gebhart/patrepeval huggingface dataset:
Extracellular DNA release, quorum sensing, and PrrF1/F2 small RNAs are key players in Pseudomonas aeruginosa tobramycin-enhanced biofilm formation (2019)

Biofilms are structured microbial communities that are the leading cause of numerous chronic infections which are difficult to eradicate. Within the lungs of individuals with cystic fibrosis (CF), <i>Pseudomonas aeruginosa</i> causes persistent biofilm infection that is commonly treated with aminoglycoside antibiotics such as tobramycin. However, sublethal concentrations of this aminoglycoside were previously shown to increase biofilm formation by <i>P. aeruginosa</i>, but the underlying adaptive mechanisms still remain elusive. Herein, we combined confocal laser scanning microscope analyses, proteomics profiling, gene expression assays and phenotypic studies to unravel <i>P. aeruginosa</i> potential adaptive mechanisms in response to tobramycin exposure during biofilm growth. Under this condition, we show that the modified biofilm architecture is related at least in part to increased extracellular DNA (eDNA) release, most likely as a result of biofilm cell death. Furthermore, the activity of quorum sensing (QS) systems was increased, leading to higher production of QS signaling molecules. We also demonstrate upon tobramycin exposure an increase in expression of the PrrF small regulatory RNAs, as well as expression of iron uptake systems. Remarkably, biofilm biovolumes and eDNA relative abundances in <i>pqs</i> and <i>prrF</i> mutant strains decrease in the presence of tobramycin. Overall, our findings offer experimental evidences for a potential adaptive mechanism linking PrrF sRNAs, QS signaling, biofilm cell death, eDNA release, and tobramycin-enhanced biofilm formation in <i>P. aeruginosa</i>. These specific adaptive mechanisms should be considered to improve treatment strategies against <i>P. aeruginosa</i> biofilm establishment in CF patients' lungs.
End-group ionisation enables the use of poly(N-(2-methacryloyloxy)ethyl pyrrolidone) as an electrosteric stabiliser block for polymerisation-induced self-assembly in aqueous media (2019)

End-group ionisation enables use of PNMEP as a steric stabiliser in aqueous PISA: colloidal stability depends on solution pH, with flocculation occurring below pH 4.5.
A palladium catalyzed route to a benzofuran analogue of idolactam V (ILV): Effects on PKC isotype selectivity (1994)

Abstract
Pathogenesis of Staphylococcus aureus Bloodstream Infections (2016)

Staphylococcus aureus, a Gram-positive bacterium colonizing nares, skin, and the gastrointestinal tract, frequently invades the skin, soft tissues, and bloodstreams of humans. Even with surgical and antibiotic therapy, bloodstream infections are associated with significant mortality. The secretion of coagulases, proteins that associate with and activate the host hemostatic factor prothrombin, and the bacterial surface display of agglutinins, proteins that bind polymerized fibrin, are key virulence strategies for the pathogenesis of S. aureus bloodstream infections, which culminate in the establishment of abscess lesions. Pathogen-controlled processes, involving a wide spectrum of secreted factors, are responsible for the recruitment and destruction of immune cells, transforming abscess lesions into purulent exudate, with which staphylococci disseminate to produce new infectious lesions or to infect new hosts. Research on S. aureus bloodstream infections is a frontier for the characterization of protective vaccine antigens and the development of immune therapeutics aiming to prevent disease or improve outcomes.
Performance analysis on a CC-NUMA prototype (1997)

Cache-coherent nonuniform memory access (CC-NUMA) machines have been shown to be a promising paradigm for exploiting distributed execution. CC-NUMA systems can provide performance typically associated with parallel machines, without the high cost associated with parallel programming. This is because a single image of memory is provided on a CC-NUMA machine. Past research on CC-NUMA machines has focused on modifications to the memory hierarchy, interconnect topology, and memory consistency protocols, which are all areas critical to achieving scalable performance. The research described here expands this focus to issues associated with operating system structures which can increase system scalability. We describe a hardware/software prototyping study which investigates how changes to the operating system of a commercial IBM AS/400® system can provide scalable performance when running transaction processing workloads. The project described was a joint effort between researchers at the IBM Thomas J. Wats on Research Center and a team from the AS/400 development laboratory in Rochester, Minnesota. This paper describes various aspects of the project, including changes made to the operating system to enable scalable performance, and the associated hardware and software performance tools developed to identify bottlenecks in the existing operating system structures.
Deacidification of soybean oil using supercritical fluid and membrane technology (2005)

