gebhart/patrepeval huggingface dataset:
MetaProSIP: Automated Inference of Stable Isotope Incorporation Rates in Proteins for Functional Metaproteomics (2014)

We propose a joint experimental and theoretical approach to the automated reconstruction of elemental fluxes in microbial communities. While stable isotope probing of proteins (protein-SIP) has been successfully applied to study interactions and elemental carbon and nitrogen fluxes, the volume and complexity of mass spectrometric data in protein-SIP experiments pose new challenges for data analysis. Together with a flexible experimental setup, the novel bioinformatics tool MetaProSIP offers an automated high-throughput solution for a wide range of (13)C or (15)N protein-SIP experiments with special emphasis on the analysis of metaproteomic experiments where differential labeling of organisms can occur. The information calculated in MetaProSIP includes the determination of multiple relative isotopic abundances, the labeling ratio between old and new synthesized proteins, and the shape of the isotopic distribution. These parameters define the metabolic capacities and dynamics within the investigated microbial culture. MetaProSIP features a high degree of reproducibility, reliability, and quality control reporting. The ability to embed into the OpenMS framework allows for flexible construction of custom-tailored workflows. Software and documentation are available under an open-source license at www.openms.de/MetaProSIP.
Model-free quantification of shear wave velocity and attenuation in tissues and its in vivo application (2013)

We validate a technique for model-free measurement of shear wave velocity and attenuation. A mechanical shaker was used to excite harmonic plane and cylindrical waves in phantoms and excised tissue. Radiation force was used to excite impulsive cylindrical waves. 2D FFT of the displacement yielded the k-space whose coordinates are frequency and the wave number. The shear wave velocity at each frequency was obtained by finding the maximum at the given frequency in k-space and dividing the frequency coordinate by the wave number coordinate. The attenuation (α) at a given frequency was calculated using α = FWHM × π/√3, where FWHM is the full width at half maximum of the k-space peak along the given frequency. This method was applied to measure shear wave velocity and attenuation of transplanted kidneys and livers, and in the thyroid tumor, and compare it to the healthy tissues. The velocities and attenuations at each frequency for various excitation methods agree within one standard deviation. The k-space estimates of velocity and attenuation agreed with those obtained using the phase gradient (velocity) and amplitude decay (attenuation). The transplanted organs and the thyroid tumor had higher velocity and lower attenuation than healthy tissues.
Cytomegalovirus induces interstitial lung disease in allogeneic bone marrow transplant recipient rats independent of acute graft-versus-host response. (1996)

Interstitial lung disease (ILD) after allogeneic bone marrow transplantation (BMTx) is an important clinical problem in terms of diagnosis, therapy, and pathogenesis. Graft-versus-host disease (GvHD) and cytomegalovirus (CMV) infection seem to be major risk factors for ILD, but their role in the pathogenesis is not well established. We previously reported CMV-induced ILD in allogeneic bone marrow recipient rats, which was prevented by antiviral drug treatment. In this paper, we describe the pathology of ILD in allogeneic bone marrow transplant recipient rats and the relation of ILD with CMV infection and GvHD. Brown Norway rats received an allogeneic (Lewis) BMTx and rat CMV infection, after an allogeneic (Lewis) lung transplantation and immunosuppression. CMV infection was recorded by the amount of infectious virus and viral antigens in the lung. ILD was monitored by the presence of diffuse histopathologic changes in the alveolar septal wall. GvHD was scored by the relative splenic weights and the presence of perivascular infiltrates in the lung. Cells expressing CMV antigens were more numerous in the alveolar septa of the allogeneic recipient lungs than in the syngeneic donor lungs (p < 0.05). The high viral load in the recipient lung of allogeneic BMTx recipient rats was accompanied by diffuse ILD, marked by extensive microvascular damage and congestion of the alveolar septa. ILD was observed neither in the syngeneic donor lung nor in both lungs of mock-infected animals. GvHD was not observed in rat-CMV-infected or in mock-infected animals. Our results indicate that CMV induces microvascular damage, resulting in ILD. This process is independent of GvHD.
Prior velocity modeling and uncertainty analysis with basin modeling and rock physics constraints (2019)

