gebhart/patrepeval huggingface dataset:
Understanding the p K a of Redox Cysteines: The Key Role of Hydrogen Bonding (2012)

Many cellular functions involve cysteine chemistry via thiol-disulfide exchange pathways. The nucleophilic cysteines of the enzymes involved are activated as thiolate. A thiolate is much more reactive than a neutral thiol. Therefore, determining and understanding the pK(a)s of functional cysteines are important aspects of biochemistry and molecular biology with direct implications for redox signaling. Here, we describe the experimental and theoretical methods to determine cysteine pK(a) values, and we examine the factors that control these pK(a)s. Drawing largely on experience gained with the thioredoxin superfamily, we examine the roles of solvation, charge-charge, helix macrodipole, and hydrogen bonding interactions as pK(a)-modulating factors. The contributions of these factors in influencing cysteine pK(a)s and the associated chemistry, including the relevance for the reaction kinetics and thermodynamics, are discussed. This analysis highlights the critical role of direct hydrogen bonding to the cysteine sulfur as a key factor modulating the equilibrium between thiol S-H and thiolate S(-). This role is easily understood intuitively and provides a framework for biochemical functional insights.
Photoemission spectromicroscopy with MAXIMUM at Wisconsin (1990)

We describe the development of the scanning photoemission spectromicroscope MAXIMUM at the Wisoncsin Synchrotron Radiation Center, which uses radiation from a 30-period undulator. The article includes a discussion of the first tests after the initial commissioning.
Optimal Cooperation Strategy in Cognitive Radio Systems with Energy Harvesting (2014)

In recent years, the excessive energy consumption in wireless communication systems has been increasingly critical, and environmental and financial considerations have motivated a trend in wireless communication technologies to resort to renewable energy sources. Energy harvesting is considered as a promising solution to alleviate such issues and has received extensive attentions. In this paper, we consider a cognitive radio system with one primary user (PU) and one secondary user (SU) and both of their transmitters operate in time-slotted mode. The SU, which harvests energy exclusively from ambient radio signal, follows a save-then-transmit protocol. In such a scenario, we investigate the SU's optimal cooperation strategy, namely, the optimal decision (to cooperate with the PU or not) and the optimal action (to spend how much time on energy harvesting and to allocate how much power for cooperative relay). We separately investigate the optimal action in non-cooperation and cooperation modes to maximize the SU's achievable throughout and derive the optimal closed-form solutions. Based on the analytical results of the optimal solutions, we propose the optimal cooperation protocol (OCP) to make the optimal decision, which simply involves a two-level test. Simulation results show that the proposed OCP outperforms the other two protocols (non-cooperation protocol and stochastic cooperation protocol) and the optimal underlay (OU) transmission mode.
Ecology of seed dormancy and germination in grasses (1998)

The caryopsis (hereafter called seed) germination stage of the life cycle of grasses is of much interest to (1) agriculturalists establishing fields of cereals to be harvested for grain, (2) range and grassland managers revegetating overgrazed or otherwise disturbed lands, (3) weed specialists attempting to control weeds in crops, pastures, lawns, and even in natural plant communities and (4) ecologists investigating plant life histories and the dynamics of plant populations, communities and ecosystems. Through experience, agriculturalists, land managers, weed biologists and ecologists have come to realize that the seeds of many grasses are difficult to germinate; consequently, much research has been done on their dormancy and germination. In fact, Simpson (1990) published a book entitled Seed Dormancy in Grasses. However, this wonderful compendium of information was written from a physiological point of view and, therefore, does not devote much attention to the ecological perspective of seed germination.
Effects of dextran 70 on hemodynamics and lung liquid and protein exchange in awake sheep. (1990)

