gebhart/patrepeval huggingface dataset:
Stability for Function Trade-Offs in the Enolase Superfamily “Catalytic Module”<sup>,</sup> (2007)

Enzyme catalysis reflects a dynamic interplay between charged and polar active site residues that facilitate function, stabilize transition states, and maintain overall protein stability. Previous studies show that substituting neutral for charged residues in the active site often significantly stabilizes a protein, suggesting a stability trade-off for functionality. In the enolase superfamily, a set of conserved active site residues (the “catalytic module”) has repeatedly been used in nature in the evolution of many different enzymes for the performance of unique overall reactions involving a chemically diverse set of substrates. This catalytic module provides a robust solution for catalysis that delivers the common underlying partial reaction that supports all of the different overall chemical reactions of the superfamily. As this module has been so broadly conserved in the evolution of new functions, we sought to investigate the extent to which it follows the stability−function trade-off. Alanine substitutions were made for individual residues, groups of residues, and the entire catalytic module of o-succinylbenzoate synthase (OSBS), a member of the enolase superfamily from Escherichia coli. Of six individual residue substitutions, four (K131A, D161A, E190A, and D213A) substantially increased protein stability (by 0.46−4.23 kcal/mol), broadly consistent with prediction of a stability−activity trade-off. The residue most conserved across the superfamily, E190, is by far the most destabilizing. When the individual substitutions were combined into groups (as they are structurally and functionally organized), nonadditive stability effects emerged, supporting previous observations that residues within the module interact as two functional groups within a larger catalytic system. Thus, whereas the multiple-mutant enzymes D161A/E190A/D213A and K131A/K133A/D161A/E190A/D213A/K235A (termed 3KDED) are stabilized relative to the wild-type enzyme (by 1.77 and 3.68 kcal/mol, respectively), the net stabilization achieved in both cases is much weaker than what would be predicted if their stability contributions were additive. Organization of the catalytic module into systems that mitigate the expected stability cost due to the presence of highly charged active site residues may help to explain its repeated use for the evolution of many different functions.
Would Diversity Really Increase the Robustness of the Routing Infrastructure Against Software Defects? (2018)

Today’s Internet routing infrastructure exhibits high homogeneity. This constitutes a serious threat to the resilience of the network, since a bug or security vulnerability in an implementation could make all routers running that implementation become simultaneously unusable. This situation could arise as a result of a defective software upgrade or a denial-of-service attack. Diversity has been proposed as a solution to increase resilience to software defects, but the benefits have not been clearly studied. In this paper, we use a graph theoretic approach to study the benefits of diversity for the robustness of a network, where robustness is the property of a network staying connected under a software failure. We address three fundamental questions: 1) How do we measure the robustness of a network under such failures? 2) How much diversity is needed to guarantee a certain degree of robust- ness? 3) Is there enough diversity already in the network or do we need to introduce more? We find that a small degree of diversity can provide good robustness. In particular, for a Tier-1 ISP network, five implementations suffice: two for the backbone routers and three for the access routers. We learn that some networks may already have enough diversity, but the diversity is not adequately used for robustness. We observe that the best way to apply diversity is to partition the network into contiguous regions using the same implementation, separating backbone and access routers and taking into account if a router is replicated. We evaluate our approach on multiple real ISP topologies, including the topology of a Tier-1 ISP.
Platinum clusters with precise numbers of atoms for preparative-scale catalysis (2017)

