gebhart/patrepeval huggingface dataset:
Hydrogen bonds and salt bridges across protein-protein interfaces (1997)

To understand further, and to utilize, the interactions across protein-protein interfaces, we carried out an analysis of the hydrogen bonds and of the salt bridges in a collection of 319 non-redundant protein-protein interfaces derived from high-quality X-ray structures. We found that the geometry of the hydrogen bonds across protein interfaces is generally less optimal and has a wider distribution than typically observed within the chains. This difference originates from the more hydrophilic side chains buried in the binding interface than in the folded monomer interior. Protein folding differs from protein binding. Whereas in folding practically all degrees of freedom are available to the chain to attain its optimal configuration, this is not the case for rigid binding, where the protein molecules are already folded, with only six degrees of translational and rotational freedom available to the chains to achieve their most favorable bound configuration. These constraints enforce many polar/charged residues buried in the interface to form weak hydrogen bonds with protein atoms, rather than strongly hydrogen bonding to the solvent. Since interfacial hydrogen bonds are weaker than the intra-chain ones to compete with the binding of water, more water molecules are involved in bridging hydrogen bond networks across the protein interface than in the protein interior. Interfacial water molecules both mediate non-complementary donor-donor or acceptor-acceptor pairs, and connect non-optimally oriented donor-acceptor pairs. These differences between the interfacial hydrogen bonding patterns and the intra-chain ones further substantiate the notion that protein complexes formed by rigid binding may be far away from the global minimum conformations. Moreover, we summarize the pattern of charge complementarity and of the conservation of hydrogen bond network across binding interfaces. We further illustrate the utility of this study in understanding the specificity of protein-protein associations, and hence in docking prediction and molecular (inhibitor) design.
Root nodulation of Sesbania rostrata (1994)

The tropical legume Sesbania rostrata can be nodulated by Azorhizobium caulinodans on both its stem and its root system. Here we investigate in detail the process of root nodulation and show that nodules develop exclusively at the base of secondary roots. Intercellular infection leads to the formation of infection pockets, which then give rise to infection threads. Concomitantly with infection, cortical cells of the secondary roots dedifferentiate, forming a meristem which has an "open-basket" configuration and which surrounds the initial infection site. Bacteria are released from the tips of infection threads into plant cells via "infection droplets," each containing several bacteria. Initially, nodule differentiation is comparable to that of indeterminate nodules, with the youngest meristematic cells being located at the periphery and the nitrogen-fixing cells being located at the nodule center. Because of the peculiar form of the meristem, Sesbania root nodules develop uniformly around a central axis. Nitrogen fixation is detected as early as 3 days following inoculation, while the nodule meristem is still active. Two weeks after inoculation, meristematic activity ceases, and nodules then show the typical histology of determinate nodules. Thus, root nodule organogenesis in S. rostrata appears to be intermediate between indeterminate and determinate types.
Novel method using white spectral probe signals to measure Brillouin gain spectra of pure silica core fibres (1992)

The beat spectrum of white spectral probe signals and a pump laser are used to directly give the Brillouin gain spectrum on an RF spectrum analyser. The measured peak gain coefficient is about 2.3 × 10−11m/W and the Brillouin linewidth is 29 MHz which can be further broadened by the additional strain distribution.
Flow Cytometric Analysis of Feline Reticulocytes (1992)

