gebhart/patrepeval huggingface dataset:
Computational Cannula Microscopy: Fluorescent Imaging Through Ultra-Thin Glass Needle (2017)

We demonstrate a fluorescent microscopy through an optical cannula (220µm diameter glass needle) for deep tissue imaging. We first show sample images captured in thin sections for the proof of principle. Then cannula is inserted deep into dissected brain tissue which captured high resolution images of microglia cells.
Constraint Management and Checking in Template-Based Circuit Designs (2009)

In a template-based design methodology, constraint management and proof are critical to accurate circuit analysis. Constraints are defined in one of three places: at the template level, at the circuit design level, or at the RTL level. Constraints are used to restrict the patterns of both logical and electrical analyses. At the circuit level, where the templates are instantiated, the constraints must be proven true to validate the logical and electrical analyses. In this paper, we show all aspects of our constraint management in our template-based design methodology. We show how we use constraints for formal equivalence checking, electrical analysis, and template verification and how we validate constraints using formal techniques and simulation assertions.
ChemInform Abstract: Air as the Renewable Carbon Source of the Future: An Overview of CO<sub>2</sub> Capture from the Atmosphere (2013)

Abstract Review: 217 refs.
CMOS-compatible, piezo-optomechanically tunable photonics for visible wavelengths and cryogenic temperatures (2019)

We demonstrate a platform for phase and amplitude modulation in silicon nitride photonic integrated circuits via piezo-optomechanical coupling using tightly mechanically coupled aluminum nitride actuators. The platform, fabricated in a CMOS foundry, enables scalable active photonic integrated circuits for visible wavelengths, and the piezoelectric actuation functions without performance degradation down to cryogenic temperatures. As an example of the potential of the platform, we demonstrate a compact (∼40 µm diameter) silicon nitride ring resonator modulator operating at 780 nm with intrinsic quality factors in excess of 1.5 million, >10 dB change in extinction ratio with 2 V applied, a switching time less than 4 ns, and a switching energy of 0.5 pJ/bit. We characterize the exemplary device at room temperature and 7 K. At 7 K, the device obtains a resistance of approximately 20 teraohms, allowing it to operate with sub-picowatt electrical power dissipation. We further demonstrate a Mach-Zehnder modulator constructed in the same platform with piezoelectrically tunable phase shifting arms, with 750 ns switching time constant and 20 nW steady-state power dissipation at room temperature.
Rate‐Reducing Resistance to <i>Fusarium solani</i> f. sp. <i>phaseoli</i> underlies Field Resistance to Soybean Sudden Death Syndrome (1997)

Yield losses occur in soybean [ Glycine max (L.) Merr.] because of sudden death syndrome (SDS) caused by Fusarium solani (Mart.) Saec. f. sp. phaseoli (Burk.) Snyd. & Hans, type A. Our objective was to determine whether tolerance or partial resistance to infection underlies field resistance to SDS. Seven field resistant cultivars and five susceptible cultivars were planted at two locations. Twenty taproots per cultivar were sampled every 7 to 21 d from the V0 to R8 growth stages, 8 to 121 days after planting (DAP). Six taproot sections per plant were tested for F. solani on a selective medium. Infection frequency (IF), the percentage of infected plants, and infection severity (IS), the percentage of infected root segments, were scored. Leaf symptoms were recorded and standardized to the R6 stage and the disease index (DX) was calculated. Infection was detected at the VI stage (within 15 DAP) and reached a maximum by about R1 (55–68 DAP). All cultivars were infected by F. solani . However, seasonal mean IF and mean IS were significantly lower among the resistant cultivar class. After R1, infection was also significantly lower among the resistant cultivar class within individual sampling dates. Also, DX and IF were correlated in each environment ( r = 0.38 and 0.61). Therefore, in the resistant cultivars Forrest, Ripley, Jack, PI520733, ExF44, ExF59, and ExF78, late season rate‐reducing (partial) resistance decreased the DX, IF, and IS. Resistance probably extends the latent period of F. solani . Among susceptible cultivars, Essex and A5403, had reduced leaf symptoms but high IF and IS suggesting tolerance to F.solani that alleviated SDS.
Rapid Identification of Periodontal Pathogens in Subgingival Plaque: Comparison of Indirect Immunofluorescence Microscopy with Bacterial Culture for Detection of Actinobacillus actinomycetemcomitans (1985)

