gebhart/patrepeval huggingface dataset:
Thermosensitive UL9 gene function is required for early stages of herpes simplex virus type 1 DNA synthesis (1995)

DNA replication of herpes simplex virus type 1 (HSV-1) is dependent on a virus-encoded sequence-specific origin-binding protein, the product of the UL9 reading frame. We have identified the mutations in the UL9 gene of three temperature-sensitive (ts) mutants of HSV-1 which are responsible for the ts phenotype (A90T in mutant tsS and V220M in tsR and tsX). The mutations are located in two different conserved helicase sequence motifs of UL9. Two further alterations (I204T and E280D) compared to the published sequence were found in the mutant, revertant and parental wild-type strain 17syn+ sequences and therefore seemed to be irrelevant for the ts phenotype. The ts function of the UL9 protein was required at early times during DNA synthesis whereas upward temperature shifts at later times did not considerably inhibit DNA synthesis.
Effective exploitation of a zero overhead loop buffer (1999)

A Zero Overhead Loop Buffer (ZOLB) is an architectural feature that is commonly found in DSP processors. This buffer can be viewed as a compiler managed cache that contains a sequence of instructions that will be executed a specified number of times. Unlike techniques such as loop unrolling, a loop buffer is a hardware technique that can be used to minimize loop overhead without the penalty of increasing code size. In addition, a ZOLB also requires relatively little space and power, which are both important considerations for most DSP applications. This paper describes strategies for generating code to effectively use a ZOLB. The authors have found that many common improving transformations used by optimizing compilers to improve code on conventional architectures are shown (1) to allow more loops to be placed in a ZOLB and (2) to further reduce loop overhead of the loops placed in a ZOLB. The results given in this paper demonstrate that this architectural feature can often be exploited with substantial improvements in execution time and slight reductions in code size.
NCBI disease corpus: A resource for disease name recognition and concept normalization (2014)

Information encoded in natural language in biomedical literature publications is only useful if efficient and reliable ways of accessing and analyzing that information are available. Natural language processing and text mining tools are therefore essential for extracting valuable information, however, the development of powerful, highly effective tools to automatically detect central biomedical concepts such as diseases is conditional on the availability of annotated corpora. This paper presents the disease name and concept annotations of the NCBI disease corpus, a collection of 793 PubMed abstracts fully annotated at the mention and concept level to serve as a research resource for the biomedical natural language processing community. Each PubMed abstract was manually annotated by two annotators with disease mentions and their corresponding concepts in Medical Subject Headings (MeSH®) or Online Mendelian Inheritance in Man (OMIM®). Manual curation was performed using PubTator, which allowed the use of pre-annotations as a pre-step to manual annotations. Fourteen annotators were randomly paired and differing annotations were discussed for reaching a consensus in two annotation phases. In this setting, a high inter-annotator agreement was observed. Finally, all results were checked against annotations of the rest of the corpus to assure corpus-wide consistency. The public release of the NCBI disease corpus contains 6892 disease mentions, which are mapped to 790 unique disease concepts. Of these, 88% link to a MeSH identifier, while the rest contain an OMIM identifier. We were able to link 91% of the mentions to a single disease concept, while the rest are described as a combination of concepts. In order to help researchers use the corpus to design and test disease identification methods, we have prepared the corpus as training, testing and development sets. To demonstrate its utility, we conducted a benchmarking experiment where we compared three different knowledge-based disease normalization methods with a best performance in F-measure of 63.7%. These results show that the NCBI disease corpus has the potential to significantly improve the state-of-the-art in disease name recognition and normalization research, by providing a high-quality gold standard thus enabling the development of machine-learning based approaches for such tasks. The NCBI disease corpus, guidelines and other associated resources are available at: http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/DISEASE/.
Validación de encuesta para determinar la flexibilidad de cadena de suministro (2018)