Hemolytic anemia was induced in five Domestic Shorthair cats (four adult males and one spayed female obtained from a breeding colony at Colorado State University, CO), and blood samples were analyzed from five other cats (two castrated male Domestic Shorthairs, one castrated male Domestic Longhair, one castrated male Persian, and one spayed female Siamese presented to the Veterinary Teaching Hospital at Colorado State University for miscellaneous problems). Blood samples taken from these cats had percentages of aggregate reticulocytes that ranged from 0% to 14.5% as determined by manual counting and were used to identify the best technique for staining cat reticulocytes for flow cytometric analysis. The best technique was mixing a blood sample (1/2,000 dilution) with 0.2 micrograms thiazole orange in 1 ml of diluent and incubating the mixture in the dark at room temperature for 30 to 60 minutes. The percentage of reticulocytes determined by flow cytometry correlated well (r = 0.88) with manually determined aggregate reticulocyte percentages; no significant differences were observed between the two techniques (P > 0.05). For the conditions used, punctate reticulocytes were not detected by flow cytometry. Samples with very high platelet numbers and very low packed cell volumes may show falsely elevated percentages of reticulocytes as determined by flow cytometry. The reproducibility of the flow cytometric technique was good; the coefficient of variation ranged from 4.8% to 17.9% in two samples with two different times of incubation. Staining of cat aggregate reticulocytes with thiazole orange and use of flow cytometric quantification is a reproducible technique that has a good correlation with the manual reticulocyte counting method.
Induction of Mixed Chimerism With MHC-Mismatched but Not Matched Bone Marrow Transplants Results in Thymic Deletion of Host-Type Autoreactive T-Cells in NOD Mice (2011)

Induction of mixed chimerism with MHC-mismatched, but not matched, donor BM transplants re-establishes thymic deletion of host-type autoreactive T-cells and prevents T1D, with donor antigen-presenting cell expression of mismatched MHC II molecules being required.
3D reality modelling: photo-realistic 3D models of real world scenes (2003)

This paper presents a 3D reality modelling system, applying lasers and digital photography to create super-accurate photo-realistic three-dimensional worlds. A key feature of the 3D reality system is its flexibility. It can be used with all common long-range scanners and digital or video cameras, without the need of any pre-calibration or static arrangement between the different sensors. The system can be used for a wide range of applications in industry and science, as well as for environmental modelling and virtual reality presentations. The 3D models are sufficiently lifelike to be used in sectors such as real estate, cultural heritage and construction. Results can be exported to all major 3D software and CAD packages or viewed via a Web browser.
Clonning of DNA fragments containing Streptomyces promoter activity. (1987)

The thiostrepton-resistance gene is expressed in Streptomyces jumonjinensis [16]-8 SANK 61185 carrying the plasmid pIJ702 but not the tyrosinase gene. We have isolated DNA fragments from various streptomycetes that restore expression of the tyrosinase gene on pIJ702 in this organism. The nucleotide sequences of two of these DNA fragments show that they contain putative ribosome binding sites and- 10 regions of possible promoters.
An ASIP-based control system for Vision Chips with highly parallel signal processing (2015)

The field of Machine Vision is still dominated by classical imaging systems consisting of a camera attached to a PC. Especially very fast processes with high requirements on minimal latency or maximal refresh rate are increasingly starting to stretch such systems to their limits. Image sensors with integrated feature extraction - so-called “Vision Chips” - already allow reducing the amount of data on chip compared to conventional imagers, thereby narrowing down the output to relevant data. Freely programmable systems are not restricted to the execution of a specific hard-wired algorithm. However, not least because of the necessary, but rather complex external circuitry, none of the proposed systems have so far been able to gain acceptance. This paper introduces an architecture of an Application-Specific Instruction Set Processor (ASIP) based control system, which can be directly incorporated into a System-on-Chip (SoC). The sensor's functional units are integrated into the micro-controller as additional data path elements, making them directly accessible as part of the instruction set. Furthermore, a parameterizable input/output (IO) controller and an Serial Peripheral Interface (SPI) based configuration interface enable the system to be used widely self-sufficient with specific algorithms. The proposed control system has been integrated into a prototypical Vision Chip and has been successfully tested.
A Ti-coated nano-SiC supported platinum electrocatalyst for improved activity and durability in direct methanol fuel cells (2014)

Nano-silicon carbide (nano-SiC) particles modified with a titanium (Ti) coating were used as a novel support for the platinum (Pt) electrocatalyst in direct methanol fuel cells. Ti-coated nano-SiC (Ti/SiC) powder was prepared by a one-pot deposition method under vacuum and a coating was formed on the nano-SiC surface. The Ti coating was strongly bonded with nano-SiC with the help of TiC and Ti5Si3. The Ti/SiC supported Pt electrocatalyst (Pt–Ti/SiC) was fabricated using a microwave-assisted reduction method. The electrocatalytic performances of the Pt–Ti/SiC for the methanol oxidation and oxygen reduction reactions were much higher than the Pt supported on the pristine nano-SiC. The electrochemical stability of the Pt–Ti/SiC was more outstanding compared with the Pt supported on Vulcan XC-72 carbon black. The superior electrocatalytic performance of the Pt–Ti/SiC can be ascribed to the anchoring effect of the Ti coating on Pt nanoparticles and the high stability of the nano-SiC support.
Drug Therapy of Depression (1967)

