gebhart/patrepeval huggingface dataset:
Deterministic Implementations for Reproducibility in Deep Reinforcement Learning (2018)

While deep reinforcement learning (DRL) has led to numerous successes in recent years, reproducing these successes can be extremely challenging. One reproducibility challenge particularly relevant to DRL is nondeterminism in the training process, which can substantially affect the results. Motivated by this challenge, we study the positive impacts of deterministic implementations in eliminating nondeterminism in training. To do so, we consider the particular case of the deep Q-learning algorithm, for which we produce a deterministic implementation by identifying and controlling all sources of nondeterminism in the training process. One by one, we then allow individual sources of nondeterminism to affect our otherwise deterministic implementation, and measure the impact of each source on the variance in performance. We find that individual sources of nondeterminism can substantially impact the performance of agent, illustrating the benefits of deterministic implementations. In addition, we also discuss the important role of deterministic implementations in achieving exact replicability of results.
A Novel Mobile Multicast Protocol in IPv6 Networks (2009)

Based on dynamic multicast agent, a novel mobile multicast protocol, named TD-DMAMoM (time and distance-aided dynamic multicast agent-based mobile multicast protocol) is presented. In TD-DMAMoM, a fast multicast handover mechanism is used to decrease the multicast interruption time when the mobile node (MN) moves from one foreign network to another. Meanwhile, the proposed protocol tries to provide fast data delivery and low multicast tree reconstruction overhead for high-speed receivers and optimal delivery path for low-speed receivers. During a multicast session in TD-DMANMoM, if a MN enters a new foreign network, the dynamic selection and updating of multicast agent is determined based on the two newly-defined metrics (i.e., time metric t and distance metric d) by the multicast subnet agent. Only when the metrics of both time t and distance d are "True", then the updating of multicast agent will be launched. Simulation results show that TD-DMAMoM has better performance than the other dynamic multicast agent-based protocols, especially in the case where the number of MNs is large.
Three-dimensional Structure of Human γ-Glutamyl Hydrolase (2002)

gamma-Glutamyl hydrolase catalyzes the cleavage of the gamma-glutamyl chain of folylpoly-gamma-glutamyl substrates and is a central enzyme in folyl and antifolyl poly-gamma-glutamate metabolism. The crystal structure of human gamma-glutamyl hydrolase, determined at 1.6-A resolution, reveals that the protein is a homodimer. The overall structure of human gamma-glutamyl hydrolase contains 11 alpha-helices and 14 beta-strands, with a fold in which a central eight-stranded beta-sheet is sandwiched by three and five alpha-helices on each side. The topology is very similar to that of the class I glutamine amidotransferase domains, with the only major differences consisting of extensions in four loops and at the C terminus. These insertions are important for defining the substrate binding cleft and/or the dimer interface. Two sequence motifs are found in common between human gamma-glutamyl hydrolase and the class I glutamine amidotransferase family and include the catalytically essential residues, Cys-110 and His-220. These residues are located in the center of a large l-shaped cleft that is closed at one end and open at the other. Several conserved residues, including Glu-114, His-171, Gln-218, and Lys-223, may be important for substrate binding. Modeling of a methotrexate thioester intermediate, based on the corresponding complex of the glutamate thioester intermediate of Escherichia coli carbamoyl-phosphate synthetase, indicates that the substrate binds in an orientation with the pteroyl group toward the open end of the cleft.
Rho Signaling Regulates Pannexin 1-mediated ATP Release from Airway Epithelia (2011)

