gebhart/patrepeval huggingface dataset:
Active transport of charged substrates by a proton/sugar co-transport system. Amino-sugar uptake in the yeast <i>Rhodotorula gracilis</i> (1981)

1. In the yeast Rhodotorula gracilis several amino sugars were actively transported. Glucosamine, which is largely protonated at physiological pH (pK 7.75) was used as a model substrate. At pH 6.75 its half-saturation constant was 1 mM and the maximal velocity was 50 nmol/min per mg dry wt. 2. Amino sugars were taken up via the monosaccharide carrier. The transport of glucosamine was strongly restricted by monosaccharides. D-Xylose inhibited competitively the uptake of glucosamine. The inhibition constant was 1 mM. Cells preloaded with D-xylose showed exchange transport on subsequent addition of glucosamine. 3. Transport of glucosamine was energized by the membrane potential. Uncoupling agents such as carbonyl cyanide m-chlorophenyl-hydrazone and the lipophilic cation TPP+ (tetraphenylphosphonium ion) at concentrations that depolarized the membrane potential inhibited the uptake of glucosamine. Conversely the transport of glucosamine partly dissipated the membrane potential, which was monitored by radioactively labelled lipophilic cations. 4. The translocated charges were electrically compensated by the extrusion of protons and K+ (1 glucosamine molecule/0.85 H+ + 0.15 K+). 5. An increase of the pH in the range 4.75-8.75 lead to a decrease of the half-saturation constant from 5 mM to 1 mM and to an optimum of the maximal velocity at pH 6.75. We suggest that this fair constancy is due to the carrier not distinguishing between the protonated form of glucosamine (pH less than 7.75) and the deprotonated form (pH greater than 7.75). The increase of V(T) (maximal transport velocity) between pH 4.75 and 6.75 is due to the increase of the membrane potential: the decrease between pH 6.75 and 8.75 is due to the deprotonization of the carrier.
A 16 Mb/s data detector and timing recovery circuit for token ring LAN (2003)

A 1.75- mu m CMOS interface circuit for a differential Manchester-coded 16-Mb/s token-ring local area network (LAN) is presented. The chip provides fixed gain and slicing functions as well as integrated clock recovery, data timing, and lock detection. When it is used in tandem with a digital controller/driver chip, a complete 16-Mb IEEE 802.5-1988 standard-compatible token-ring transceiver is realized. Block-level functionality of the interface circuit is discussed, following by more detailed subcircuit descriptions and a presentation of measured results. The measured jitter transfer function of the PLL phase-locked to a high-transition-density data stream is shown.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Controlling the Formation of DNA Origami Structures with External Signals (2012)

Degradable Newkome-type and polylysine dendrons functionalized with spermine surface units are used to control the formation of DNA origami structures. The intact dendrons form polyelectrolyte complexes with the scaffold strands, therefore blocking the origami formation. Degradation of the dendron with an optical trigger or chemical reduction leads to the release of the DNA scaffold and efficient formation of the desired origami structure. These results provide new insights towards realizing responsive materials with DNA origami.
Timing ECO optimization via Bézier curve smoothing and fixability identification (2011)

Due to the rapidly increasing design complexity in modern IC design, more and more timing failures are detected at late stages. Without deferring time-to-market, metal-only ECO is an economical technique to correct these late-found failures. Typically, a design undergoes many ECO runs in design houses; the usage of spare cells is of significant importance. Hence, in this paper, we aim at timing ECO using the least number of spare cells. We observe that a path with good timing is desired to be geometrically smooth. Different from negative slack and gate delay used in most of prior work, we propose a new metric of timing criticality — fixability — considering the smoothness of critical paths. To measure the smoothness of a path, we use Bezier curve as the golden path. Furthermore, in order to concurrently fix timing violations, we derive the dominance property to divide violated paths into independent segments. Based on Bezier curve smoothing, fixability identification, and the dominance property, we develop an efficient algorithm to fix violations. Compared with the state-of-the-art works, experimental results show that our algorithm not only effectively resolves all timing violations with few spare cells but also achieves 22.8X and 42.6X speedups.
Energy-conscious, deterministic i/o device scheduling in hard real-time systems (2003)

Energy consumption is an important design parameter for embedded and portable systems. Software-controlled (or dynamic) power management (DPM) has emerged as an attractive alternative to inflexible hardware solutions. However, DPM via I/O device scheduling for real-time systems has not been considered before. We present an online I/O device scheduler, which we call low-energy device scheduler (LEDES), for hard real-time systems that reduces the energy consumption of I/O devices. LEDES takes as inputs a predetermined task schedule and a device-usage list for each task and it generates a sequence of sleep/working states for each device such that the energy consumption of the device is minimized. It also guarantees that real-time constraints are not violated. We then present a more general I/O device scheduler, which we call multistate constrained low-energy scheduler (MUSCLES), for handling I/O devices with multiple power states. MUSCLES generates a sequence of power states for each I/O device while guaranteeing that real-time constraints are not violated. We present several realistic case studies to show that LEDES and MUSCLES reduce energy consumption significantly for hard real-time systems.
Crystal structure of the NEMO ubiquitin‐binding domain in complex with Lys 63‐linked di‐ubiquitin (2009)