We present a methodology for prior velocity modeling that facilitates incorporation of information regarding the geological history of a basin as well as different types of well data. Our approach relies on linking velocity models to the basin modeling outputs of porosity, mineral volume fractions and pore pressure through rock physics models. We account for basin modeling uncertainties by defining prior probability distributions on uncertain parameters and performing Monte Carlo basin simulations. We perform probabilistic calibration of the basin model outputs by defining data likelihood distributions to represent data uncertainty. Outputs of the basin models exhibiting acceptable fits to calibration data are used in rock physics modeling to obtain multiple velocity realizations. We apply our methodology to a 2D real field case and demonstrate that the geologically and physically consistent velocity models obtained by our approach are comparable to tomographic inversion in terms of quality of the corresponding depth migrated seismic images. Presentation Date: Tuesday, September 17, 2019 Session Start Time: 1:50 PM Presentation Start Time: 3:55 PM Location: 217B Presentation Type: Oral
Oxygen Sensing and the Transcriptional Regulation of Oxygen-Responsive Genes in Yeast (1998)

The budding yeast Saccharomyces cerevisiae is a facultative aerobe that responds to changes in oxygen availability (and carbon source) by initiating a biochemically complex program that ensures that energy demands are met under two different physiological states: aerobic growth, supported by oxidative and fermentative pathways, and anaerobic growth, supported solely by fermentative processes. This program includes the differential expression of a large number of genes, many of which are involved in the direct utilization of oxygen. Research over the past decade has defined many of the cis-sites and trans-acting factors that control the transcription of these oxygen-responsive genes. However, the manner in which oxygen is sensed and the subsequent steps involved in the transduction of this signal have not been precisely determined. Heme is known to play a pivotal role in the expression of these genes, acting as a positive modulator for the transcription of the aerobic genes and as a negative modulator for the transcription of the hypoxic genes. Consequently, cellular concentrations of heme, whose biosynthesis is oxygen-dependent, are thought to provide a gauge of oxygen availability and dictate which set of genes will be transcribed. But the precise role of heme in oxygen sensing and the transcriptional regulation of oxygen-responsive genes is presently unclear. Here, we provide an overview of the transcriptional regulation of oxygen-responsive genes, address the functional roles that heme and hemoproteins may play in this regulation, and discuss possible mechanisms of oxygen sensing in this simple eukaryotic organism.
Determination of elemental composition in geochemical exploration using a 14-MeV neutron generator (1981)

The use of prompt neutron-gamma techniques is well established in the areas of geochemical exploration and environmental monitoring. However, the problems associated with the determination of absolute composition, as compared to elemental identification, can be substantial. For example, in borehole work, the concentration of water can significantly modify the gamma-ray spectrum of the surrounding material. In marine work, the presence of Cl in the water can seriously mask important gamma-ray lines from elements of environmental interest. In order to study these problems, the authors have been using a 14-MeV pulsed neutron generator and a IGe detector system for field measurements where the amount of water in the material has been varied. In addition, they have been doing systematic laboratory measurements of monoelemental samples in water, to determine the detection sensitivity, linearity, and the gamma-ray lines most useful for analysis. These have included elements of environmental interest, e.g. Cd, Ni, Cr and Zn, in the presence of Cl.
Food purchase diversity across U.S. markets (2000)

Growth in the number of food products and brands carried by grocery stores implies a preference for diversity. We examine the factors that affect the variety of food purchases across U.S. markets. Three measures of variety, based on market-level sales of both grocery categories and RTE cereal brands, are regressed on various population and market characteristics. We find that markets with a high proportion of low-income individuals exhibit less variety both in terms of grocery categories and breakfast cereal brands. We also find that racial diversity and average store size are important factors in explaining diversity of grocery purchases across markets, but are less important in explaining the variety of cereal brand purchases. [EconLit citations: D120, L660.] © 2000 John Wiley & Sons, Inc.
Domisilica: Providing Ubiquitous Access to the Home (1997)

