivalent, varies from 0.9 to 1.4 per cent. He stated elsewhere<sup>2</sup>that solutions with tonicity
The IBM System/360 Model 91: Floating-Point Execution Unit (1967)

The principal requirement for the Model 91 floating-point execution unit was that it be designed to support the instruction-issuing rate of the processor. The chosen solution was to develop separate, instruction-oriented algorithms for the add, multiply, and divide functions. Linked together by the floating-point instruction unit, the multiple execution units provide concurrent instruction execution at the burst rate of one instruction per cycle.
Antibiotic Resistance: Current Perspectives (2017)

Antibiotic resistance is one of the most serious challenges that the world is currently facing. The number of people succumbing to drug-resistant infections is increasing every day, but the rate of drug discovery has failed to match the requisite demands. Most of the currently known antibiotics target the three essential pathways of central dogma. However, bacteria have evolved multiple mechanisms to survive these antibiotics. Consequently, there is an urgent necessity to target auxiliary pathways for the discovery of new drugs. Metabolism-related and stress-associated pathways are ideal in this regard. The stringent response pathway regulated by the signaling nucleotides (p)ppGpp is an attractive target as inhibition of the pathway would in turn decrease the persistence and long-term survival of pathogenic bacteria. In this perspective, we focus on the recent design of small molecule analogues of (p)ppGpp that have yielded promising results in terms of growth and biofilm inhibition. Additionally, we discuss how targeting small RNAs and riboswitches, as well as antimicrobial peptides, would help combat drug-resistant infections in the near future.
A thermodynamic theory of RF Power transmitters with an example (2009)

The continuing evolution of wireless communication standards and the associated increases in functionality for mobile wireless voice and data devices are driving the growing demand for transmitters that offer enhanced performance and greater flexibility while simultaneously consuming less power. Transmitter solutions are typically spawned by separate analysis and design of the RF power amplifier and the modulator functions. One trend in the industry has been to combine these functions while enhancing efficiency and maintaining waveform quality. However, the treatment of architectural synthesis has not been unified. The ideas presented in this paper unify the analysis and synthesis philosophy under the theoretical umbrella of thermodynamics and Shannon's theorem.
Universal Cellular Automata Based on the Collisions of Soft Spheres (2003)

Fredkin’s Billiard Ball Model (BBM) is a continuous classical mechanical model of computation based on the elastic collisions of identical finite-diameter hard spheres. When the BBM is initialized appropriately, the sequence of states that appear at successive integer time steps is equivalent to a discrete digital dynamics. Here we discuss some models of computation that are based on the elastic collisions of identical finite-diameter soft spheres: spheres which are very compressible and hence take an appreciable amount of time to bounce off each other. Because of this extended impact period, these Soft Sphere Models (SSMs) correspond directly to simple lattice gas automata—unlike the fast-impact BBM. Successive time steps of an SSM lattice gas dynamics can be viewed as integer-time snapshots of a continuous physical dynamics with a finite-range soft-potential interaction. We present both two-dimensional and three-dimensional models of universal CAs of this type, and then discuss spatially efficient computation using momentum conserving versions of these models (i.e., without fixed mirrors). Finally, we discuss the interpretation of these models as relativistic and as semiclassical systems, and extensions of these models motivated by these interpretations. Cellular automata (CA) are spatial computations. They imitate the locality and uniformity of physical law in a stylized digital format. The finiteness of the information density and processing rate in a CA dynamics is also physically realistic. These connections with physics have been exploited to construct CA models of spatial processes in Nature and to explore artificial “toy” universes. The discrete and uniform spatial structure of CA computations also makes it possible to “crystallize” them into efficient hardware [17, 21]. Here we will focus on CAs as realistic spatial models of ordinary (nonquantum- coherent) computation. As Fredkin and Banks pointed out [2], we can demonstrate the computing capability of a CA dynamics by showing that certain patterns of bits act like logic gates, like signals, and like wires, and that we can put these pieces together into an initial state that, under the dynamics, exactly simulates the logic circuitry of an ordinary computer.
Estimating variance components and breeding values for number of oocytes and number of embryos in dairy cattle using a single-step genomic evaluation (2017)

