gebhart/patrepeval huggingface dataset:
A Channelization Model of Landscape Evolution (2001)

The geomorphic evolution of many landscapes is fundamentally determined by the evolution of the river channels and their interactions with hillslopes. Consequently, models of landscape evolution ought to track the evolution of the channel geometry so as to quantify the rate of erosion of channel bottoms and to follow the changes in hillslope-channel coupling over time. Unfortunately, the spatial resolution required to describe channel morphology adequately is computationally impractical. It is also beyond the resolution of most digital elevation data. What is required is a parameterization scheme for approximating fine scale channel morphology at a coarse pixel scale. Such a parameterization is already implicitly employed in most models by assuming channel equilibrium, which ties the width and depth of a model channel to the square root of discharge through a pixel. Channel fluxes are thereby predictable, and a closed form of the governing equations is attained. In reality, mountain river channels do not take a simple equilibrium form and show great spatial variability and evident disequilibrium geometry. Since the time scales of changes in channel geometry, bedrock channel erosion, and hillslope response are all closely related, it is reasonable to infer that the spatio-temporal development of the landscape is determined by their interaction and that channel disequilibrium is a fundamental factor in the dynamics of landscape evolution. If this is the case, we need an alternative sub-grid scale parameterization that aggregates channel properties such as surface morphology, roughness, cross-sectional geometry, so that the time dependent behavior of these properties can be estimated at the coarse pixel scale. We introduce such a parameterization measure, which we term <i>channelization</i>, after extensive investigation of the pixel resolution dependence of topographic relief. We focus in particular on the effect of coarse graining on digital elevation data for derived measures such as channel slope and upstream area and demonstrate that we can approximately correct for this effect. We show that a very simple geomorphic model can be constructed around the channelization parameter and the resolution-invariant topographic measures. This model demonstrates that channel disequilibrium may play a significant role in mountain landscape dynamics. It also shows how geomorphic models in general could be modified to incorporate such sub-pixel scale complexities and to better model these dynamics.
Supplementary Figure 1 from Basal Subtype and MAPK/ERK Kinase (MEK)-Phosphoinositide 3-Kinase Feedback Signaling Determine Susceptibility of Breast Cancer Cells to MEK Inhibition (2023)

Supplementary Figure 1 from Basal Subtype and MAPK/ERK Kinase (MEK)-Phosphoinositide 3-Kinase Feedback Signaling Determine Susceptibility of Breast Cancer Cells to MEK Inhibition
Combined Use of Streaming Potential and UV/Vis To Assess Surface Modification of Fabrics via Soil Release Polymers (2019)

Polymers have become a widespread part of laundry detergent formulations because of their benefits which are usually delivered via surface modification of fibers. Therefore, there is a growing interest in understanding their deposition on fabrics. In this work, we have used streaming potential to assess changes in surface charge of polyester and knitted cotton after modification via soil release polymers (SRPs). Results identify a relationship between the measured zeta potential for the modified fabrics and the charge of the polymer. The effects of parameters, such as agitation speed and bulk concentration during deposition, have been investigated. Streaming potential data were then correlated to adsorption isotherms from UV absorbance data, and a Langmuir–Freundlich model was proposed to describe the isotherms for polyester. The stain removal index for some common hydrophobic stains was determined via image analysis. A link between SRP deposition efficiency and their effectiveness on greasy soil removal was observed.
Abstract 5400: Antiangiogenic gene therapy with VB111 is active in glioblastoma xenografts (2011)