ATP released from airway epithelial cells promotes purinergic receptor-regulated mucociliary clearance activities necessary for innate lung defense. Cell swelling-induced membrane stretch/strain is a common stimulus that promotes airway epithelial ATP release, but the mechanisms transducing cell swelling into ATP release are incompletely understood. Using knockdown and knockout approaches, we tested the hypothesis that pannexin 1 mediates ATP release from hypotonically swollen airway epithelia and investigated mechanisms regulating this activity. Well differentiated primary cultures of human bronchial epithelial cells subjected to hypotonic challenge exhibited enhanced ATP release, which was paralleled by the uptake of the pannexin probe propidium iodide. Both responses were reduced by pannexin 1 inhibitors and by knocking down pannexin 1. Importantly, hypotonicity-evoked ATP release from freshly excised tracheas and dye uptake in primary tracheal epithelial cells were impaired in pannexin 1 knockout mice. Hypotonicity-promoted ATP release and dye uptake in primary well differentiated human bronchial epithelial cells was accompanied by RhoA activation and myosin light chain phosphorylation and was reduced by the RhoA dominant negative mutant RhoA(T19N) and Rho and myosin light chain kinase inhibitors. ATP release and Rho activation were reduced by highly selective inhibitors of transient receptor potential vanilloid 4 (TRPV4). Lastly, knocking down TRPV4 impaired hypotonicity-evoked airway epithelial ATP release. Our data suggest that TRPV4 and Rho transduce cell membrane stretch/strain into pannexin 1-mediated ATP release in airway epithelia.
Semiconductor laser-diode-pumped solid-state lasers: status and future (1988)

Semiconductor laser diode pumping of solid-state lasers is an idea whose time has come. Early experiments in the 1960s proved the scientific feasibility of diode pumping, but the cryogenically cooled, relatively low-efficiency diodes of the day precluded demonstration of the high-efficiency, power, compactness, and operating life that the concept promises. Since then, the room-temperature efficiency, power, diode packing density, and life of AlGaAs laser diodes have increased spectacularly,1 largely due to the introduction of MOCVD wafer scale processing of single- and multiple-quantum-well diode structures: single-100-μm-wide-stripe laser diodes can produce >3-W cw and >8-W quasi-cw (150-μs pulse); centimeter long linear (bar) diode arrays can produce >13-W cw and >130-W quasi-cw; 2-D arrays of stacked bars can produce >3.3-kW/cm2 quasi-cw; high-power diodes are now approaching2 wall plug efficiencies of 60%. The recent availability of such high-performance laser diodes and arrays has enabled significant progress toward the full realization of the original vision.
Cu(II)-Inhibitory Effect on Photosystem II from Higher Plants. A Picosecond Time-Resolved Fluorescence Study (1996)

The influence of Cu(II) inhibition on the primary reactions of photosystem II (PSII) electron transport was studied by picosecond time-resolved fluorescence on isolated PSII membranes. The fluorescence decay from Cu(II)-inhibited PSII centers showed a dominant amplitude of a fast phase (100-300 ps) similar to PSII centers in the uninhibited "open state" and minor contributions of components around 600 ps and 2.6 ns. These data indicate efficient primary charge separation in PSII membranes incubated with Cu(II). The quantum yield of primary reactions in the inhibited PSII centers was similar to that of "open" PSII centers. Kinetic analysis of the decay curves in the framework of the exciton/radical pair equilibrium model showed no significant changes in the rate constants associated with the charge separation/recombination equilibrium. However, in closed centers (QA reduced), a decrease in the rate constant K23, associated with the back-reaction of a relaxed radical pair, by a factor of 4 was calculated. The free energy losses upon primary charge separation (delta G1) and during subsequent radical pair relaxation (delta G2) were also determined in Cu(II)-inhibited centers and were compared with uninhibited centers. No changes in the delta G1 values and a significant decrease in the delta G2 values were found as compared with those of control PSII centers in the "closed" state. These data indicate that Cu(II) does not affect primary radical pair formation, but strongly affects the formation of a relaxed radical pair, by neutralizing the negative charge on QA- and eliminating the repulsive interaction between Pheo- and QA- and/or by modifying the general dielectric properties of the protein region, surrounding these cofactors. Moreover, a close attractive interaction between Pheo-, QA-, and Cu2+ can be proposed. Our results are in good agreement with very recent EPR results indicating an additional effect of Cu2+ on the acceptor side [Jegerschöld et al. (1995) Biochemistry 34, 12747-12758].
The Plausibility of Life (2017)

