gebhart/patrepeval huggingface dataset:
A unified approach to ranking in probabilistic databases (2009)

The dramatic growth in the number of application domains that naturally generate probabilistic, uncertain data has resulted in a need for efficiently supporting complex querying and decision-making over such data. In this paper, we present a unified approach to ranking and top-k query processing in probabilistic databases by viewing it as a multi-criteria optimization problem, and by deriving a set of features that capture the key properties of a probabilistic dataset that dictate the ranked result. We contend that a single, specific ranking function may not suffice for probabilistic databases, and we instead propose two parameterized ranking functions , called PRF ω and PRF e , that generalize or can approximate many of the previously proposed ranking functions. We present novel generating functions -based algorithms for efficiently ranking large datasets according to these ranking functions, even if the datasets exhibit complex correlations modeled using probabilistic and/xor trees or Markov networks . We further propose that the parameters of the ranking function be learned from user preferences, and we develop an approach to learn those parameters. Finally, we present a comprehensive experimental study that illustrates the effectiveness of our parameterized ranking functions, especially PRF e , at approximating other ranking functions and the scalability of our proposed algorithms for exact or approximate ranking.
Object tracking and detection after occlusion via numerical hybrid local and global mode-seeking (2008)

Given an object model and a black-box measure of similarity between the model and candidate targets, we consider visual object tracking as a numerical optimization problem. During normal tracking conditions when the object is visible from frame to frame, local optimization is used to track the local mode of the similarity measure in a parameter space of translation, rotation and scale. However, when the object becomes partially or totally occluded, such local tracking is prone to failure, especially when common prediction techniques like the Kalman filter do not provide a good estimate of object parameters in future frames. To recover from these inevitable tracking failures, we consider object detection as a global optimization problem and solve it via Adaptive Simulated Annealing (ASA), a method that avoids becoming trapped at local modes and is much faster than exhaustive search. As a Monte Carlo approach, ASA stochastically samples the parameter space, in contrast to local deterministic search. We apply cluster analysis on the sampled parameter space to redetect the object and renew the local tracker. Our numerical hybrid local and global mode-seeking tracker is validated on challenging airborne videos with heavy occlusion and large camera motions. Our approach outperforms state-of-the-art trackers on the VIVID benchmark datasets.
Parkinsonian features of eight pathologically diagnosed cases of diffuse lewy body disease (1995)

Premortem diagnosis of diffuse Lewy body disease (DLBD) is difficult, and knowledge of the parkinsonian features of DLBD might facilitate the diagnosis. In this study, we compared the parkinsonian syndrome of DLBD and Parkinson's disease (PD). We retrospectively reviewed the charts of Columbia-Presbyterian Medical Center (CPMC) Brain Bank cases (1989-1993) with pathologically diagnosed DLBD or PD, and the literature on the parkinsonian features in DLBD patients presenting with parkinsonism. Parkinsonism accompanied or preceded cognitive/psychiatric changes in most CPMC cases (DLBD 100%, PD 88%). DLBD had an earlier mean age of onset than PD did (57 versus 64 years), a similar male:female ratio (1.7:1 versus 1.9:1), and similar mean disease duration (12-13 years). Cognitive/psychiatric changes were less frequent in PD than in DLBD (65 versus 100%) (p = 0.025). Rest tremor was specifically mentioned in 29% of DLBD versus 56% of PD (p = 0.10). Bradykinesia was less common in PD (56% versus 86%) (p = 0.05). All those with PD responded to L-Dopa, as did all those with DLBD who received L-Dopa. In conclusion, there are subtle differences between PD and DLBD in age of onset, frequency of cognitive/psychiatric changes, bradykinesia, and rest tremor. However, even when taken together, these cannot be used to distinguish these entities.
Analysis of Fibrogenic Processes in Denervated Tissues of Spinal Cord Injury Patients (1989)