RESEARCH into the nature of depression and its treatment by drugs is hobbled by the fact that depressions do not constitute a single homogeneous entity. The term "depression" is employed to refer to a symptom, a syndrome, or a diagnostic entity.<sup>1</sup>It has been unclear whether so-called antidepressant drugs are to be regarded as specifically effective for treatment of the symptom, syndrome, or diagnostic entity. Our research has led us to the conclusion that it is important to evaluate the potential usefulness of drug treatments in distinct syndromes of depression. In our series of studies, we began by comparing the therapeutic efficacy of antidepressant drugs among heterogeneous groups of patients whose presenting symptom was predominantly depression of mood. Although it was possible to demonstrate a significant average difference in therapeutic response between a tricyclic antidepressant, imipramine, and placebo, the difference was not striking.<sup>2</sup>A subsequent study, which
LYR71, a derivative of trimeric resveratrol, inhibits tumorigenesis by blocking STAT3-mediated matrix metalloproteinase 9 expression (2008)

Tumor migration/invasion is the main cause of tumor progression and STAT3 is needed to enhance tumor migration/invasion by up-regulating MMP-9. Thus, agents that inhibit STAT3 activation may be used as an anticancer drug. We present herein that 6-methyl-2-propylimino-6, 7-dihydro-5H-benzo [1, 3]-oxathiol-4-one (LYR71) , a derivative of trimeric resveratrol, has an anticancer activity through inhibition of STAT3 activation. We found that LYR71 suppressed STAT3 activation and inhibited the expression and activity of MMP-9 in RANTES-stimulated breast cancer cells. In addition, LYR71 reduced RANTES-induced MMP-9 transcripts by blocking STAT3 recruitment, dissociating p300 and deacetylating histone H3 and H4 on the MMP-9 promoter. Furthermore, LYR71 inhibited tumor migration/invasion in RANTES-treated breast cancer cells and consequently blocked tumor progression in tumor-bearing mice. Taken together, the results of this study suggest that LYR71 can be therapeutically useful due to the inhibition effect of STAT3-mediated MMP-9 expression in breast cancer cells.
A method to extend the low frequency operation of load commutated inverters (2002)

A novel method for extending the range of thyristor-based load-commutated inverters (LCIs) is proposed. Using conventional single- and three phase LCI topologies, voltage and current waveforms are generated containing a dominant higher-frequency (leading power factor) switching component. A lower-frequency load component is concurrently produced, enabling an LCI to supply lagging power factor and even DC loads. A state-space model is used to apply methods of optimal control in order to improve three-phase LCI operation. Both simulation and experimental results are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Echo Separation in Multidimensional Waveform Encoding SAR Remote Sensing Using an Advanced Null-Steering Beamformer (2012)

In order to reap the potential benefits that waveform diversity can provide for spaceborne synthetic aperture radar remote sensing, echoes from different subpulses constituting a complete transmit waveform should be effectively separated at first. This paper presents a new separation approach implemented by an advanced null-steering beamformer on satellite. Compared with common null-steering beamforming, our approach will take into account the characteristics of echo signal from the scene and accordingly embed the finite-impulse response (FIR) filtering process into the modified null-steering beamformer to deal with the issue of pulse extension. In this paper, echo signals generated by multidimensional encoded waveform will be analyzed in detail; based on this analysis, FIR filter and the new null-steering beamformer are derived. Simulation results show that much better separation performance can be obtained by our approach than by conventional null-steering beamforming.
Antimicrobial Peptides Past, Present and Future (2016)

