gebhart/patrepeval huggingface dataset:
Controlled Mather-Thurston theorems (2020)

Classical results of Milnor, Wood, Mather, and Thurston produce flat connections in surprising places. The Milnor-Wood inequality is for circle bundles over surfaces, whereas the Mather-Thurston Theorem is about cobording general manifold bundles to ones admitting a flat connection. The surprise comes from the close encounter with obstructions from Chern-Weyl theory and other smooth obstructions such as the Bott classes and the Godbillion-Vey invariant. Contradiction is avoided because the structure groups for the positive results are larger than required for the obstructions, e.g. $\operatorname{PSL}(2,\mathbb{R})$ versus $\operatorname{U}(1)$ in the former case and $C^1$ versus $C^2$ in the latter. This paper adds two types of control strengthening the positive results: In many cases we are able to (1) refine the Mather-Thurston cobordism to a semi-$s$-cobordism (ssc) and (2) provide detail about how, and to what extent, transition functions must wander from an initial, small, structure group into a larger one. The motivation is to lay mathematical foundations for a physical program. The philosophy is that living in the IR we cannot expect to know, for a given bundle, if it has curvature or is flat, because we can't resolve the fine scale topology which may be present in the base, introduced by a ssc, nor minute symmetry violating distortions of the fiber. Small scale, UV, "distortions" of the base topology and structure group allow flat connections to simulate curvature at larger scales. The goal is to find a duality under which curvature terms, such as Maxwell's $F \wedge F^\ast$ and Hilbert's $\int R\ dvol$ are replaced by an action which measures such "distortions." In this view, curvature results from renormalizing a discrete, group theoretic, structure.
Modes of Retrotransposition of Long Interspersed Element-1 by Environmental Factors (2012)

Approximately 42% of the human genome is composed of endogenous retroelements, and the major retroelement component, long interspersed element-1 (L1), comprises ∼17% of the total genome. A single human cell has more than 5 × 10(5) copies of L1, 80∼100 copies of which are competent for retrotransposition (RTP). Notably, L1 can induce RTP of other retroelements, such as Alu and SVA, and is believed to function as a driving force of evolution. Although L1-RTP during early embryogenesis has been highlighted in the literature, recent observations revealed that L1-RTP also occurs in somatic cells. However, little is known about how environmental factors induce L1-RTP. Here, we summarize our current understanding of the mechanism of L1-RTP in somatic cells. We have focused on the mode of L1-RTP that is dependent on the basic helix-loop-helix/per-arnt-sim (bHLH/PAS) family of transcription factors. Along with the proposed function of bHLH/PAS proteins in environmental adaptation, we discuss the functional linking of L1-RTP and bHLH/PAS proteins for environmental adaptation and evolution.
Drift-Induced Selection Between Male and Female Heterogamety (2017)

Evolutionary transitions between male and female heterogamety are common in both vertebrates and invertebrates. Theoretical studies of these transitions have found that, when all genotypes are equally fit, continuous paths of intermediate equilibria link the two sex chromosome systems. This observation has led to a belief that neutral evolution along these paths can drive transitions, and that arbitrarily small fitness differences among sex chromosome genotypes can determine the system to which evolution leads. Here, we study stochastic evolutionary dynamics along these equilibrium paths. We find non-neutrality, both in transitions retaining the ancestral pair of sex chromosomes, and in those creating a new pair. In fact, substitution rates are biased in favor of dominant sex determining chromosomes, which fix with higher probabilities than mutations of no effect. Using diffusion approximations, we show that this non-neutrality is a result of "drift-induced selection" operating at every point along the equilibrium paths: stochastic jumps off the paths return with, on average, a directional bias in favor of the dominant segregating sex chromosome. Our results offer a novel explanation for the observed preponderance of dominant sex determining genes, and hint that drift-induced selection may be a common force in standard population genetic systems.
Seismically Driven Fractured Reservoir Characterization Using an Integrated Approach – Joanne Field, UK (2009)

The Joanne Field is an Upper Cretaceous Chalk reservoir in the UK sector of the Central North Sea. Over the production life of the field it has become increasingly apparent that the presence of fracturing has a significant impact upon the efficacy of the
Lignin peroxidase mediated silver nanoparticle synthesis in Acinetobacter sp. (2017)