Hoy en dia la flexibilidad en la cadena de suministro (CS) es una de las caracteristicas mas representativa de la CS, ya que esta se ve reflejada en la capacidad con la que las empresas responden a los cambios y necesidades de los clientes. En este articulo se presenta una validacion estadistica de una encuesta disenada para conocer los 3 diferentes tipos de flexibilidades y los beneficios obtenidos en una CS. Los resultados muestran que la encuesta es valida y fiable para ser utilizada para futuros analisis.
Eccentric Exercise Impairs Respiratory Function And Increases Susceptibility To Permeability Transition In Skeletal Muscle Mitochondria (2009)

Unaccustomed eccentric exercise has been consistently associated with distinct signs of muscle damage and with a subsequent increased muscle bioenergetic dependence on anaerobic metabolism; however, the mechanisms that underlie these long-term energetic alterations are not accurately clarified. PURPOSE: To ascertain the effects of eccentric exercise on skeletal muscle mitochondrial function. METHODS: Twenty-four male Charles-River CD-1 mice (12 wks; ∼40 g) were randomly divided in 3 groups (n=8/group): control (C), sacrificed immediately (Ecc0h) and 48h after the exercise (Ecc48h). The exercise consisted of 120 min continuous downhill running at an average velocity of 16m/min. Blood was drawn for plasma creatine kinase (CK) activity and myoglobin (Mb) and interleukin-6 (IL-6) content assays. Skeletal muscle mitochondria were isolated for in vitro assessment of oxygen consumption and transmembrane potential (Dψ) using malate+pyruvate (MP) and succinate plus rotenone (SR). Mitochondrial osmotic swelling and Ca2+ fluxes were also measured to study mitochondrial susceptibility to permeability transition (mtPT). RESULTS: Eccentric exercise increased CK activity (1061±14 vs 119±17 vs 256±48 U/L, p<0.05), Mb and IL-6 content (5.9±0.8 vs 2.4±0.4 vs 2.8±0.5 pg/mL, p<0.05) in Ecc0h compared to C and Ecc48h, respectively. State 3 (177±10 vs 243±7 vs 218±11 nmolO2/mg prot/min, p<0.05) and maximal Dψ (191±2 vs 201±2 vs 200±1 mV, p<0.05) decreased in Ecc0h compared to C and Ecc48h, respectively with MP but not with SR. State 4 with SR increased in Ecc0h compared to C and Ecc48h (83±3 vs 74±4 vs 63±4 nmolO2/mg prot/min, respectively, p<0.05). Respiratory control ratio decreased in Ecc0h with MP (5.6±0.9 vs 8.4±0.4 vs 8.4±0.5, p<0.05) and SR (3.1±0.1 vs 3.4±0.1 vs 3.7±0.2, p<0.05) compared to C and Ecc48, respectively. No differences were found in ADP/O and lag phase with both substrates between groups. Compared to C and Ecc48h, Ecc0h showed enhanced swelling amplitude and increased Ca2+ release. CONCLUSION: Eccentric exercise resulted in transiently impairment of skeletal muscle mitochondrial function and increased susceptibility to Ca2+-induced mPT. However, mice were able to turn mitochondrial function back to baseline 48h after eccentric exercise. FCT grants SFRH/BPD/4225/2007; SFRH/BD/30906/2006.
Dynamic Recurrent Neural Network for Biped Robot Equilibrium Control: Preliminary Results (2006)

The purpose of the research addressed in this paper is to develop a real time neural control algorithm for the balance of a biped robot. Our approach is based on dynamic recurrent neural networks and dynamic backpropagation through time algorithm. The neural architecture and its learning process are validated on the control of the ROBIAN biped torso. The neural controller described is trained to compensate, by the torso’s joint motions, applied external perturbations. The algorithm is embedded in the real time electronic unit of the robot and online learning is achieved. The learning behavior and the control performances are the preliminary results presented in this paper. These experimental results show the ability and efficiency of the proposed approach.
Vector-quantized Image Modeling with Improved VQGAN (2021)