We studied the effect of intravenous dextran 70 infusion on lung liquid and protein exchange to determine whether its effects were due to altered hemodynamics or to altered microvascular permeability. In each of six instrumented awake sheep with chronic lung lymph fistulas, we performed three experiments: 1) control, 2) a 30-minute infusion of 1 l of 6% dextran 70, and 3) an infusion of 1 l of 0.9% NaCl. In addition to pulmonary hemodynamics and lymph dynamics, we measured the plasma-to-lung lymph equilibration rate of [125I] albumin. We followed all the sheep for 10 hours, including a 2-hour baseline period. Dextran was more effective in expanding plasma volume (63 +/- 15% [mean +/- SD]) than saline (11 +/- 6%) at the end of the 30-minute infusion. Pulmonary vascular pressures increased after dextran and remained elevated for 8 hours, whereas after saline the pressures returned to baseline within 1 hour. After dextran, lung lymph flow increased and remained elevated. It was only transiently increased after saline. We confirmed that dextran equilibrated rapidly with lung lymph (half-time, less than 0.6 hour), even though it maintained plasma volume expansion for the whole body (half-time, 11.1 +/- 2.7 hours). The dextran increased both plasma and lymph total macromolecular osmotic pressure but did not increase the plasma-interstitial (lymph) osmotic pressure difference in the lung, except transiently during the infusion. The lymph/plasma protein concentration ratio increased after dextran due mainly to plasma protein dilution. There were no differences in the half-time of tracer albumin equilibration between plasma and lung lymph (control, 2.2 +/- 0.6 hours; saline, 2.0 +/- 0.6 hours; dextran, 2.3 +/- 0.6 hours). Dextran 70 increased liquid filtration mainly by increasing microvascular pressure and possibly filtration surface area. There was no evidence for a change in the leakiness of the lung microvascular barrier to albumin.
ChemInform Abstract: MOLECULAR DESIGN BY CYCLOADDITION REACTIONS PART 12, SYNTHESES OF FLUORANTHENE AND DIAZAFLUORANTHENE DERIVATIVES (1974)

Abstract Während bei der Umsetzung der Cumalinsäurederivate‐(I) mit.
Supplementary Table 1 from Pericytes Elicit Resistance to Vemurafenib and Sorafenib Therapy in Thyroid Carcinoma via the TSP-1/TGFβ1 Axis (2023)

&lt;p&gt;Supplementary Table 1 Antibodies list and experimental conditions for immunohistochemistry (IHC)&lt;/p&gt;
Genetic structure of bloodworm, Arenicola loveni (Annelida; Arenicolidae) suggests risk of local extinction in the face of overexploitation is lower than expected (2020)

The bloodworm, Arenicola loveni, is commonly used as bait by fishers and may be vulnerable to local extinction owing to its K-selected life history strategies and overexploitation. Accurate population data that can inform management is, however, outdated, whereas demand for bloodworm continues or is even increasing. This study provides genetic data on the population structure of A. loveni sampled at seven sites in the Western Cape and one in the Eastern Cape Provinces of South Africa. Mitochondrial cytochrome oxidase I (COI) data indicate that the population forms two lineages that should be managed separately: a western lineage that contains mostly samples from Saldanha Bay and a southern lineage that contains samples from the south coast (Muizenberg to Swartkops). High haplotypic, but low nucleotide diversity for the nuclear internal transcribed spacer (ITS) and COI genes, suggest that populations from both lineages have a recent common ancestry. Low pairwise Fixation index (Fst) values among most populations on the south coast, and common haplotypes shared among localities, indicate some degree of connectivity among populations. The presence of many private haplotypes at each site, however, indicates that local populations also rely heavily on regional recruitment. Gene flow among populations, and the absence of this between the western and southern lineages, is most likely attributed to larval dispersal facilitated by the predominant oceanic circulation patterns. These results suggest that although individual populations may be protected against local extinction through recruitment from elsewhere, reliance on local recruits may render populations vulnerable should baiting pressure increase.
Low-temperature transition in barium sodium niobateBa2NaNb5O15 (1997)

In order to examine a low-temperature transition in barium sodium niobate ${\mathrm{Ba}}_{2}$${\mathrm{NaNb}}_{5}$${\mathrm{O}}_{15}$ (BSN), an in situ observation was made in the temperature range between room temperature and 25 K by a transmission electron microscope. It was revealed that satellite reflection spots characterizing the incommensurate structure, which appear around 573 K, do not disappear even around 25 K. On the other hand, it was found that microdomains elongating along the [010] direction with a width of about 10 nm appear around 200 K, together with the appearance of both new satellite spots at the (h,k,l+1/2) points with h,k,l integers and new faint diffuse streaks through the (h,k+1/2,l+1/2) points along the [100] direction. It is concluded that the low-temperature transition in BSN is a transition from the 1q quasicommensurate state to the 2q one in which two modulated waves arise along the [100] and [010] directions.
PI3Kγ inhibition reduces blood pressure by a vasorelaxant Akt/L-type calcium channel mechanism (2011)