Uncontrolled antibiotic use lead to increasing the level of resistant bacterial species. Antimicrobial peptides (AMPs) are one of the few alternatives in the fight with everyday growing bacterial resistance to commonly used antibiotics. AMPs general application could be also as endotoxin neutralizing agents or as an adjuvants to regular antimicrobial therapy. In this review we were focused on the most recent data that concern the diverse use of AMPs, their activities and modes of actions.
Experimental demonstration of a wafer-level flexible probe for optical waveguide testing (2007)

A flexible optical probe that accomplishes wafer-level directional coupling of light into optical waveguides is investigated theoretically and experimentally. Simulated results indicate high coupling efficiencies in excess of 80% for a range of parameters. Probe fabrication was implemented using SU8 as flexible waveguide material. Coupling of light from flexible probe to an S-shaped test waveguide demonstrated 11% efficiency compared to direct butt coupling. These results may lead to increased yield, shorter development cycles and overall savings in PLC packaging costs.
Subsets of the Zinc Finger Motifs in dsRBP-ZFa Can Bind Double-Stranded RNA (1999)

dsRBP-ZFa is a Xenopus zinc finger protein that binds dsRNA and RNA-DNA hybrids with high affinity and in a sequence-independent manner. The protein consists of a basic N-terminal region with seven C2H2 zinc finger motifs and an acidic C-terminal region that is not required for binding. The last four zinc finger motifs, and the linkers that join them, are nearly identical repeats, while the first three motifs and their linkers are each unique. To identify which regions of the protein are involved in nucleic acid binding, we examined the ability of five protein fragments to bind dsRNA and RNA-DNA hybrids. Our studies reveal that a fragment encompassing the three N-terminal, unique zinc finger motifs and another encompassing the last three of the nearly identical motifs have binding properties similar to the full-length protein. Since these two fragments do not share zinc finger motifs of the same sequence, dsRBP-ZFa must contain more than one type of zinc finger motif capable of binding dsRNA. As with the full-length protein, ssRNA and DNA do not significantly compete for dsRNA binding by the fragments.
Sensitive Detection of Human IgG in ELISA Using a Monoclonal Anti-IgG-Peroxidase Conjugate (2004)

Enzyme–antibody (Ab) conjugates specific for IgG are widely used in indirect immunological assays and have been until recently routinely prepared with polyclonal IgG-specific animal Abs. The use of monoclonal Abs (MAbs) could permit a better standardization of the IgG-specific conjugate reagents but is expected to result in lower reactivity due to the recognition of a single epitope by the MAbs. In this work, we have characterized a monoclonal anti-human IgG-peroxidase (HRP) reagent and compared its reactivity with commercial reagents. The murine C5-1 anti-human IgG MAb was selected for conjugation because of its high affinity (Ka = 1.9 × 10−10M), pan-IgG reactivity and absence of cross-reactivity with various structures including animal IgGs. The specific activity and binding kinetics of the C5-1:HRP conjugate were similar to the ones of two polyclonal anti-IgG:HRP conjugates when tested with immobilized human IgG. The C5-1:HRP conjugate could detect low amounts of human IgG much more effectively than two commercial monoclonal conjugates although it was slighty less effective than a polyclonal conjugate. However, the C5-1 conjugate yielded reduced background reactivity compared to the polyclonal conjugate, resulting in similar signal-to-noise ratios. These results indicate that the C5-1:HRP conjugate could be a suitable substitute for anti-human IgG conjugates prepared from animal antisera.
Pulsatile administration of gonadotrophin releasing hormone and oral administration of naltrexone in hypothalamic amenorrhoea (1993)

Between 1979 and 1990, 73 patients suffering from hypothalamic amenorrhoea were treated by pulsatile administration of gonadotrophin releasing hormone (GnRH) in 359 treatment cycles. Seventy-two pregnancies were achieved. In 64 favourable patients in whom hypothalamic amenorrhoea constituted the only reason for infertility, a pregnancy rate of 29% per cycle could be obtained. Patients who conceived during pulsatile GnRH required an average of only 2.4 cycles per conception. Twelve out of 24 patients with hypothalamic amenorrhoea who exhibited an ovulatory response to pulsatile GnRH, ovulated during oral administration of naltrexone; such responsiveness to opioid antagonism was, however, restricted to the less serious grades. In conclusion, pulsatile administration of GnRH continues to be a highly effective mode of treatment of infertility due to hypothalamic amenorrhoea of various aetiologies. A subgroup of these patients may be successfully treated by the oral administration of naltrexone.
A Hierarchical Partitioning Strategy for an Efficient Parallelization of the Multilevel Fast Multipole Algorithm (2009)