Pretraining language models with next-token prediction on massive text corpora has delivered phenomenal zero-shot, few-shot, transfer learning and multi-tasking capabilities on both generative and discriminative language tasks. Motivated by this success, we explore a Vector-quantized Image Modeling (VIM) approach that involves pretraining a Transformer to predict rasterized image tokens autoregressively. The discrete image tokens are encoded from a learned Vision-Transformer-based VQGAN (ViT-VQGAN). We first propose multiple improvements over vanilla VQGAN from architecture to codebook learning, yielding better efficiency and reconstruction fidelity. The improved ViT-VQGAN further improves vector-quantized image modeling tasks, including unconditional, class-conditioned image generation and unsupervised representation learning. When trained on ImageNet at \(256\times256\) resolution, we achieve Inception Score (IS) of 175.1 and Fr'echet Inception Distance (FID) of 4.17, a dramatic improvement over the vanilla VQGAN, which obtains 70.6 and 17.04 for IS and FID, respectively. Based on ViT-VQGAN and unsupervised pretraining, we further evaluate the pretrained Transformer by averaging intermediate features, similar to Image GPT (iGPT). This ImageNet-pretrained VIM-L significantly beats iGPT-L on linear-probe accuracy from 60.3% to 73.2% for a similar model size. VIM-L also outperforms iGPT-XL which is trained with extra web image data and larger model size.
Probabilistic Assessment of the Friendship Trail Bridge (2011)

The analysis performed in this study is theoretical and uses data found in the open literature rather than actual data for the bridge. The results presented indicate that the bridge is unlikely to meet a service life of an additional 20 years at reliability levels required by prevailing design codes while foregoing routine maintenance. In the light of the lower than typical reliability predicted by the analysis, more frequent bridge inspections will be needed to maintain safety in the event the bridge is repaired. vii The predictions are critically dependent on assumptions relating to the corrosion rate and statistical distributions of the load and the resistance. The validity of these assumptions needs to be verified from appropriate field inspection of the bridge. Without such verification, it will be unwise to base decisions exclusively on the reported theoretical analysis.
Informed web content delivery (2005)

With the maturation of the World Wide Web, a variety of technologies have been created to optimize content delivery, such as caching, content delivery networks, and prefetching. While these techniques can be effective, it remains unclear how and when they are best used. This dissertation examines current Web performance practices and optimizations and provides a tool to improve Web performance by facilitating informed optimization of Web site content delivery to the end user. 
This dissertation first examines Web site performance from a user perspective by characterizing whole-page performance. While many performance optimizations are very effective on individual objects, they may not be effective across the whole page. Similarly, other optimizations may only be effective at the page level. Using our Medusa proxy, we find that the optimization that has the largest impact is parallel connections. Other performance optimizations only provide incremental benefit. In some cases this is due to limited opportunity for use, and, in these cases, clients would see better performance if these optimizations were more heavily used. 
This dissertation then examines Web site performance from a Web site perspective by analyzing the properties of a wide variety of web servers, focusing on content delivery. We find that our workload contains a much higher degree of uncacheable responses than previously found and that current practices impede Web site performance. We also performed a simulation analysis to estimate the potential performance benefits of content delivery networks (CDNs) for these Web sites. Our results indicate that Web sites benefit from the use of a CDN, but that CDNs can decrease the average request rate more than the peak request rate. 
Lastly, this dissertation presents the design and implementation of the Cassandra Toolkit, a tool that identifies performance problems and estimates the effect of performance optimizations on a Web site (e.g., a cache or CDN). We also validate the Cassandra Toolkit against a real optimization by comparing the Cassandra Toolkit's cache analysis with a real cache on actual Web site workloads. Finally, we show how the Cassandra Toolkit can optimize several real Web sites in different ways.
Embedded monitors for detecting and preventing intrusions in cryptographic and application protocols. (2003)