Subnanometer noble metal clusters have enormous potential, mainly for catalytic applications. Because a difference of only one atom may cause significant changes in their reactivity, a preparation method with atomic-level precision is essential. Although such a precision with enough scalability has been achieved by gas-phase synthesis, large-scale preparation is still at the frontier, hampering practical applications. We now show the atom-precise and fully scalable synthesis of platinum clusters on a milligram scale from tiara-like platinum complexes with various ring numbers (n = 5-13). Low-temperature calcination of the complexes on a carbon support under hydrogen stream affords monodispersed platinum clusters, whose atomicity is equivalent to that of the precursor complex. One of the clusters (Pt<sub>10</sub>) exhibits high catalytic activity in the hydrogenation of styrene compared to that of the other clusters. This method opens an avenue for the application of these clusters to preparative-scale catalysis.The catalytic activity of a noble metal nanocluster is tied to its atomicity. Here, the authors report an atom-precise, fully scalable synthesis of platinum clusters from molecular ring precursors, and show that a variation of only one atom can dramatically change a cluster's reactivity.
An extended phase-locked loop for clock synchronization applications (2002)

Proposes a new tracking loop suited to track an unmodulated sine wave corrupted by an additive disturbance with inphase (I) and quadrature (Q) components correlated, Situations of this kind arise often in clock recovery circuits, where one of the sources of disturbance is the self-noise that must be described in terms of cyclostationary processes and leads to I and Q components with different power spectral densities and often correlated. The new loop explores this correlation by extracting the I component which is then used to perform some cancellation of the Q component, allowing an improvement relative to a conventional PLL. A small signal analysis of the new loop is presented and its performance derived. Numerical results of the tracking performance are presented for unipolar RZ signaling and bipolar data with elementary pulses time limited to two time slots, this latter case with an absolute value non-linearity to regenerate the discrete line at the clock rate. Both examples show that considerable improvements may be achieved relatively to the conventional PLL if the self noise is the main source of disturbance.
Semiconductor laser far-field shaping by means of an angle-selective facet coating (1991)

An optical short-wave pass filter, applied as a coating on a semiconductor laser facet, is observed to decrease the far-field width perpendicular to the active layer. The resulting far field has a higher coupling efficiency to circular optics. Combination of this coating with a highly reflective coating on the rear facet gives an improvement of the available external differential efficiency and maintains the threshold current of the uncoated laser. The experimental results obtained can be explained in the framework of a simple model.
Photoelectrical properties of molecular layer consisting of chlorophyll a∕ferredoxin heterostructure (2004)

Photoelectrical properties of biomolecular heterostructures are investigated. Ferredoxin and chlorophyll a were used as an electron acceptor and a sensitizer in the heterostructure by mimicking the photosynthesis. Self-assembly layer of ferredoxin was formed on Au-coated glass, and then chlorophyll a was deposited onto the ferredoxin layer by Langmuir–Blodgett method. The photoinduced current flow was observed by repeated step illumination of 488nm light irradiation. The rectifying property by the scanning-tunneling-spectroscopy-based current–voltage characteristic was achieved in the ferredoxin∕chlorophyll a heterostructure. The ferredoxin∕chlorophyll a heterostructure was functioned as the molecular diode and switching device with photocurrent generation and rectifying property. Proposed molecular diode can be usefully applied for the development of molecular-scale bioelectronic devices such as the diode, switch, and solar cell.
Optical Transmission of Polymer Pillars for Chip I/O Optical Interconnections (2004)

In the pursuit of high-density wafer-level input-output optical interconnections, microscopic polymer pillars have recently been fabricated. The optical performance of these pillars is critical for their potential application to gigascale integration. In the present work, the optical transmission of these pillars is analyzed and measured. It is shown that these polymer pillars act as precision many-moded waveguides, thus, verifying the cross-sectional uniformity, smoothness of surfaces, and optical quality of the material.
Expression Mechanisms Underlying NMDA Receptor‐Dependent Long‐Term Potentiation (1999)

