gebhart/patrepeval huggingface dataset:
Statistical density modification using local pattern matching (2003)

A method for improving crystallographic phases is presented that is based on the preferential occurrence of certain local patterns of electron density in macromolecular electron-density maps. The method focuses on the relationship between the value of electron density at a point in the map and the pattern of density surrounding this point. Patterns of density that can be superimposed by rotation about the central point are considered equivalent. Standard templates are created from experimental or model electron-density maps by clustering and averaging local patterns of electron density. The clustering is based on correlation coefficients after rotation to maximize the correlation. Experimental or model maps are also used to create histograms relating the value of electron density at the central point to the correlation coefficient of the density surrounding this point with each member of the set of standard patterns. These histograms are then used to estimate the electron density at each point in a new experimental electron-density map using the pattern of electron density at points surrounding that point and the correlation coefficient of this density to each of the set of standard templates, again after rotation to maximize the correlation. The method is strengthened by excluding any information from the point in question from both the templates and the local pattern of density in the calculation. A function based on the origin of the Patterson function is used to remove information about the electron density at the point in question from nearby electron density. This allows an estimation of the electron density at each point in a map, using only information from other points in the process. The resulting estimates of electron density are shown to have errors that are nearly independent of the errors in the original map using model data and templates calculated at a resolution of 2.6 A. Owing to this independence of errors, information from the new map can be combined in a simple fashion with information from the original map to create an improved map. An iterative phase-improvement process using this approach and other applications of the image-reconstruction method are described and applied to experimental data at resolutions ranging from 2.4 to 2.8 A.
Hot cracking during laser welding of steel: influence of the welding parameters and prevention of cracks (2017)

In continuous wave keyhole-mode laser welding of high strength steel alloys hot cracking can occur. The hot crack susceptibility depends on the mutual interaction of several factors like the welding parameters, the alloy composition and the weld fixturing. In this paper we focus on the influence of the welding parameters and investigate the dependency of the laser power, the welding speed and the laser wavelength on the crack formation. X-ray images are used to visualize the hot crack patterns, which exhibit a pronounced periodicity. To influence the hot crack formation, the incident energy input into the process was adapted. For specific welding parameters, we show exemplarily the prevention of hot cracking by the use of a twin-spot optics.
Diagnosing and predicting mixed culture fermentations with unicellular and guild-based metabolic models (2019)

ABSTRACT Multi-species microbial communities determine the fate of materials in the environment and can be harnessed to produce beneficial products from renewable resources. In a recent example, fermentations by microbial communities have produced medium-chain fatty acids (MCFAs). Tools to predict, assess, and improve the performance of these communities, however, are limited. To provide such tools, we constructed two metabolic models of MCFA-producing microbial communities based on available genomic, transcriptomic and metabolomic data. The first model is a unicellular model (iFermCell215), while the second model (iFermGuilds789) separates fermentation activities into functional guilds. Ethanol and lactate are fermentation products known to serve as substrates for MCFA production, while acetate is another common co-metabolite during MCFA production. Simulations with iFermCell215 predict that low molar ratios of acetate-to-ethanol favor MCFA production, whereas the products of lactate and acetate co-utilization are less dependent on the acetate-to-lactate ratio. In simulations of an MCFA-producing community fed a complex organic mixture derived from lignocellulose, iFermGuilds789 predicted that lactate was an extracellular co-metabolite that served as a substrate for butyrate (C4) production. Extracellular hexanoic (C6) and octanoic acids (C8) were predicted by iFermGuilds789 to be from community members that directly metabolize sugars. Modeling results provide several hypotheses that can improve our understanding of microbial roles in a MCFA-producing microbiome and inform strategies to increase MCFA production. Further, these models represent novel tools for exploring the role of mixed microbial communities in carbon recycling in the environment, as well as on beneficial reuse of organic residues. IMPORTANCE Microbiomes are vital to human health, agriculture, and protecting the environment. Predicting behavior of self-assembled or synthetic microbiomes, however, remains a challenge. In this work, we used unicellular and guild-based metabolic models to investigate production of medium-chain fatty acids by a mixed microbial community that is fed multiple organic substrates. Modeling results provided insights into metabolic pathways of three medium-chain fatty acid-producing guilds and identified potential strategies to increase production of medium-chain fatty acids. This work demonstrates the role of metabolic models in augmenting multi-omic studies to gain greater insights into microbiome behavior.
Endoplasmic reticulum localization of the low density lipoprotein receptor mediates presecretory degradation of apolipoprotein B (2002)