The Domisilica project is exploring future computing environments centered around the home. We envision a future in which objects in the home, such as appliances and rooms, are enhanced with computational capabilities that make them accessible away from the home. Our approach has been to add computational power to real world objects located in the home, and to provide a centralized model of the home which can be used to integrate a wide variety of services and is accessible remotely. This paper focuses on issues of interface modes and accessibility which arose as we developed Domisilica. These include extending the affordances of real world objects to provide new services, providing remote access through a variety of connections both impoverished and broad, and providing universal access for all types of people including people with disabilities, children, and older adults. KEYWORDS: Computing in the home, ubiquitous computing, dynamically generated interfaces, multimodal interfaces ...
Insights into Fast Lithium and Sodium-Ion Conduction in Solid Electrolyte and Cathode Materials (2016)

Major advances in rechargeable batteries require the discovery and characterisation of new materials. It is clear that a complete understanding of the properties of electrode and electrolyte materials for both Li- and Na-ion batteries requires fundamental knowledge of their underlying structural, ion diffusion and surface properties on the atomic- and nano-scales. In this context, advanced materials modelling [1] combined with structural and electrochemical techniques are now powerful tools for investigating these properties. This talk will highlight recent studies [2,3] in the following areas: (i) structural and mechanistic insights into fast lithium-ion conduction in Li 4 SiO 4 -Li 3 PO 4 solid electrolytes; (ii) ion diffusion pathways in polyanionic cathode materials such as Li-sulfates (e.g. LiFeSO 4 OH) and Na-phosphates (e.g. Na 2 FePO 4 F, NaFePO 4 ). References [1] M.S. Islam; C.A.J. Fisher, Chem. Soc. Rev. , 43 , (2014) 185. [2] Y. Deng et al., J. Amer. Chem. Soc ., 137 (2015) 9136. [3] S.M. Wood et al., J. Phys. Chem. C., 119 (2015) 15935.
Indications for Therapy for Fungemia in Postoperative Patients (1982)

We reviewed the clinical courses of 63 surgical patients who had experienced one or more days of fungemia, to determine the clinical setting for such infections and to define indications for systemic therapy. Fifty-one patients experienced fungemia as a late complication of intraperitoneal infection. Candida was identified as part of a polymicrobial flora in 70%. If untreated, the mortality was 83% (30 of 36). No untreated patients with fungemia for more than one day survived. Adequate therapy with amphotericin B (total dose, greater than 3 mg/kg) improved survival to 67% (ten of 15). Autopsies performed in 20 cases revealed visceral Candida microabscesses in seven, with the gastrointestinal tract (12) and intraabdominal abscess (five) as the most common sources of fungi. These data support the concept of Candida as an important participant in polymicrobial infection and recommend therapy with amphotericin B for patients with intraperitoneal infection experiencing fungemia.
INTERPOLATION AND RANGE EXTRAPOLATION OF HRTFS (2004)

The Head Related Transfer Function (HRTF) characterizes the scat-tering properties of a person’s anatomy (especially the pinnae, head and torso), and exhibits considerable person-to-person variability. It is usually measured as a part of a tedious experiment, and this leads to the function being sampled at a few angular locations. When the HRTF is needed at intermediate angles its value must be interpolated. Further, its range dependence is also neglected, which is invalid for nearby sources. Since the HRTF arises from a scattering process, it can be characterized as a solution of a scatter-ing problem. In this paper, we show that by taking this viewpoint and performing some analysis we can express the HRTF in terms of a series of multipole solutions of the Helmholtz equation. This approach leads to a natural solution to the problem of HRTF inter-polation. Furthermore, we show that the range-dependence of the HRTF in the near-field can also be obtained by extrapolation from measurements at one range. 1.
Microbiological quality of non-sterile pharmaceutical products (2014)