Abstract Membrane processing has been used for oil purification, but low flux and membrane instability are major impediments. A technique that combines membrane processing and supercritical CO 2 was investigated. A specialized, high‐pressure, dead‐end membrane cell was designed, fabricated, and connected to two ISCO (Lincoln, NE) supercritical fluid extraction (SFE) systems. The cell has a base with a grooved bottom for permeate removal, plus a porous metal disc for membrane support; a cell body with threaded connections; and a cap with an inlet assembly. One SFE pump provided the appropriate pressure on the feed stream, the second maintained pressure on the permeate at a slightly lower pressure. The sample consisted of 50% TAG and 50% FFA. For example, for separations at 45°C and a transmembrane pressure of 7‐atm, the β (selectivity factor) values (TAG, FFA) for the SE and BW membranes were 0.56, 3.63 and 0.60, 2.63, respectively, whereas the β values (TAG, FFA) for the DK and NF90 membranes were 0.58, 1.37 and 0.70, 1.28, respectively.
Detailed gasification process of woody biomass-derived char with H<sub>2</sub>O and CO<sub>2</sub> gasifying agents (2020)

To effectively utilize renewable biomass resources, gasification technology is being actively developed. Many studies have been performed regarding the gasification of biomass-derived char (i.e., biochar), where the gasification rate varies greatly with experimental device and biomass type, even when the same gasification temperature is used. In addition, the pore development mechanism during gasification i.e., the relation between the gasification reaction rate and interface area, has been rarely studied. Herein, the gasification rate of wooden biochar with H2O and CO2 gasifying agents using same experimental apparatus and char samples were investigated. The development of micro- and mesopores in the biochar during gasification with H2O and CO2 agents was examined in detail. The results showed that (1) gasification rate constant of biochar was approximately 3–10 times higher under H2O gasifying agent than under CO2 agent at 1073–1273 K; (2) this study reported the most typical values of frequency factor A and activation energy E on Arrhenius plot at high temperature region; and (3) the specific surface area of the micro and mesopores increased with proceeding H2O and CO2 gasification, and the reaction rate is proportional to the interface area during the gasification process.
Development of a system for steady state observation of micro droplet evaporation behavior (2021)

One of the unique droplet behaviors is the Leidenfrost phenomenon. When a droplet comes into contact with a wall that is hotter than the boiling point of the liquid, a thin vapor film formed between the wall and the droplet blocks the heat transfer from the wall to the droplet, causing the droplet to float on the wall and greatly increasing the evaporation time. This phenomenon is also used for micro droplets. For example, by understanding the behavior of micro-droplets in the Leidenfrost state of fuel sprayed inside an engine, we have been able to improve the efficiency of the system. In addition, we are developing a mist CVD method, which is one of the functional thin film fabrication methods, and we are successfully utilizing the Leidenfrost phenomenon to achieve the film deposition. The Leidenfrost phenomenon has been indirectly demonstrated by experiments, but it has not yet been directly observed and needs to be demonstrated. In this study, we developed a droplet diameter measurement program using Python and a special observation device capable of optical observation of microdroplets to observe mist droplets at high temperatures. As a result, it was found that the measurement program could recognize droplets with high accuracy, but it was difficult to obtain accurate droplet diameters due to misrecognition of out-of-focus droplets. In the future, it is necessary to develop a new observation method and a new measurement program that takes into account the unfocused droplets.
Biogenic Nanoscale Colloids in Wastewater Effluents (2010)