Mutations in the low density lipoprotein (LDL) receptor (LDLR) cause hypercholesterolemia because of inefficient LDL clearance from the circulation. In addition, there is a paradoxical oversecretion of the metabolic precursor of LDL, very low density lipoprotein (VLDL). We recently demonstrated that the LDLR mediates pre-secretory degradation of the major VLDL protein, apolipoprotein B (apoB). Kinetic studies suggested that the degradation process is initiated in the secretory pathway. Here, we evaluated the ability of several LDLR variants that are stalled within the secretory pathway to regulate apoB secretion. Both a naturally occurring mutant LDLR and an LDLR consisting of only the ligand-binding domains and a C-terminal endoplasmic reticulum (ER) retention sequence were localized to the ER and not at the cell surface. In the presence of either of the ER-localized LDLRs, apoB secretion was essentially abolished. When the ligand-binding domain of the truncated receptor was mutated the receptor was unable to block apoB secretion, indicating that the inhibition of apoB secretion depends on the ability of the LDLR to bind to its ligand. These findings establish LDLR-mediated pre-secretory apoB degradation as a pathway distinct from reuptake of nascent lipoproteins at the cell surface. The LDLR provides an example of a receptor that modulates export of its ligand from the ER.
Novel free space and fiber laser cavities demonstrating extreme sensitivities in Intracavity Phase Interferometry systems (2018)

A method to enhance the sensitivity of sensors based on Intracavity Phase Interferometry by a factor of up to 10,000 is demonstrated in a free space laser. This technique is then implemented in fiber lasers.
Short peptide analogs as alternatives to collagen in pro-regenerative corneal implants (2018)

Although biomaterials comprising full-length recombinant human collagen and extracted animal collagen have been evaluated and used clinically, these macromolecules provide only a limited number of functional groups amenable to chemical modification or crosslinking and are demanding to process. Synthetic, customizable analogs that are functionally equivalent, and can be readily scaled-up are therefore very desirable for pre-clinical to clinical translation. Here, we demonstrate, using cornea regeneration as our test bed, that collagen-like-peptides conjugated to multifunctional polyethylene glycol (CLP-PEG) when grafted into mini-pigs as corneal implants were functionally equivalent to recombinant human collagen-based implants that were successfully tested in patients. We also show for the first time that these materials affected regeneration through stimulation of extracellular vesicle production by endogenous host cells that have migrated into the CLP-PEG scaffolds.
A Capacity Planning Framework for Multi-tier Enterprise Services with Real Workloads (2007)

With complexity of systems increasing and customer requirements for QoS growing, new methods and modeling techniques that explain large-systems' behavior and help predict their future performance are required to effectively tackle the emerging performance issues. To accurately answer capacity planning questions for an existing production system with a real workload mix, we propose a new capacity planning framework that is based on the following three components: i) a Workload Profiler that dynamically builds the workload profile; ii) a Regression-based Solver that is used for deriving the CPU demand of client transactions on a given hardware; and iii) an Analytical model that is based on a network of queues representing the different tiers. To validate our approach, we conduct a detailed case study using the access logs from two heterogeneous production servers that represent customized client accesses to a popular and actively used HP Open View Service Desk application.
High Efficiency Free Electron Laser. (1982)