To test the hypothesis that altered collagen metabolism is a contributing factor in the apparent delayed wound healing in denervated regions of spinal cord injury (SCI) patients, a tissue implant (PVA) was used to directly measure collagen deposition. Sterile PVA implants were placed subcutaneously in the inner aspect of the upper arm above the cord injury (innervated) and in the inner aspect of the upper leg below the cord injury (denervated) of 20 spinal cord injury patients and compared to eight healthy volunteers. On day 14, the implants were removed and analyzed histologically by trichrome stain and biochemically for hydroxyproline as a measure of collagen deposition. No remarkable histologic differences were observed in the sponge material removed from the upper regions compared to the lower denervated regions of the spinal cord injury patients. Sponges from both areas were infiltrated with fibroblasts containing well-developed rough endoplasmic reticulum and large quantities of trichrome-positive collagen. Likewise, upper and lower histology of controls was identical and nondistinguishable from the corresponding sections obtained from the spinal cord injury patients. Quantitation of the hydroxyproline in the arms of the spinal cord injury patients (n = 20) showed 4.3 +/- 0.7 nmol hydroxyproline per milligram of sponge compared to 4.1 +/- 0.4 nmol/mg in the denervated regions of the lower limb. The hydroxyproline content in the arms of control volunteers was 5.2 +/- 0.7 nmol/mg compared to 3.9 +/- 0.8 nmol/mg in the leg (n = 8). These observations suggest that fibrogenic processes in denervated regions are not reduced significantly compared to innervated regions.
Multisensing Emissive Pyrimidine (2011)

Fluorescent nucleoside analogs, commonly used to explore nucleic acid dynamics, recognition and damage, frequently respond to a single environmental parameter. Herein we address the development of chromophores that can simultaneously probe more than one environmental factor while having each associated with a unique spectroscopic signature. We demonstrate that an isomorphic emissive pyridine-modified 2-deoxy-uridine 1, containing multiple sensory elements, responds to changes in acidity, viscosity, and polarity. Protonation of the pyridine moiety (pK(a) 4.4) leads to enhanced emission (λ(em) =388 nm) and red-shifted absorption spectra (λ(abs) =319 nm), suggesting the formation of an intramolecular hydrogen bond with the neighboring pyrimidine carbonyl. This "locked" conformation can also be mimicked by increasing solvent viscosity, resulting in a stark enhancement of emission quantum yield. Finally, increasing solvent polarity substantially impacts the chromophore's Stokes shift [from 5.8×10(3) cm(-1) at E(T) (30)=36.4 kcal mol(-1) to 9.3 ×10(3) cm(-1) at E(T) (30)=63.1 kcal mol(-1)]. The opposite effect is seen for the impact of solvent polarity of the protonated form. The characteristic photophysical signature induced by each parameter facilitates the exploration of these environmental factors both individually and simultaneously.
Tissue plasminogen activator promotes the effects of corticotropin-releasing factor on the amygdala and anxiety-like behavior (2004)

Stress-induced plasticity in the brain requires a precisely orchestrated sequence of cellular events involving novel as well as well known mediators. We have previously demonstrated that tissue plasminogen activator (tPA) in the amygdala promotes stress-induced synaptic plasticity and anxiety-like behavior. Here, we show that tPA activity in the amygdala is up-regulated by a major stress neuromodulator, corticotropin-releasing factor (CRF), acting on CRF type-1 receptors. Compared with WT, tPA-deficient mice responded to CRF treatment with attenuated expression of c-fos (an indicator of neuronal activation) in the central and medial amygdala but had normal c-fos responses in paraventricular nuclei. They exhibited reduced anxiety-like behavior to CRF but had a sustained corticosterone response after CRF administration. This effect of tPA deficiency was not mediated by plasminogen, because plasminogen-deficient mice demonstrated normal behavioral and hormonal changes to CRF. These studies establish tPA as an important mediator of cellular, behavioral, and hormonal responses to CRF.
Presentación del prototipo final a la Competición "Chem-E-Car" en el 10º Congreso Mundial de Ingeniería Química (2019)