Metals present in environment render the bacteria to attain certain resistance machinery to survive, one of which is transformation of metal ions to nano forms. Various enzymes and proteins have been suggested to play significant role in synthesis of silver nanoparticles (AgNPs) in bacteria. In present study, we have purified lignin peroxidase from secreted enzyme extract of Acinetobacter sp. employing diethyl aminoethyl cellulose ion exchange and Biogel P-150 gel filtration column chromatography. The purified fraction has a specific activity of 1.571 U/mg with substrate n-propanol and 6.5-fold purification. The tetrameric enzyme, with molecular weight of 99 kDa, consisted of dimers of two polypetides of 23.9 and 24.6 kDa as revealed by native and SDS-PAGE. On exposure to purified enzyme, spherical polydispersed AgNPs of ~ 50 nm were obtained as observed under transmission electron microscope. Optimum activity of the purified enzyme was obtained at pH 2 and 60 °C with n-propanol as substrate. This is the first report describing the reduction of extracellular silver ions by lignin peroxidase purified from Acinetobacter sp.
FINAL REPORT DOE/ER/63705-1 (2005)

Our DOE project is one of the efforts that comprised the Vertical Transport and Mixing Program [VTMX] of the Environmental Sciences Division of the Office of Biological and Environmental Research in Department of Energy and was supported originally by DOE grant ER 62847. The Advanced Regional Prediction System [ARPS] computer code was used to simulate flow in the Salt Lake Valley. The simulations provided evidence that atmospheric forcing interacts with the Jordan Narrows, the Traverse Range and other complex mountain terrain at the south end of the Salt Lake Valley to produce lee rotors, hydraulic jumps and other effects. This continuation grant was designed to allow us to complete our work on VTMX. The primary outcome of this grant was the completion of the dissertation of Dr. Ying Chen. In that work, several turbulence models were tested, a new surface vegetation model was developed, and Weather Research and Forecast code simulations were compared with ARPS runs.
From Connected People, Connected Things, to Connected Intelligence (2020)

People tend to overestimate what can be done in one year and to underestimate what can be done in ten years. To get prepared, people have started to ask what the next generation would look like while 5G mobile cellular network is still at its first year of commercial deployment. In this paper, we first take a look back to see what 5G has achieved from its inception up to the year 2020, and then we have an outlook towards another 10 years ahead to the year 2030 where 6G is expected to be enrolled to the market. While 5G gradually opens up the curtain of internet of everything and brings vertical transform to change the society, 6G is believed to open a new era of `Internet of Intelligence' with connected people, connected things, and connected intelligence, solving human challenges in many aspects and helping perfect the world we all live in.
Software license management with smart cards (1999)

This paper describes public-key protocols for binding software licenses to tamper-resistant smart cards, for transferring licenses between cards, and for purchasing them on-line. The protocols support software distribution both through retail stores and over the Internet. The user can transfer licenses from several cards onto a single card to avoid juggling between several cards in the reader. The protocols are based on signed delegation certificates that are mostly stored outside the smart card. A smart card reader and cards capable of public-key signatures are the only new hardware needed. The protocols are easy for the user and simple to implement and analyze. We prove the security of the transfer protocol. 1
Cisplatin Ototoxicity, Increased DPOAE Amplitudes, and Magnesium Deficiency (2000)

Abstract Outer hair cell (OHC) metabolism is blocked by cisplatin. Concurrent changes in the renal handling of magnesium occur because of the damage cisplatin causes to the renal proximal tubule cells within the thick ascending loop of Henle. Although there is no evidence of cisplatin within the OHCs, there are significant levels of intracellular calcium, the antagonist to magnesium at the cell membrane. The OHC motile response is dependent on intracellular calcium. When the calcium current is suppressed by an antagonist, the extracellular OHC microphonic potential decreases. Magnesium deficiency is known to produce hyperexcitabililty within the central nervous system, including fatal audiogenic seizures. In addition, increases in the amplitude of the auditory brainstem response wave V occur with aminoglycoside therapy and magnesium deficiency. This paper illustrates the amplitude growth of distortion product otoacoustic emissions in two patients treated with cisplatin and explores the possible underlying reasons why this may be related to magnesium metabolism. Abbreviations: DPOAEs = distortion product otoacoustic emissions, OAEs = otoacoustic emissions, OHC = outer hair cell, TEOAEs = transient otoacoustic emissions
Testing the efficacy of lionfish traps in the northern Gulf of Mexico (2020)

Spearfishing is currently the primary approach for removing invasive lionfish (Pterois volitans/miles) to mitigate their impacts on western Atlantic marine ecosystems, but a substantial portion of lionfish spawning biomass is beyond the depth limits of SCUBA divers. Innovative technologies may offer a means to target deepwater populations and allow for the development of a lionfish trap fishery, but the removal efficiency and potential environmental impacts of lionfish traps have not been evaluated. We tested a collapsible, non-containment trap (the 'Gittings trap') near artificial reefs in the northern Gulf of Mexico. A total of 327 lionfish and 28 native fish (four were species protected with regulations) recruited (i.e., were observed within the trap footprint at the time of retrieval) to traps during 82 trap sets, catching 144 lionfish and 29 native fish (one more than recruited, indicating detection error). Lionfish recruitment was highest for single (versus paired) traps deployed <15 m from reefs with a 1-day soak time, for which mean lionfish and native fish recruitment per trap were approximately 5 and 0.1, respectively. Lionfish from traps were an average of 19 mm or 62 grams larger than those caught spearfishing. Community impacts from Gittings traps appeared minimal given that recruitment rates were >10X higher for lionfish than native fishes and that traps did not move on the bottom during two major storm events, although further testing will be necessary to test trap movement with surface floats. Additional research should also focus on design and operational modifications to improve Gittings trap deployment success (68% successfully opened on the seabed) and reduce lionfish escapement (56% escaped from traps upon retrieval). While removal efficiency for lionfish demonstrated by traps (12-24%) was far below that of spearfishing, Gittings traps appear suitable for future development and testing on deepwater natural reefs, which constitute >90% of the region's reef habitat.
Tissue-Engineered Solutions in Plastic and Reconstructive Surgery: Principles and Practice (2017)

