gebhart/patrepeval huggingface dataset:
Linker‐insertion mutagenesis of Pseudomonas aeruginosa outer membrane protein OprF (1993)

The oprF gene, expressing Pseudomonas aeruginosa major outer membrane protein OprF, was subjected to semi-random linker mutagenesis by insertion of a 1.3 kb Hincll kanamycin-resistance fragment from plasmid pUC4KAPA into multiple blunt-ended restriction sites in the oprF gene. The kanamycin-resistance gene was then removed by Pstl digestion, which left a 12 nucleotide pair linker residue. Nine unique clones were identified that contained such linkers at different locations within the oprF gene and were permissive for the production of full-length OprF variants. In addition, one permissive site-directed insertion, one non-permissive insertion and one carboxy-terminal insertion leading to proteolytic truncation were also identified. These mutants were characterized by DNA sequencing and reactivity of the OprF variants with a bank of 10 OprF-specific monoclonal antibodies. Permissive clones produced OprF variants that were shown to be reactive with the majority of these monoclonal antibodies, except where the insertion was suspected of interrupting the epitope for the specific monoclonal antibody. In addition, these variants were shown to be 2-mercaptoethanol modifiable, to be resistant to trypsin cleavage in intact cells and partly cleaved to a high-molecular-weight core fragment in outer membranes and, where studied, to be accessible to indirect immunofluorescenee labelling in intact cells by monoclonal antibodies specific for surface epitopes. Based on these data, a revised structural model for OprF is proposed.
Changes in the structure-function relationship of elastin and its impact on the proximal pulmonary arterial mechanics of hypertensive calves (2008)

Extracellular matrix remodeling has been proposed as one mechanism by which proximal pulmonary arteries stiffen during pulmonary arterial hypertension (PAH). Although some attention has been paid to the role of collagen and metallomatrix proteins in affecting vascular stiffness, much less work has been performed on changes in elastin structure-function relationships in PAH. Such work is warranted, given the importance of elastin as the structural protein primarily responsible for the passive elastic behavior of these conduit arteries. Here, we study structure-function relationships of fresh arterial tissue and purified arterial elastin from the main, left, and right pulmonary artery branches of normotensive and hypoxia-induced pulmonary hypertensive neonatal calves. PAH resulted in an average 81 and 72% increase in stiffness of fresh and digested tissue, respectively. Increase in stiffness appears most attributable to elevated elastic modulus, which increased 46 and 65%, respectively, for fresh and digested tissue. Comparison between fresh and digested tissues shows that, at 35% strain, a minimum of 48% of the arterial load is carried by elastin, and a minimum of 43% of the change in stiffness of arterial tissue is due to the change in elastin stiffness. Analysis of the stress-strain behavior revealed that PAH causes an increase in the strains associated with the physiological pressure range but had no effect on the strain of transition from elastin-dominant to collagen-dominant behavior. These results indicate that mechanobiological adaptations of the continuum and geometric properties of elastin, in response to PAH, significantly elevate the circumferential stiffness of proximal pulmonary arterial tissue.
Supplementary Table 1 from Distinct Subtypes of Gastric Cancer Defined by Molecular Characterization Include Novel Mutational Signatures with Prognostic Capability (2023)

&lt;p&gt;Supplementary Table 1: Published publications and cohorts&lt;/p&gt;
Economic‐Based Optimization (2008)

This chapter contains sections titled: Economic-Based Performance Objective Functions Batch and Semibatch Reactors Flow Reactors Summary Problems Bibliography
Extended vs standard lymph node dissection in robot‐assisted radical prostatectomy for intermediate‐ or high‐risk prostate cancer: a propensity‐score‐matching analysis (2013)

Robot-assisted eLND achieved an increased lymph node yield and higher detection rate of lymph node metastases; however, robotic eLND did not alter biochemical outcomes in a short-term follow-up.
Retroreflective screens and their application to autostereoscopic displays (1997)

An autostereoscopic display is described that enables a viewer, or viewers, to view 3D TV or computer graphics images without the need to wear special glasses or other head-wear. The display is based upon a retroreflective screen which provides the display with a number of unique features. One of these features is the capability to produce a large screen (greater than 80' diagonal) multiviewer autostereoscopic display whereby each viewer can see the same or a completely different image. Each image can occupy the entire screen without crosstalk between multiple images occurring. Retroreflective material has the characteristic that light incident on it is returned to the viewer along exactly the same path as the incident light. This is in contrast to reflections from other surfaces where in general the angle of incident is equal to the angle of reflection. Incident light returned from a retroreflective screen can be structured such that scatter or other disturbances can be minimized. This results in a very narrow viewing angle over which the incident image can be observed. Sine the majority of the light incident on the screen is returned to the originating source the screen can be considered to have a 'gain' when compared with a similar configuration where the light is incident on a conventional projection screen.
Formation and manipulation of ferrofluid droplets with magnetic fields in a microdevice: a numerical parametric study (2020)

