gebhart/patrepeval huggingface dataset:
High performance Nanogold-silver in situ hybridisation. (1998)

Conventional in situ hybridisation (ISH) usually requires the presence of at least 10-50 copies of the nucleic acid sequence in question per cell. In situ PCR has been proposed as an alternative method, which may yield single-copy sensitivity, but shows a relatively high rate of false-negative or even false-positive reactions. Very recently, possible alternatives have been described, which can be performed in routine laboratories without the need for expensive equipment. Streptavidin-Nanogold-Silver ISH is an easy-to-perform assay, which can be applied to detect low copy numbers of nucleic acid sequences in paraffin sections and cytological preparations. Its combination with labelled tyramides (TSATM = tyramide signal amplification, also known as CARD = catalysed reporter deposition) can achieve single gene copy sensitivity in detecting DNA viruses and also shows very high sensitivity for RNA detection. Possible applications include the early recognition of viral infection, cancer-associated genes, genetic diseases, and also the specific detection of mRNA.
Cover Picture: Reconstructing the Discontinuous and Conformational β1/β3‐Loop Binding Site on hFSH/hCG by Using Highly Constrained Multicyclic Peptides (ChemBioChem 1/2015) (2014)

The cover picture shows the X-ray crystal structure of hCGβ (the “pregnancy hormone”, in blue) in complex with a monoclonal antibody (mAb3468, in green) that binds with sub-nanomolar affinity (PDB ID: 1QFW). The structure illustrates the molecular complexity of the discontinuous and conformational β1/β3 binding site on hCGβ, and further suggests that the binding surfaces of hCGβ and mAb3468 only interact efficiently when they adopt the correct secondary and tertiary structures. On p. 91 ff., P. Timmerman et al. present a new synthetic methodology for manufacturing small (3.5–5 kDa), peptide-based mimics of the highly discontinuous β1/β3 epitope on hCGβ that retain both the secondary and tertiary structures as well as the strong binding to mAb3468, while neglecting 75 % of the total protein. Synthesis of these mimics involves the use of multiple constraints, including cyclization with a synthetic scaffold and connecting the loops both via oxime linkages and natural disulfide bonds. These constraints were shown to be essential for the binding properties of these mimics.
BIOLOGICAL EXPRESSIONS OF LYMPHOCYTE ACTIVATION (1973)

A population of thymus-derived lymphocytes has been identified that, upon activation by the nonspecific plant mitogen concanavalin A, suppresses the development of plaque-forming cell responses in fresh or 48-h antigen-stimulated cultures of mouse spleen cells. Suppressor cells can inhibit both primary and secondary IgM and IgG responses in vitro. X-irradiation before activation of peripheral thymus-derived cells by concanavalin A abrogates generation of suppressor cells. After a 48 h activation period, however, the function of concanavalin A-activated suppressor cells is radioresistant. As yet uncertain is whether these suppressor cells are a population of cells distinct from thymus-derived "helper" cells. In certain important regards, the cells mediating these two opposing functions share similar characteristics; the effect observed may be determined by the circumstances of activation or the numbers of activated cells, and may consequently represent different functions of a single thymus-derived regulator cell population.
Expression and localization of utrophin in differentiating PC12 cells (2000)

To ascertain the role of utrophin in cultured neuronal cells, we investigated its expression and distribution along the NGF-induced differentiation of PC12 cells grown on different substrata. Utrophin mRNA was measured by RT-PCR assay and utrophin protein was quantified by immunoblot analysis. The distribution of utrophin and beta-dystroglycan was analyzed by confocal microscopy. We demonstrate that utrophin protein was increased 4-fold during differentiation of cells grown laminin. Concomitant with this up-regulation, utrophin was enriched at the growth cones in differentiating cells, where it co-localizes with beta-dystroglycan. These data suggest the presence of a utrophin-beta-dystroglycan complex in PC12 cells that participates in the formation and/or stabilization of the growth cone-extracellular matrix adhesion.
Will PI3K pathway inhibitors be effective as single agents in patients with cancer? (2011)

The phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) axis regulates essential cellular functions including cell survival, proliferation, metabolism, migration, and angiogenesis. The PI3K pathway is activated in human cancers by mutation, amplification, and deletion of genes encoding components of this pathway. The critical role of PI3K in cancer has led to the development of drugs targeting the effector mechanisms of this signaling network. Recent studies have shown that inhibition at multiple levels of the PI3K pathway results in FOXO-dependent feedback reactivation of several receptor tyrosine kinases (RTKs) which, in turn, limit the sustained inhibition of this pathway and attenuates the action of therapeutic antagonists. This suggests that if used as single agents, PI3K pathway inhibitors may have limited clinical activity. We propose herein that to successfully target the output of the PI3K pathway in cancer cells, combination therapies that hinder these compensatory mechanisms should be used. Thus, combination therapies that target RTKs, PI3K, and mTOR activities may be required to maximize the clinical benefit derived from treatment with these inhibitors.
Analysis and implementation of distributed algorithms for multi-robot systems (2008)

Distributed algorithms for multi-robot systems rely on network communications to share information. However, the motion of the robots changes the network topology, which affects the information presented to the algorithm. For an algorithm to produce accurate output, robots need to communicate rapidly enough to keep the network topology correlated to their physical configuration. Infrequent communications will cause most multi-robot distributed algorithms to produce less accurate results, and cause some algorithms to stop working altogether. The central theme of this work is that algorithm accuracy, communications bandwidth, and physical robot speed are related. 
This thesis has three main contributions: First, I develop a prototypical multi-robot application and computational model, propose a set of complexity metrics to evaluate distributed algorithm performance on multi-robot systems, and introduce the idea of the robot speed ratio, a dimensionless measure of robot speed relative to message speed in networks that rely on multi-hop communication. The robot speed ratio captures key relationships between communications bandwidth, mobility, and algorithm accuracy, and can be used at design time to trade off between them. I use this speed ratio to evaluate the performance of existing distributed algorithms for multi-hop communication and navigation. Second, I present a definition of boundaries in multi-robot systems, and develop new distributed algorithms to detect and characterize them. Finally, I define the problem of dynamic task assignment, and present four distributed algorithms that solve this problem, each representing a different trade-off between accuracy, running time, and communication resources. 
All the algorithms presented in this work are provably correct under ideal conditions and produce verifiable real-world performance. They are self-stabilizing and robust to communications failures, population changes, and other errors. All the algorithms were tested on a swarm of 112 robots. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Multiphase Compositional Modeling in Small-Scale Pores of Unconventional Shale Reservoirs (2013)

Abstract Compositional modeling of hydraulically stimulated naturally fractured liquid-rich shale (LRS) reservoirs is a complex process that is yet to be understood. The flow and multiphase mass transfer in the nano-, meso-, and macro-scale pores, as in Eagle Ford, Woodford and Bakken is of great interest. Understanding the production mechanisms from such reservoirs is crucial in the overall effort to increase the ultimate hydrocarbon production. Thus, we focused on deciphering the physical fundamentals of various recovery mechanisms via reservoir modeling. The starting point was examining the phase behavior issues in unconventional reservoirs. Specifically, we constructed phase diagrams using a new correlation to shift the critical properties of components in the nano and meso-scale pores. The correlation was applied to three recently published Eagle Ford fluid samples. The new phase behavior correlation was used in a dual-permeability compositional model to determine the nature of pore-to-pore flow and, eventually, the hydrocarbon production from wells. In the simulation models we allowed for the phase behavior differences between fracture and matrix and included a multi-level flow hierarchy from matrix (nano, meso, and macropores) to fractures and finally to the well. To make computation accurate we resorted to a series of detailed logarithmic local grid refinement (LS-LGR) in various strategic subdomains in the matrix and fracture. As a result of this modeling study, we have concluded several reasons why hydrocarbon fluids can move in the shale reservoir nano, meso, and macro-scale pores and why we are able to produce from such low-permeability reservoirs. For instance, favorable phase envelope shift of hydrocarbon mixtures in the nano- and meso-scale pores is one of the contributing factors to economic production in gas-condensate and bubble-point systems. Also noted, when the phase envelope is crossed in gas-condensate systems, a large gas-to-oil volume split in the nano, meso, and macro-pores plays a crucial role in hydrocarbon recovery during depletion. For the bubble-point oil region, the low viscosity of the liquid phase and the delay in gas bubble evolution appears as the main reason for favorable oil production. Furthermore, ‘rubblizing’ the reservoir in the vicinity of hydraulic fractures creates another favorable environment for improved drainage, which is why multi-stage hydraulic fracturing is so critical in successful development of shale reservoirs.
Transmission analysis for OFDM signals over hybrid RF-optical high-throughput satellite (2018)

