gebhart/patrepeval huggingface dataset:
Functional Antibody Arrays through Metal Ion‐Affinity Templates (2006)

Immobile but active. Unmodified antibodies can be immobilized in an active state on arrays of patterned features coupled with metal-ions by using dip-pen nanolithography and microcontact printing. Their immunoreactivity was determined by atomic force and fluorescence microscopy after the arrays had been exposed to their corresponding protein or virus antigens. An example of a functional antibody array used to capture the influenza virus is shown in the AFM image. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2268/2006/z600271_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
ChemInform Abstract: Systematic Search in Conformational Analysis (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Asymmetric Dihydroxylation of Chiral γ‐Amino α,β‐ Unsaturated Esters: Turning the Mismatched into the Matched Case via Protective Group Tuning. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Six-port based wave-correlator with application to beam direction finding (2001)

Six-port technology is well known for its ability to accurately measure the scattering parameters of a microwave network. In this paper a six-port based wave-correlator, which is operated as a two-channel wave receiver, is reported. A novel method for calibrating the six-port based wave-correlator by using only one phase shifter is proposed. The calibration procedure offers simple formulas for determining the calibration parameters, and their validity and accuracy are confirmed by measurements. In addition, an application of the proposed wave-correlator to beam direction finding is discussed. Experimental proof at X-band frequency was carried out and satisfactory results were obtained.
Modulation depth characteristics of a liquid crystal television spatial light modulator (1988)

The performance of a commercially available liquid crystal TV display was characterized in terms of its modulation depth. Measurements of screen transmittance and modulation depth, as a function of signal level, showed that the primary limitations of the device as a spatial light modulator were due to the nature of the video scan format and the display drive electronics. The resolution of the device, as measured by the modulation transfer function, is limited more by the physical pixel spacing than by pixel crosstalk. The optical flatness of the screen was characterized interferometrically, both with and without polarizers, to show the improvement in wavefront quality obtained by replacing the original polarizers.
Predictive linear transforms for noise robust speech recognition (2007)

It is well known that the addition of background noise alters the correlations between the elements of, for example, the MFCC feature vector. However, standard model-based compensation techniques do not modify the feature-space in which the diagonal covariance matrix Gaussian mixture models are estimated. One solution to this problem, which yields good performance, is joint uncertainty decoding (JUD) with full transforms. Unfortunately, this results in a high computational cost during decoding. This paper contrasts two approaches to approximating full JUD while lowering the computational cost. Both use predictive linear transforms to modify the feature-space: adaptation-based linear transforms, where the model parameters are restricted to be the same as the original clean system; and precision matrix modelling approaches, in particular semi-tied covariance matrices. These predictive transforms are estimated using statistics derived from the full JUD transforms rather than noisy data. The schemes are evaluated on AURORA 2 and a noise-corrupted resource management task.
Temporal properties of low power wireless links (2005)

Recently, several studies have analyzed the statistical properties of low power wireless links in real environments, clearly demonstrating the differences between experimentally observed communication properties and widely used simulation models. However, most of these studies have not performed in depth analysis of the temporal properties of wireless links. These properties have high impact on the performance of routing algorithms.Our first goal is to study the statistical temporal properties of links in low power wireless communications. We study short term temporal issues, like lagged autocorrelation of individual links, lagged correlation of reverse links, and consecutive same path links. We also study long term temporal aspects, gaining insight on the length of time the channel needs to be measured and how often we should update our models.Our second objective is to explore how statistical temporal properties impact routing protocols. We studied one-to-one routing schemes and developed new routing algorithms that consider autocorrelation, and reverse link and consecutive same path link lagged correlations. We have developed two new routing algorithms for the cost link model: (i) a generalized Dijkstra algorithm with centralized execution, and (ii)a localized distributed probabilistic algorithm.
Quinacrine, A Chromosome Stain Specific for Deoxyadenylate-Deoxythymidylate-Rich Regions in DNA (1972)

Fluorescence of quinacrine in the presence of different polynucleotides was studied to attempt to identify the specific nucleotides responsible for the fluorescence of stained chromosome preparations. A marked enhancement of fluorescence was seen in the presence of bihelical polynucleotides, such as poly(dA-dT), poly(dA).poly(dT), and poly(rA).poly(rU), but not in the presence of single-stranded polynucleotides, such as poly(dA), poly(dT), poly(rA), or poly(rU) alone. The higher was the GC content of natural DNAs, the more they quenched. Quenching was also seen with poly(dG) or poly(rG) alone, but not with poly(dC) or poly(rC) alone. Native and denatured DNA were both effective in quenching fluorescence. Thus, a bihelical conformation is not required for fluorescence quenching. Nearly all of these properties are shared with proflavine. In contrast, acridine orange, which stains most areas of chromosome preparations, shows enhanced fluorescence in the presence of all members of a series of natural DNAs. These data suggest that base-pairs composed of AT (rather than GC) residues are responsible for the observed fluorescence of specific chromosome regions after treatment with quinacrine, and support the proposal of Ellison and Barr (Chromosoma, in press) that the highly localized quinacrine fluorescence in their cytological preparations reflects the presence of DNA that has a high (A + T)/(G + C) ratio.
NETREACT: Distributed Event Detection in Sensor Data Streams with Disaggregated Packet Processing Pipelines (2022)