Abstract Introduction: Glioblastoma is a highly vascular tumor with marked endothelial dependence. While anti-angiogenic therapy has shown transient clinical benefit for the treatment of glioblastoma, persistent vascularization is seen with a normalization of blood vessels within the tumor. VB-111 is a dual-action, anti-angiogenic and vascular disrupting agent for cancer treatment aimed specifically at destroying newly formed and existing tumor blood vessels in a safe and efficient manner. VB-111 consists of a replication incompetent adenovirus together with an endothelial angiogenic-specific promoter and a pro-apoptotic Fas chimera transgene. Methods: Intracranial xenografts were established in nude rats with a luciferase expressing U87 glioma cell line. Rats were treated intravenously with VB-111 at 1011 viral particles or placebo at 21 days post tumor cell implantation. Tumor growth was followed by in vivo bioluminescent imaging and 7T MRI. Rats were sacrificed when moribund or when marked neurologic deficit was observed. Tumors were evaluated by standard histologic methods for vessel density and necrosis. Results: Untreated rats bearing U87 tumors showed a median survival of 38 days (95% CI 35.1-40.9 days), while animals treated with VB-111 showed a median survival of 48 days (95% CI 42.1-53.9 days). Log rank analysis of survival distributions between these two groups showed a significant difference (p=0.024) in favor of treatment. Luciferase activity, used as a surrogate for tumor volume, began separating between the two groups in week two post treatment and showed a continued trend for reduced activity in the treatment group thereafter. MRI imaging confirmed decreased tumor size in representative animals from the VB-111 group. Conclusions: VB-111's Dual action therapy is promising for glioblastoma. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5400. doi:10.1158/1538-7445.AM2011-5400
Amperometric Determination of Total Cholesterol at Gold Electrodes Covalently Modified with Cholesterol Oxidase and Cholesterol Esterase with Use of Thionin as an Electron Mediator (1999)

Immobilization of cholesterol oxidase (EC 1.1.3.6) (ChOx) on a gold electrode was attempted by cross-linking using glutaraldehyde between ChOx molecules and a self-assembled monolayer of 2-aminoethanethiolate. The resulting electrode (ChOx/Au) exhibits an amperometric response to free cholesterol in the presence of thionin as an electron mediator, and a steady-state response is obtained approximately 60 s after injection of cholesterol into the electrolyte solution. Coimmobilization of cholesterol esterase (EC 3.1.1.13) (ChE) and ChOx (ChE/ChOx/Au) allows the amperometric determination of both esterified cholesterol and free cholesterol. Cyclic voltammetry of the ChE/ChOx/Au and the dependence of the amperometric response to cholesterol on the concentration of thionin suggest that thionin is encapsulated in the enzyme film on the electrode surface. Apparent Michaelis constants of the ChOx/Au and the ChE/ChOx/Au electrodes suggest that the amperometric response was controlled by penetration of the reaction substrate into the films of the enzyme(s). The concentration of total (free and esterified) cholesterol in human serum samples, determined by using the techniques developed in the present study, is in good agreement with that determined by the well-established technique using colorimetry.
Using Model-Based Design in an IEC 62304-Compliant Software Development Process. (2010)

IEC 62304 [1] is an international standard (hereafter referred to as the Standard) that specifies software development life cycle processes to improve the safety of medical devices. It defines a series of activities and tasks that are required for medical device software engineering. We will discuss how MathWorks tools for Model-Based Design, which have been used to create high-integrity software [2-4], can be used to create control system and signal processing software in a manner compliant with the Standard. Software development processes
Mass-balanced through-wafer electrostatic x/y-scanner for parallel probe data storage (2008)

In this work we describe the design, fabrication and testing of a mass-balanced planar x/y-scanner designed for parallel-probe storage applications (see Fig. 1a). We explore electrostatic actuation as an alternative to electromagnetic actuation. To increase the shock resistance, mass-balancing is used and the scanner is fabricated by deep reactive ion etching through a complete wafer. To move the scan table in both positive and negative x and y directions, four comb drives are used. The comb-drive fingers are tapered to increase the generated force without decreasing the minimum trench width.
Rare-earth ion exchanged Cu-SSZ-13 zeolite from organotemplate-free synthesis with enhanced hydrothermal stability in NH3-SCR of NOx (2018)