The results of an experimental program to investigate the free electron laser (FEL) are presented. The experimental results indicate that to the limits of the present sensitivity the FEL is behaving in accordance with theoretical models. This suggests that improving the current and emittance of FEL accelerators will have a profound effect on improving the performance of FELs.
Enabling "Hinge" model in polarization-mode-dispersion statistics using variable differential-group-delay-based emulator (2006)

By slow polarization coupling and reorganizing applied differential group delay (DGD) to each section of a variable DGD-based polarization-mode-dispersion (PMD) emulator, we realize slow dynamics with negligible distortion of generated PMD statistics to enable a "hinge" model for system evaluation.
Boundary macroblock padding in MPEG-4 video decoding using a graphics coprocessor (2002)

MPEG-4 is the latest multimedia coding standard that supports object-based coding and manipulation of natural video and synthetic graphics objects. Due to its various features and high coding efficiency, MPEG-4 is becoming popular in video streaming applications. Many graphics coprocessors provide the acceleration of inverse discrete cosine transform (IDCT) and motion compensation for real-time video decoding. Therefore, it is desired to use the graphics coprocessors to accelerate MPEG-4 video decoding as well. Since MPEG-4 video decoding for rectangular video objects is similar to other video coding standards, e.g., MPEG-2, the IDCT and motion compensation can still be executed on the graphics coprocessors. However, we have found that boundary macroblock padding, which is an essential processing step in decoding arbitrarily shaped video objects, could not be efficiently accelerated on the graphics coprocessors due to its complexity. Although we can implement the boundary macroblock padding on the host processor, the frame data processed on the graphics coprocessor need to be transferred to the host processor for padding. In addition, the padded data on the host processor need to be sent back to the graphics coprocessor to be used as a reference for subsequent frames. To avoid this overhead, we present two approaches of boundary macroblock padding. In the first approach, the boundary macroblock padding is partitioned into two tasks, one of which the host processor can perform without the overhead of data transfers. In the second approach, we propose two new instructions and an algorithm that can be easily adopted in the next-generation graphics coprocessors or mediaprocessors, which gives a performance improvement of up to a factor of nine compared to that with the Pentium III.
Accurate Single-Ended Distributed Temperature Sensing (2008)

Abstract Distributed temperature sensing (DTS) is a technique to obtain real-time temperature well logs which are used for several applications such as production allocation, heavy oil thermal recovery (e.g., steam-assisted gravity drainage, SAGD) steam-well management, and well-integrity monitoring. This system is based on measuring scattered light at more than one wavelength from an optical fiber placed along the well. An issue arises when the attenuation of the optical fiber changes with time by different amounts at the different wavelengths used causing degradation in accuracy of the measurement. This differential loss can be compensated for by connecting both ends of the optical fiber to the DTS instrument in a double-ended (DE) configuration. However, it is not always possible to operate in DE configuration because of other constrains in the design such as lack of space or restricted number of penetrations in completion equipment. Single-ended (SE) operation configuration has been used in these cases, exposing the monitoring system to potential loss of accuracy. An accurate single-ended (ASE) DTS system which provides differential loss measurement and compensation to single-ended installations is described. The instrument uses more than one light source to compensate for the optical-fiber differential losses at the relevant wavelengths. This compensation is applied continuously without the need of external recalibration. A system operating on this principle has been used for some time on single-mode fibers, and recent technical advances have enabled its application to multimode fibers. Laboratory-test and field-test results are presented showing a dramatic improvement in accuracy in cases where differential losses have developed. Comparative data using DE, SE, and ASE DTS systems are presented showing cases in which optical fibers were subjected to extreme environments where the effect of differential loss is accentuated. Examples are shown in which errors of up to 100°C caused by differential loss were automatically corrected in real time by the ASE DTS instrument.
Farnesyl Transferase Inhibition for the Treatment of Tauopathies (2018)

