gebhart/patrepeval huggingface dataset:
Microbiological characteristics of pristine and contaminated deep vadose sediments from an arid region (1993)

The unsaturated (vadose) zone in arid and semiarid regions can be >100 m thick and may receive little or no moisture recharge from the surface. The microbiological properties of the vadose zone are of interest because of the potential for microorganisms to impact the fate and transport of contaminants in these environments. At numerous sites in the western United States, large volumes of wastewater or process water have been disposed of directly to the surface or shallow subsurface and have subsequently migrated through the vadose zone to the groundwater. The purpose of this study was to determine and compare the microbial properties of pristine and impacted vadose zone sediments. Vadose zone sediments from depths ranging from 24 to 90 m were obtained from 3 boreholes drilled on the Hanford site in south‐central Washington State. One borehole was located in a pristine area and the other two were located in areas where wastewater had been disposed of directly to the surface and near subsurface. An open‐flow centrifugation method was used to determine unsaturated hydraulic conductivity for the sediments, allowing construction of characteristic curves relating the hydraulic conductivity (K) to the volumetric water content (8). By comparing the volumetric water content of sediments obtained prior to centrifugation to their water content over a range of K(θ), it could be determined which vadose zone samples had been subjected to artificial recharge. Elevated concentrations of nitrate and the presence of carbon tetrachloride in vadose sediments were also used as indicators that sediments had been impacted by past waste disposal practices. Those vadose zone paleosol samples receiving artificial recharge had higher populations of culturable bacteria (log 1.0–6.6 CFU g−1) and were able to mineralize organic substrates more rapidly than a pristine paleosol. Thus, the in situ microbial population was stimulated by increased moisture from artificial recharge and/or from contaminants. In contrast, culturable bacteria were near or below detection in unimpacted fluvial and flood sands. The few culturable microorganisms that were present in unimpacted vadose sediments were either associated with the sediments at the time of deposition or transported from the surface during the last major proglacial flood, approximately 13,000 years ago.
A 12-bit resolution, 200-MSample/second phase modulator for a 2.5GHz carrier with discrete carrier pre-rotation in 65nm CMOS (2011)

A digital-to-RF phase modulator based on a single current-steering DAC is presented, including a carrier pre-rotation scheme that prevents phase inaccuracy due to carrier feedthrough. The phase modulator has been fabricated in a standard 65-nm CMOS process and draws 1.9 mW from a 1-V supply. The modulator achieves 12-bit resolution at a measured 200 MSamples/second, state-of-the-art performance in both resolution and sampling speed. It has sufficient speed to allow for oversampling to shape the output spectrum and therefore reduce filtering requirements, as demonstrated through a 32x oversampled 8-PSK signal at 6.25 MSymbols/second with under 6.1% EVM.
Molecular Layer Deposition of Hybrid Organic−Inorganic Alucone Polymer Films Using a Three-Step ABC Reaction Sequence (2009)

Thin film growth using molecular layer deposition (MLD) or atomic layer deposition (ALD) is based on sequential, self-limiting surface reactions. In this work, MLD is used to grow a hybrid organic−inorganic polymer film based on a three-step ABC reaction sequence using trimethylaluminum (TMA), ethanolamine (EA), and maleic anhydride (MA) as the reactants. This three-step ABC sequence avoids the use of homobifunctional organic precursors by employing a homotrifunctional inorganic reactant (TMA), a heterobifunctional organic reactant (EA), and a ring-opening organic reactant (MA). The resulting hybrid organic−inorganic polymer film is an alucone with an approximate formula of (−AlCH3−OCH2CH2NH−C(O)CHCHCOO−)n. The growth of this ABC alucone film was monitored using in situ Fourier transform infrared (FTIR) measurements at 90−170 °C. The three sequential surface reactions displayed self-limiting growth. The FTIR difference spectra monitored the absorbance from the surface species during the three surface reactions. The gain and loss of absorbance helped to determine the reaction mechanism for the ABC alucone film growth. Transmission electron microscope (TEM) measurements on ZrO2 nanoparticles also displayed the growth of very conformal ABC alucone films. The ABC alucone growth per cycle was also measured on Si wafers using X-ray reflectivity. ABC alucone growth rates were temperature dependent and varied from 24 Å per cycle at 90 °C to 4.0 Å per cycle at 170 °C. X-ray photoelectron spectroscopy also determined the composition of the ABC alucone films. The robust and efficient growth of the ABC alucone hybrid organic−inorganic films may be useful in applications requiring flexible or sacrificial films.
OKID as a general approach to linear and bilinear system identification (2014)