Rare-earth Y exchanged Al-rich Cu-CHA shows significantly improved hydrothermal stability in NH<sub>3</sub>-SCR reaction.
Penile transplantation: the US experience and institutional program set-up (2018)

Penile transplantation using vascularized composite allografts is an emerging technique to treat genital loss. In the United States, this procedure has been performed successfully at Massachusetts General Hospital in a patient who had previously undergone treatment for penile cancer. The Johns Hopkins Medical Institutions has developed a research protocol to perform penile transplantation in patients with genital loss secondary to trauma. The process of selecting the appropriate candidate for genitourinary (GU) vascularized composite allograft surgery is rigorous including extensive physical examination, laboratory testing, imaging and psychological evaluations. After transplantation, limiting the potential complications associated with immunosuppression is critical given that the procedure is intended to improve quality of life and is not life-saving. Ultimately, penile transplant is a surgical intervention which may have numerous applications. Optimization of the pre-operative screening process, surgical technique, and immunosuppressive protocol is required to establish this method as the standard treatment for patients with genital loss and limited reconstructive options.
Nonisentropic propagation of sound in uniform ducts using Euler equations (1986)

The problem of sound propagation in uniform ducts is examined using the Euler equations. First, a numerical spatial marching technique is examined for the case of no mean flow. The technique uses an initial value formulation. It is found that the scheme is stability limited, in agreement with previous results obtained using the Helmholtz equation. Also duct mode analysis is performed and the following is observed. When the mean flow in the duct is treated as isentropic, the solutions agree with existing solutions. However, this implies no pressure gradient for the mean flow in the streamwise direction. If a mean pressure gradient is imposed, it is found that the lowest mode attenuates as it propagates against the flow direction. It is also found that the same mode grows due to an instability, if it propagates downstream. This instability is related to combustion instability.
Characterization of the receptor protein tyrosine phosphatase gene product PTP gamma: binding and activation by triphosphorylated nucleosides. (1995)

A full-length cDNA for a novel isoform of the human receptor tyrosine phosphatase gamma gene (PTPRG) was overexpressed in Sf9 insect cells, and the gene product, PTP gamma, was purified and characterized. The protein was expressed as a M(r) approximately 185,000 protein accompanied by a M(r) approximately 120,000 putative cleavage product on SDS-PAGE analysis. The protein undergoes N-linked glycosylation and constitutive phosphorylation of serine residues. When assayed for tyrosine-specific phosphatase activity, PTP gamma dephosphorylated myelin basic protein at a pH optimum of 7.5 and a Km of 12.6 microM; reduced carboxyamidomethylated and maleylated lysozyme (RCM-lysozyme) at a pH optimum of 6.0 and a Km of 12 microM; and p-nitrophenylphosphate with a pH optimum of 5.5 and a Km of 3.5 mM. Phosphatase activity was inhibited by ZnCl2 and sodium orthovanadate; Mg2+, Mn2+, and Ca2+ ions were ineffective. The partially purified form of the enzyme was allosterically activated by triphosphorylated nucleosides, with a preference for purines. This activation was prevented by Mg2+ addition and did not occur when a purified form of the enzyme was utilized, suggesting that its activation depends on specific activating factors or conformational constraints. Interestingly, PTP gamma protein was specifically bound by an ATP-agarose matrix through its intracellular domain, suggesting a link between binding of nucleotides and activation of the phosphatase.
Evaluation of Control Interfaces for Desktop Virtual Environments (2015)