In the 150 years since Darwin, the field of evolutionary biology has left a glaring gap in understanding how animals developed their astounding variety and complexity. The standard answer has been that small genetic mutations accumulate over time to produce wondrous innovations such as eyes and wings. Drawing on cutting-edge research across the spectrum of modern biology, Marc Kirschner and John Gerhart demonstrate how this stock answer is woefully inadequate. Rather they offer an original solution to the longstanding puzzle of how small random genetic change can be converted into complex, useful innovations. In a new theory they call facilitated variation,” Kirschner and Gerhart elevate the individual organism from a passive target of natural selection to a central player in the 3-billion-year history of evolution. In clear, accessible language, the authors invite every reader to contemplate daring new ideas about evolution. By closing the major gap in Darwin’s theory Kirschner and Gerhart also provide a timely scientific rebuttal to modern critics of evolution who champion intelligent design.”
Improving Reinforcement Learning with Confidence-Based Demonstrations (2017)

Reinforcement learning has had many successes, but in practice it often requires significant amounts of data to learn high-performing policies. One common way to improve learning is to allow a trained (source) agent to assist a new (target) agent. The goals in this setting are to 1) improve the target agent's performance, relative to learning unaided, and 2) allow the target agent to outperform the source agent. Our approach leverages source agent demonstrations, removing any requirements on the source agent's learning algorithm or representation. The target agent then estimates the source agent's policy and improves upon it. The key contribution of this work is to show that leveraging the target agent's uncertainty in the source agent's policy can significantly improve learning in two complex simulated domains, Keepaway and Mario.
Feedback Control Engineering for Cooperative Community Development: Tools for Financial Management Advice for Low-Income Individuals (2018)

Individuals who manage their financial life to "make ends meet" have a complicated decision-making task. Their challenge is especially arduous if they live in an underprivileged community and have very low income (that is, they are part of the 10.7% of the world's population that survives on under $1.90 per day [1]). Most individuals in this situation are self-employed and face uncertain income levels (that is, they are day laborers and only hired periodically). They have inefficient or even nonexistent health services in their community and possibly poor available educational training. Furthermore, they may not have the financial services like insurance to help them cope with sudden and unpredictable events or "shocks" (the effects of adverse weather on crops).
Surface lysine and tyrosine residues are required for interaction of the major herpes simplex virus type 1 DNA-binding protein with single-stranded DNA (1992)

Modification of the herpes simplex virus type 1 major DNA-binding protein (ICP8) with reagents and conditions specific for arginine, lysine, and tyrosine residues indicates that surface lysine and tyrosine residues are required for the interaction of this protein with single-stranded DNA. Modification of either of these two amino acids resulted in a loss and/or modification of binding activity as judged by nitrocellulose filter assays and gel shift. Modification specific for arginine residues did not affect binding within the limits of the assays used. Finally, quenching of the intrinsic tryptophan fluorescence of ICP8 in the presence of single-stranded DNA either suggests involvement of this amino acid in the binding reaction or reflects a conformational change in the protein upon binding.
Carrier leakage in InGaN quantum well light-emitting diodes emitting at 480 nm (2003)

Pulsed light–current characteristics of InGaN/GaN quantum well light-emitting diodes have been measured as a function of temperature, with sublinear behavior observed over the whole temperature range, 130–330 K. A distinctive temperature dependence is also noted where the light output, at a fixed current, initially increases with temperature, before reaching a maximum at 250 K and then decreases with subsequent increases in temperature. On the basis of a drift diffusion model, we can explain the sublinear light–current characteristics and the temperature dependence by the influence of the large acceptor ionization energy in Mg-doped GaN together with a triangular density of states function characteristic of localized states. Without the incorporation of localization effects, we are unable to reproduce the temperature dependence whilst maintaining emission at the observed wavelength. This highlights the importance of localization effects on device performance.
Functionalized borazines as precursors for new silica gels (2003)