In this paper, a theoretical investigation of the performance of a communication scenario where a geostationary-orbit satellite provides radio-frequency broadband access to the users through orthogonal-frequency-division multiplexing technology and has an optical feeder link is presented. The interface between the radio frequency and the optical parts is achieved by using radio-on-fiber technology for optical-electro and electro-optical conversion onboard and no further signal processing is required. The proposed scheme has significant potential, but presents limitations related to the noise. The noise in both forward and reverse links is described, and the system performance for an example scenario with 1280 MHz bandwidth for QPSK, 16QAM, and 64QAM subcarrier modulation is estimated. The obtained results show that under certain conditions regarding link budget and components choice, the proposed solution is feasible.
High-resolution doppler-free two-photon spectroscopic studies of molecules. II. Theν2bands ofNH314 (1976)

Detailed studies involving high-resolution Doppler-free two-photon spectroscopic measurements of the ${\ensuremath{\nu}}_{2}$ vibrational bands in $^{14}\mathrm{NH}_{3}$ are presented. Using the technique of combining fixed-frequency ir sources with molecular Stark tuning presented in the preceding paper, we have used two successive $Q(5,4)$ vibrational-rotational transitions to study the spectroscopic and collisional properties of the ${\ensuremath{\nu}}_{2}$ vibrational manifold. We report (1) precise transition energies for the $({\ensuremath{\nu}}_{2},J,K)=({0}^{\ensuremath{-}},5,4)\ensuremath{\rightarrow}({2}^{\ensuremath{-}},5,4)$ two-photon transition, (2) pressure-broadening and pressure-shift data, (3) optical Stark shift parameters, and (4) excited-state transition matrix elements. An observation of collisional narrowing arising from $^{14}\mathrm{NH}_{3}$-Ne collisions is also reported.
Mode Specific Backscattering in a Quantum Point Contact (2015)

We demonstrate a scanning gate grid measurement technique consisting in measuring the conductance of a quantum point contact (QPC) as a function of gate voltage at each tip position. Unlike conventional scanning gate experiments, it allows investigating QPC conductance plateaus affected by the tip at these positions. We compensate the capacitive coupling of the tip to the QPC and discover that interference fringes coexist with distorted QPC plateaus. We spatially resolve the mode structure for each plateau.
Multivariate curve resolution of time course microarray data (2006)

Profiles extracted by MCR-WALS exhibit a strong correlation with cell cycle-associated genes, but also suggest new insights into the regulation of those genes. The unique features of the MCR-WALS algorithm are its freedom from assumptions about the underlying linear model other than the non-negativity of gene expression, its ability to analyze non-log-transformed data, and its use of measurement error information to obtain a weighted model and accommodate missing measurements.
Optimal Path Planning Using Generalized Voronoi Graph and Multiple Potential Functions (2020)