A new phenomenon called in-network computing has recently emerged with the aim of offloading calculations beyond the traditional task of packet forwarding to network switches. One of the most studied in-network computing applications is processing of sensor data streams. Existing works such as FastReact focus on solving this problem using flexible SmartNICs. In this paper, we propose NETREACT: an improved ASIC-oriented design for distributed event detection in sensor data streams to achieve a disaggregated processing pipeline. In contrast to existing approaches, NETREACT distributes the event detection task among a set of switches while leveraging the capabilities of the Intel Tofino platform in terms of boosting throughput and reducing latency. The proposed event-rule disaggregation method has the advantage of overcoming the hardware resource constraints and improving the overall network performance.
Global Optimization of Transmitter Placement for Indoor Wireless Communication Systems (2002)

The DIRECT (DIviding RECTangles) algorithm JONESJOTi, a variant of Lipschitzian methods for bound constrained global optimization, has been applied to the optimal transmitter placement for indoor wireless systems. Power coverage and BER (bit error rate) are considered as two criteria for optimizing locations of a specified number of transmitters across the feasible region of the design space. The performance of a DIRECT implementation in such applications depends on the characteristics of the objective function, the problem dimension, and the desired solution accuracy. Implementations with static data structures often fail in practice because of unpredictable memory requirements. This is especially critical in S⁴W (Site-Specific System Simulator for Wireless communication systems), where the DIRECT optimization is just one small component connected to a parallel 3D propagation ray tracing modeler running on a 200-node Beowulf cluster of Linux workstations, and surrogate functions for a WCDMA (wideband code division multiple access) simulator are also used to estimate the channel performance. Any component failure of this large computation would abort the entire design process. To make the DIRECT global optimization algorithm efficient and robust, a set of dynamic data structures is proposed here to balance the memory requirements with execution time, while simultaneously adapting to arbitrary problem size. The focus is on design issues of the dynamic data structures, related memory management strategies, and application issues of the DIRECT algorithm to the transmitter placement optimization for wireless communication systems. Results for two indoor systems are presented to demonstrate the effectiveness of the present work.
Photon Correlation Study of Background Suppressed Single InGaN Nanocolumns (2015)

We report on a linearly polarized non-classical light emission from a single InGaN/GaN nanocolumn, which is a site-controlled nanostructure allowing for pixel-like large-scale integration. We have developed a shadow mask technique to reduce background emissions arising from nitride deposits around single nanocolumns and defect states of GaN. The signal to background ratio is improved from to , which allows for detailed polarization-dependent measurement and photon-correlation measurements. Polarization-dependent measurements show that linearly polarized emissions arise from excitonic recombination involving a heavy-hole-like electronic state, corresponding to the bulk exciton of an in-plane polarized A exciton. The second-order coherence function at time zero g (2)(0) is 0.52 at 20 K without background correction. This value is explained in terms of a statistical mixture of a single-photon emission with residual weak background emissions, as well as efficient carrier injection from other localized states.
Surface reconstructions on germanium (1989)

Total-energy pseudopotential calculations have been used to investigate a number of surface reconstructions on germanium. The system of buckled dimers on the (001) surface of germanium can be represented by a spin system. The interactions between the dimers are represented by interactions between the spins. The values of the interaction parameters in an effective Hamiltonian that describes the system of dimers have been determined by calculating the energies of the (2*1), c(4*2), p(2*2) and p(4*1) arrangements of buckled dimers. The Hamiltonian gives a prediction of 380+or-100 K for the temperature of the order-disorder phase transition on the surface. The mechanism responsible for stabilising the Takayanagi reconstruction of the (111) surface of germanium has been investigated by calculating the energies of the (3*3) Takayanagi structure and of sub-elements of this structure. It is shown that the Takayanagi reconstruction is stabilised by an interaction between the adatoms and the dimers in the second layer of atoms. The surface stresses of the complete Takayanagi structure and of the Takayanagi structure without adatoms have been calculated and it is found that the surface energy is not related to the magnitude of the surface stress. preliminary results for the c(2*8) reconstruction of the (111) surface of germanium are presented.
Identification of Novel Human WW Domain-containing Proteins by Cloning of Ligand Targets (2021)