In microbiological terms, pharmaceutical products can be divided into two groups: sterile and non-sterile. Non-sterile drugs must satisfy the appropriate microbiological purity criteria which are included in pharmacopoeial monographs. Pharmacopoeial studies are prepared specifically with a view to ensuring that the medicinal product is therapeutically effective and safe for the patient. The analysis comprised the results of microbiological purity tests performed before the products are marketed. Total of 1285 samples of non-sterile drugs manufactured by different pharmaceutical plants in Polish were taken into study. The microbiological quality of drugs was assessed in accordance with the criteria included in the European Pharmacopoeia (EP). An analysis of test results demonstrated that the percentage of non-compliant samples was 1.87%. The groups of drugs, which the most often did not satisfy EPs' requirements, were drugs containing raw materials of natural origin (5.7%). The samples of studied drugs that did not meet the criteria contained in EP, exceed the maximum allowable microbiological count limits and contained microbes whose presence is prohibited. The most common non-compliance was the excessive levels of the maximum acceptable fungal count (n = 12) and the excessive the maximum acceptable aerobic microbial count (n = 10).
Smart cards: a guide to building and managing smart card applications (1998)

Evolution of the Smart Card Industry and Market Trends. Smart Card Architectures. Standards and Specifications. Security and Cryptography. Manufacturing the Smart Card. DESIGN CONSIDERATIONS. System Implementation Considerations. Functional Design and Data Layout Considerations. Operating Systems and the Card-to-Terminal Interface. System and Data Integrity. IMPLEMENTATION. Smart Card Development Skills, Methods, and Tools. Smart Card Testing and Certification. Implementing and Operating a Smart Card System. The Future of the Industry. Glossary. Appendices. Index.
Discriminative duration modeling for speech recognition with segmental conditional random fields (2011)

This paper describes a new approach to modeling duration for LVCSR using SCARF, a toolkit for speech recognition with segmental conditional random fields. We utilize SCARF's ability to integrate long-span, segment-level features to design and test duration models that help discriminate between correct and incorrect word hypotheses. We show that the duration distributions of correct and incorrect word hypotheses differ. Given a word hypothesis in the lattice and its duration, conditional length probabilities are integrated to the SCARF system as duration features. We evaluate three kinds of duration features on Broadcast News: word, pre- and post-pausal durations, and word span confusions. Adding the duration features to SCARF results in an up to 0.3% improvement over a state of-the-art discriminatively trained baseline of 15.3% WER on a Broadcast News task.
Human amygdala activation during rapid eye movements of rapid eye movement sleep: an intracranial study (2016)

The amygdaloid complex plays a crucial role in processing emotional signals and in the formation of emotional memories. Neuroimaging studies have shown human amygdala activation during rapid eye movement sleep (REM). Stereotactically implanted electrodes for presurgical evaluation in epileptic patients provide a unique opportunity to directly record amygdala activity. The present study analysed amygdala activity associated with REM sleep eye movements on the millisecond scale. We propose that phasic activation associated with rapid eye movements may provide the amygdala with endogenous excitation during REM sleep. Standard polysomnography and stereo-electroencephalograph (SEEG) were recorded simultaneously during spontaneous sleep in the left amygdala of four patients. Time-frequency analysis and absolute power of gamma activity were obtained for 250 ms time windows preceding and following eye movement onset in REM sleep, and in spontaneous waking eye movements in the dark. Absolute power of the 44-48 Hz band increased significantly during the 250 ms time window after REM sleep rapid eye movements onset, but not during waking eye movements. Transient activation of the amygdala provides physiological support for the proposed participation of the amygdala in emotional expression, in the emotional content of dreams and for the reactivation and consolidation of emotional memories during REM sleep, as well as for next-day emotional regulation, and its possible role in the bidirectional interaction between REM sleep and such sleep disorders as nightmares, anxiety and post-traumatic sleep disorder. These results provide unique, direct evidence of increased activation of the human amygdala time-locked to REM sleep rapid eye movements.
Demonstrating Miniaturised, entangled photon-pair sources on board nano satellites to enable future QKD missions (2017)