This work advances the understanding of the complex world of system identification, i.e. the set of techniques to find mathematical models of dynamical systems from measured input-output data, and exploits well-established approaches for linear systems to address nonlinear system identification problems. We focus on observer/Kalman filter identification (OKID), a method for simultaneous identification of a linear state-space model and the associated Kalman filter from noisy input-output measurements. OKID, developed at NASA, resulted in a very successful algorithm known as OKID/ERA (OKID followed by eigensystem realization algorithm). We show how ERA is not the only method to complete the OKID process, developing novel algorithms based on the preliminary estimation of the Kalman filter output residuals. The new algorithms do not only show potential for better performance, they also cast light on OKID, explicitly establishing the Kalman filter as central to linear system identification in the presence of noise, paralleling its role in signal estimation and filtering. The Kalman filter embedded in the OKID core equation is capable of converting the original problem, affected by random noise, into a purely deterministic problem. The new interpretation leads to the extension of OKID to output-only system identification, providing a new tool for applications in structural health monitoring, and raises OKID to the level of a unified approach for input-output and output-only linear system identification. Any algorithm for linear system identification formulated in the absence of noise can now optimally handle noisy data via a preliminary step consisting in solving the OKID core equation. The OKID framework developed for linear system identification is then extended to bilinear systems, which are of interest because several natural phenomena are inherently bilinear and also because high-order bilinear models are universal approximators for a wide class of nonlinear systems. The formulation of an optimal bilinear observer for bilinear state-space models, similar to the Kalman filter in the linear case, leads to the development of an extension of OKID to bilinear system identification. This is the first application of OKID to nonlinear problems, not only because bilinear systems are themselves nonlinear, but also because one can think of bilinear OKID as a technique to find bilinear approximations of nonlinear systems. Furthermore, the same strategy adopted in this work could be used to extend OKID directly to other classes of nonlinear models.
End-to-end available bandwidth (2002)

The available bandwidth (avail-bw) in a network path is of major importance in congestion control, streaming applications, QoS verification, server selection, and overlay networks. We describe an end-to-end methodology, called Self-Loading Periodic Streams (SLoPS), for measuring avail-bw. The basic idea in SLoPS is that the one-way delays of a periodic packet stream show an increasing trend when the stream's rate is higher than the avail-bw. We implemented SLoPS in a tool called pathload. The accuracy of the tool has been evaluated with both simulations and experiments over real-world Internet paths. Pathload is non-intrusive, meaning that it does not cause significant increases in the network utilization, delays, or losses. We used pathload to evaluate the variability ('dynamics') of the avail-bw in some paths that cross USA and Europe. The avail-bw becomes significantly more variable in heavily utilized paths, as well as in paths with limited capacity (probably due to a lower degree of statistical multiplexing). We finally examine the relation between avail-bw and TCP throughput. A persistent TCP connection can be used to roughly measure the avail-bw in a path, but TCP saturates the path, and increases significantly the path delays and jitter.
Isolation of germline cells from Drosophila embryos by flow cytometry (2006)

Primordial germ cells (PGC) are the earliest identifiable germ cells in the embryo. To understand the molecular basis of germline development, isolation of pure PGC is required. We report here the use of fluorescence-activated cell sorting (FACS) to isolate pure populations of Drosophila pole cells, which are the presumptive primordial germ cells in flies. In order to fluorescently mark pole cells, we used an EGFP-vasa transgenic line that expresses green fluorescent protein (GFP) specifically and continuously in the germ line throughout the life cycle. The purity of FACS-sorted pole cells from embryos was confirmed by microscopic inspection and quantitative polymerase chain reaction. Moreover, by optimizing the sample preparation and the sorting protocol, embryonic gonads could also be isolated. This technique opens the way for genome-wide transcriptome analysis of germline cells. In a pilot experiment, we generated a cDNA library from purified embryonic gonad and identified a novel germline-specific gene, RpL22-like.
<title>Multiscale geometric image analysis: diffusion and cores and variable conductance diffusion and object calculation</title> (1994)