The size, surface area, metal complexation capacity, organic pollutant sorption potential, reactivity with disinfectants, and elevated nitrogen content of biogenic organic nanoscale material (BONM) can potentially affect aquatic environments. BONM in effluents from 11 full-scale wastewater treatment plants (WWTPs), which use a range of biological processes, were characterized in two ways. First, BONM was measured by hydrodynamic size-exclusion chromatography coupled with an online organic carbon and UV detector. Second, BONM was isolated from the wastewater using rotary evaporation and dialysis and then characterized by elemental analysis, transmission electron microscopy, and Fourier transform infrared spectroscopy. The wastewaters contained 6-10 mg/L of dissolved organic carbon (DOC). BONM accounted for 5%-50% of the DOC in wastewater effluent organic matter, and the largest size fraction (>10 kDa) of organic carbon correlated with the organic carbon content determined after rotary evaporation and dialysis. Membrane bioreactor WWTPs had the lowest fraction of BONM (<10% of the DOC), followed by conventional activated sludge (10% to 30% of the DOC), with other processes (e.g., trickling filters, aerated lagoons) containing larger BONM percentages. BONM had a lower carbon to nitrogen ratio (6.2 ± 1.7) compared with the literature values for humic or fulvic acids, exhibited chemical bonds that were indicative of amides and polysaccharides, and contained fibril entangled networks. This work has important implications for operations efficiency of WWTPs, including controlling membrane fouling and release of organic nitrogen into sensitive environments.
Carbohydrate Libraries by the Random Glycosylation Approach (2001)

This chapter describes a strategy that utilizes unprotected glycosyl acceptors that are glycosylated randomly to fashion mixtures of oligosaccharides in a very straightforward manner. The assembly of libraries of oligosaccharide mixtures is greatly simplified while the analysis and purification remains challenging.
Synthesis of Mayolene-16 and Mayolene-18:  Larval Defensive Lipids from the European Cabbage Butterfly (2002)

A tandem Wittig approach has been employed for the synthesis of both (11S,9Z,12Z,15Z)- and (11R,9Z,12Z,15Z)-hydroxyoctadeca-9,12,15-trienoic acid (11-hydroxylinolenic acid, 11-HLA) from (R)-glyceraldehyde acetonide. From (11R)-HLA we have prepared the corresponding palmitic acid and stearic acid esters, mayolene-16 (1) and mayolene-18 (2), insect defensive compounds recently identified from Pieris rapae larvae. In addition, we describe the synthesis of three macrocyclic oligomers (24-26) derived from (11R)-HLA.
A mmWave Bridge Concept to Solve the Cellular Outdoor-to-Indoor Challenge (2020)

Wireless indoor coverage and data capacity are important aspects of cellular networks. With the ever-increasing data traffic, demand for more data capacity indoors is also growing. The lower frequencies of the legacy frequency bands of macro outdoor cells manage to provide coverage inside buildings, however, new frequencies foreseen for the 5th generation (5G) of mobile communications in the millimeter wave (mmWave) spectrum penetrate very poorly into buildings. Therefore, a massive densification of the network would require to deploy a large number of indoor small cells, which would lead to high deployment costs to install the necessary wired/optical backhaul. Hence, other methods are needed that allow an increase of the data capacity indoors, bearing a lower cost than a fiber deployment. We propose a cost-efficient out-of-band repeater architecture that provides more data capacity indoors than an outdoor macro/micro network can provide to indoor, without adversely affecting a legacy network, and which readily works with the established cellular infrastructure as well as standard handsets/smartphones. This proposal is compared to conventional in- and out-of-band repeaters and relay nodes in order to highlight the advantages of our solution. While the data capacity for a single link is similar to that of repeaters and relays, a macro cell can be effectively offloaded. Cell capacities corresponding to at least 3-4 times that of a repeater or relay solution can be provided, depending on the number of parallel installed links and the bandwidth in the mmWave spectrum.
Connexions: DSP education for a networked world (2002)