Overall our findings suggest that PI3Kγ inhibition could be a novel tool to modulate calcium influx in vascular smooth muscle cells, thus relaxing resistance arteries and lowering blood pressure.
Modulation of ozone-induced airway hyperresponsiveness and inflammation by interleukin-13 (2008)

The present study aimed to determine whether the T-helper cell type 2-derived cytokines, interleukin (IL)-4 and -13, can modulate the lung response to ozone exposure. IL-13(-/-), IL-4/13(-/-) and IL-13-overexpressing transgenic (Tg) mice were exposed to ozone (3 ppm; 3 h) or air. Wild-type (Wt) Balb/c mice and transgenic-negative littermates (IL-13Wt) were used as controls for gene-deficient and IL-13Tg mice, respectively. IL-4/13(-/-) and IL-13(-/-) mice developed a lesser degree of ozone-induced airway hyperresponsiveness (AHR) while IL-13Tg mice developed a greater degree of AHR compared with ozone-exposed wild-type or IL-13Wt mice, respectively. Ozone caused a time-dependent increase of bronchoalveolar lavage (BAL) neutrophils and macrophages in wild-type mice, maximal at 20-24 h, which was attenuated in the IL-13(-/-) and IL-4/13(-/-) mice. In IL-13Tg mice, there was a greater increase in BAL neutrophils after ozone exposure compared with IL-13Wt mice. Using quantitative real-time PCR, ozone-induced mRNA expression for IL-6 and keratinocyte chemokine was further enhanced in IL-13(-/-) and IL-4/13(-/-) mice, and was inhibited in IL-13Tg mice. Macrophage inflammatory protein (MIP)-3alpha/CCL20 expression was enhanced after ozone exposure in wild-type mice, inhibited in IL-13(-/-) and IL-4/13(-/-) mice, while in IL-13Tg mice it was enhanced. A similar pattern of expression was observed with lipopolysaccharide-induced cytokine (LIX/CXCL5/ENA-78) expression. In conclusion, interleukin-13 augments ozone-induced airway hyperresponsiveness and neutrophilic inflammation, possibly through modulation of certain cytokines induced by ozone exposure.
Overlap number of graphs (2011)

Abstract An overlap representation of a graph G assigns sets to vertices so that vertices are adjacent if and only if their assigned sets intersect with neither containing the other. The overlap number φ( G ) (introduced by Rosgen) is the minimum size of the union of the sets in such a representation. We prove the following: (1) An optimal overlap representation of a tree can be produced in linear time, and its size is the number of vertices in the largest subtree in which the neighbor of any leaf has degree 2. (2) If δ( G )⩾2 and G ≠ K 3 , then φ( G )⩽| E ( G )| − 1, with equality when G is connected and triangle‐free and has no star‐cutset. (3) If G is an n ‐vertex plane graph with n ⩾5, then φ( G )⩽2 n − 5, with equality when every face has length 4 and there is no star‐cutset. (4) If G is an n ‐vertex graph with n ⩾14, then φ( G )⩽ n 2 /4 − n /2 − 1, with equality for even n when G arises from K n /2, n /2 by deleting a perfect matching. © 2011 Wiley Periodicals, Inc. J Graph Theory
Platelets Adhere to Sulfatides by von Willebrand Factor Dependent and Independent Mechanisms (1991)

Unstimulated human platelets from normal volunteers adhere to sulfatides (galactosylceramide-I3-sulfate) as single cells but do not adhere appreciably to other lipids including gangliosides, neutral glycolipids, phospholipids or cholesterol-3-SO4. Platelet adhesion to sulfatide is saturable and dose-dependent, reaches maximal levels in 90 to 120 min, and is not divalent cation-dependent. Because sulfatides bind von Willebrand factor (vWf) with specificity and high affinity and platelet adhesion to structurally related sulfated glycolipids is approximately proportionate to their ability to bind vWf, we examined whether vWf mediates platelet adhesion to sulfatides. Platelets from a patient with severe Type I von Willebrand's disease adhere poorly to sulfatides. However, adhesion to levels seen with normal platelets is restored by the addition of vWf. Adhesion of normal platelets can be partially inhibited by a monospecific antibody to vWf. Normal platelet adhesion to sulfatides, however, is not increased following preincubation with vWf. Both vWf binding and platelet adhesion to sulfatides can be inhibited by the sulfated polysaccharide dextran sulfate at low concentration, fucoidan at high concentrations, but not by heparin, fibrinogen, fibronectin, or the synthetic peptides Gly-Arg-Gly-Asp-Ser-Pro or Gly-Arg-Gly-Glu-Ser-Pro. Thus, adhesion to sulfatides appears to be of two types; vWf dependent (50-75%) and vWf independent (25-50%).
ATM switch routers for combined connection-oriented and connectionless transport (2002)