In this article, we present a novel nonuniform sampling technique, based on the pipeline of rapidly exploring random tree (RRT), for efficiently computing high-quality collision-free paths while maintaining fast asymptotic convergence to the optimal solution. Our nonuniform sampling method focuses on the area where the optimal path may exist so that the path planning process can be further accelerated. First, the environment map is initialized with the generalized Voronoi graph and a heuristic path is calculated. Second, the heuristic path is discretized to construct the multiple potential functions (MPF), where the MPF provides a nonuniform sampling distribution for the path planner. As a meta-algorithm, our method is applicable to other RRT methods and helps to improve the performance of the underlying algorithm dramatically. We also prove the probabilistic completeness and the asymptotic optimality of our algorithm. The time cost and path length are selected to demonstrate the effectiveness of our algorithm. Through a series of simulation and real-world experiments, it is confirmed that the proposed algorithm achieves convincing performance compared with the state-of-the-art path planning algorithms.
Trehangelins ameliorate inflammation-induced skin senescence by suppressing the epidermal YAP-CCN1 axis (2022)

Trehangelins (THG) are newly identified trehalose compounds derived from broth cultures of an endophytic actinomycete, Polymorphospora rubra. THG are known to suppress Cellular Communication Network factor 1 (CCN1), which regulates collagen homeostasis in the dermis. Although the physical properties of THG suggest a high penetration of the stratum corneum, the effect of THG on the epidermis has not been reported. Here we describe a possible mechanism involved in skin aging focusing on the effect of THG on epidermal CCN1. This study shows that: (1) THG suppress epidermal CCN1 expression by inhibiting the translocation of Yes-Associated Protein (YAP) to nuclei. (2) Epidermal CCN1, localized at the basement membrane, regulates the balance between the growth and differentiation of keratinocytes. (3) Keratinocytes secrete more CCN1 than fibroblasts, which leads to disruption of the basement membrane and extracellular matrix components. (4) The secretion of CCN1 from keratinocytes is increased by ultraviolet B exposure, especially in aged keratinocytes, and deteriorates the elastic fiber structures in the underlying dermis. (5) Topical application of THG ameliorates the structure of the basement membrane in ex vivo human skin explants. Taken together, THG might be a promising treatment for aged skin by suppressing the aberrant YAP-CCN1 axis.
Random Fourier Features for Kernel Ridge Regression: Approximation Bounds and Statistical Guarantees (2018)

Random Fourier features is one of the most popular techniques for scaling up kernel methods, such as kernel ridge regression. However, despite impressive empirical results, the statistical properties of random Fourier features are still not well understood. In this paper we take steps toward filling this gap. Specifically, we approach random Fourier features from a spectral matrix approximation point of view, give tight bounds on the number of Fourier features required to achieve a spectral approximation, and show how spectral matrix approximation bounds imply statistical guarantees for kernel ridge regression. Qualitatively, our results are twofold: on the one hand, we show that random Fourier feature approximation can provably speed up kernel ridge regression under reasonable assumptions. At the same time, we show that the method is suboptimal, and sampling from a modified distribution in Fourier space, given by the leverage function of the kernel, yields provably better performance. We study this optimal sampling distribution for the Gaussian kernel, achieving a nearly complete characterization for the case of low-dimensional bounded datasets. Based on this characterization, we propose an efficient sampling scheme with guarantees superior to random Fourier features in this regime.
Anomalous Diffusion and the Generalized Langevin Equation (2018)

The generalized Langevin equation (GLE) is a stochastic integro-differential equation that is commonly used to describe the velocity of microparticles that move randomly in viscoelastic fluids. Such particles commonly exhibit what is known as anomalous subdiffusion, which is to say that their position mean-squared displacement (MSD) scales sublinearly with time. While it is common in the literature to observe that there is a relationship between the MSD and the memory structure of the GLE, and that there exist special cases where explicit solutions exist, this connection has never been fully characterized. Here, we establish a class of memory kernels for which the GLE is well-defined, we investigate the associated regularity properties of solutions, and we prove that large-time asymptotic behavior of the particle MSD is entirely determined by the tail behavior of the GLE's memory kernel.
Measurements of Soil Redox Potential (2009)