Connexions is a new approach to authoring, teaching, and learning that aims to fully exploit modern information technology. Available free of charge to anyone under open-content and open-source licenses, Connexions offers custom-tailored, current course material, is adaptable to a wide range of learning styles, and encourages students to explore the links among courses and disciplines. In contrast to the traditional process of textbook writing and publishing, Connexions fosters world-wide, cross-institution communities of authors, instructors, and students, who collaboratively and dynamically fashion “modules” from which courses are constructed. We believe the ideas and philosophy embodied by Connexions have the potential to change the very nature of textbook writing and publishing, producing a dynamic, interconnected educational environment that is pedagogically sound, both time and cost efficient, and fun. This paper overviews the philosophy and technology behind Connexions and describes a nascent community developing material for DSP education.
ChemInform Abstract: Heteroepitaxial Film Growth of Layered Compounds with the ZrCuSiAs‐Type and ThCr2Si2‐Type Structures: From Cu‐Based Semiconductors to Fe‐Based Superconductors (2010)

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.
ChemInform Abstract: Three Synthetic Route to a Sterically Hindered Tetrazole. A New One‐Step Mild Conversion of an Amide into a Tetrazole. (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.
Hydrodynamic Micromanipulation of Individual Cells onto Patterned Attachment Sites on Biomicroelectromechanical System Chips (2003)

We report on a simple methodology to move selected single live cells to a desired location on a flat substrate, such as a patterned biomicroelectromechanical system chip. A macroscopic syringe-and-tube-based hydrodynamic manipulation system is used to achieve controlled cell navigation onto hydrophilic sites for cell attachment. Centimeter-per-second flow velocities generated by the system get downgraded to micrometers-per-second flow at the height of settled cells as a result of viscous flow in the medium. By pushing/pulling two syringes that produce two orthogonal flows, fine manipulation in any horizontal direction is feasible. After attachment of the desired cell(s) onto the selected hydrophilic site, all other unwanted cells are washed away from the surrounding hydrophobic surface with faster flow. This simple methodology is applicable for rapid cell pattern formation with high precision.
Sensor-Based Technique for Manually Scanned Hand-Held Optical Coherence Tomography Imaging (2015)

Hand-held optical coherence tomography (OCT) imaging probes offer flexibility to image sites that are otherwise challenging to access. While the majority of hand-held imaging probes utilize galvanometer- or MEMS-scanning mirrors to transversely scan the imaging beam, these probes are commonly limited to lateral fields-of-view (FOV) of only a few millimeters. The use of a freehand manually scanned probe can significantly increase the lateral FOV. However, using the traditional fixed-rate triggering scheme for data acquisition in a manually scanned probe results in imaging artifacts due to variations in the scan velocity of the imaging probe. These artifacts result in a structurally inaccurate image of the sample. In this paper, we present a sensor-based manual scanning technique for OCT imaging, where real-time feedback from an optical motion sensor is used to trigger data acquisition. This technique is able to circumvent the problem of motion artifacts during manual scanning by adaptively altering the trigger rate based on the instantaneous scan velocity, enabling OCT imaging over a large lateral FOV. The feasibility of the proposed technique is demonstrated by imaging several biological and nonbiological samples.
Quality assurance and printing accuracy analysis of 3D printing in medical applications (2022)

Despite its recent introduction into clinical medical practice, three-dimensional (3D) printing is having a significant impact on patient care by generating patient-specific 3D anatomic models and surgical guides from volumetric medical imaging data sets (e.g., high-resolution computed tomography (CT), magnetic resonance imaging (MRI), etc). These models are transforming care by providing new but not limited to methods of data visualization, patient-specific prostheses and surgical guides. However, there is a lack of standardization, particularly in terms of quality assurance (QA) to ensure that the 3D printed model accurately represents the corresponding patient’s anatomy and pathology. This becomes even more problematic given multiple printing technologies, variability across vendors, and inter printer capabilities, all of which have an impact on printing accuracy and precision. In this study, we investigated printing accuracy on a diverse selection of 3D printers commonly used in the medical field. A specially designed 3D printing QA phantom was periodically printed on 16 printers used in our practice, covering five distinct printing technologies and eight different vendors. Longitudinal data were acquired over a period of six months with the QA phantom printed monthly on each printer. Qualitative assessment and quantitative measurements were obtained for each printed phantom. The accuracy and precision were assessed by comparing quantitative measurements with reference values of the phantom. Data were then compared among printer models, vendors, and printing technologies. Longitudinal trends were also analyzed. Results revealed differences in accuracy across printers. It was found that material jetting and vat photopolymerization printers were most accurate. Printers using the same 3D printing technology but from different vendors also showed differences in accuracy, most notably between vat photopolymerization printers from two different vendors. Furthermore, differences in accuracy were found between printers from the same vendor using the same printing technology, but different models/generations. These results show how factors such as printing technology, vendor, and model can impact 3D printing accuracy, which should be appropriately considered in practice to avoid potential detrimental consequences.
Terahertz sources based on intracavity frequency mixing in mid-infrared quantum cascade lasers with passive nonlinear sections (2011)

