gebhart/patrepeval huggingface dataset:
Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks of Mycobacterium tuberculosis (2021)

Abstract The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states, underlies its success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a major reason why the tuberculosis (TB) mortality rate is so high, with over 1.8 million deaths annually. To develop new TB therapeutics that better treat the infection (faster and more completely), a systems-level approach is needed to reveal the complexity of network-based adaptations of Mtb. Here, we report a new predictive model called PRIME ( P henotype of R egulatory influences I ntegrated with M etabolism and E nvironment) to uncover environment-specific vulnerabilities within the regulatory and metabolic networks of Mtb. Through extensive performance evaluations using genome-wide fitness screens, we demonstrate that PRIME makes mechanistically accurate predictions of context-specific vulnerabilities within the integrated regulatory and metabolic networks of Mtb, accurately rank-ordering targets for potentiating treatment with frontline drugs.
Topologically-Aware Overlay Construction and Server Selection. (2002)

A number of large-scale distributed Internet applications could potentially benefit from some level of knowledge about the relative proximity between its participating host nodes. For example, the peformance of large overlay networks could be improved if the application-level connectivity between the nodes in these networks is congruent with the underlying IP-level topology. Similarly, in the case of replicated web content, client nodes could use topological information in selecting one of multiple available servers. For such applications, one need not find the optimal solution in order to achieve significant practical benefits. Thus, these applications, and presumably others like them, do not require exact topological information and can instead use sufficiently informative hints about the relative positions of Internet hosts. In this paper, we present a binning scheme whereby nodes partition themselves into bins such that nodes that fall within a given bin are relatively close to one another in terms of network latency. Our binning strategy is simple (requiring minimal support from any measurement infrastructure), scalable (requiring no form of global knowledge, each node only needs knowledge of a small number of well-known landmark nodes) and completely distributed (requiring no communication or cooperation between the nodes being binned). We apply this binning strategy to the two applications mentioned above: overlay network construction and server selection. We test our binning strategy and its application using simulation and Internet measurement traces. Our results indicate that the performance of these applications can be significantly improved by even the rather coarse-grained knowledge of topology offered by our binning scheme.
Biological Methods in Biodiesel Production and Their Environmental Impact (2021)

This publication presents the technologies of enzymatic biodiesel production in comparison to the conventional methods using acid and base catalysts. Transesterification with conventional catalysts has some disadvantages, and for this reason, alternative methods of biodiesel production have been investigated. These solutions include the replacement of chemical catalysts with biological ones, which show substrate specificity in relation to fats. Replacing chemical with biological catalysts causes elimination of some disadvantages of chemical processes, for instance: high temperatures of reaction, problematic process of glycerol purification, higher alcohol-to-oil molar ratios, and soap formation. Moreover, it causes operational cost reduction and has a positive environmental impact. This is due to the lower temperature of the process, which in turn translates into lower cost of equipment and lower GHG emissions associated with the need to provide less heat to the process. The increase of biofuels’ demand has led to the technology of enzymatic biodiesel production being constantly being developed. This research mainly focuses on the possibility of obtaining cheaper and more effective biocatalysts, as well as increasing the durability of enzyme immobilization on different materials.
Security Assessment of Dynamically Obfuscated Scan Chain Against Oracle-guided Attacks (2021)

Logic locking has emerged as a promising solution to protect integrated circuits against piracy and tampering. However, the security provided by existing logic locking techniques is often thwarted by Boolean satisfiability (SAT)-based oracle-guided attacks. Criteria for successful SAT attacks on locked circuits include: (i) the circuit under attack is fully combinational, or (ii) the attacker has scan chain access. To address the threat posed by SAT-based attacks, we adopt the dynamically obfuscated scan chain (DOSC) architecture and illustrate its resiliency against the SAT attacks when inserted into the scan chain of an obfuscated design. We demonstrate, both mathematically and experimentally, that DOSC exponentially increases the resiliency against key extraction by SAT attack and its variants. Our results show that the mathematical estimation of attack complexity correlates to the experimental results with an accuracy of 95% or better. Along with the formal proof, we model DOSC architecture to its equivalent combinational circuit and perform SAT attack to evaluate its resiliency empirically. Our experiments demonstrate that SAT attack on DOSC-inserted benchmark circuits timeout at minimal test time overhead, and while DOSC requires less than 1% area and power overhead.
What about computational super-resolution in fluorescence Fourier light field microscopy? (2020)

Recently, Fourier light field microscopy was proposed to overcome the limitations in conventional light field microscopy by placing a micro-lens array at the aperture stop of the microscope objective instead of the image plane. In this way, a collection of orthographic views from different perspectives are directly captured. When inspecting fluorescent samples, the sensitivity and noise of the sensors are a major concern and large sensor pixels are required to cope with low-light conditions, which implies under-sampling issues. In this context, we analyze the sampling patterns in Fourier light field microscopy to understand to what extent computational super-resolution can be triggered during deconvolution in order to improve the resolution of the 3D reconstruction of the imaged data.
Position control of a 3 DOF platform for haptic shape rendering (2012)