Soil redox potentials (Eh) are commonly measured and operationally defined using platinum (Pt) electrodes, but there are variations in the methodology and instrumentation for measuring the associated voltages that may lead to imprecise and inaccurate estimates of oxidation–reduction intensity in the soil environment. Most field measurements of Eh are either made manually using a volt meter or automatically with a recording device such as a data logger. A mesocosm experiment was conducted to evaluate the impact of these two measurement approaches on resulting Eh values in three different wetland soils. Noticeable differences were observed between data collected using a multimeter (simple volt meter) and those collected with a data logger. Because the multimeter permitted the observed voltages to drift while the Pt and reference electrodes equilibrated following closure of the circuit, it was initially suspected that these were the more accurate data. By adding a 10‐Mohm resistor (standard component of commercially available multimeters) to a closed circuit containing the Pt and reference electrodes, data loggers could be modified to collect data similar to those obtained using a multimeter. Further testing, however, demonstrated that the voltage drift observed when using a closed 10‐Mohm circuit was an artifact of alterations in the electrochemical soil environment surrounding the Pt electrode. By using an instrument with very high (200 Gohm) input resistance, the artifactual drift could be essentially eliminated. Our comparisons and experiments suggest that the most accurate measurements of soil Eh and soil redox status are obtained using volt meters with high input resistance (e.g., 200 Gohm). Accurate Eh values also are obtained using data loggers (20 Gohm resistance) in the standard configuration that maintains an open circuit except during the actual instantaneous voltage measurement.
Adaptive power management in LTE terminal modem (2014)

The high-speed communication environment and high-performance mobile devices have leveraged each other. Long Term Evolution (LTE) supports high bandwidth and low latency for data transfer. However, high bandwidth transfer will spend the mobile device's battery power rapidly. To extend the user equipment (UE)'s battery life time, LTE adopts enhanced Discontinuous Reception (DRX) mechanism. Even though LTE supports DRX framework to reduce power consumption, DRX not only depends on base-station but also needs sufficient idle time to operate efficiently. In this paper, we propose a novel adaptive power management technique of LTE model which reduces the active (i.e. non-DRX period) power consumption. Our experimental results shows that a communication modem with the proposed method improves energy saving by 40.72% compared to previous modem.
On establishing a benchmark for evaluating static analysis alert prioritization and classification techniques (2008)

Benchmarks provide an experimental basis for evaluating software engineering processes or techniques in an objective and repeatable manner. We present the FAULTBENCH v0.1 benchmark, as a contribution to current benchmark materials, for evaluation and comparison of techniques that prioritize and classify alerts generated by static analysis tools. Static analysis tools may generate an overwhelming number of alerts, the majority of which are likely to be false positives (FP). Two FP mitigation techniques, alert prioritization and classification, provide an ordering or classification of alerts, identifying those likely to be anomalies. We evaluate FAULTBENCH using three versions of a FP mitigation technique within the AWARE adaptive prioritization model. Individual FAULTBENCH subjects vary in their optimal FP mitigation techniques. Together, FAULTBENCH subjects provide a precise and general evaluation of FP mitigation techniques.
Effects of Selective Serotonin Reuptake Inhibitors on Objective and Subjective Sleep Quality (2000)

The purpose of this paper is to review the effects of selective serotonin (5-HT) reuptake inhibitors on objective and subjective sleep and awakening quality measures. Polysomnography (PSG) demonstrated in both healthy volunteers and depressed patients a decrease in sleep efficiency and total sleep time, a lengthening of sleep latency and a deterioration in sleep continuity, including an increase in the number of awakenings and wake time during the total sleep period. Sleep architecture mostly showed an increase in S1 and S2 and a decrease in S3, S4 and REM sleep as well as a lengthening of REM latency. Objective awakening quality, if measured at all by psychometry, generally showed no decrements. Concerning subjective sleep and awakening quality, normals demonstrated either no changes or a tendency towards a deterioration, while in patients some improvement was observed. Reasons for this discrepancy will be discussed. Novel 5-HT reuptake inhibitors with additional modes of action such as 5-HT2 antagonism (e.g. trazodone, nefazodone) are more likely to improve objective and subjective sleep quality, although some shortcomings may be inherent in regard to comorbidity (e.g. sleep-related breathing disorders). Thus, PSG seems to be a necessity for diagnosis and treatment of complex sleep disorders.