Tau inclusions are a shared feature of many neurodegenerative conditions and tau mutations lead to frontotemporal dementia. Approaches to treatment of these conditions have focused directly on the tau protein by targeting its post-translational modifications, its levels and its tendency to aggregate. We discovered a novel regulatory pathway for tau degradation that operates through the Rhes protein, a GTPase. Rhes is farnesylated and treatment with the farnesyl transferase inhibitor, lonafarnib, reduced Rhes, attenuated behavioral abnormalities, significantly reduced atrophy, tau inclusions, sumoylation and ubiquitination, as well as microgliosis in the rTg4510 tauopathy mouse. Direct reduction of Rhes levels reproduced the results observed with lonafarnib. The mechanism of lonafarnib action, as mediated by Rhes to reduce tau pathology, operates through the lysosome without involvement of the proteasome. Finally we show that the developmental increase in Rhes levels can be homeostatically regulated in the presence of tau mutations as a protective mechanism through which cells sense abnormal tau before any pathology is present. The extensive human trials of lonafarnib for other conditions, makes this drug ideal for repurposing to treat tauopathies.
On crop height estimation with UAVs (2014)

Remote sensing by Unmanned Aerial Vehicles (UAVs) is changing the way agriculture operates by increasing the spatial-temporal resolution of data collection. Micro-UAVs have the potential to further improve and enrich the data collected by operating close to the crops, enabling the collection of higher spatio-temporal resolution data. In this paper, we present a UAV-mounted measurement system that utilizes a laser scanner to compute crop heights, a critical indicator of crop health. The system filters, transforms, and analyzes the cluttered range data in real-time to determine the distance to the ground and to the top of the crops. We assess the system in an indoor testbed and in a corn field. Our findings indicate that despite the dense canopy and highly variable sensor readings, we can precisely fly over crops and measure its height to within 5cm of measurements gathered using current measurement technology.
Critical regions for the sweetness of brazzein<sup>1</sup> (2003)

Brazzein is a small, heat-stable, intensely sweet protein consisting of 54 amino acid residues. Based on the wild-type brazzein, 25 brazzein mutants have been produced to identify critical regions important for sweetness. To assess their sweetness, psychophysical experiments were carried out with 14 human subjects. First, the results suggest that residues 29-33 and 39-43, plus residue 36 between these stretches, as well as the C-terminus are involved in the sweetness of brazzein. Second, charge plays an important role in the interaction between brazzein and the sweet taste receptor.
Pheromone‐Binding Proteins of Scarab Beetles<sup>a</sup> (1998)

We have characterized pheromone binding proteins (PBPs) present in the antennae of several species of scarab beetles. In most cases there was only one class of PBP, which was expressed in both sexes. Both Anomala osakana++ and Popillia japonica possess a single PBP, highly homologous to each other. In species the same PBP seems to recognize both enantiomers of japonilure, which have opposite biological functions, i.e., the sex pheromone and the behavioral antagonist (stop signal). The purified PBP of A. osakana binds both enantiomers apparently with the same low affinity. Unexpectedly, these ligands were bound by moth PBPs, which utilize pheromones with unrelated structures. These findings suggest that the ligand specificity in this class of proteins may not be as high as it has been postulated.
Input Shaping Control of Double-Pendulum Bridge Crane Oscillations (2008)

Large amplitude oscillation of crane payloads is detrimental to safe and efficient operation. Under certain conditions, the problem is compounded when the payload creates a double-pendulum effect. Most crane control research to date has focused on single-pendulum dynamics. Several researchers have shown that single-mode oscillations can be greatly reduced by properly shaping the inputs to the crane motors. This paper builds on those previous developments to create a method for suppressing double-pendulum payload oscillations. The input shaping controller is designed to have robustness to changes in the two operating frequencies. Experiments performed on a portable bridge crane are used to verify the effectiveness of this method and the robustness of the input shaper.
Identification via a Parallel Hit Progression Strategy of Improved Small Molecule Inhibitors of the Malaria Purine Uptake Transporter that Inhibit <i>Plasmodium falciparum</i> Parasite Proliferation (2019)