Reproductive technologies such as multiple ovulation and embryo transfer (MOET) and ovum pick-up (OPU) accelerate genetic improvement in dairy breeding schemes. To enhance the efficiency of embryo production, breeding values for traits such as number of oocytes (NoO) and number of MOET embryos (NoM) can help in selection of donors with high MOET or OPU efficiency. The aim of this study was therefore to estimate variance components and (genomic) breeding values for NoO and NoM based on Dutch Holstein data. Furthermore, a 10-fold cross-validation was carried out to assess the accuracy of pedigree and genomic breeding values for NoO and NoM. For NoO, 40,734 OPU sessions between 1993 and 2015 were analyzed. These OPU sessions originated from 2,543 donors, from which 1,144 were genotyped. For NoM, 35,695 sessions between 1994 and 2015 were analyzed. These MOET sessions originated from 13,868 donors, from which 3,716 were genotyped. Analyses were done using only pedigree information and using a single-step genomic BLUP (ssGBLUP) approach combining genomic information and pedigree information. Heritabilities were very similar based on pedigree information or based on ssGBLUP [i.e., 0.32 (standard error = 0.03) for NoO and 0.21 (standard error = 0.01) for NoM with pedigree, 0.31 (standard error = 0.03) for NoO, and 0.22 (standard error = 0.01) for NoM with ssGBLUP]. For animals without their own information as mimicked in the cross-validation, the accuracy of pedigree-based breeding values was 0.46 for NoO and NoM. The accuracies of genomic breeding values from ssGBLUP were 0.54 for NoO and 0.52 for NoM. These results show that including genomic information increases the accuracies. These moderate accuracies in combination with a large genetic variance show good opportunities for selection of potential bull dams.
Gold Glyconanoparticles as Water-Soluble Polyvalent Models To Study Carbohydrate Interactions (2001)

Glycosphingolipid clustering and interactions at the cell membrane can be modeled by gold glyconanoparticles prepared with biologically significant oligosaccharides. Such water-soluble gold glyconanoparticles with highly polyvalent carbohydrate displays (see picture, gray hemisphere: gold nanoparticle) have been obtained by a simple and versatile strategy.
Printed, Sub-3V Digital Circuits on Plastic from Aqueous Carbon Nanotube Inks (2010)

Printing electronic components on plastic foils with functional liquid inks is an attractive approach for achieving flexible and low-cost circuitry for applications such as bendable displays and large-area sensors. The challenges for printed electronics, however, include characteristically slow switching frequencies and associated high supply voltages, which together impede widespread application. Combining printable high-capacitance dielectrics with printable high-mobility semiconductors could potentially solve these problems. Here we demonstrate fast, flexible digital circuits based on semiconducting carbon nanotube (CNT) networks and high-capacitance ion gel gate dielectrics, which were patterned by jet printing of liquid inks. Ion gel-gated CNT thin-film transistors (TFTs) with 50 microm channel lengths display ambipolar transport with electron and hole mobilities >20 cm(2)/V.s; these devices form the basis of printed inverters, NAND gates, and ring oscillators on both polyimide and SiO(2) substrates. Five-stage ring oscillators achieve frequencies >2 kHz at supply voltages of 2.5 V, corresponding to stage delay times of 50 micros. This performance represents a substantial improvement for printed circuitry fabricated from functional liquid inks.
Platforms and networks in triterpenoid pharmacology (2007)

Abstract Using the pentacyclic, naturally occurring triterpenoids, oleanolic, ursolic, and betulinic acids, as starting materials, we have developed a new series of multifunctional drugs for potential clinical use. These agents have anti‐inflammatory, anti‐oxidative, anti‐proliferative, pro‐apoptotic, and differentiating activities. Two synthetic oleanane triterpenoids, 2‐cyano‐3,12‐dioxooleana‐1,9(11)‐dien‐28‐oic acid (CDDO) and its C‐28 methyl ester (CDDO‐Me), are presently in Phase I clinical trials in cancer patients. Three themes are emphasized in this review: (1) The importance of the unique structures of the triterpenoid platforms that have been used as a start for new synthesis; (2) The concept that these new drugs interact with entire physiological networks, rather than solely with single molecular targets; and (3) The coupling in real time between the triterpenoid platforms and the physiological networks with which they interact, as seen in the reversibility of the Michael reactions, which mediate their activity. We suggest that further development of such new, multifunctional drugs will most likely occur in the more flexible environment of small biotech or pharmaceutical companies. Drug Dev Res 68:174–182, 2007. © 2007 Wiley‐Liss, Inc.
Fentanyl Midazolam combination for endoscopy sedation is safe and effective (1998)