Haptics is related to the touch feeling: within the framework of virtual reality, the human machine interaction which relies mainly on the hearing and sight may be enhanced by adding the touch sense. Thus, force feedback and tactile feedback systems are now increasingly developed to improve interaction. In this paper, we propose a new haptic device able to render the shape and surface of different objects. For that purpose, a position controlled platform has been designed. The paper introduces the design and the control strategies used to render the accurate shapes of convex or concave surfaces. Experimental and psychophysical results are given to assess the quality of the approach.
Diagnostic test for lymphoproliferative disease virus infection of turkeys, using the polymerase chain reaction (1994)

Lymphoproliferative disease virus, a type-C retrovirus, is the etiologic agent of a naturally acquired lymphoproliferative disorder in turkeys. The disease is characterized by rapid induction of lymphoproliferative lesions with morphologic and histopathologic features resembling those of reticuloendotheliosis. Owing to lack of overt clinical manifestations, early detection of lymphoproliferative disease virus is essential for preventing the rapid horizontal spread of the disease that can decimate flocks. We describe development of a simple, rapid, sensitive, and highly specific assay, using the polymerase chain reaction, capable of providing differential diagnosis of the disease soon after infection.
A doppler guided retrograde catheterization system (1992)

A Doppler guided retrograde catheterization system was developed to accurately catheterize the aortic root and left ventricular chamber without X-ray. This system consists of a 20 MHz, 0.076 mm thick x 1.016 mm diameter pulsed Doppler crystal integrated into the tip of a 100 cm multipurpose triple lumen catheter. Two lumens (0.61 mm) are used for electrodes; a third lumen (1.245 mm) may be used for guidewire and pressure determination; and the system is attached to a flow velocimeter. In an aortic arch flow model, the principles of Doppler signal guidance were confirmed with flow toward the catheter tip demonstrating positive signals and flow away from the catheter tip demonstrating negative signals. The magnitude and polarity (direction) of the detected phasic and mean velocities were utilized to guide catheterization in six dogs. Using the reversal of Doppler signal polarity to indicate branch entry and manipulating the catheter so as to maintain maximal positive axial velocity, the Doppler catheter was successfully advanced from the femoral artery to the aortic valve. Branches detected by the Doppler system were confirmed by fluoroscopy. The aortic valve was audible when approached and the left ventricular chamber was recognized by its characteristic pressure waveform. The Doppler guided retrograde catheterization system offers new technology to perform left heart catheterization without X-ray and may prove useful in a variety of settings including the development of invasive ultrasonic diagnostic and therapeutic technology.
A multistage approach for production and workforce planning in long-cycle product environments (1994)

Abstract Aggregate production planning (APP) has been studied extensively for the past two decades. The APP problem, also called production and workforce scheduling, is to determine the optimal workforce and production level in each period of the planning horizon in order to satisfy demand forecasts for these periods. The advantages of the APP are low cost of data collection and computational cost of the running model; the accuracy of data; and, effective managerial understanding of the results. If the product of concern takes longer than one period, it is called a long-cycle product. Examples of long-cycle products are aircraft, ships, buildings and special machines. A detailed model incorporating dynamic productivity and long-cycle products considerations is presented to solve the problem of production and workforce planning. Using a multistage production system approach, a search technique is developed to solve this class of problems where the objective function is linear and some of the constraint coefficients are dynamically nonlinear. The model provides a better solution than an aggregate production planning model, often used to solve these problems.
Ray scattering model for spherical transparent particles (2008)

We propose a model for the reflectance of a particle medium made of identical, large, spherical, and absorbing particles in a clear binder. A 3D geometrical description of light scattering is developed by relying on the laws of geometrical optics. The amount of light backscattered by a single particle is determined as a function of its absorbance and refractive index. Then, we consider a set of coplanar particles, called a particle sublayer, whose reflectance and transmittance are functions of the particle backscattering ratio and the particle concentration. The reflectance of an infinite particle medium is derived from a description of multiple reflections and transmissions between many superposed particle sublayers. When the binder has a refractive index different from that of air, the medium's reflectance factor accounts for the multiple reflections occurring beneath the air-binder interface as well as for the measuring geometry. The influences of various parameters, such as the refractive indices and the particle absorption coefficient, are examined.
Local Geomagnetic Field Modelling Closes the Gap Between MWD and GyroDirectional Surveying (1999)