Long-term potentiation (LTP) is currently the best available cellular model for learning and memory in the mammalian brain. In the CA1 region of the hippocampus, as well as in many other areas of the CNS, its induction requires a rise in postsynaptic Ca2+ via activation of NMDA receptors. What happens after the rise in postsynaptic Ca2+ is less clear. This paper summarizes experiments performed over the last decade in slice preparations that address the site of expression of LTP. While a large number of laboratories have contributed importantly to this issue, this review will rely primarily on experiments performed in the authors' laboratory. The experiments to be discussed can be broadly divided into two groups: those designed to determine if an increase in glutamate release occurs during LTP and those designed to determine if a change in postsynaptic sensitivity to glutamate occurs during LTP. Experiments in the first category include the analysis of dual-component excitatory postsynaptic currents (EPSCs), paired-pulse facilitation, saturating release probability, the use of MK-801 to measure release probability, and glial glutamate transporter currents to measure directly the synaptic release of glutamate. Experiments in the second category include analysis of miniature EPSC amplitudes, measurements of synaptic potency, the consequences of loading cells with the constitutively activated form of CaM kinase II, and the evidence that during LTP postsynaptically silent synapses become functional. We will argue that, while numerous experiments fail to support a presynaptic expression mechanism, many experiments do point to a postsynaptic expression mechanism. The decrease in synaptic failures during LTP, the only generally accepted experimental result that supports a presynaptic expression mechanism, can be explained by postsynaptically silent synapses. Future directions for research in this field include activity-dependent targeting of glutamate receptors and the functional consequences of phosphorylation of AMPA receptors.
A Method of Measuring Relaxation of Stress for Aluminum Alloys (1970)

A method of measuring stress relaxation by the use of stressing frames, wherein a constant strain is maintained on the specimen, is discussed. The elastic strain introduced into the specimen during loading, at the start of the exposure, and the elastic strain relieved during unloading, at the end of the exposure, are measured. The difference in elastic strains can be used to determine the amount of stress relaxation that has taken place. The method seems to produce reliable measurements and has the advantages that it requires no very costly equipment, and the tests require little or no attention during the exposure periods. Although each test yields only one stress-time data point, many tests can be run simultaneously.
[Correlation of skinfold thickness with bone density and estradiol, FSH and prolactin level in a sample of 231 women]. (1995)

Skin thickness was measured by means of ultrasound and correlated with the results of bone densitometry and hormonal parameters. Skin thickness and bone density were significantly correlated (p < 0.0001). These results indicated that not only bone, but also skin is a hormone-dependent organ, which responds to the menopausal decrease in sexual steroids. Hence, skin ultrasound, just like bone densitometry, can be useful implemented in the differential diagnostic procedure, as well as the therapy of the menopausal syndrome. Additionally, the estrogen-dependent postmenopausal decrease in collagen tissue can be assessed by ultrasound and a successful therapeutic outcome achieved by optimizing the dosage of estrogen substitution.
Tracking the changes of hippocampal population nonlinear dynamics in rats learning a memory-dependent task (2011)

Neurobiological processes associated with learning are known to be highly nonlinear, dynamical, and time-varying. Characterizing the time-varying functional input-output properties of neural systems is a critical step to understand the neurobiological basis of learning. In this paper, we present a study on tracking of the changes of neural dynamics in rat hippocampus during learning of a memory-dependent delayed nonmatch-to-sample (DNMS) task. The rats were first trained to perform the DNMS task without a delay between the sample and response events. After reaching a performance level, they were subjected to the DNMS task with variable delays with a 5s mean duration. Spike trains were recorded from hippocampal CA3 (input) and CA1 (output) regions during all training sessions and constitute the input-output data for modeling. We applied the time-varying Generalized Laguerre-Volterra Model to study the changes of the CA3-CA1 nonlinear dynamics using these data. Result showed significant changes in the Volterra kernels after the introduction of delays. This result suggests that the CA3-CA1 nonlinear dynamics established in the initial training sessions underwent a functional reorganization as animals were learning to perform the task that now requires delays.
Sublingual vs. vaginal misoprostol for induction of labor (2006)

The administration of misoprostol 25 mug by the sublingual route was neither more effective nor safer than the same dose administered vaginally.
Current Oral Rabies Vaccination in Europe: An Interim Balance (1988)