There are two main approaches for intrusion detection: signature-based and anomaly-based. Signature-based detection employs pattern matching to match attack signatures with observed data making it ideal for detecting known attacks. However, it cannot detect unknown attacks for which there is no signature available. Anomaly-based detection builds a profile of normal system behavior to detect known and unknown attacks as behavioral deviations. However, it has a drawback of a high false alarm rate. In this thesis, we describe our anomaly-based IDS designed for detecting intrusions in cryptographic and application-level protocols. Our system has several unique characteristics, such as the ability to monitor cryptographic protocols and application-level protocols embedded in encrypted sessions, a very lightweight monitoring process, and the ability to react to protocol misuse by modifying protocol response directly.
Interpreting DNA Mixtures in Structured Populations (1999)

Abstract DNA profiles from multiple-contributor samples are interpreted by comparing the probabilities of the profiles under alternative propositions. The propositions may specify some known contributors to the sample and may also specify a number of unknown contributors. The probability of the alleles carried by the set of people, known or unknown, depends on the allelic frequencies and also upon any relationships among the people. Membership of the same subpopulation implies a relationship from a shared evolutionary history, and this effect has been incorporated into the probabilities. This acknowledgment of the effects of population structure requires account to be taken of all people in a subpopulation who are typed, whether or not they contributed to the sample.
Specialised pacemaking cells in the rabbit urethra (2000)

1. Collagenase dispersal of strips of rabbit urethra yielded, in addition to normal spindle-shaped smooth muscle cells, a small proportion of branched cells which resembled the interstitial cells of Cajal dispersed from canine colon. These were clearly distinguishable from smooth muscle in their appearance under the phase-contrast microscope, their immunohistochemistry and their ultrastructure. They had abundant vimentin filaments but no myosin, a discontinuous basal lamina, sparse rough endoplasmic reticulum, many mitochondria and a well-developed smooth endoplasmic reticulum. 2. Interstitial cells were non-contractile but exhibited regular spontaneous depolarisations in current clamp. These could be increased in frequency by noradrenaline and blocked by perfusion with calcium-free solution. In voltage clamp they showed abundant calcium-activated chloride current and spontaneous transient inward currents which could be blocked by chloride channel blockers. 3. The majority of smooth muscle cells were vigorously contractile when stimulated but did not show spontaneous electrical activity in current clamp. In voltage clamp, smooth muscle cells showed very little calcium-activated chloride current. 4. We conclude that there are specialised pacemaking cells in the rabbit urethra that may be responsible for initiating the slow waves recorded from smooth muscle cells in the intact syncitium.
Determination of the internal piezoelectric potentials and indium concentration in InGaN based quantum wells grown on relaxed InGaN pseudo-substrates by off-axis electron holography (2020)

Micro light emitting diodes have been grown by metal organic vapor phase epitaxy on standard GaN and partly relaxed InGaNOS substrates with the purpose of incorporating higher concentrations of indium for identical growth conditions. Green emission has been demonstrated at wavelengths of 500 nm for the GaN template and 525 and 549 nm for the InGaNOS substrates, respectively. The structure, deformation, indium concentration and piezoelectric potentials have been measured with nm-scale spatial resolution in the same specimens by transmission electron microscopy. We show by off-axis electron holography that the piezoelectric potential and information about the indium concentration from the mean inner potential are obtained simultaneously. By separating the components using a model, we show that for higher concentrations of indium in the quantum wells (QWs) grown on InGaNOS substrates, the piezoelectric potentials are reduced. The measurements of the indium concentrations by electron holography have been verified by combining energy dispersive x-ray spectrometry, x-ray diffraction and from the tensile deformation made by precession electron diffraction. A discussion of the limitations of these advanced aberration-corrected transmission electron microscopy techniques when applied to nm-scale QW structures is given.
Efficient 2D and 3D Facade Segmentation Using Auto-Context (2017)

This paper introduces a fast and efficient segmentation technique for 2D images and 3D point clouds of building facades. Facades of buildings are highly structured and consequently most methods that have been proposed for this problem aim to make use of this strong prior information. Contrary to most prior work, we are describing a system that is almost domain independent and consists of standard segmentation methods. We train a sequence of boosted decision trees using auto-context features. This is learned using stacked generalization. We find that this technique performs better, or comparable with all previous published methods and present empirical results on all available 2D and 3D facade benchmark datasets. The proposed method is simple to implement, easy to extend, and very efficient at test-time inference.
Theoretischer Bezugsrahmen (2004)