We present a novel hierarchical partitioning strategy for the efficient parallelization of the multilevel fast multipole algorithm (MLFMA) on distributed-memory architectures to solve large-scale problems in electromagnetics. Unlike previous parallelization techniques, the tree structure of MLFMA is distributed among processors by partitioning both clusters and samples of fields at each level. Due to the improved load-balancing, the hierarchical strategy offers a higher parallelization efficiency than previous approaches, especially when the number of processors is large. We demonstrate the improved efficiency on scattering problems discretized with millions of unknowns. In addition, we present the effectiveness of our algorithm by solving very large scattering problems involving a conducting sphere of radius 210 wavelengths and a complicated real-life target with a maximum dimension of 880 wavelengths. Both of the objects are discretized with more than 200 million unknowns.
Maximum likelihood event estimation and list-mode image reconstruction on GPU hardware (2009)

The scintillation detectors commonly used in SPECT and PET imaging and in Compton cameras require estimation of the position and energy of each gamma ray interaction. Ideally, this process would yield images with no spatial distortion and the best possible spatial resolution. In addition, especially for Compton cameras, the computation must yield the best possible estimate of the energy of each interacting gamma ray. These goals can be achieved by use of maximum-likelihood (ML) estimation of the event parameters, but in the past the search for an ML estimate has not been computationally feasible. Now, however, graphics processing units (GPUs) make it possible to produce optimal, real-time estimates of position and energy, even from scintillation cameras with a large number of photodetectors. In addition, the mathematical properties of ML estimates make them very attractive for use as list entries in list-mode ML image reconstruction. This two-step ML process-using ML estimation once to get the list data and again to reconstruct the object-allows accurate modeling of the detector blur and, potentially, considerable improvement in reconstructed spatial resolution.
DPP-4 Inhibition by Sitagliptin Improves the Myocardial Response to Dobutamine Stress and Mitigates Stunning in a Pilot Study of Patients With Coronary Artery Disease (2010)

The augmentation of GLP-1 (7-36) by inhibition of DPP-4 improves global and regional LV performance in response to stress and mitigates postischemic stunning in humans with coronary artery disease. Clinical Trial Registration- URL: http://www.isrctn.org. Unique identifier: ISRCTN78649100.
Fabulous (1990)

Through words and pictures on a computer screen, FABULOUS acquaints students with how to prepare a food item and to build a menu before they ever get into the kitchen
Two different monoclonal antibodies to alpha‐tubulin inhibit the bending of reactivated sea urchin spermatozoa (1982)

Two monoclonal antibodies reactive for alpha-tubulin but not for beta-tubulin have been prepared, characterized in terms of their relative binding to tubulins from different sources by a solid-phase binding assay, immunoautoradiography, and indirect immunofluorescence, and utilized to study flagellar motility. Our results demonstrate that alpha-tubulins from different species, and even from different tissues of the same species, are nonidentical. Especially interesting was the observation that one of the antibodies, Ab2, immunofluorescently stained microtubules of chick embryo fibroblast cells, but was completely unreactive for microtubules of rat kangaroo (PtK2) fibroblasts; a different antibody, Ab1, stained both cell types. Results of these and additional experiments clearly show that Ab1 and Ab2 recognize discrete and different epitopes on alpha-tubulin. Monoclonal antitubulins Ab1 and Ab2 each inhibited the bend amplitude of reactivated sea urchin spermatozoa without affecting beat frequencies or the ability of the outer doublet microtubules to slide past each other in elastase-digested models. These results, together with those obtained previously using rabbit polyclonal antitubulin antibodies [Asai and Brokaw, 1980], demonstrate that inhibition of bend amplitude is a common property of antitubulin antibodies and is not due to the binding of antibodies to one specific site on the axoneme. Our results suggest that tubulin subunit conformational changes may occur on the outer doublet lattice and may be integrally involved in the mechanism and control of flagellar bending.