Trialkynylborazines have been prepared in excellent yields by reacting alkynyl-bis(diisopropylamino)borane with powdered ammonium chloride in toluene. These were subsequently used in hydrosilylations with trichlorosilane and trialkoxysilanes using platinum on charcoal as heterogeneous catalyst. This reaction is stereoselective and gives the β-isomers as major product. The tris(β-tricholorsilylvinyl)-substituted derivative (Cl3SiCHCH)3B3N3H3 was isolated in pure form and transformed into a highly functionalized silica gel by a sol–gel process. This gel has a specific surface of about 315 m2 g−1 and is the first containing intact borazine rings. The structures of (iPr2N)2B–CCH, B,B′,B″-(HCCH)3B3N3H3,B,B′,B″-(Me3SiCCH)3B3N3H3 and B,B′,B″-(Cl3Si–CHCH)3B3N3H3 were determined by X-ray structure analyses and are reported.
Transient Expression of Olig1 Initiates the Differentiation of Neural Stem Cells into Oligodendrocyte Progenitor Cells (2004)

In order to develop an efficient strategy to induce the in vitro differentiation of neural stem cells (NSCs) into oligodendrocyte progenitor cells (OPCs), NSCs were isolated from E14 mice and grown in medium containing epidermal growth factor and fibroblast growth factor (FGF). Besides supplementing the medium with oligodendrogenic factors such as Sonic Hedgehog (Shh), FGF-2, and PDGF, we attempted to initiate the gene transcription program for OPC differentiation by transfection of the Olig1 gene, a transcription factor known to be involved in the induction of oligodendrocyte lineage formation during embryogenesis. Whereas addition of Shh, FGF-2, and PDGF could induce OPC differentiation in 12% of the NSCs, the transient expression of Olig1 by use of Nucleofector gene transfection initiated OPC differentiation in 55% of the NSCs. Our results show that nonviral transfection of genes encoding for oligodendrogenic transcription factors may be an efficient way to initiate the in vitro differentiation of NSCs into OPCs.
Epidemiology, Clinical Manifestations, and Outcomes of<i>Streptococcus suis</i>Infection in Humans (2014)

Streptococcus suis, a bacterium that affects pigs, is a neglected pathogen that causes systemic disease in humans. We conducted a systematic review and meta-analysis to summarize global estimates of the epidemiology, clinical characteristics, and outcomes of this zoonosis. We searched main literature databases for all studies through December 2012 using the search term "streptococcus suis." The prevalence of S. suis infection is highest in Asia; the primary risk factors are occupational exposure and eating of contaminated food. The pooled proportions of case-patients with pig-related occupations and history of eating high-risk food were 38.1% and 37.3%, respectively. The main clinical syndrome was meningitis (pooled rate 68.0%), followed by sepsis, arthritis, endocarditis, and endophthalmitis. The pooled case-fatality rate was 12.8%. Sequelae included hearing loss (39.1%) and vestibular dysfunction (22.7%). Our analysis identified gaps in the literature, particularly in assessing risk factors and sequelae of this infection.
Fabry–Pérot Resonator Antenna With High Aperture Efficiency Using a Double-Layer Nonuniform Superstrate (2018)

Due to the nonuniform electromagnetic (EM) field amplitude distribution over its aperture, the Fabry-Pérot resonator antenna (FPRA) suffers from relatively low aperture efficiency. In this communication, an FPRA with high aperture efficiency is proposed based on a double-layer nonuniform superstrate (DNS). The DNS is designed to have a constant reflection phase but a varying reflection magnitude, thereby obtaining a uniform EM field amplitude distribution over the FPRA's aperture and, hence improving the directivity and the corresponding aperture efficiency. As an example, a cylindrical FPRA with an aperture diameter of 3.5 λ (where λ is the wavelength in free space) is presented. In comparison with a uniform superstrate, the proposed DNS enhances the FPRA's directivity from 19.6 to 20.4 dBi and correspondingly improves the aperture efficiency from 76.3% to 91.7%.
A Trust Evaluation to Help On-line Consumer to Choose the Provider in Auction Web Site (2007)