Recent advances in microsurgery, imaging, and transplantation have led to significant refinements in autologous reconstructive options; however, the morbidity of donor sites remains. This would be eliminated by successful clinical translation of tissue-engineered solutions into surgical practice. Plastic surgeons are uniquely placed to be intrinsically involved in the research and development of laboratory engineered tissues and their subsequent use. In this article, we present an overview of the field of tissue engineering, with the practicing plastic surgeon in mind. The Medical Research Council states that regenerative medicine and tissue engineering "holds the promise of revolutionizing patient care in the twenty-first century." The UK government highlighted regenerative medicine as one of the key eight great technologies in their industrial strategy worthy of significant investment. The long-term aim of successful biomanufacture to repair composite defects depends on interdisciplinary collaboration between cell biologists, material scientists, engineers, and associated medical specialties; however currently, there is a current lack of coordination in the field as a whole. Barriers to translation are deep rooted at the basic science level, manifested by a lack of consensus on the ideal cell source, scaffold, molecular cues, and environment and manufacturing strategy. There is also insufficient understanding of the long-term safety and durability of tissue-engineered constructs. This review aims to highlight that individualized approaches to the field are not adequate, and research collaboratives will be essential to bring together differing areas of expertise to expedite future clinical translation. The use of tissue engineering in reconstructive surgery would result in a paradigm shift but it is important to maintain realistic expectations. It is generally accepted that it takes 20-30 years from the start of basic science research to clinical utility, demonstrated by contemporary treatments such as bone marrow transplantation. Although great advances have been made in the tissue engineering field, we highlight the barriers that need to be overcome before we see the routine use of tissue-engineered solutions.
c-Abl Tyrosine Kinase Adopts Multiple Active Conformational States in Solution (2016)

Protein tyrosine kinases of the Abl family have diverse roles in normal cellular regulation and drive several forms of leukemia as oncogenic fusion proteins. In the crystal structure of the inactive c-Abl kinase core, the SH2 and SH3 domains dock onto the back of the kinase domain, resulting in a compact, assembled state. This inactive conformation is stabilized by the interaction of the myristoylated N-cap with a pocket in the C-lobe of the kinase domain. Mutations that perturb these intramolecular interactions result in kinase activation. Here, we present X-ray scattering solution structures of multidomain c-Abl kinase core proteins modeling diverse active states. Surprisingly, the relative positions of the regulatory N-cap, SH3, and SH2 domains in an active myristic acid binding pocket mutant (A356N) were virtually identical to those of the assembled wild-type kinase core, indicating that Abl kinase activation does not require dramatic reorganization of the downregulated core structure. In contrast, the positions of the SH2 and SH3 domains in a clinically relevant imatinib-resistant gatekeeper mutant (T315I) appear to be reconfigured relative to their positions in the wild-type protein. Our results demonstrate that c-Abl kinase activation can occur either with (T315I) or without (A356N) global allosteric changes in the core, revealing the potential for previously unrecognized signaling diversity.
Operando Analysis of Interphase Dynamics in Anode-Free Solid-State Batteries with Sulfide Electrolytes (2021)

Sulfide solid electrolytes (SEs) show promise for Li metal solid-state batteries due to their high ionic conductivities and relative ease of manufacturing. However, many sulfide SEs suffer from limited electrochemical stability against Li metal electrodes. In this work, we use a suite of operando analytical techniques to investigate the dynamics of solid electrolyte interphase (SEI) formation and the associated effects on Li plating. We contrast a sulfide SE that forms an electrically insulating SEI (Li 6 PS 5 Cl) with an SE that forms an SEI with electrically conducting phases present (Li 10 GeP 2 S 12 ). Using anode-free cell configurations, where the Li/SE interface is formed against a current collector, we perform complimentary operando video microscopy and operando X-ray photoelectron spectroscopy (XPS) experiments. The combination of these techniques allows for the interpretation of electrochemical voltage traces during Li plating. The electrically insulating nature of the SEI in Li 6 PS 5 Cl facilitates Li metal nucleation and plating after the initial SEI formation. In contrast, in cells that form an electronically conducting SEI, the onset of Li plating is suppressed, which is attributed to a low Faradaic efficiency from continuous SE decomposition. The insights in this study reveal how interphase dynamics control the transition from SEI formation to plating in anode-free solid-state batteries.
New high gain pulse-triggered power transistors with amorphous saturable CT cores (1984)