We present a numerical model that describes the microfluidic generation and manipulation of ferrofluid droplets under an external magnetic field. We developed a numerical Computational Fluid Dynamics (CFD) analysis for predicting and optimizing continuous flow generation and processing of ferrofluid droplets with and without the presence of a permanent magnet. More specifically, we explore the dynamics of oil-based ferrofluid droplets within an aqueous continuous phase under an external inhomogeneous magnetic field. The developed model determines the effect of the magnetic field on the droplet generation, which is carried out in a flow-focusing geometry, and its sorting in T-junction channels. Three-channel depths (25 μm, 30 μm, and 40 μm) were investigated to study droplet deformation under magnetic forces. Among the three, the 30 μm channel depth showed the most consistent droplet production for the studied range of flow rates. Ferrofluids with different loadings of magnetic nanoparticles were used to observe the behavior for different ratios of magnetic and hydrodynamic forces. Our results show that the effect of these factors on droplet size and generation rate can be tuned and optimized to produce consistent droplet generation and sorting. This approach involves fully coupled magnetic-fluid mechanics models and can predict critical details of the process including droplet size, shape, trajectory, dispensing rate, and the perturbation of the fluid co-flow for different flow rates. The model enables better understanding of the physical phenomena involved in continuous droplet processing and allows efficient parametric analysis and optimization.
Integrating the CEREC technology at UT College of Dentistry. (2012)

The computer-aided design/computer-aided manufacturing (CAD/CAM) has evolved during the past 25 years, and this evolution has improved the speed and precision in which dentists can deliver high quality esthetic restorations. CEREC is an acronym for "ceramic reconstruction" and is one of the CAD/CAM systems available to dentists in private practice. The University of Tennessee College of Dentistry was one of the first dental schools in the United States to embrace this technology and integrate it into the four-year curriculum. In a dental school setting, this technology can prove to be an educational tool for the dental students, cost effective for the University and provide exceptional service for the patients.
Macrophage Killing of Bacterial and Fungal Pathogens Is Not Inhibited by Intense Intracellular Accumulation of the Lipoglycopeptide Antibiotic Oritavancin (2012)

Intact phagocytic effector function is fundamental to host defense against microbial pathogens. Concern has been raised regarding the potential that accumulation of certain agents, including cationic amphiphilic antibiotics, within macrophages could cause a mixed-lipid storage disorder, resulting in macrophage dysfunction in recipients. The ability of 2 macrophage cell lines (HL-60; RAW 264.7) to kill archetypal Gram-positive (Staphylococcus aureus), Gram-negative (Acinetobacter baumannii), and fungal (Candida albicans) pathogens was tested following exposure of the macrophages to the lipoglycopeptide antibiotic oritavancin. Oritavancin did not affect killing of C. albicans but markedly enhanced killing of S. aureus by both macrophages. Oritavancin modestly reduced killing of A. baumannii by HL-60 cells but not by RAW 264.7 cells. Thus, macrophage killing of microbes remains intact despite substantial intracellular accumulation with a lipoglycopeptide antibiotic.
Potential of RFID Systems to Detect Object Orientation (2011)

In this paper we present a novel method for estimating the inclination of passive UHF RFID tags, for use in supply chains to monitor the handling of tagged items. Based on observations of the polarization, a Bayesian estimator of the tag inclination is constructed. The Bayesian estimator has been analyzed and evaluated in a experimental setup. The results shows great potential as the estimator is very robust when determining the inclination.
Spatial atomic layer deposition for coating flexible porous Li-ion battery electrodes (2017)

Ultrathin atomic layer deposition (ALD) coatings on the electrodes of Li-ion batteries can enhance the capacity stability of the Li-ion batteries. To commercialize ALD for Li-ion battery production, spatial ALD is needed to decrease coating times and provide a coating process compatible with continuous roll-to-roll (R2R) processing. The porous electrodes of Li-ion batteries provide a special challenge because higher reactant exposures are needed for spatial ALD in porous substrates. This work utilized a modular rotating cylinder spatial ALD reactor operating at rotation speeds up to 200 revolutions/min (RPM) and substrate speeds up to 200 m/min. The conditions for spatial ALD were adjusted to coat flexible porous substrates. The reactor was initially used to characterize spatial Al2O3 and ZnO ALD on flat, flexible metalized polyethylene terephthalate foils. These studies showed that slower rotation speeds and spacers between the precursor module and the two adjacent pumping modules could significantly increase the reactant exposure. The modular rotating cylinder reactor was then used to coat flexible, model porous anodic aluminum oxide (AAO) membranes. The uniformity of the ZnO ALD coatings on the porous AAO membranes was dependent on the aspect ratio of the pores and the reactant exposures. Larger reactant exposures led to better uniformity in the pores with higher aspect ratios. The reactant exposures were increased by adding spacers between the precursor module and the two adjacent pumping modules. The modular rotating cylinder reactor was also employed for Al2O3 ALD on porous LiCoO2 (LCO) battery electrodes. Uniform Al coverages were obtained using spacers between the precursor module and the two adjacent pumping modules at rotation speeds of 25 and 50 RPM. The LCO electrodes had a thickness of ∼49 μm and pores with aspect ratios of ∼12–25. Coin cells were then constructed using the ALD-coated LCO electrodes and were tested to determine their battery performance. The capacity of the Al2O3 ALD-coated LCO battery electrodes was measured versus the number of charge-discharge cycles. Both temporal and spatial ALD processing methods led to higher capacity stability compared with uncoated LCO battery electrodes. The results for improved battery performance were comparable for temporal and spatial ALD-coated electrodes. The next steps are also presented for scale-up to R2R spatial ALD using the modular rotating cylinder reactor.
High Quality Factor 1D Photonic Crystal Cavities in Silicon (2009)