El proyecto consistio en la presentacion del prototipo Chem-E-Car desarrollado en la UCM en la competicion mundial que se celebro durante el transcurso del Congreso Mundial de Ingenieria Quimica (Barcelona, 30 septiembre-2 de octubre de 2017).
ChemInform Abstract: Bioactive Marine Metabolites. Part 54. Toxadocials B (I), C (II) and Toxadocic Acid A (III): Thrombin‐Inhibitory Aliphatic Tetrasulfates from the Marine Sponge, Toxadocia cylindrica. (1994)

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.
MUM: a middleware for the provisioning of continuous services to mobile users (2004)

Advances in wireless solutions and portable devices are enabling new challenging service scenarios where mobile users are willing to access ubiquitous and continuous services. This calls for novel middleware capable of tailoring service contents to client characteristics and of following client movements at provision time. The paper proposes MUM, a dynamic and flexible middleware to support continuous services to mobile users in ubiquitous scenarios. MUM performs service configuration by dynamically distributing middleware components to intermediate nodes along the client-server path and provides service session continuity by automatically migrating the session state in response to user movements during service provisioning. MUM exploits mobile agents to move both middleware components and session state, where and when needed, while it allows service developers to continue using the traditional client/server model for MUM-based application components. In addition, The work presents the implementation of a Video-on-Demand service on top of MUM, with the goal of verifying the feasibility of our approach when applied to the challenging multimedia application area. First experimental results show that, notwithstanding the application-level approach, the MUM configuration/session migration times are compatible even with the strict requirements imposed by multimedia distribution over the best-effort Internet.
Silicon Integrated Waveguide Devices for Filtering and Wavelength Demultiplexing (2010)

Following different approaches, we have realized a number of different silicon integrated demultiplexers for WDM-based on-chip optical interconnects. We compare these devices based on their size, transmission loss, pass-band shape and tolerance against process variations.
A REVIEW OF ASSEMBLED POLYACRYLONITRILE-BASED CARBON NANOFIBER PREPARED ELECTROSPINNING PROCESS (2011)

Electrospinning is a very simple and versatile process by which polymer nanofibers with diameters ranging from a few nanometers to several micrometers can be produced using an electrostatically driven jet of polymer solution (or polymer melt). Significant progress has been made in this process throughout the last decade and the resultant nanostructures have been exploited to a wide range of applications. An important feature of the electrospinning process is that electrospinning nanofibers are produced in atmospheric air and at room temperature. This paper reviews the assembled polyacrylonitrile (PAN)-based carbon nanofibers with various processing parameters such as electrical potential, distance between capillary and collector drum, solution flow rate (dope extrusion rate), and concentration of polymer solution. The average fiber diameter would increase with increasing concentration of the polymer solution and the flow rate. Therefore, the screen distance could also increase but the average electrical potential of the fibers diameter decreases. Electrospinning process can be conducted at higher electrical potentials, lower flow rate, nearer screen distance, and higher concentrations of dope.
Simulation of fluid flow and collection efficiency for an SEA multi-element probe (2014)

Numerical simulations of fluid flow and collection efficiency for a Science Engineering Associates (SEA) multi-element probe are presented. Simulation of the flow field was produced using the Glenn-HT Navier-Stokes solver. Three dimensional unsteady results were produced and then time averaged for the collection efficiency results. Three grid densities were investigated to enable an assessment of grid dependence. Collection efficiencies were generated for three spherical particle sizes, 100, 20, and 5 micron in diameter, using the codes LEWICE3D and LEWICE2D. The free stream Mach number was 0.27, representing a velocity of approximately 86 ms. It was observed that a reduction in velocity of about 15-20 occurred as the flow entered the shroud of the probe.Collection efficiency results indicate a reduction in collection efficiency as particle size is reduced. The reduction with particle size is expected, however, the results tended to be lower than previous results generated for isolated two-dimensional elements. The deviation from the two-dimensional results is more pronounced for the smaller particles and is likely due to the effect of the protective shroud.
Moles and Site-Specific Risk of Nonfamilial Cutaneous Malignant Melanoma in Womene (1989)