NEMO is essential for activation of the NF-kappaB signaling pathway, which is regulated by ubiquitination of proteins. The C-terminal leucine zipper of NEMO and its adjacent coiled-coil region (CC2-LZ) reportedly bind to linear ubiquitin chains with 1 microM affinity and to Lys 63-linked chains with 100 microM affinity. Here we report the crystal structure of the CC2-LZ region of mouse NEMO in complex with Lys 63-linked di-ubiquitin (K63-Ub(2)) at 2.7A resolution. The ubiquitin-binding region consists of a 130A-long helix and forms a parallel coiled-coil dimer. The Ile 44-centered hydrophobic patch of ubiquitin is recognized in the middle of the NEMO ubiquitin-binding region. NEMO interacts with each K63-Ub(2)via a single ubiquitin-binding site, consistent with low affinity binding with K63-Ub(2).
Inferring Network-Wide Quality in P2P Live Streaming Systems (2007)

This paper explores how to remotely monitor network-wide quality in mesh-pull P2P live streaming systems. Peers in such systems advertise to each other buffer maps which summarize the chunks of the video stream that they currently have cached and make available for sharing. We demonstrate how buffer maps can be exploited to monitor network-wide quality. We show that the information provided in a peer's advertised buffer map correlates with that peer's viewing-continuity and startup latency. Given this correlation, we remotely harvest buffer maps from many peers and then process these buffer maps to estimate the video playback quality. We apply this methodology to a popular P2P live streaming system, namely, PPLive. To harvest buffer maps, we build a buffer-map crawler and also deploy passive sniffing nodes. We process the harvested buffer maps and present results for network-wide playback continuity, startup latency, playback lags among peers, and chunk propagation patterns. The results show that this methodology can provide reasonably accurate estimates of ongoing video playback quality throughout the network.
A Reinforced Rigid Fixation Device for Unstable Intertrochanteric Fractures (1999)

A 120 degrees blade plate reinforced by a strut is introduced for the treatment of unstable intertrochanteric and proximal subtrochanteric fractures. Mechanical tests showed that the strength of this reinforced resistance device was 11,758 N. This strength is two and three times greater than that of the Gamma nail and sliding hip screw, respectively, and five times greater with the strut than without it. Three hundred fifty-eight patients older than 60 years of age were treated with this method between 1987 and 1991 (mean followup, 16 months). Six months after surgery the fracture had united in 82% of the patients who were walking without aid or using only a cane. Weightbearing began when the patient's general overall condition allowed such activity (average, 5 days; mode, 3 days). A chi squared test showed no difference regarding the results between stable and unstable fractures. Intraoperative and postoperative complication rates were 3% and 7.1%, respectively. The failure of fixation rate was 5.4%. Mechanical tests and clinical results showed that immediate weightbearing can be allowed in all types of intertrochanteric fractures. This reinforced device is effective in treating unstable intertrochanteric fractures and is especially indicated for the most unstable types (Evans' Grades 4 and 5).
Understanding retiming through maximum average-weight cycles (1991)

Article Free Access Share on Understanding retiming through maximum average-weight cycles Author: Marios C. Papaefthymiou Laboratory for Computer Science, Massachusetts Institute of Technology, Cambridge, MA Laboratory for Computer Science, Massachusetts Institute of Technology, Cambridge, MAView Profile Authors Info & Claims SPAA '91: Proceedings of the third annual ACM symposium on Parallel algorithms and architecturesJune 1991 Pages 338–348https://doi.org/10.1145/113379.113410Published:01 June 1991Publication History 9citation308DownloadsMetricsTotal Citations9Total Downloads308Last 12 Months9Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Microbial Conversion of Waste Glycerol from Biodiesel Production into Value-Added Products (2013)

Biodiesel has gained a significant amount of attention over the past decade as an environmentally friendly fuel that is capable of being utilized by a conventional diesel engine. However, the biodiesel production process generates glycerol-containing waste streams which have become a disposal issue for biodiesel plants and generated a surplus of glycerol. A value-added opportunity is needed in order to compensate for disposal-associated costs. Microbial conversions from glycerol to valuable chemicals performed by various bacteria, yeast, fungi, and microalgae are discussed in this review paper, as well as the possibility of extending these conversions to microbial electrochemical technologies.
A Model-Driven Framework for Domain Specific Process Design and Governance. (2017)