Tracking and analyzing the movement trajectories of individuals and groups is an important problem with applications in crowd management and the development of transportation systems. However, real-world tracking is limited due to the size of the trackable area and the precision with which a person can be tracked. Experiments in virtual environments have many advantages, including practically unlimited sizes and the precise measurement of spatial behavior. However, the generalizability of research using virtual environments to real-world scenarios is often limited by the translation of participants’ movements to those of their avatars. We compared human movement patterns in virtual environments with different control interfaces: a handheld joystick, a mouse-and-keyboard setup, and a keyboard-only setup. With each of these controls, participants completed several movement-related tasks of varying difficulty in a limited amount of time. Questionnaires indicated that participants preferred the mouse-and-keyboard setup over the other two setups. Standard performance measures suggested that the joystick underperformed in a variety of tasks. Movement trajectories in the final task indicated that each of the control setups produced somewhat realistic behavior, despite some apparent differences from real-world trajectories. Overall, the results indicated that, given limited resources, mouse-and-keyboard setups consistently outperform joysticks and produce realistic movement patterns.
Cost-effective Cloud Edge Traffic Engineering with Cascara. (2021)

Inter-domain bandwidth costs comprise a significant amount of the operating expenditure of cloud providers, but have received little attention in research and practice. Traffic engineering systems at the cloud edge must strike a fine balance between minimizing costs and maintaining the latency expected by clients. The nature of this tradeoff is complex due to non-linear pricing schemes prevalent in the market for inter-domain bandwidth. We quantify this tradeoff and uncover several key insights from the link-utilization between a large cloud provider and Internet service providers. Based on these insights, we propose CASCARA, a cloud edge traffic engineering framework to optimize inter-domain bandwidth allocations with non-linear pricing schemes. CASCARA exploits the abundance of latency-equivalent peer links on the cloud edge to minimize costs without impacting latency significantly. Extensive evaluation on production traffic demands of a commercial cloud provider shows that CASCARA saves 11–50% in bandwidth costs per cloud PoP, while bounding the increase in client latency by 3 milliseconds.
A performance study of wormhole routed networks through analytical modeling and experimentation (1993)

The individual processors of a parallel computer cooperate by exchanging information over an interconnection network. This dissertation studies the performance of such multicomputer interconnection networks. Here an analytical model that uses a new concept called the distributed queue is presented. This model is used to predict both the latency and maximum possible throughput of wormhole routed k-ary n-cube networks. Comparisons with experiments on a parallel computer called the High-speed Network Evaluation Testbed (Hnet) prove the model's accuracy. Using this model the performance of networks for different worm sizes, node topologies and length to width ratios (for the 2-dimensional mesh) are compared. The model is also used to compare the performance of different topologies within the k-ary n-cube family subject to equal cost constraints. A combined cost constraint which includes both node cost and network packaging cost is presented. Next this dissertation evaluates interconnection network performance in an experimental manner, with parallel applications generating Hnet network traffic. Both a latency-tolerant parallel sorting algorithm and a latency-sensitive parallel sparse matrix multiply algorithm are used to compare the performance of different networks. The effect on performance of variations in network topology, routing algorithm and application algorithm are explored.
Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions (2020)

We consider the problem of solving LP relaxations of MAP-MRF inference problems, and in particular the method proposed recently in (Swoboda, Kolmogorov 2019; Kolmogorov, Pock 2021). As a key computational subroutine, it uses a variant of the Frank-Wolfe (FW) method to minimize a smooth convex function over a combinatorial polytope. We propose an efficient implementation of this subproutine based on in-face Frank-Wolfe directions, introduced in (Freund et al. 2017) in a different context. More generally, we define an abstract data structure for a combinatorial subproblem that enables in-face FW directions, and describe its specialization for tree-structured MAP-MRF inference subproblems. Experimental results indicate that the resulting method is the current state-of-art LP solver for some classes of problems. Our code is available at https://pub.ist.ac.at/~vnk/papers/IN-FACE-FW.html.
Design of New Chiral Auxiliaries for the Stereoselective Nucleophilic Addition to α-Alkoxy Aldehydes: A Remarkable Remote Protecting Group Effect (1993)

The MgBr2·OEt2 mediated addition of allyltributyltin to an α-alkoxyaldehyde bearing a protected 2-hydroxytetrahydropyranyl group was shown to be highly diastereoselective. The sense and the level of induction was shown depend on the nature of the protecting group at C-3.
ACM International Conference on Multimedia Retrieval (ICMR) 2017s (2017)