We report on our progress developing highly-miniaturised, polarisation-entangled, photon pair sources for CubeSats. We have a correlated photon-pair source in orbit in the NUS Galassia 2U CubeSat. We also have an entangled photon pair source in production and a high brightness (1Mcps) entangled photon-pair source in development for our upcoming satellite missions. All our sources are proof-of-principle demonstrations that the hardware necessary for entanglement-based QKD can be miniaturised and made sufficiently robust for operation in nano-satellites. The photon pairs they produce are measured with liquid crystal-based Bell state analysers and Geiger-mode avalanche photo-diodes within the source. These space missions allow our on-the-ground radiation, thermal and vibration tests to be validated and the real-world operation and aging of the source in space to be studied. A BBM92 QKD-capable design of the source has been used in a phase A study of a satellite-to-satellite QKD demonstration mission by the University of New South Wales, Canberra. This mission study uses two 6U CubeSats in LEO and aims to demonstrate QKD over separations of increasing distances as the two CubeSats drift apart.
Reactive Biomaterial for the Treatment of Herbicide Contaminated Drinking Water: Atrazine Dechlorination (2012)

The herbicide atrazine is used for control of broadleaf weeds, principally in corn, sorghum, and sugarcane [1]. Atrazine is currently used in 70 countries at an estimated annual rate of 111,000 tons [2, 3]. Atrazine is typically applied early in the planting season. However, Heavy rainfall events, shortly after application may lead to detectable atrazine concentrations in waterways and in drinking-water supplies. The United States Environmental Protection Agency established a 3 ppb limit of atrazine in drinking water. In some instances, municipal water treatment plants use chemicals and other treatment processes, such as activated carbon, to reduce atrazine to below the 3 ppb legal limit for drinking water.
Towards A Marketplace for Multi-domain Cloud Network Slicing: Use Cases (2019)

Dynamic end-to-end cloud network slices following a Slice-as-a-Service (SaaS) paradigm offer promising opportunities in support of diverse vertical industries attached to different administrative domains. This paper presents a distributed Marketplace model to dynamically create cloud network slices involving different slice resource providers. Portrayed through the lens of three reference use case scenarios, we discuss potential attributes of having a Marketplace and the outcomes feeding the use case requirements within a Slice Marketplace scope. Effective selection, negotiation, and proper monitoring and enforcement of service level agreements between multiple administrative and technological domains are among the prime challenges towards the realization of a distributed Marketplace of federated network and cloud resource providers.
Multiobjective design optimization of counterweight balancing of a robot arm using genetic algorithms (1995)

We present a hybrid approach to optimize the counterweight balancing of a robot arm, which uses a combination of a genetic algorithm (GA) with the min-max multiobjective optimization method to get the Pareto optimal set of solutions. This set corresponds to several possible robot designs from which the most appropriate has to be chosen by the designer. Our approach is compared to a more traditional min-max search technique in which a combination of random and sequential search was used to generate the Pareto optimal solutions. Our results show how the GA is able to get solutions with a lower deviation from the ideal vector.
Prise en charge d’une rectocolite hémorragique réfractaire (2014)

Un homme de 43 ans, suivi pour une rectocolite hemorragique (RCH) diagnostiquee 8 ans auparavant, consulte en raison d’une diarrhee sanglante evoluant depuis plus d’une semaine. Sa RCH etait initialement une forme etendue jusqu’au sigmoide et avait repondu favorablement a un traitement salicyle topique et oral. Le traitement par mesalasine orale propose par la suite avait ete poursuivi en entretien a raison de 2 g/j. L’episode actuel s’est brutalement installe il y a 10 [...]