Using a tapered photonic crysal cavity approach we designed cavities with theoretical Quality factors Q=2 × 107 and measured experimental Q= 7.5 × 105. Non-linear broadening of the cavity resonance has also been observed.
The WE 640AA condenser microphone (2014)

In 1916 Edward Wente, working for Western Electric an AT&amp;T subsidiary, invented a microphone that was the foundation of the modern condenser microphone. Wente's early condenser microphone designs continued to be developed until Western Electric produced the WE 361 in 1924 followed by the Model 394 condenser microphone in 1926. Western Electric used the WE 394 microphone as part of the “Master Reference System” to rate audio transmission quality of the telephone network. The WE 394 was too large for some measurement purposes so in 1932 Bell Labs engineers H. Harrison and P. Flanders designed a smaller version. The diaphragm had a diameter of 0.6 in. However, this design proved too difficult to manufacture and F. Romanow, also at Bell Labs, designed the 640A “1 in.” microphone in 1932. Years later it was discovered that the 640A sensitivity varied by almost 6 dB from -650 C to 250 C. To reduce the thermal sensitivity, Bell Labs engineers M. Hawley and P. Olmstead carefully changed some of the 640A materials. The modified microphone was designated as the 640AA, which became the worldwide standard microphone for measuring sound pressure. This talk will describe some more details of the history of the 640AA microphone.
CERMINE -- Automatic Extraction of Metadata and References from Scientific Literature (2014)

CERMINE is a comprehensive open source system for extracting metadata and parsed bibliographic references from scientific articles in born-digital form. The system is based on a modular workflow, whose architecture allows for single step training and evaluation, enables effortless modifications and replacements of individual components and simplifies further architecture expanding. The implementations of most steps are based on supervised and unsupervised machine-learning techniques, which simplifies the process of adjusting the system to new document layouts. The paper describes the overall workflow architecture, provides details about individual implementations and reports evaluation methodology and results. CERMINE service is available at http://cermine.ceon.pl.
Genetic Methodologies and Applications (2013)

There have been tremendous advances in the molecular technologies and data-analytic methods at our disposal for studying the genetic bases of complex d diseases and traits. These advances have enabled the creation of comprehensive catalogs of different forms of human genetic variation, as well as large-scale studies focused on specific diseases or traits. This chapter outlines the general principles behind some of these advances and discusses their application to studying complex genetic traits, with a focus on neuropsychiatric disease in particular. Different genetic strategies that are underway in psychiatric genetics include studies of <italic>de novo</italic> variation in exome sequencing, large deletion and duplication copy number variants, rare and low-frequency variants segregating in populations, and common polymorphisms.
A New Single-Phase Five-Level Inverter Topology for Single and Multiple Switches Fault Tolerance (2018)

Reliability of power inverters is of dominant importance in various applications, including industrial, military, aerospace, and commercial applications. Therefore, developing fault tolerant (FT) power inverters is extremely needed from the viewpoints of system availability and avoiding harmful consequences. Tolerating various types of faults, preserving full output ratings after the fault, and being cost-effective represent the main challenges for most of existing FT solutions. In this paper, a new FT single-phase five-level inverter topology is proposed. The proposed topology can effectively tolerate both of single or multiple switches faults whether they are of open- or short-circuit fault types. Moreover, the proposed topology does not deteriorate system efficiency in postfault operation compared to the previously developed FT solutions. Evaluation of the effectiveness and robustness of the proposed topology is verified in both of simulation and experimental environments. Different case studies are investigated in order to cover various types and locations of switches' faults. Moreover, comprehensive comparisons are provided to validate the superiority of the proposed topology over the previously addressed techniques.
Discriminative feature selection for hidden Markov models using Segmental Boosting (2008)