ACM ICMR is the premier International Conference on Multimedia Retrieval, and from 2011 it "illuminates the state of the arts in multimedia retrieval".
Myocardial iron quantification using T2* and native T1mapping - a 250 patient study (2015)

Background The management of iron overload has been transformed by the use of T2* as a surrogate marker of cardiac iron loading. The presence of iron however not only changes T2*, but also T2 and T1. Recent advances make T1 mapping a possible complementary technique to T2*. Preliminary data are encouraging, but the relative advantages and disadvantages and optimal mathematical model for the relationship between T1 and T2* remain unknown. Methods This was a single centre prospective study of 250 patients (age 37 ± 13 years) referred with potential iron overload for T2* assessment, with 50 healthy volunteers (age 44 ± 11 years) as a reference comparison group. Each participant underwent short axis septal T2* (standard Siemens sequence using 8 different TE) at 1.5T and in addition myocardial T1 mapping (ShMOLLI sequence). Results Image quality 27% of patients required more than one T2* acquisition to obtain optimal images for analysis compared with 12% for T1 mapping. ShMOLLI images were uninterpretable in 2 patients due to the presence of an MRI conditional pacemaker, and the positioning of a PORT-A-CATH implantable venous access system. It is known that some patients were unable to complete T2* sequences (21 heart beat scan), but these were not captured by the inclusion criteria of the study. There was an exponential relationship between T1 and T2* across all patients and healthy volunteers (R 2 =0.71, p<0.001, figure 1). This was composed of a tight curvefit below T2* of 20ms (R 2 =0.83, p<0.001, figure 2A) and almost no correlation above 20ms (R 2 =0.07, figure 2B). The lower limit of normal (2SD below the mean) T1 from the healthy volunteers was 895ms. In patients with T2* above 20ms, T1 was normal in 55%, high in 1% and low in 44%. The derived equivalent T1 cutpoints for published T2* cutoffs for mild, moderate and severe iron were 20ms (846ms); 14ms (705ms) and 10ms (636ms). If T1 is accurate for iron, then using the lower limit of normal for T1 (895ms) would suggest that the normal limit for T2* would be 29ms. However, of the 50 healthy volunteers, 8 (16%) had T2*s lower than this, possibly due to relatively lower precision of T2* measurements.
Synthesis of lithium cobalt oxide using low-pressure spray pyrolysis (2013)

A low pressure spray pyrolysis (LPSP) process was applied to synthesize crystalline lithium cobalt oxide as a battery cathode material via a liquid route. The effects of temperature and pressure of reactor on the synthesized particles characteristics were systematically investigated. Reactor temperatures of 800, 1000 and 1200 °C with pressures of 760 and 300 Torr were applied as operating conditions. The characterizations results show that the synthesized particles were highly crystalline and nearly spherical in shape. The results concluded that the low-pressure spray pyrolysis method has ability in control of particles morphology, crystallinity and atomic lithium-to-cobalt ratio.
Cloning and functional expression of a TEA‐sensitive A‐type potassium channel from rat brain (1991)

A rat brain cDNA (Raw3) related to the Drosophila Shaw K+ channel family has been characterized. Raw3 cRNA leads to the formation of TEA-insensitive, fast inactivating (A-type) K+ channels when injected into Xenopus laevis oocytes. Raw3 channels have markedly different properties from the previously cloned rat A-type K+ channel RCK4, Raw3 channels operate in the positive voltage range.
Analysis of parameter-independent PLLs with bang-bang phase-detectors (2002)

The parameter-independent design of Phase-Locked Loops (PLLs) is investigated for the case that a bang-bang phase-detector is used. Two self-biased CMOS PLL structures are proposed and compared, one leading to a completely parameter- and frequency independent behavior. If the PLL frequency operation is constant and known in advance, however, both structures can be made independent of the transistor V/sub t/ and /spl beta/ parameters.