Jede Untersuchung verfügt über eine akademische Theorie als Fundament. Ist diese Theorie nur unzureichend ausgeformt, fällt das wissenschaftliche Gebäude durch Instabilität auf. Für die politikwissenschaftlichen Baustellen betreiben die Architekten Forschung, welches Fundament unter dem Gebäude des Parteiensystems zu finden sei. Jene Erkundungen gehen den Fragen nach, wie Parteien entstehen, welche Schichten sie an sich binden, welche Rolle sie in der politischen Ordnung einnehmen, wie sie staatliche Organe mit ihren Repräsentanten beschicken.
Conversion of α,β-Unsaturated Aldehydes into Saturated Esters: An Umpolung Reaction Catalyzed by Nucleophilic Carbenes (2005)

N-Heterocyclic carbenes derived from benzimidazolium salts are effective catalysts for generating homoenolate species from alpha,beta-unsaturated aldehydes. These nucleophilic intermediates can be protonated, and the resulting activated carbonyl unit is trapped with an alcohol nucleophile, thereby promoting a highly efficient conversion of an alpha,beta-unsaturated aldehyde into a saturated ester. A kinetic resolution of secondary alcohols can be achieved using chiral imidazoylidene catalysts. [reaction: see text]
Doubly Resonant Photonic Antenna for Single Infrared Quantum Dot Imaging at Telecommunication Wavelengths (2017)

Colloidal quantum dots (CQDs) have drawn strong interest in the past for their high prospects in scientific, medical, and industrial applications. However, the full characterization of these quantum emitters is currently restricted to the visible wavelengths, and it remains a key challenge to optically probe single CQDs operating in the infrared spectral domain, which is targeted by a growing number of applications. Here, we report the first experimental detection and imaging at room temperature of single infrared CQDs operating at telecommunication wavelengths. Imaging was done with a doubly resonant bowtie nanoaperture antenna (BNA) written at the end of a fiber nanoprobe, whose resonances spectrally fit the CQD absorption and emission wavelengths. Direct near-field characterization of PbS CQDs reveal individual nanocrystals with a spatial resolution of 75 nm (λ/20) together with their intrinsic 2D dipolar free-space emission properties and exciton dynamics (blinking phenomenon). Because the doubly resonant BNA is strongly transmissive at both the CQD absorption and the emission wavelengths, we are able to perform all-fiber nanoimaging with a standard 20% efficiency InGaAs avalanche photodiode (APD). The detection efficiency is predicted to be 3000 fold larger than with a conventional circular aperture tip of the same transmission area. Double resonance BNA fiber probes thus offer the possibility of exploring extreme light-matter interaction in low band gap CQDs with current plug-and-play detection techniques, opening up new avenues in the fields of infrared light-emitting devices, photodetectors, telecommunications, bioimaging, and quantum information technology.
Optimization of coal liquefaction reactors (1983)

Abstract The method of Lagrangian multipliers of classical calculus is applied to obtain the optimum operating conditions of three continuous stirred tank reactors (CSTR) in series, to liquefy coal with minimum gas yield. In the formulation of the problem, the gas conversion was assumed to be the cost function. Results obtained were supported by the experimental findings in terms of liquefaction temperatures, reaction times, and conversion of coal into various liquefaction products.
Sigma-delta modulation for audio DSP (1993)

An automated procedure is presented for the design of high-order sigma delta single stage modulators for use with high-quality digital audio systems. Immediate application to data conversion is discussed, with the advantage of relaxed analogue component specifications due to the one-bit quantiser. Further, a novel application is presented, applying the relatively new technique of digital bitstream processing to a digital audio mixing structure. Initial simulations confirm the viability of this approach from a feasibility viewpoint, and the ultimate simplicity of the one bit signal format suggests considerable application opportunities in commercial digital audio products.