The field trial for the oral immunization of foxes against rabies in the Federal Republic of Germany began in 1983 and since the end of 1985 has had the specific goal of the elimination of rabies in large interdependent areas of that country. To meet this goal it was necessary to develop methods for the large-scale production of the SAD (Street Alabama Dufferin) clone B19 vaccine as well as to develop a bait that could be mass-produced (the Tübingen fox bait). It has been shown that after a single vaccination campaign in the field approximately 75% of the fox population is immune to rabies and that after one or two repeated campaigns vaccination in many areas could be discontinued. Participation in the field trial in circumscribed border areas was extended to Italy in 1985 and to Austria, Luxembourg, Belgium, and France in 1986. For the first time, through the use of oral immunization, a method for the elimination of rabies is available that is effective, safe, inexpensive, and practical. Further, this method meets the requirements of animal-protection societies, does not interfere with the preservation of endangered species, and therefore represents a significant political factor.
The Ecological and Behavioral Research of Andrias davidianus and its protection (2011)

This paper deals with some aspects of ecological and behavioral study of Andrias davidianus based on observations of its natural habits and pattern of activities.
Relaxation effects in graphite intercalation compounds (1986)

The ac susceptibility bridge technique is applied to the measurement of a long spin-lattice relaxation time associated with the magnetic anomaly which has been reported for ${\mathrm{FeCl}}_{3}$ graphite intercalation compounds at 1.75 K. Investigations of this relaxation mechanism show that the specific heat of the spin system at low temperatures contributes to an anomaly in the relaxation time near the temperature of the magnetic anomaly. Our results indicate that the graphite layers between the magnetic intercalant layers act as nonmagnetic spacing layers allowing the c-axis spin-spin coupling to be varied.
Damage Behavior of Yarn Embedded in Concrete Using Acoustic Emission Analysis (2011)

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Gas-Phase Dehydrogenation of Saturated and Aromatic Cyclic Hydrocarbons by Pt<i><sub>n</sub></i><sup>+</sup> (<i>n </i>= 1−4) (1997)

Small platinum clusters are readily generated by electron ionization of Pt4(PF3)8 in an FT-ICR mass spectrometer. Ptn+ (n = 1−4), cluster ions of a given n value may then be isolated and reacted with a variety of gaseous saturated and aromatic cyclic hydrocarbons. The present experiments thus illuminate catalytic dehydrogenation behavior intermediate between that of single-atom and bulk platinum. Extensive chemisorption (dehydrogenation of the hydrocarbon) and physisorption (nondissociative adsorption of intact neutral reagent molecule on the cluster) occur, depending on the particular reagent species. For example, each of the clusters exhibits chemisorption with at least one ligand for every neutral reactant species except for hexafluorobenzene. In general, the extent of chemisorption increases with cluster size. Also, some of the reactions do not proceed by a previously proposed C−H bond insertion mechanism. The detailed reaction pathways and product relative yields depend on the metal cluster ion, the reagent neutral species, and the stability of the final product.
OVERVIEW OF ANIMAL DETECTION AND ANIMAL WARNING SYSTEMS IN NORTH AMERICA AND EUROPE (2003)

The purpose of animal detection and animal warning systems is to prevent or reduce the number of animal-vehicle collisions. These systems are specifi cally aimed at large animals (e.g., ungulates) that can cause human death, injury and property damage. Animal detection systems detect large animals before they enter the road and then warn drivers that a large animal is on or near the road at that time. Animal warning systems detect vehicles and then warn the animals through a variety of audio and visual signals. This paper lists all animal detection and animal warning systems known to the authors in September 2003. We identifi ed 27 locations where systems are or have been in place in North America and Europe. In addition, we identifi ed 20 sites for which an animal detection or animal warning systems are planned. We described the main characteristics of the systems and reviewed them with respect to operation and maintenance. We conclude that animal detection and animal warning systems have the potential to be an effective mitigation tool. However, further research and development is needed before they can be applied on a wide scale.
Transient electrowetting on dielectric for activating droplets in bioprinting applications (2016)