Emerging resistance to current antimalarial medicines underscores the importance of identifying new drug targets and novel compounds. Malaria parasites are purine auxotrophic and import purines via the <i>Plasmodium falciparum</i> equilibrative nucleoside transporter type 1 (PfENT1). We previously showed that PfENT1 inhibitors block parasite proliferation in culture. Our goal was to identify additional, possibly more optimal chemical starting points for a drug discovery campaign. We performed a high throughput screen (HTS) of GlaxoSmithKline's 1.8 million compound library with a yeast-based assay to identify PfENT1 inhibitors. We used a parallel progression strategy for hit validation and expansion, with an emphasis on chemical properties in addition to potency. In one arm, the most active hits were tested for human cell toxicity; 201 had minimal toxicity. The second arm, hit expansion, used a scaffold-based substructure search with the HTS hits as templates to identify over 2000 compounds; 123 compounds had activity. Of these 324 compounds, 175 compounds inhibited proliferation of <i>P. falciparum</i> parasite strain 3D7 with IC<sub>50</sub> values between 0.8 and ∼180 μM. One hundred forty-two compounds inhibited PfENT1 knockout (<i>pfent1</i>Δ) parasite growth, indicating they also hit secondary targets. Thirty-two hits inhibited growth of 3D7 but not <i>pfent1</i>Δ parasites. Thus, PfENT1 inhibition was sufficient to block parasite proliferation. Therefore, PfENT1 may be a viable target for antimalarial drug development. Six compounds with novel chemical scaffolds were extensively characterized in yeast-, parasite-, and human-erythrocyte-based assays. The inhibitors showed similar potencies against drug sensitive and resistant <i>P. falciparum</i> strains. They represent attractive starting points for development of novel antimalarial drugs.
Versatile and High-Throughput Polyelectrolyte Complex Membranes via Phase Inversion (2019)

High-flux filtration membranes constructed through scalable and sustainable methods are desirable for energy-efficient separations. Often, these criteria are difficult to be reconciled with one another. Polymeric membranes can provide high flux but frequently involve organic solvents in processing steps. Solubility of many polymeric membranes in organic media also restricts their implementation in solvent filtration. In the present work, we report a simple and high-throughput aqueous processing approach for polyelectrolyte complex (PEC) membranes with controllable porosity and stability in various aqueous and organic environments. PECs are materials composed of oppositely charged polymer chains that can form solids in aqueous environments, yet which can be dissolved in very specific salt solutions capable of breaking the interpolymer ion pairs. By exploiting the salt-induced dissolution and subsequent reformation of the complex, nano- to microporous films are rapidly synthesized which resemble membranes obtained through conventional solvent-phase inversion techniques. PECs remain stable in organic solvents because of the low dielectric constant of the environment, which enhances electrostatic interactions, making them suitable for a wide range of water and solvent filtration applications. Here, we elucidate how the polymer-phase behavior can be manipulated to exercise morphological control, test membrane performance for water and solvent filtration, and quantify the mechanical stability of PECs in relevant conditions.
Measurement of the comb dynamics for feedback control of an etalon-based coupled optoelectronic oscillator (2008)

The response of an optical frequency comb from an etalon-based coupled optoelectronic oscillator to changes in drive current, optoelectronic loop phase, modulator bias, and laser cavity length has been measured. It is found that controlling the phase of the optoelectronic loop is best suited for control of the pulse repetition rate, whereas controlling the laser cavity length is best for stabilization of the optical carrier frequency. Moreover, by measuring the instabilities of the carrier frequency at the fixed-point frequency of the optoelectronic phase, changes to the optoelectronic phase can be decoupled from changes to the laser cavity.