There are two basic principles associated with multiscale geometry: 1) geometry involves analysis that is invariant to certain spatial transformations, including translation, rotation, and zoom, and 2) the dimension of scale is as critical as the dimensions giving spatial position, corresponding intuitively to level of detail in image space. Considered together, image space and scale is called scale space. Three families of methods based on these principles are achieving impressive results in image analysis —particularlyin their insensitivity to irrelevant detail (including image noise) and intensity blurring, and in their ability to produce stable object descriptions and pixel classifications into objects. The three families are multiscale medial axis or core-based analysis (CBA), variable conductance difftision (VCD), and multiscale geometric statistical pattern recognition (MGSPR). This pair of tutorials (morning and afternoon) covered the basic mathematics of multiscale geometry as well as all three of these families of methods. It included algorithms for computation and also illustrative results of the applications of the methods to both 2D and 3D medical images of various modalities. The morning tutorial covered the mathematics of diffusion and scale space and the definition, effect on scale space geometry, and application of cores. The afternoon tutorial covered the mathematics, algorithms, and applications of variable conductance diffusion, including approaches involving MGSPR, and it covered algorithms for segmenting objects both via VCD and via CBA.
Protein Crystals Nucleated and Grown by Means of Porous Materials Display Improved X-ray Diffraction Quality (2022)

Well-diffracting protein crystals are indispensable for X-ray diffraction analysis, which is still the most powerful method for structure-function studies of biomolecules. A promising approach to growing such crystals is the use of porous nucleation-inducing materials. However, while protein crystal nucleation in pores has been thoroughly considered, little attention has been paid to the subsequent growth of crystals. Although the nucleation stage is decisive, it is the subsequent growth of crystals outside the pore that determines their diffraction quality. The molecular-scale mechanism of growth of protein crystals in and outside pores is theoretically considered. Due to the low degree of metastability, the crystals that emerge from the pores grow slowly, which is a prerequisite for better diffraction. This expectation has been corroborated by experiments carried out with several types of porous material, such as bioglass ("Naomi's Nucleant"), buckypaper, porous gold and porous silicon. Protein crystals grown with the aid of bioglass and buckypaper yield significantly better diffraction quality compared with crystals grown conventionally. In all cases, visually superior crystals are usually obtained. Our theoretical conclusion is that heterogeneous nucleation of a crystal outside the pore is an exceptional case. Rather, the protein crystals nucleating inside the pores continue growing outside them.
Safe and flexible ion gel based composite electrolyte for lithium batteries (2016)

Safe and flexible electrolyte functioning well at wide temperature range and deformable conditions by incorporating ion gel in electrospun membranes.
Bacillus licheniformis BT5.9 Isolated from Changar Hot Spring, Malang, Indonesia, as a Potential Producer of Thermostable α-amylase. (2013)

A total of 34 bacterial isolates were obtained from soil samples collected from Changar Hot Spring, Malang, Indonesia. Of these, 13 isolates produced a zone of hydrolysis in starch-nutrient agar medium and generated various amylases in liquid medium. One isolate was selected as the best amylase producer and was identified as Bacillus licheniformis BT5.9. The improvement of culture conditions (initial medium pH of 5.0, cultivation temperature of 50°C, agitation speed of 100 rpm and inoculum size of 1.7 × 10(9) cells/ml) provided the highest amylase production (0.327 U/ml).
Decision letter: Long term intrinsic cycling in human life course antibody responses to influenza A(H3N2): an observational and modeling study (2022)

Cross-sectional serological data and mathematical models suggest the existence of long-term periodicity in human antibody responses arising from multiple exposures to influenza A(H3N2), providing insights into the interactions between exposure histories and future risks of infections.
In vivo diffusion-weighted MRI detection of myocardial fibrosis in hypertrophic cardiomyopathy patients (2015)

Background Recent studies have demonstrated the potential of in vivo diffusion-weighted MRI (DWI) in detecting myocardial replacement fibrosis for chronic myocardial infarction [1-3]. Despite the potential of this contrastfree technique, detecting diffuse myocardial fibrosis with DWI has not been established. Current cardiac MRI (CMR) techniques to detect diffuse myocardial fibrosis include late gadolinium enhancement (LGE) [4], pre/ post contrast T1 mapping [5], and extracellular volume (ECV) mapping [6]. We propose the application of a recently developed cardiac DWI technique [7] to detect diffuse myocardial fibrosis in HCM patients and compare its performance with established CMR techniques.
Electrical Energy Conversion for Low Temperature Electrolysis - Challenges and Future Trends (2021)

Low temperature electrolysis brings the possibility of achieving the production of fuels and chemical feedstocks without any carbon footprint. Power electronic converters are vital components of future electrolyser systems in terms of overall cost and efficiency. This paper presents the current state of art in power electronics for low temperature electrolysis and all the major steps of designing an electrolysis system are discussed from the modeling of electrolysers to the system architecture. The most promising routes are pointed out and backed up with results from both experimental and theoretical studies found in the literature.
Link Setup Time Reduction by FILS on IEEE 802.11-Based Inter-Vehicular Communications (2021)