We examined the relationship between self-reported mole counts and cutaneous melanoma with respect to anatomic site in 110 case and 231 control female nurses. Counts of moles on the lower leg were better predictors of melanoma risk than were counts of moles on the arm. The relative risk for the highest quintile of lower leg mole counts versus no lower leg moles was 4.2. Mole counts at each site (arm, thigh, and lower leg) were associated with risk of melanoma of the trunk and lower leg, but none were associated with the risk of melanoma of the upper extremity. The absence of direct site-specificity suggests that mole counts primarily indicate systemic melanoma risk, rather than direct risk from the moles themselves.
A low power input amplifier for bio-signal acquisition in 28 nm FDSOI technology (2017)

In this paper a low power amplifier for bio-signal acquisition is described. The design takes benefit of UTBB-FDSOI 28nm technology and exploits bulk under the buried oxide as a second gate of FET device. This amplifier exhibits low supply current of 25nA, while keeping input noise at 24 μV in bio-signal frequency band. The gain of the amplifier is 71dB.
Clinical Science (1983)

A three-dimensional finite element model has been developed for the purpose of analyzing the stress distribution in a human mandibular right first molar. The model takes into account the non-symmetric geometry and loading, and the material inhomogeneities of the tooth. Comparisons with existing two-dimensional analyses are given.
Vertical bulb unit commissioned in Japan (2004)

The sexually dimorphic nucleus of the rat medial preoptic area (SDN-POA) has a volume five times larger in the adult male compared with that of the adult female. In the present study, the effects of discrete electrolytic destruction of the SDN-POA or other specific medial preoptic (MPOA) regions on masculine sexual behavior were determined in adult, sexually experienced male rats. Small lesions encompassing the SDN-POA had no effect on the maintenance of copulatory behavior. Lesions of similar size placed within the ventral or anterio-dorsal MPOA also did not consistently affect the display of masculine sexual behavior. However, animals that received small lesions within their dorsal MPOA showed a substantial, long-term decrease in number of mounts, intromissions, and ejaculations compared to these parameters in sham-lesioned control rats, thus indicating a lesion-induced disruption of those neural mechanisms mediating these behaviors. Collectively these data suggest that the SDN-POA is not critical for a full expression of male sexual behavior and that the dorsal MPOA may be more important than other MPOA regions for copulatory behavior.
Efficient car recognition policies (2002)

This paper addresses the challenges of producing recognition systems that consider both of these objectives. In general, a "(recognition) policy" specifies when to apply which "imaging operators", which can range from low-level edge-detectors and region-growers through high-level token-combination-rules and expectation-driven object-detectors. Given the costs of these operators and the distribution of possible images, we can determine both the expected cost and expected accuracy of any such policy. Our task is to find a maximally effective policy - typically one with sufficient accuracy, whose cost is minimal. We compare various ways to produce such policies in general, and show that policies that select the operators that maximize information gain per unit cost work effectively.
Chemoenzymatic synthesis of daptomycin analogs active against daptomycin-resistant strains (2020)

Daptomycin is a last resort antibiotic for the treatment of infections caused by many Gram-positive bacterial strains, including vancomycin-resistant Enterococcus (VRE) and methicillin- and vancomycin-resistant Staphylococcus aureus (MRSA and VRSA). However, the emergence of daptomycin-resistant strains of S. aureus and Enterococcus in recent years has renewed interest in synthesizing daptomycin analogs to overcome resistance mechanisms. Within this context, three aromatic prenyltransferases have been shown to accept daptomycin as a substrate, and the resulting prenylated analog was shown to be more potent against Gram-positive strains than the parent compound. Consequently, utilizing prenyltransferases to derivatize daptomycin offered an attractive alternative to traditional synthetic approaches, especially given the molecule's structural complexity. Herein, we report exploiting the ability of prenyltransferase CdpNPT to synthesize alkyl-diversified daptomycin analogs in combination with a library of synthetic non-native alkyl-pyrophosphates. The results revealed that CdpNPT can transfer a variety of alkyl groups onto daptomycin's tryptophan residue using the corresponding alkyl-pyrophosphates, while subsequent scaled-up reactions suggested that the enzyme can alkylate the N1, C2, C5, and C6 positions of the indole ring. In vitro antibacterial activity assays using 16 daptomycin analogs revealed that some of the analogs displayed 2-80-fold improvements in potency against MRSA, VRE, and daptomycin-resistant strains of S. aureus and Enterococcus faecalis. Thus, along with the new potent analogs, these findings have established that the regio-chemistry of alkyl substitution on the tryptophan residue can modulate daptomycin's potency. With additional protein engineering to improve the regio-selectivity, the described method has the potential to become a powerful tool for diversifying complex indole-containing molecules. KEY POINTS: • CdpNPT displays impressive donor promiscuity with daptomycin as the acceptor. • CdpNPT catalyzes N1-, C2-, C5-, and C6-alkylation on daptomycin's tryptophan residue. • Differential alkylation of daptomycin's tryptophan residue modulates its activity.
Abstract 447: Integrated omics modeling of transcriptional regulation in medulloblastoma subtypes (2020)