A recently described protein module consisting of 35-40 semiconserved residues, termed the WW domain, has been identified in a number of diverse proteins including dystrophin and Yes-associated protein (YAP). Two putative ligands of YAP, termed WBP-1 and WBP-2, have been found previously to contain several short peptide regions consisting of PPPPY residues (PY motif) that mediate binding to the WW domain of YAP. Although the function(s) of the WW domain remain to be elucidated, these observations strongly support a role for the WW domain in protein-protein interactions. Here we report the isolation of three novel human cDNAs encoding a total of nine WW domains, using a newly developed approach termed COLT (cloning of ligand targets), in which the rapid cloning of modular protein domains is accomplished by screening cDNA expression libraries with specific peptide ligands. Two of the new genes identified appear to be members of a family of proteins, including Rsp5 and Nedd-4, which have ubiquitin-protein ligase activity. In addition, we demonstrate that peptides corresponding to PY and PY-like motifs present in several known signaling or regulatory proteins, including RasGAP, AP-2, p53BP-2 (p53-binding protein-2), interleukin-6 receptor-alpha, chloride channel CLCN5, and epithelial sodium channel ENaC, can selectively bind to certain of these novel WW domains.
DFT-based interpolation with simple leakage suppression (2011)

For pilot-aided channel estimation in OFDM systems with a large number of subcarriers, an efficient discrete Fourier transform(DFT)-based interpolator is proposed. To suppress the leakage in a conventional DFT-based interpolator, the proposed method simply reuses the channel frequency response (CFR) estimates at leftmost and rightmost pilot subcarriers.
Reinforcement learning for autonomous dynamic soaring in shear winds (2014)

Dynamic soaring (DS) is an aerobatic maneuver whereby a gliding aircraft harnesses energy from horizontal wind that varies in strength and/or direction to support flight. Typical approaches to dynamic soaring in autonomous unmanned aerial vehicles (UAVs) use nonlinear optimizers to generate energy-gaining trajectories, which are then followed using traditional controllers. The effectiveness of such a strategy is limited by both the local optimality of the generated trajectory, as well as controller tracking errors. In this paper, we investigate a reinforcement learning (RL) approach working in continuous space to control a DS aircraft flying in shear wind conditions. The RL controller operates in two stages: In the first stage, it observes a traditional sample-based controller flying a locally optimal DS trajectory generated a priori. In the second stage, the sample-based controller is removed and authority is passed to the RL algorithm. We show that by deviating from the original planned trajectory, the RL controller is able to achieve better performance than its baseline teacher controller.
Perspective distortion modeling, learning and compensation (2015)

We describe a method to model perspective distortion as a one-parameter family of warping functions. This can be used to mitigate its effects on face recognition, or synthesis to manipulate the perceived characteristics of a face. The warps are learned from a novel dataset and, by comparing one-parameter families of images, instead of images themselves, we show the effects on face recognition, which are most significant when small focal lengths are used. Additional applications are presented to image editing, videoconference, and multi-view validation of recognition systems.
Microarrays in Disease Diagnosis and Prognosis (2007)

Abstract Progress in microarray technologies will soon lead to their application in clinical practice. These high‐throughput technologies are expected to have a major impact on molecular pathology, initially in tumour classification and tumour staging.
Deep Sequencing of the Murine Olfactory Receptor Neuron Transcriptome (2015)

The ability of animals to sense and differentiate among thousands of odorants relies on a large set of olfactory receptors (OR) and a multitude of accessory proteins within the olfactory epithelium (OE). ORs and related signaling mechanisms have been the subject of intensive studies over the past years, but our knowledge regarding olfactory processing remains limited. The recent development of next generation sequencing (NGS) techniques encouraged us to assess the transcriptome of the murine OE. We analyzed RNA from OEs of female and male adult mice and from fluorescence-activated cell sorting (FACS)-sorted olfactory receptor neurons (ORNs) obtained from transgenic OMP-GFP mice. The Illumina RNA-Seq protocol was utilized to generate up to 86 million reads per transcriptome. In OE samples, nearly all OR and trace amine-associated receptor (TAAR) genes involved in the perception of volatile amines were detectably expressed. Other genes known to participate in olfactory signaling pathways were among the 200 genes with the highest expression levels in the OE. To identify OE-specific genes, we compared olfactory neuron expression profiles with RNA-Seq transcriptome data from different murine tissues. By analyzing different transcript classes, we detected the expression of non-olfactory GPCRs in ORNs and established an expression ranking for GPCRs detected in the OE. We also identified other previously undescribed membrane proteins as potential new players in olfaction. The quantitative and comprehensive transcriptome data provide a virtually complete catalogue of genes expressed in the OE and present a useful tool to uncover candidate genes involved in, for example, olfactory signaling, OR trafficking and recycling, and proliferation.
Formal aspects of workflow management, Part 2: Distributed scheduling (1997)