PURPOSE: To investigate the use of the opioid Fentanyl with low dose Midazolam as sedation for gastrointestinal endoscopy. BACKGROUND: Among opiates Fentanyl demonstrates extensive analgesia and reduced respiratory depression, with rapid elimination (T 1/2 20 min). Midazolam is a benzodiazepine with a longer elimination phase (T 1/2 3.9 hrs.) but extensive amnesia. A Fentanyl/Midazolam combination allows a lower dose of Midazolam to be used. Overall this combination may result in better patient comfort, more rapid recovery and eadier discharge times. METHODS: We measured pre and post procedure oxygen saturations (O 2 sat) and blood pressare (B.P.) in a sequential series of 235 patients undergoing upper and lower gastrointestinal endoscopy with sedation. We studied a total of 265 procedures. The average dose of Fentanyl used was 113lag and the average dose of Midazolam was 2.79mg. All patients had 02 at a rate of 2IJmin. RESULTS: The average pre-procedure 02 sat was 95.6% (off oxygen) and the post procedure 02 sat was 95.9% on 2 L O2/min. A total of 5 patients (2.13%) during endoscopy transiently developed 02 sats of less than 90%. The average pre procedure B.P. was 126/74 and the average post procedure B.P. was 119/69. A total of 20 patients had a drop of > 25% in systolic B.P., representing a hypotension rate of 8.51%. In none of these patients was this mild hypotension clinically significant and all but 2 patients rapidly responded to Trendelenburg manoeuvre. The 2 patients refractory to Trendelenburg rapidly responded to 500 or 1000mls saline. CONCLUSION: The use of combination Fentanyl and low dose Midazolam (with 02 2L/min.) as sedation in GI endoscopy is safe with no serious adverse effects in 235 patients. Other studies by our group show improved patient comfort and more rapid discharge time with this combination. Earlier studies showed desaturation rates of 32% without supplemental 02 in another cohort of 210 patients.
Production and Characterization of Arbovirus Antibody in Mouse Ascitic Fluid (1967)

SummarySpecific high-titered arbovirus CF antibody was obtained in mouse ascitic fluid. Primary and secondary immunization consisting of multiple closely spaced injections produced an antibody response similar to that found after one primary and one secondary injection, but resulted in higher-titered yet similarly specific reagents. Subcutaneous inoculation was shown to be more effective than intraperitoneal inoculation for primary immunization, whereas the reverse was true for secondary immunization. CF and HI antibody in hyperimmune ascitic fluid was found only in the 7S gamma G-immunoglobulin region. AC activity was found in the 19S portion of the gamma globulin region of unheated ascitic fluid; it was heat labile when isolated from 7S gamma G-immunoglobulins and heat stable in their presence. Nonspecific inhibitors in the HI test were shown to be lipoproteins that were not associated with 19S or 7S globulins.
A fast algorithm for context-aware buffer insertion (2000)

We study the problem of performing buffer insertion in the context of a given layout in a practical situation, there are restrictions on where buffers may be inserted while routing over such regions may be possible (e.g., due to the presence of macro cells). As a result, it is desirable to perform route planning and biffer insertion simultaneously. Further it is necessary that such an algorithm be aware of the tradeoff between cost (e.g. total capacitance) and delay. In this context we propose the Delay Reduction to Cost Ratio (DRCR) problem and present a fast algorithm for the same. Solutions identified by the algorithm are characterized with respect to the overall cost vs. performance tradeoff curve. Computational experiments demonstrate the viability of the approach.
Tyrosine Phosphatase SHP-1 Is Involved in CD66-Mediated Phagocytosis of Opa52-ExpressingNeisseria gonorrhoeae (1999)

Opa proteins of Neisseria gonorrhoeae bind to CD66 receptors on human phagocytes, thereby inducing efficient uptake of the bacteria in the absence of opsonins. The interaction of Opa proteins and CD66 receptors leads to activation of Src family tyrosine kinases, a process that is of critical importance for the efficient, CD66-mediated internalization. Here we show that during Opa-mediated stimulation of CD66 the activity of the host cell tyrosine phosphatase SHP-1 is strongly downregulated, concomitant with increases in the tyrosine phosphorylation of several cellular proteins. Since the SHP-1 tyrosine phosphorylation level itself is influenced by Opa-induced events, this phosphatase comprises an important regulatory checkpoint of the pathogen-triggered signaling cascade in human phagocytes.
Genetically encoded short peptide tag for versatile protein labeling by Sfp phosphopantetheinyl transferase (2005)

An 11-residue peptide with the sequence DSLEFIASKLA was identified from a genomic library of Bacillus subtilis by phage display as an efficient substrate for Sfp phosphopantetheinyl transferase-catalyzed protein labeling by small molecule-CoA conjugates. We name this peptide the "ybbR tag," because part of its sequence is derived from the ybbR ORF in the B. subtilis genome. The site of Sfp-catalyzed ybbR tag labeling was mapped to the underlined Ser residue, and the ybbR tag was found to have a strong tendency for adopting an alpha-helical conformation in solution. Here we demonstrate that the ybbR tag can be fused to the N or C termini of target proteins or inserted in a flexible loop in the middle of a target protein for site-specific protein labeling by Sfp. The short size of the ybbR tag and its compatibility with various target proteins, the broad substrate specificity of Sfp for labeling the ybbR tag with small-molecule probes of diverse structures, and the high specificity and efficiency of the labeling reaction make Sfp-catalyzed ybbR tag labeling an attractive tool for expanding protein structural and functional diversities by posttranslational modification.