Abstract Medulloblastoma (MB) is one of the most common pediatric brain tumors. Current treatment options carry substantial risk for lifelong cognitive and neurological impairment. Consequently, there is a pressing need to elucidate molecular mechanisms with the ultimate goal of developing targeted tumor-specific therapies. In a recent study on proteomes and phospho-proteomes of primary MB tumors, we identified proteomic MB subtypes that were not apparent from transcriptional or methylation data. To identify gene regulatory circuitries that drive these MB subtypes, we have now mapped accessible chromatin and 3D chromosome conformation in 23 and 13 MB tumors from the same cohort, using ATAC-seq and Hi-C respectively. We identify subtype-specific accessible regulatory chromatin regions, including a subset of regions not identifiable by the enhancer mark H3K27ac. We associate regulatory regions to their target gene promoters by correlating transcription with ATAC-seq signal strength, and confirm these relationships using the newly generated Hi-C data. Using an unpublished adaptation of the GSEA algorithm, which we tailored for an enrichment analysis of non-coding regulatory elements instead of genes, we identify transcription factors and master regulators with binding sites specific to an MB subtype. By associating these master regulators with their transcriptional targets, we have derived models of regulatory circuitry in MB which implicate central mechanisms of MB pathogenesis and may inform future therapeutic targeting. Citation Format: Owen S. Chapman, Tobias Ehrenberger, Tenley C. Archer, Maxwell P. Gold, Filip Mundt, Miriam Adam, Clarence K. Mah, Karsten Krug, Sahaana Chandran, Jesse R. Dixon, Scot L. Pomeroy, Ernest Fraenkel, Jill P. Mesirov, Lukas Chavez. Integrated omics modeling of transcriptional regulation in medulloblastoma subtypes [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 447.
Interacting Multiple Model and Probabilistic Data Association Filter on Radar Tracking for ATM System (2012)

According to the International Civil Aviation Organization’s plan, the Communications, Navigation, Surveillance, and Air Traffic Management (CNS/ATM) system based on the Global Navigation Satellite System (GNSS) technology should be implemented to replace the traditional Air Traffic Control (ATC) system based on ground-based radar. The major concern of the CNS/ATM system may experience service interruption when the GNSS signal blocked by either intentional or unintentional radio-frequency interference. To maintain the normal operation of the CNS/ATM system, a promising approach is to use the existing ground-based radar system to provide navigation and surveillance services for the ATM system. To utilize the existing radar system as a backup solution, the tracking capability of the radar system has to be enhanced to be compatible with standard GNSS positioning services. This study implements a tracking algorithm to improve the aircraft tracking performance of the radar system. The proposed tracking algorithm is called the Interacting Multiple Model and Probabilistic Data Association filter (IMMPDAF). The IMMPDAF can accurately track an aircraft in a cluttered environment under various maneuver modes. The procedure of implementing the IMMPDAF into a radar system is discussed. The tracking performance of the IMMPDAF is compared with that of a filter that uses the nearest neighbor method as well as the standard Kalman filter. Additionally, the computation loads of these filters are evaluated. Finally, real radar data collected by the Civil Aeronautics Administration of Taiwan are used to demonstrate the tracking performance improvement with the IMMPDAF.