This paper demonstrates the need for an ATM network to support both connection-oriented and connectionless networking in order to be an effective integrated services network. It identifies two key properties for an efficient solution that offers both networking modes: the use of a common addressing scheme and a common routing protocol for both modes. To enhance PNNI (private network-to-network interface) based ATM networks to support both networking modes, we propose a datagram protocol called CL-ATM (connectionless ATM) that uses the same addressing scheme and routing protocol as connection-oriented ATM. ATM switches with CL-ATM packet forwarding modules are referred to as ATM switch routers. This paper also addresses the problem of how two different integrated services networks, each supporting both networking modes, can interwork. Specifically, it shows how a network based on IP interworks with a network of ATM switch routers.
Sign-Magnitude SC: Getting 10X Accuracy for Free in Stochastic Computing for Deep Neural Networks (2018)

Stochastic computing (SC) is a promising computing paradigm for applications with low precision requirement, stringent cost and power restriction. One known problem with SC, however, is the low accuracy especially with multiplication. In this paper we propose a simple, yet very effective solution to the low-accuracy SC-multiplication problem, which is critical in many applications such as deep neural networks (DNNs). Our solution is based on an old concept of sign-magnitude, which, when applied to SC, has unique advantages. Our experimental results using multiple DNN applications demonstrate that our technique can improve the efficiency of SC-based DNNs by about 32X in terms of latency over using bipolar SC, with very little area overhead (about 1%).
Analyzing the influence of virtual lanes on the performance of infiniband networks (2002)

InfiniBand is very likely to become the de facto standard for communication between processing nodes and I/O devices as well as for interprocessor communication. The InfiniBand Architecture (IBA) supports up to 15 data virtual lanes per physical link, primarily intended for traffic prioritization, deadlock avoidance, and quality of service. However, virtual lanes may also contribute to improve performance by reducing the influence of the head-of-line blocking effect on input physical ports. On the other hand, when virtual lanes are used, crossbar complexity may be increased.The main goal of this paper is to show at what extent the use of virtual lanes may contribute to improve network performance on an InfiniBand environment, obtaining the trade-off between the number of virtual lanes and performance improvement. Different configurations (crossbar organization, crossbar bandwidth, and link bandwidth) are used. Evaluation results using up*/down* routing show that two virtual lanes are often enough to achieve the most of the improvement on performance, allowing the use of the remaining virtual lanes for other purposes. Additionally, by increasing the crossbar bandwidth, a lower complexity crossbar configuration can be used.
Supplementary Information from Adrenomedullin Blockade Suppresses Growth of Human Hormone–Independent Prostate Tumor Xenograft in Mice (2023)

&lt;p&gt;PDF file 114K, described the legends of all the supplementary figures&lt;/p&gt;
In Vivo Dynamics of Swi6 in Yeast: Evidence for a Stochastic Model of Heterochromatin (2004)

The mechanism for transcriptional silencing of pericentric heterochromatin is conserved from fission yeast to mammals. Silenced genome regions are marked by epigenetic methylation of histone H3, which serves as a binding site for structural heterochromatin proteins. In the fission yeast Schizosaccharomyces pombe, the major structural heterochromatin protein is Swi6. To gain insight into Swi6 function in vivo, we have studied its dynamics in the nucleus of living yeast. We demonstrate that, in contrast to mammalian cells, yeast heterochromatin domains undergo rapid, large-scale motions within the nucleus. Similar to the situation in mammalian cells, Swi6 does not permanently associate with these chromatin domains but binds only transiently to euchromatin and heterochromatin. Swi6 binding dynamics are dependent on growth status and on the silencing factors Clr4 and Rik1, but not Clr1, Clr2, or Clr3. By comparing the kinetics of mutant Swi6 proteins in swi6(-) and swi6(+) strains, we demonstrate that homotypic protein-protein interactions via the chromoshadow domain stabilize Swi6 binding to chromatin in vivo. Kinetic modeling allowed quantitative estimation of residence times and indicated the existence of at least two kinetically distinct populations of Swi6 in heterochromatin. The observed dynamics of Swi6 binding are consistent with a stochastic model of heterochromatin and indicate evolutionary conservation of heterochromatin protein binding properties from mammals to yeast.
Room-Temperature Valley Coherence in a Polaritonic System (2019)