Local Geomagnetic Field Modelling Closes the Gap Between MWD and Gyro Directional Surveying Tor Inge Waag; Tor Inge Waag SINTEF Petroleum Research AS Search for other works by this author on: This Site Google Scholar Torkildsen Torgeir; Torkildsen Torgeir Statoil Search for other works by this author on: This Site Google Scholar Odd Helge Inderhaug; Odd Helge Inderhaug Norsk Hydro Search for other works by this author on: This Site Google Scholar Inge M. Carlsen Inge M. Carlsen Saga Petroleum Search for other works by this author on: This Site Google Scholar Paper presented at the SPE Annual Technical Conference and Exhibition, Houston, Texas, October 1999. Paper Number: SPE-56699-MS https://doi.org/10.2118/56699-MS Published: October 03 1999 Cite View This Citation Add to Citation Manager Share Icon Share Twitter LinkedIn Get Permissions Search Site Citation Waag, Tor Inge, Torgeir, Torkildsen, Inderhaug, Odd Helge, and Inge M. Carlsen. "Local Geomagnetic Field Modelling Closes the Gap Between MWD and Gyro Directional Surveying." Paper presented at the SPE Annual Technical Conference and Exhibition, Houston, Texas, October 1999. doi: https://doi.org/10.2118/56699-MS Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll ProceedingsSociety of Petroleum Engineers (SPE)SPE Annual Technical Conference and Exhibition Search Advanced Search This paper was prepared for presentation at the 1999 SPE Annual Technical Conference and Exhibition held in Houston, Texas, 3–6 October 1999. Keywords: field anomaly, variation, torgeir torkildsen, society of petroleum engineers, gyro directional, local field anomaly, correction, upstream oil & gas, drilling operation, directional drilling Subjects: Drilling Operations, Reservoir Characterization, Formation Evaluation & Management, Information Management and Systems, Directional drilling This content is only available via PDF. 1999. Society of Petroleum Engineers You can access this article if you purchase or spend a download.
ChemInform Abstract: Enantiomeric Excess and Absolute Configuration Determination of cis‐ Dihydrodiols from Bacterial Metabolism of Monocyclic Arenes. (1991)

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.
Phenotypic Analysis of Microalgae Populations Using Label-Free Imaging Flow Cytometry and Deep Learning (2021)

Environmental factors such as temperature, nutrients, and pollutants affect the growth rates and physical characteristics of microalgae populations. As algae play a vital role in marine ecosystems, the monitoring of algae is important to observe the state of an ecosystem. However, analyzing these microalgae populations using conventional light microscopy is time-consuming and requires experts to both identify and count the algal cells, which in turn considerably limits the volume of the samples that can be measured in each experiment. In this work we use a high-throughput and field-portable imaging flow cytometer to perform automated label-free phenotypic analysis of marine microalgae populations using image processing and deep learning. The imaging flow cytometer provides color intensity and phase images of microalgae contained in a liquid sample by capturing and reconstructing the lens-free color holograms of the continuously flowing liquid at a flow rate of 100 mL/h. We extracted the spatial and spectral features of each algal cell in a sample from these holographic images and performed automated algae identification using convolutional neural networks. These features, alongside the composition and growth rate of the algae within the samples, were analyzed to understand the interactions between different algae populations as well as the effects of toxin exposure. As proof of concept, we demonstrated the effectiveness of the system by analyzing the impact of various concentrations of copper on microalgae monocultures and mixtures.
FeOx/FeP hybrid nanorods neutral hydrogen evolution electrocatalysis: insight into interface (2018)

The introduction of the FeO<sub>x</sub>/FeP interface effect not only facilitates the water adsorption and dissociation in neutral HER, but also modifies the Δ<italic>G</italic>(<sub>H*</sub>) of FeP, exhibiting remarkable catalytic activity with a Tafel slope as low as 47 mV dec<sup>−1</sup>.
Design of the RFID for Storage of Biological Information (2009)

Recent advances in RFID (radio frequency identification) technology promises to create a wireless circuitry capable of interfacing with biological systems for acquisition, identification and processing of biological data based on radio frequency interaction. Thus, the RFID tag can be attached not only to consumer products and form part of the supply chain, but also to animals, plants and in particular human body. This paper describes the strategy for the design of a novel RFID tag, which stores vital biological information such as body temperature and blood pressure and heartbeat in accordance with the EPC global Class-1 standard. Biological data is obtained from a sensor technology that is based on resistance deviation-to-pulse width converter. The integrated chip consists of an analog front end, command interpreter, collision avoidance block, data storage, sensors, and interface circuitry. The system is capable of supporting heartbeats in the range of 40~200 beats per a minute and blood pressure 0~300mmHg. The proposed system employs collision free algorithm that supports access to single tag within a multiple tag environment. The approach facilitates intelligent management of patients in hospitals as part of an integrated healthcare management system.
Batch fabricated scanning near field optical microscope/atomic force microscopy microprobe integrated with piezoresistive cantilever beam with highly reproducible focused ion beam micromachined aperture (2003)