Current BPM approaches and standards have not sufficiently reduced the Business-IT gap. Indeed, today's solutions are mostly domainindependent and platform-dependent, which limits the ability of business matter experts to express business intent and enact process change. In contrast, the tool presented in this paper supports an approach that focuses on BPM and SOA environments in a domain-dependent and platform-independent way. We propose to add a domain specific-layer on top of current solutions so that business stakeholders can design and understand their processes in a more intuitive way. This significantly improves the agility and governance of processes. The demo shows the appropriateness and the feasibility of the approach.
An Integrated Risk Predictor for Pulmonary Nodules (2016)

Abstract It is estimated that over 1.5 million lung nodules are detected annually in the United States. Most of these are benign but frequently undergo invasive and costly procedures to rule out malignancy. A risk predictor that can accurately differentiate benign and malignant lung nodules could be used to more efficiently route benign lung nodules to non-invasive observation by CT surveillance and route malignant lung nodules to invasive procedures. The majority of risk predictors developed to date are based exclusively on clinical risk factors, imaging technology or molecular markers. Assessed here are the relative performances of previously reported clinical risk factors and proteomic molecular markers for assessing cancer risk in lung nodules. From this analysis an integrated model incorporating clinical risk factors and proteomic molecular markers is developed and its performance assessed on a previously reported prospective collection of lung nodules that enrolled 475 patients from 12 sites with lung nodules between 8 and 30mm in diameter. In this analysis it is found that the molecular marker is most predictive. However, the integration of clinical and molecular markers is superior to both clinical and molecular markers separately. Clinical Trial Registration: Registered at ClinicalTrials.gov ( NCT01752101 ).
Holomorphic embedding approach as an alternative method for solving the power flow problem (2017)

This paper presents results of the implementation and description of the basic formulation for the Holomorphic Embedding Load Flow Method (HELM). The approach is a noniterative technique proposed as an alternative method to solve the power flow problem. The basic formulation of the method is implemented by generation of an interface to use the data structure of the traditional MATPOWER. This is a free code tool which is developed in Matlab. Additionally, the same data files of this tool are used as input data for study carried out in this work. Also, the output results are adapted to have similar characteristics to the MATPOWER's output. Experiments and results for seven power systems demonstrate the validity of the new tool.
RhoA-GDP Regulates RhoB Protein Stability (2008)

RhoA plays a significant role in actin stress fibers formation. However, silencing RhoA alone or RhoA and RhoC did not completely suppress the stress fibers suggesting a residual "Rho-like" activity. RhoB, the third member of the Rho subclass, is a shortlived protein barely detectable in basal conditions. In various cell types, the silencing of RhoA induced a strong up-regulation of both total and active RhoB protein levels that were rescued by re-expressing RhoA and related to an enhanced half-life of the protein. The RhoA-dependent regulation of RhoB does not depend on the activity of RhoA but is mediated by its GDP-bound form. The stabilization of RhoB was not dependent on isoprenoid biosynthesis, Rho kinase, extracellular signal-regulated kinase, p38 mitogen-activated kinase, or phosphatidylinositol 3'-OH kinase pathways but required RhoGDIalpha. The forced expression of RhoGDIalpha increased RhoB half-life, whereas its knock-down antagonized the induction of RhoB following RhoA silencing. Moreover, a RhoA mutant (RhoAR68E) unable to bind RhoGDIalpha was significantly less efficient as compared with wild-type RhoA in reversing RhoB up-regulation upon RhoA silencing. These results suggest that, in basal conditions, RhoGDIalpha is rate-limiting and the suppression of RhoA makes it available to stabilize RhoB. Our results highlight RhoGDIalpha-dependent cross-talks that regulate the stability of RhoGTPases.
Operational characteristics of a harware-based pattern matcher (1983)

The design and operation of a new class of hardware-based pattern matchers, such as would be used in a backended database processor in a full-text or other retrieval system, is presented. This recognizer is based on a unique implementation technique for finite state automata consisting of partitioning the state table among a number of simple digital machines. It avoids the problems generally associated with implementing finite state machines, such as large state table memories, complex control mechanisms, and state encodings. Because it consists primarily of memory, with its high regularity and density, needs only limited static interconnections, and operates at a relatively low speed, it can be easily constructed using integrated circuit techniques. After a brief discussion of other pattern-matching hardware, the structure and operation of the partitioned finite state automaton is given, along with a simplified discussion of how the state tables are partitioned. The expected performance of the resulting system and the state table partitioning programs is then discussed.
Aquaporins as Targets for Drug Discovery (2007)