Abstract The emerging field of valleytronics aims to coherently manipulate an electron and/or hole’s valley pseudospin as an information bearing degree of freedom (DOF). Monolayer transition metal dichalcogenides, due to their strongly bound excitons, their degenerate valleys and their seamless interfacing with photons are a promising candidate for room temperature valleytronics. Although the exciton binding energy suggests room temperature valley coherence should be possible, it has been elusive to-date. A potential solution involves the formation of half-light, half-matter cavity polaritons based on 2D material excitons. It has recently been discovered that cavity polaritons can inherit the valley DOF. Here, we demonstrate the room temperature valley coherence of valley-polaritons by embedding a monolayer of tungsten diselenide in a monolithic dielectric cavity. The extra decay path introduced by the exciton-cavity coupling, which is free from decoherence, is the key to room temperature valley coherence preservation. These observations paves the way for practical valleytronic devices.
HERO: Hierarchical EMC-constrained routing (1992)

The authors point out that, in order to perform the design of printed circuit boards as time- and cost-efficiently as possible, electromagnetic compatability (EMC) phenomena have to be taken into account during layout synthesis. The EMC router HERO offers a robust framework for incorporating EMC constraints and cost criteria into routing. Using HERO, it will not be possible to obtain a completely failsafe layout, in general. However, experimental results for typical boards prove that a great number of EMC problems can be avoided during layout synthesis and that the effects of EMC phenomena can be reduced substantially. Detailed reports of EMC design rule violations provide effective input to the succeeding EMC verification phase. Violations of EMC design rules are mainly caused by an inappropriate placement. Therefore, it seems to be of great promise to combine hierarchical placement methods with this approach for hierarchical routing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Power Density and Efficiency Enhancement in ICN DC–DC Converters Using Topology Morphing Control (2018)

This paper introduces a new approach for output voltage regulation in impedance control network (ICN) resonant dc-dc converters, in which the rectifier of the ICN converter alternates between full-bridge and half-bridge topologies. This approach, termed topology morphing control, allows the ICN converter to maintain soft switching across power levels while substantially reducing the output capacitance requirement and improving partial-power efficiencies compared to the conventional burst mode (on/off) control. A closed-loop control architecture for the ICN converter is also introduced, which regulates the converter's output voltage under input voltage and load variations while ensuring smooth transitions between the multiple operating modes of the proposed topology morphing control. A prototype 1-MHz, 120-W step-down ICN resonant converter designed for an input voltage range of 18-36 V, an output voltage of 12 V, and a 10:1 output power range has been built and tested with both burst mode control and the proposed topology morphing control. The topology morphing control reduces the output capacitance requirement in the prototype ICN converter by 57% and reduces converter losses at partial power levels by up to 46.5%. The prototype ICN converter is also tested under closed-loop control and is shown to successfully regulate its output voltage in the face of input voltage and load variations.
Towards FHE in Embedded Systems: A Preliminary Codesign Space Exploration of a HW/SW Very Large Multiplier (2015)

The integration of fully homomorphic encryption (FHE) into embedded systems is limited due to its huge computational requirements. FHE requires multiplications of operands up to millions of bits. Current implementations use high-end and parallel processors, leading to high-power consumption. We propose a hardware-software system to benefit from the best of hardware (performance/low-power) and software (flexibility) capabilities. In this letter, we present our first codesign results for hardware dedicated multiplication units, which is used as atomic operations by the software layer. We report FPGA implementation results for those units and software performance estimations of their use in multiplications up to 16 millions-bit operands. In range of 10 W power consumption, our analysis show that good FHE performance is affordable.