In scanning near field optical microscope (SNOM), an optical probe with aperture diameter well below the optical wavelength is moved over the sample. The sample-probe distance control is one of the key problems in SNOM. Our earlier approach allowed for fabrication of the piezo-SNOM/atomic force microscopy (AFM) probe, however, reproductivity of the process and optical quality of the device were not satisfactory. Now we report an innovative processing sequence, which offers highly reproductive batch processing, typical for semiconductor technology and renders it possible to produce cantilevers playing role of an AFM detector as well as a nanoaperture detector. Moreover, illumination of the aperture is easier because of a wide input opening and its big cone angle. The throughput is in the range of 10−5 and higher. Apertures in hollow pyramids have been formed by direct ion beam drilling with a focused beam of 30 keV Ga+ ions. Direct focused ion beam (FIB) drilling is a reproducible process for hole formation at the 30–100 nm diameter range. Formation of smaller apertures is possible if a special FIB drilling/deposition procedure is applied.
Dust and molecular gas in magellanic type galaxies (2000)

Der Gehalt an Staub und molekularem Gas stellt eine entscheidende Größe für unser Verständnis der Entwicklung von\nGalaxien dar, da beide Bestandteile des interstellaren Mediums eng mit der Entstehung von Sternen verknüpft sind. Am\nIRAM 30m Millimetre Radio Telescope (MRT) und am Swedish Eso Submillimetre Telescope (SEST) wurden von mir die CO (1-0)\nund CO (2-1) Linienübergänge und die thermische Kontinuumsstrahlung von Staub bei 1.3 mm in einer FIR limitierten\nStichprobe von Galaxien des Magellanschen Typs beobachtet. Die Daten erlauben Aussagen über die Staubmasse und -\ntemperatur, die räumliche Verteilung von Staub und molekularem Gas, den Umrechnungsfaktor von CO zu molekularem\nWasserstoff, das Verhältnis von Gas zu Staub und die Effizienz der Sternenentstehung in Zwerggalaxien.
Sex Determination Based on Raman Spectroscopy of Saliva Traces for Forensic Purposes (2016)

The forensic analysis of body fluids has made great strides in recent years. Body fluids can easily be identified, and DNA analysis can be used to link a stain found at a crime scene to a specific person. When no reference DNA profile is available and the recovered DNA does not yield a match in a database, it would be incredibly useful if the evidence could still provide investigators with useful information. Biocatalytic and immunoassays can be used to determine a donor's sex, race, and other phenotypic characteristics. However, these tests depend on chemical reactions and are destructive to the sample. Here, we used Raman spectroscopy and multivariate data analysis to develop a nondestructive technique that could be used at a crime scene to determine the sex of a saliva donor. Our internally cross-validated classification model correctly identified 44 (92%) of the 48 donors used for model training. Subsequent external validation correctly identified 11 (92%) of the 12 donors saved for testing. This proof-of-concept study demonstrates the value of Raman spectroscopy as a forensic tool, and indicates that it can be used to elucidate phenotypic information about a body fluid donor. Future studies will expand to other body fluids and additional donor characteristics, such as race and age.
Antiangiogenic Role of Somatostatin Receptor 2 in a Model of Hypoxia-Induced Neovascularization in the Retina: Results from Transgenic Mice (2007)

These results suggest that sst(2) may be protective against angiogenesis. The immediate clinical importance lies in the establishment of a potential pharmacological target based on sst(2) pharmacology.
Microwave-Enhanced Ionothermal CuAAC for the Synthesis of Glycoclusters on a Calix[4]arene Platform (2008)

A tetra-azido calix[4]arene derivative was allowed to react with ethynyl tetra- O-benzyl- C-galactoside in the presence of CuI and i-Pr 2EtN in three different ionic liquids, that is, [C 8dabco][N(CN) 2], [C 8dabco][Br], and Ammoeng 110. Reactions were performed at 80 degrees C by thermal and MW dielectric heating. In all cases, multiple cycloadditions took place to give a triazole-linked tetra- C-galactosyl-calix[4]arene in up to 90% yield. The [C 8dabco][N(CN) 2] ionic liquid was also used to perform the multiclick reactions with propargyl O-lactoside and S-sialoside.
Formation of Highly Aligned Collagen Nanofibers by Continuous Cyclic Stretch of a Collagen Hydrogel Sheet (2016)

A collagen sheet with highly aligned collagen fibers is fabricated by continuous cyclic stretch. The rearrangement of the collagen fibers depends on the different process parameters of the cyclic stretch, including magnitude, frequency, and period of stretch. The collagen fibers are aligned perpendicularly to the direction of the stretch. Corneal stromal cells and smooth muscle cells cultivated on the highly aligned collagen sheet show alignment along the collagen fibers without the stretch during culture. Thus, the sheet can be a suitable scaffold for use in regenerative medicine.