A new high gain pulse-triggered power transistor (PTPT) with amorphous saturable CT (current transformer) is presented. In the PTPT, a current transformer plays an important role in the astable multivibrator operation. The base of power transistors can be directly driven by the collector current through the current transformer. This positive feedback operation holds the on state of the power transistor by initiating the small trigger pulse to the primary winding of the current transformer. Turn off operation can be also achieved applying trigger pulse. This behavior corresponds to the so called GTO (GATE TURN-OFF THYRISTOR). A turn off technique is developed to extinguish the conducting power transistor. In this paper, the switching characteristics of PTPT and its experimental results are described. New applications using PTPT are also introduced.
Self-Assembly of Surfactant-like Peptides (2007)

Inspired by recent work describing surfactant-like peptides, we have carried out a systematic study on peptides with the underlying composition of V6D2, altering the absolute sequence to determine the importance of the surfactant-like structure. All of the peptides examined here formed self-assembled structures in water. However, in contrast to other reports, we have found a surprising diversity of structures including fibers, tapes, and twisted ribbons but an absence of the vesicles and nanotubes described previously. Further investigations demonstrated that peptide purity plays a significant role in the outcome of the self-assembly. Different batches behave very differently, which can be linked to the compositions of these batches. This work shows that there is a need for not only rational design but also ease of synthesis of the building blocks for self-assembled structures.
Nanoholes fabricated by self-assembled gallium nanodrill on GaAs(100) (2007)

Self-assembled nanodrill technology based on droplet epitaxy growth was developed to obtain nanoholes on a GaAs(100) surface. In this technology, the gallium droplets act like “electrochemical drills” etching away the GaAs substrate beneath to give rise to nanoholes more than 10nm deep. The driving force of the nanodrill is attributed to the arsenic desorption underneath the gallium droplet at high growth temperatures and Ga-rich condition. This nanodrill technology provides an easy and flexible method to fabricate nanohole templates on GaAs(100) surface and has great potential for developing quantum dots and quantum dot molecules for quantum computation applications.
Cavity quantum-electrodynamical time-dependent density functional theory within Gaussian atomic basis. II. Analytic energy gradient (2022)

Following the formulation of cavity quantum electrodynamical time-dependent density functional theory (cQED-TDDFT) models [Flick et al., ACS Photonics 6, 2757-2778 (2019); Yang et al., J. Chem. Phys. 155, 064107 (2021)], here we report the derivation and implementation of the analytic energy gradient for the polaritonic states of a single photochrome within the cQED-TDDFT models. Such gradient evaluation is also applicable to a complex of explicitly-specified photochromes, or, with proper scaling, a set of parallel-oriented, identical-geometry, non-interacting molecules in the microcavity.
Stimulatory Effect of a Sulfonylurea Analogue and Its Polymer Conjugate on Insulin Secretion from Rat Islets (1994)

Abstract A sulfonylurea with a polymerizable end group (a glyburide analogue) was synthesized. This monomer was copolymerized with N, N ‐dimethylacrylamide (DMAAm). In vitro bioactivity was evaluated by adding these sulfonylurea monomers and copolymers into normal rat islet cultures and measuring the insulin concentration in the supernatant. The sulfonylurea monomer showed a stimulatory effect on rat islets at glucose concentrations of 50 and 100 mg/dL, with equivalent stimulation indices for glyburide, the potent sulfonylurea drug, while no effect was observed at a glucose concentration of 200 mg/dL. The sulfonylurea polymer stimulated Langerhans islets to secrete insulin at a low glucose concentration of 50 mg/dL, with 80% bioactivity of its monomeric compound. However, at 100 and 200 mg/dL glucose concentrations, there was no significant stimulation in insulin secretion. Because it is suggested that the sulfonylurea receptors are located in the lipid phase on the ATP‐sensitive K + channels, the solubilization of sulfonylurea into, and its diffusion through, the lipid phase in the cell membrane may affect the interactions of sulfonylurea with its receptors. In the case of the sulfonylurea polymer, the sulfonylurea unit in the polymer can interact with its receptor as can be seen by the increased insulin secretion at a glucose concentration of 50 mg/dL, but its interaction would be interfered with to some extent by a large hydrophilic polymer backbone. Thus, less change in insulin secretion was observed at higher glucose concentrations by the addition of this particular sulfonylurea polymer.