We address the feature selection problem for hidden Markov models (HMMs) in sequence classification. Temporal correlation in sequences often causes difficulty in applying feature selection tech niques. Inspired by segmental k-means segmentation (SKS) [B. Juang and L. Rabiner, 1990], we propose Segmentally Boosted HMMs (SBHMMs), where the state-optimized features are constructed in a segmental and discriminative manner. The contributions are twofold. First, we introduce a novel feature selection algorithm, where the temporal dynamics are decoupled from the static learning procedure by assuming that the sequential data are piecewise independent and identically distributed. Second, we show that the SBHMM consistently improves traditional HMM recognition in various domains. The reduction of error compared to traditional HMMs ranges from 17% to 70% in American Sign Language recognition, human gait identification, lip reading, and speech recognition.
The variable natural history of idiopathic dilated cardiomyopathy. (2012)

IDCM exhibits a highly variable natural history and standard clinical predictors have limited ability to classify IDCM patients into broad prognostic categories. These findings suggest that there are important host-environmental factors still unappreciated in the biology of IDCM.
SINR Coverage Enhancement of 6G UAV-Assisted Networks Deploying IRS (2022)

The objective of the work is to enhance the signal-to-interference-plus-noise ratio (SINR) coverage probability in UAV-assisted 6G wireless networks. Therefore, the work analyzed and compared the coverage probability of conventional and IRS-assisted UAV communications models. The research obtained that the employment of IRS in UAV-assisted wireless networks enhances the SINR coverage probability significantly. Moreover, the installment of IRS in UAV networks reduces the energy consumption of the network.
Incorporating cost of control into the design of a load balancing controller (2004)

Load balancing is widely used in computing systems as a way to optimize performance by reducing bottleneck utilizations, such as adjusting the size of buffer pools to balance resource demands in a database management system. Load balancing is generally approached as a constrained optimization problem in which only the benefits of load balancing are considered. However, the costs of control are important as well. Herein, we study the value of including in controller design the trade-off between the cost of transient imbalances in resource utilizations and the cost of changing resource allocations. An example of the latter are actions such as resizing buffer pools that can reduce throughputs. This is because requests for data in pools whose memory is reduced immediately have longer access times whereas requests for data in pools whose memory is increased must fill this memory with data from disk before accessed times are reduced. We frame our study of control costs in terms of the widely used linear quadratic regulator (LQR). We develop a cost model that allows us to specify the LQR Q and R matrices based on the impact on system performance of changing resource allocations and transient load imbalances. Our studies of a DB2 universal database server using benchmarks for online transaction processing and decision support workloads show that incorporating our cost model into the MIMO LQR controller results in a 14% improvement in performance beyond that achieved by dynamically allocating the size of buffers without properly considering the cost of control.
A New Solution for Life Without Blood (1995)

The faster neurological recovery of dogs treated with the "intracellular-type" maintenance solution supports the biochemical data showing the benefits of this type of blood substitute for extending the safe limits of hypothermic cardiac arrest procedures to > 3 hours.
A Novel Crystallization-Induced Diastereomeric Transformation Based on a Reversible Carbon−Sulfur Bond Formation. Application to the Synthesis of a γ-Secretase Inhibitor (2007)

This paper describes a remarkably efficient process for the preparation of gamma-secretase inhibitor 1. The target is synthesized in only five steps with an overall yield of 58%. The key operation is a highly selective and practical, crystallization-driven transformation for the conversion of a mixture of tertiary benzylic alcohols into the desired sulfide diastereomer with 94:6 dr. This unprecedented process is based upon a reversible carbon-sulfur bond formation under acidic conditions.
A novel feedforward noise shaping for word-length reduction (2016)

In this paper, we present a novel approach to shape the quantization noise during word-length reduction. In comparison to the traditional feedback noise shaping, our approach is feedforward and thus inherently stable. It can achieve one or multiple frequency notches in the quantization noise spectrum with controlled notch width and notch depth while keeping the out-of-band noise level lower than the feedback noise shaping. Results from a digital communication example demonstrate the performance of this new noise shaping method.
Biological Active Analogues of the Opioid Peptide Biphalin: Mixed α/β3-Peptides (2013)

Natural residues of the dimeric opioid peptide Biphalin were replaced by the corresponding homo-β(3) amino acids. The derivative 1 containing hβ(3) Phe in place of Phe showed good μ- and δ-receptor affinities (Ki(δ) = 0.72 nM; Ki(μ) = 1.1 nM) and antinociceptive activity in vivo together with an increased enzymatic stability in human plasma.
The Role of α-Folate Receptor-Mediated Transport in the Antitumor Activity of Antifolate Drugs (2004)

Antifolate drugs, particularly ZD9331, have the potential for increased efficacy in tumors that highly overexpress the alpha-FR.