We report the design and performance of terahertz quantum cascade laser sources based on intracavity difference frequency generation in dual-wavelength mid-infrared quantum cascade lasers with a passive nonlinear section at the exit facet, designed for giant second-order nonlinear susceptibility. These devices operate in the mid-infrared at λ1=8.4 μm and λ2=9.5 μm, with terahertz output at the difference frequency, λ3≈73 μm. Terahertz output of approximately 100 nW was observed up to a heat sink temperature of 210 K.
[Changes in immunological status among newly-diagnosed HIV-infected in Denmark 1995-2005]. (2008)

Newly-diagnosed homosexual men present at an earlier stage of disease progression and with a better preserved immune system today than 5-10 years ago, presumably due to a combination of frequent HIV testing and increased risk behaviour among young homosexuals in particular. Increased preventive measures targeting known risk groups are necessary to prevent further spread.
Coverage Extension via Side-Lobe Transmission in Multibeam Satellite System (2017)

peer reviewed
Synthesis of N‐Protected 3,3‐Difluoroazetidin‐2‐ones. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Implementation of dipolar direct current (DDC) collision‐induced dissociation in storage and transmission modes on a quadrupole/time‐of‐flight tandem mass spectrometer (2011)

Means for effecting dipolar direct current collision-induced dissociation (DDC CID) on a quadrupole/time-of-flight in a mass spectrometer have been implemented for the broadband dissociation of a wide range of analyte ions. The DDC fragmentation method in electrodynamic storage and transmission devices provides a means for inducing fragmentation of ions over a large mass-to-charge range simultaneously. It can be effected within an ion storage step in a quadrupole collision cell that is operated as a linear ion trap or as ions are continuously transmitted through the collision cell. A DDC potential is applied across one pair of rods in the quadrupole collision cell of a QqTOF hybrid mass spectrometer to effect fragmentation. In this study, ions derived from a small drug molecule, a model peptide, a small protein, and an oligonucleotide were subjected to the DDC CID method in either an ion trapping or an ion transmission mode (or both). Several key experimental parameters that affect DDC CID results, such as time, voltage, low mass cutoff, and bath gas pressure, are illustrated with protonated leucine enkephalin. The DDC CID dissociation method gives a readily tunable, broadband tool for probing the primary structures of a wide range of analyte ions. The method provides an alternative to the narrow resonance conditions of conventional ion trap CID and it can access more extensive sequential fragmentation, depending upon conditions. The DDC CID approach constitutes a collision analog to infrared multiphoton dissociation (IRMPD).
On the Removal of Nitrogeneous Gam from Town Gas (1955)

都市ガス中に少量の気相ガムが生成し, 圧迭機轟ガバナーなどの供給綱に堆積し, 供給に支障を来すおそれがある。これはオイルガス中のジオレフィンと発生炉ガス中に比較的多量に存在する酸化窒素が, 酸素の存在の下に重合してガムとなるためであることを確かめた。これに対する対策として, 発生炉ガス中の酸化窒素を乾式脱硫器によつて除去する方法, および既にガス中に生成したガムを水洗によつて除去する方法の2つの方法が適当で, 両者の実験室的および工業的規模の試験成績によりその有用性を示した。