Bio-printing is now facing a big challenge of cell viability with using extrusion based printing or jetting based printing principles. One of the causes is due to the high shear stress and pressure gradient of cell included flows. Digital microfluidics which was activated by electrowetting on dielectrics (EWOD) principles involved potential advantages such as low shear stress induced and high speed activation promisingly overcomes this challenge. Although much efforts has been devoted to understand the phenomenon physically as well as to apply it to activating droplets, there is no complete study about the transient state of EWOD from which it can be used for supporting EWOD based droplet activated system design. This paper will systematically introduce several physical aspects of transient EWOD including dependence of response speed on viscosity and drop’s volume. The results showed that the response speed of droplets strongly depends on drop’s viscosity and size. It also revealed the existence of a critical point of liquid viscosity where the behavior of droplet changes from underdamped to overdamped regimes.
The Relationship of Host Range, Physiology, and Genotype to Virulence on Cantaloupe in <i>Pseudomonas syringae</i> from Cantaloupe Blight Epidemics in France (2000)

ABSTRACT In 1993, a bacterial blight caused important losses of cantaloupe (Cucumis melo var. cantalupensis) in southwestern France and has now been reported in all cantaloupe-growing regions of France. The causal agent of this blight is Pseudomonas syringae, although on a worldwide basis this bacterium has not been a major pathogen of melon for over 50 years. To identify the pathovar of the cantaloupe pathogen, we employed biochemical tests, plasmid and chromosomal profiling, and host range studies for 23 strains from cantaloupe and 47 reference strains of 14 pathovars of P. syringae. Numerical analysis of 119 traits, serological typing, syringomycin production, and BOX-polymerase chain reaction profiles did not allow us to differentiate among pathovars related to P. syringae pv. syringae. Host range studies of cantaloupe and references strains on 18 plant species showed that virulence to sugar beet was a common feature of strains virulent on cantaloupe, but was not common to strains avirulent on cantaloupe. Virulence to other species of plants varied among strains, but the overall extent of the host range was proportional to aggressiveness to cantaloupe. We propose that the strains attacking cantaloupe in France be considered P. syringae pv. aptata and that adequate host range testing may reveal that this pathovar is the cause of cantaloupe blight reported in other parts of the world.
Modulation of colonization by black-pigmented Bacteroides species in squirrel monkeys by immunization with Bacteroides gingivalis (1989)

Periodontal diseases are inflammatory responses thought to be triggered by specific microorganisms colonizing in the gingival crevice. Theoretically, periodontal diseases could be prevented if the etiologic organisms were not allowed to colonize the subgingival area. The humoral immune response is one mechanism which may modulate bacterial colonization in the gingival crevice. To test the effect of systemic humoral immunity on subgingival colonization by bacteria, squirrel monkeys (Saimiri sciureus) were immunized with Bacteroides gingivalis, a black-pigmented Bacteroides sp. and putative periodontal pathogen. Immunized and sham-immunized monkeys were orally inoculated with 10(10) viable B. gingivalis during ligation of five teeth in one quadrant with bacterium-soaked suture material and distribution over the entire dentogingival margin. Immunization resulted in an increased level of immunoglobulin G anti-B. gingivalis in serum and was associated with a strong trend toward a statistically significant reduction in colonization of the gingival crevice by black-pigmented bacteroides.
Synthesis of 5-substituted imidazo[4,5-b]pyridinones by annelation of 4-amino-5-ethoxalyl-1H-imidazole derivatives with active methylene compounds (1999)

A new synthetic route to imidazo[4,5-b]pyridinones with a range of substituents at the 6-position has been developed. These compounds can be prepared in four steps from readily available 5-chloro-4-nitroimidazoles. The key step involves construction of the pyridine ring by annelation of 4-amino-5-ethoxalylimidazoles with active methylene compounds under dehydrating conditions or by acylation with substituted acetyl chlorides followed by spontaneous cyclisation. An exception is the reaction in which cyclisation of a phenylacetyl derivative occurs to give a seven-membered ring, forming an imidazo[4,5-b]azepinedione.