This paper reports the performance of link setup time reduction outlined by IEEE 802.11ai, which is also known as Fast Initial Link Setup (FILS), in real intermittent inter-vehicular communications. Fast link establishment is a significant concern in communications between mobile devices with high mobility, such as passing vehicles on roads, because short link setup times enable vehicles to transfer larger amounts of application data. However, secure links are also important because they prevent both unauthorized access by unauthenticated users and misinformation circulation by malicious persons. Conventional security protocols such as IEEE 1609.2 and IEEE 802.11i/IEEE 802.1X, which is also known as theWi-Fi Protected Access 2 Extensible Authentication Protocol (WPA2-EAP), archive user authentication in vehicular networks but often take several seconds to establish a secure link due to numerous frame exchanges. In contrast, FILS is designed to establish a secure WPA2-EAP link in 100 ms using cached authentication information. However, since the effectiveness of FILS in real vehicular networks has not yet been reported, this paper describes experiments that clarify its setup time reduction abilities in 2.4 GHz IEEE 802.11n-based inter-vehicular communications by measuring the initial link setup times between two passing vehicles in a real environment. The results show that FILS significantly reduces the initial link setup times between the passing vehicles to around 150 ms and increases the size of application data transferred between vehicles. Additionally, it is demonstrated that FILS always establishes a secure link, while Protected EAP (PEAP) sometimes fails. Finally, in communications between vehicles passing each other at the relative speed of 80 km/h, we confirm that the FILS link setup time reduction effectively increases transferrable application data sizes by 10MB compared with WPA2-PEAP.
Adenovirus 5 E1A Interacts with E4orf3 To Regulate Viral Chromatin Organization (2019)

Human adenovirus expresses several early proteins that control various aspects of the viral replication program, including an orchestrated expression of viral genes. Two of the earliest viral transcriptional units activated after viral genome entry into the host cell nucleus are the E1 and E4 units, which each express a variety of proteins. Chief among these are the E1A proteins that function to reprogram the host cell and activate transcription of all other viral genes. The E4 gene encodes multiple proteins, including E4orf3, which functions to disrupt cellular antiviral defenses, including the DNA damage response pathway and activation of antiviral genes. Here we report that E1A directly interacts with E4orf3 via the conserved N terminus of E1A to regulate the expression of viral genes. We show that E4orf3 indiscriminately drives high nucleosomal density of viral genomes, which is restrictive to viral gene expression and which E1A overcomes via a direct interaction with E4orf3. We also show that during infection E1A colocalizes with E4orf3 to nuclear tracks that are associated with heterochromatin formation. The inability of E1A to interact with E4orf3 has a significant negative impact on overall viral replication, the ability of the virus to reprogram the host cell, and the levels of viral gene expression. Together these results show that E1A and E4orf3 work together to fine-tune the viral replication program during the course of infection and highlight a novel mechanism that regulates viral gene expression.<b>IMPORTANCE</b> To successfully replicate, human adenovirus needs to carry out a rapid yet ordered transcriptional program that executes and drives viral replication. Early in infection, the viral E1A proteins are the key activators and regulators of viral transcription. Here we report, for the first time, that E1A works together with E4orf3 to perfect the viral transcriptional program and identify a novel mechanism by which the virus can adjust viral gene expression by modifying its genome's nucleosomal organization via cooperation between E1A and E4orf3.
Kinetic modeling and optimization of operating parameters for transvinylation of lauric acid (2012)

Abstract The transition metal complex catalyzed transvinylation of carboxylic acid with vinyl acetate monomer is of significant interest to industry. The palladium complex catalyzed transvinylation of lauric acid using vinyl acetate monomer is a reversible reaction. In present article, design of experiments (DOE) statistics is used to study effects of various operating parameters on transvinylation of lauric acid. The kinetic parameters forward and backward rate constants and the thermodynamic parameters such as equilibrium constant and energy of activation of the transvinylation of lauric acid were estimated using the Dynochem model. The optimum operating parameters for the transvinylation of lauric acid were then predicted using the Dynochem model and verified by performing the actual experiments to validate the model. It was found that the experimental results match with the predicted one. © 2012 Wiley Periodicals, Inc. Int J Chem Kinet 44: 624–634, 2012
Improved oil recovery surfactants based on lignin (1991)

The limited supply and increasing cost of petroleum-based surfactants for chemical enhanced oil recovery have led Texaco to study renewable resources as sources of improved oil recovery (lOR) surfactants. The starting material of choice is lignin, the second most abundant organic chemical on earth. Lignins are produced in large quantities as waste in pulp and paper mills and are very inexpensive.