The intracellular hydric balance is an essential process of mammalian cells. The water movement across cell membranes is driven by osmotic and hydrostatic forces and the speed of this process is dependent on the presence of specific aquaporin water channels. Since the molecular identification of the first water channel, AQP1, by Peter Agre's group, 13 homologous members have been found in mammals with varying degree of homology. The fundamental importance of these proteins in all living cells is suggested by their genetic conservation in eukaryotic organisms through plants to mammals. A number of recent studies have revealed the importance of mammalian AQPs in both physiology and pathophysiology and have suggested that pharmacological modulation of aquaporins expression and activity may provide new tools for the treatment of variety of human disorders, such as brain edema, glaucoma, tumour growth, congestive heart failure and obesity in which water and small solute transport may be involved. This review will highlight the physiological role and the pathological involvement of AQPs in mammals and the potential use of some recent therapeutic approaches, such as RNAi and immunotherapy, for AQP-related diseases. Furthermore, strategies that can be developed for the discovery of selective AQP-drugs will be introduced and discussed.
X‐Ray Photoelectron and Scanning Auger Electron Spectroscopic Studies of Oxidized Graphite Electrode Surfaces (1987)

The surfaces of electrochemically modified graphite electrodes have been studied using ESCA, scanning Auger microscopy, and chemical titration. Quantitative evaluation of surface functionalities after electro‐oxidation in sulfuric acid provides an understanding of their mechanistic role in synthetic uses of the carbon electrode. Specifically concentrations of acid and phenolic groups are correlated with the level of oxidation on the electrode. A plateau is reached at between 4 and 22 C/cm2.
Interference Management in Femtocells (2012)

Increase in system capacity and data rates can be achieved efficiently in a wireless system by getting the transmitter and receiver closer to each other. Femtocells deployed in the macrocell significantly improve the indoor coverage and provide better user experience. The femtocell base station called as Femtocell Access Point (FAP) is fully user deployed and hence reduces the infrastructure, maintenance and operational cost of the operator while at the same time providing good Quality of Service (QoS) to the end user and high network capacity gains. However, the mass deployment of femtocell faces a number of challenges, among which interference management is of much importance, as the fundamental limits of capacity and achievable data rates mainly depends on the interference faced by the femtocell network. To cope with the technical challenges including interference management faced by the femtocells, researchers have suggested a variety of solutions. These solutions vary depending on the physical layer technology and the specific scenarios considered. Furthermore, the cognitive capabilities, as a functionality of femtocell have also been discussed in this survey. This article summarises the main concepts of femtocells that are covered in literature and the major challenges faced in its large scale deployment. The main challenge of interference management is discussed in detail with its types in femtocells and the solutions proposed over the years to manage interference have been summarised. In addition an overview of the current femtocell standardisation and the future research direction of femtocells have also been provided.
TOWARDS CONTINUOUS CONTROL FOR MOBILE ROBOT NAVIGATION: A REINFORCEMENT LEARNING AND SLAM BASED APPROACH (2019)

Abstract. We introduce a new autonomous path planning algorithm for mobile robots for reaching target locations in an unknown environment where the robot relies on its on-board sensors. In particular, we describe the design and evaluation of a deep reinforcement learning motion planner with continuous linear and angular velocities to navigate to a desired target location based on deep deterministic policy gradient (DDPG). Additionally, the algorithm is enhanced by making use of the available knowledge of the environment provided by a grid-based SLAM with Rao-Blackwellized particle filter algorithm in order to shape the reward function in an attempt to improve the convergence rate, escape local optima and reduce the number of collisions with the obstacles. A comparison is made between a reward function shaped based on the map provided by the SLAM algorithm and a reward function when no knowledge of the map is available. Results show that the required learning time has been decreased in terms of number of episodes required to converge, which is 560 episodes compared to 1450 episodes in the standard RL algorithm, after adopting the proposed approach and the number of obstacle collision is reduced as well with a success ratio of 83% compared to 56% in the standard RL algorithm. The results are validated in a simulated experiment on a skid-steering mobile robot.
Multi-Material Additive Manufacturing of Sustainable Innovative Materials and Structures (2019)

This paper highlights the multi-material additive manufacturing (AM) route for manufacturing of innovative materials and structures. Three different recycled thermoplastics, namely acrylonitrile butadiene styrene (ABS), polylactic acid (PLA), and high impact polystyrene (HIPS) (with different Young's modulus, glass transition temperature, rheological properties), have been selected (as a case study) for multi-material AM. The functional prototypes have been printed on fused deposition modelling (FDM) setup as tensile specimens (as per ASTM D638 type-IV standard) with different combinations of top, middle, and bottom layers (of ABS/PLA/HIPS), at different printing speed and infill percentage density. The specimens were subjected to thermal (glass transition temperature and heat capacity) and mechanical testing (peak load, peak strength, peak elongation, percentage elongation at peak, and Young's modulus) to ascertain their suitability in load-bearing structures, and the fabrication of functional prototypes of mechanical meta-materials. The results have been supported by photomicrographs to observe the microstructure of the analyzed multi-materials.