Workflows are composite activities that achieve interoperation of a variety of system and human tasks. Workflows must satisfy subtle domain-specific integrity and organizational requirements. Consequently, flexibility in execution is crucial. A promising means to achieve flexibility is through declarative specifications (Part 1) with automatic distributed scheduling techniques (Part 2). We address the problem of scheduling workflows from declarative specifications given in terms of intertask dependencies and event attributes. Our approach involves distributed events, which are automatically set up to exchange the necessary messages. Our approach uses symbolic reasoning to (a) determine the initial constraints on events or guards, (b) preprocess the guards, and (c) execute the events. It has been implemented. workflows, temporal logic, scheduling. This is a greatly extended and revised version of a paper that appears in the Proceedings of the International Conference on Data...
National Survey on the English Language in Finland : Uses, Meanings and Attitudes (2011)

This volume reports on a large-scale national survey on Finns’ uses of, attitudes to and perceptions of English in the 2000s when the significance of English for many Finns and in many societal domains in Finnish society was clearly in the process of becoming more pronounced. The survey was conducted in the autumn 2007. Data were collected with the help of an extensive questionnaire which covered the respondents’ learning of, contacts with and uses of English, their attitudes to English and language mixing, and their predictions about the role of English in Finland in the future. The data set consisted of 1 495 responses, collected by random sampling. The survey confirms that English has a strong presence in Finland. English is the most widely studied language and the foreign language most commonly used. Finns also assess their own skills in English as relatively good. In addition, Finns’ overall attitudes to English are quite positive and pragmatic and they do not consider English a threat to the Finnish language and culture. Instead, the knowledge of English is considered an essential resource in the increasingly multicultural and globalizing world. The survey also revealed some socio-demographic differences. In general, the proficiency in and use of English are highest among younger generations and respondents who live in cities, who are at least relatively well educated and whose professional position is managerial or expert. The survey also identified a small minority who have not studied English, who assess their skills in English as minimal and who do not need or use English much. They are typically older people with little education. On the whole, the survey foregrounded three broad respondent categories: the ‘haves’, ‘have-nots’, and ‘have-it-alls’ of English.
Characterizing outage capacity for space-time communication over wideband wireless channels (2003)

We provide a compact characterization of the outage rates for wideband wireless communication, quantifying the effects of frequency and spatial diversity. Our information-theoretic computations yield the following findings. (a) Complex models typically employed in simulations can be replaced by simple, bandwidth-dependent, tap delay line models without loss of generality. (b) The spectral efficiency (i.e., the achievable rate, divided by the bandwidth) is well approximated as a Gaussian random variable, so that it is only necessary to specify its mean and variance to obtain outage rates. (c) The mean spectral efficiency depends only on the spatial diversity, while the variance depends on the spatial and frequency diversity via a product. Our definitions of frequency and spatial diversity have physically motivated interpretations, and are not based on high signal-to-noise ratio (SNR) asymptotics as in prior work.
Structure-Based Prototyping of Allosteric Inhibitors of Human Uridine/Cytidine Kinase 2 (UCK2) (2022)

Pyrimidine nucleotide biosynthesis in humans is a promising chemotherapeutic target for infectious diseases caused by RNA viruses. Because mammalian cells derive pyrimidine ribonucleotides through a combination of <i>de novo</i> biosynthesis and salvage, combined inhibition of dihydroorotate dehydrogenase (DHODH; the first committed step in <i>de novo</i> pyrimidine nucleotide biosynthesis) and uridine/cytidine kinase 2 (UCK2; the first step in salvage of exogenous nucleosides) strongly attenuates viral replication in infected cells. However, while several pharmacologically promising inhibitors of human DHODH are known, to date there are no reports of medicinally viable leads against UCK2. Here, we use structure-based drug prototyping to identify two classes of promising leads that noncompetitively inhibit UCK2 activity. In the process, we have identified a hitherto unknown allosteric site at the intersubunit interface of this homotetrameric enzyme. By reducing the <i>k</i><sub>cat</sub> of human UCK2 without altering its <i>K</i><sub>M</sub>, these new inhibitors have the potential to enable systematic dialing of the fractional inhibition of pyrimidine salvage to achieve the desired antiviral effect with minimal host toxicity.
High efficiency, multi-mJ, sub 10 fs, optical parametric amplifier at 3 kHz (2012)

We present a short-pulse pumped optical parametric amplifier (OPA) with a broadband spectrum from 670 nm to 1000 nm, supporting 5.7 fs pulses with &gt; 32 % pump-to-signal conversion efficiency resulting in pulse energies of 2.5 mJ.