Auction on the Websites, such as eBay, is common activity for most people; but the anonymity on the web is vulnerable to malicious participants who exploit possible cheating techniques. The paper, based on the notion of transitive trust; leads to a system where reputation values correspond to the left principal eigenvector of a matrix of normalized local trust value. In addition, the paper also proposes several new and suitable metrics for the auction in the viewpoints of social network.
Study of Biodegradable Polylactide/Poly(butylene adipate-<i>co</i>-terephthalate) Blends (2005)

Both polylactide (PLA) and poly(butylene adipate-co-terephthalate) (PBAT) are biodegradable polymers. They are thermoplastics which can be processed using most conventional polymer processing methods. PLA is high in strength and modulus (63 MPa and 3.4 GPa, respectively) but brittle (strain at break 3.8%) while PBAT is flexible and tough (strain at break approximately 710%). In view of their complementary properties, blending PLA with PBAT becomes a natural choice to improve PLA properties without compromising its biodegradability. In this study, PLA and PBAT were melt blended using a twin screw extruder. Melt elasticity and viscosity of the blends increased with the concentration of PBAT. Crystallization of the PLA component, phase morphology of the blend, mechanical properties, and toughening mechanism were investigated. The blend comprised an immiscible, two-phase system with the PBAT evenly dispersed in the form of approximately 300 nm domains within the PLA matrix. The PBAT component accelerated the crystallization rate of PLA but had little effect on its final degree of crystallinity. With the increase in PBAT content (5-20 wt %), the blend showed decreased tensile strength and modulus; however, elongation and toughness were dramatically increased. With the addition of PBAT, the failure mode changed from brittle fracture of the neat PLA to ductile fracture of the blend as demonstrated by tensile test and scanning electron microcopy (SEM) micrographs. Debonding between the PLA and PBAT domains induced large plastic deformation in PLA matrix ligaments.
RuvAB and RecG Are Not Essential for the Recovery of DNA Synthesis Following UV-Induced DNA Damage in <i>Escherichia coli</i> (2004)

Abstract Ultraviolet light induces DNA lesions that block the progression of the replication machinery. Several models speculate that the resumption of replication following disruption by UV-induced DNA damage requires regression of the nascent DNA or migration of the replication machinery away from the blocking lesion to allow repair or bypass of the lesion to occur. Both RuvAB and RecG catalyze branch migration of three- and four-stranded DNA junctions in vitro and are proposed to catalyze fork regression in vivo. To examine this possibility, we characterized the recovery of DNA synthesis in ruvAB and recG mutants. We found that in the absence of either RecG or RuvAB, arrested replication forks are maintained and DNA synthesis is resumed with kinetics that are similar to those in wild-type cells. The data presented here indicate that RecG- or RuvAB-catalyzed fork regression is not essential for DNA synthesis to resume following arrest by UV-induced DNA damage in vivo.
Draft Genome Sequences of <i>Vibrio</i> sp. Strains Isolated from Tetrodotoxin-Bearing Scavenging Gastropod (2014)

Vibrio sp. strains JCM 18905 and JCM 19053 were isolated from a tetrodotoxin (TTX)-bearing scavenging gastropod, and Vibrio sp. strain JCM 18904 was isolated from a sea cucumber. All these are closely related to Vibrio alginolyticus. Their comparative genome information is useful for studies of TTX production in bacteria.
Activity Server: You can run but you can't hide. (1991)

The activity server is a software utility that provides high-level information on what a user or a number of users are doing by combining data inputs from various sources. These sources are: 1) thejinger server, 2) the phone server, and 3) the location server. The finger server provides information on users' activities or lack thereof on hosts within a local network; the phone server abstracts information from call progress of users' digital phones whereas the location server abstracts information from active badge sightings. Responses from all these unobtrusive data gathering sources are put together to form a composite model of the activities of users. Information may be collected only from or on behalf of participating users; each user within the user community can determine how much of his own information the activity server may receive. The main attributes of the activity server are: 1) it maintains history of all the participating users, 2) it synchronizes among the many, possibly conflicting, pieces of information from three sources, 3) it distinguishes interdependence of activities among users, and 4) it provides a high-level abstraction about users' activities.