The sensitivity of indirect immunofluorescence microscopy using specific polyclonal or monoclonal serodiagnostic reagents for Actinobacillus actinomycetemcomitans in subgingival dental plaque ranged from 82-100% as compared with culture on selective or non-selective media. This bacterium was found in 100% of the periodontally diseased sites examined in localized juvenile periodontitis patients and was statistically related to clinical indices of periodontal disease including the Gingival Index, Plaque Index, and Pocket Depth. Indirect immunofluorescence microscopy is a useful technique for the rapid and reliable determination of A. actinomycetemcomitans in human subgingival dental plaque which may be applied to the clinical diagnosis, treatment, and monitoring of periodontitis associated with A. actinomycetemcomitans.
Virtual Traffic Lights: System Design and Implementation (2018)

Traffic congestion is a daunting problem that is affecting the daily lives of billions of people across the world. Recently, a promising new traffic control scheme known as Virtual Traffic Lights (VTL) has been proposed for mitigating traffic congestion. VTL is an infrastructure free traffic control scheme that leverages the presence of Vehicle-to-Vehicle (V2V) communications. Such infrastructure free scheme has several benefits, such as alleviating traffic congestion; reducing the large cost of traffic lights and traffic control systems; reducing carbon emission, etc. This paper reports a DSRC-based prototype design effort on VTL using Dedicated Short Range Communications (DSRC) technology. The experiments performed show the feasibility of implementing VTL with DSRC technology. Preliminary results of the field tests conducted in Pittsburgh with vehicles using VTL equipment indicate that VTL is capable of coordinating traffic at intersections and reducing the commute time of people.
Laser-produced plasma light source for EUVL (2010)

This paper describes the development of laser-produced-plasma (LPP) extreme-ultraviolet (EUV) source architecture for advanced lithography applications in high volume manufacturing. EUV lithography is expected to succeed 193nm immersion technology for sub-22nm critical layer patterning. In this paper we discuss the most recent results from high EUV power testing and debris mitigation testing on witness samples and normal incidence collectors. Subsystem performance will be shown including the CO2 drive laser, debris mitigation, normal incidence collector and coatings, droplet generation, laser-to-droplet targeting control, intermediate-focus (IF) metrology and system use and experience. In addition, a number of smaller lab-scale experimental systems have also been constructed and tested. This presentation reviews the experimental results obtained on systems with a focus on the topics most critical for an HVM source.
Studying viscoelasticity in soft tissues with supersonic shear imaging (2004)

In this work, a 3D analytical formulation of the mechanical Green’s function in a viscoelastic medium is derived and presented. Based on a Voigt model to take into account viscoelasticity, this mathematical formulation is validated experimentally using the supersonic shear imaging technique (SSI). Taking benefit of the ultrasonic remote generation of a moving shear source radiating low-frequency shear waves in the medium, this technique has been studied and validated for soft tissue elasticity mapping in previous works. It is shown here that the spatial and temporal shape of shear waves induced in soft tissues using SSI can be accurately modeled with the viscoelastic Green’s function. The influences of important parameters such as viscosity, elasticity, or diffraction on the shear wave shape are carefully studied and discriminated. In a second part, taking advantage of the previous modeling, the inverse problem consisting of recovering shear elasticity and viscosity is presented and validated using the Green’s function-based simulation tool. Experiments on tissue-mimicking phantoms presenting different viscoelastic properties are presented. The influence of out-of-plane shear propagation on the inversion algorithm is discussed.
Development of Epitope-Blocking ELISA for Universal Detection of Antibodies to Human H5N1 Influenza Viruses (2009)

The epitope-blocking ELISA based on a unique 5F8 mAb provided highly sensitive and 100% specific detection of antibodies to H5N1 influenza viruses in human sera.
Synthesis of C‐4 substituted pyrimidine nucleoside analogs. Preparation of several 4‐(2‐oxoalkylidene)‐2(1<i>H</i>)‐pyrimidinone ribonucleosides (1994)

Abstract A series of 4‐(1‐alkynyl)‐2(1 H )‐pyrimidinone ribonucleosides were synthesized from the Pd‐catalyzed coupling of terminal alkynes to the 4‐chloropyrimidin‐2‐one ribonucleoside ( 2 ). These compounds were hydrated, using three different methods, to afford the 4‐(2‐oxoalkylidene)‐2(1 H )‐pyrimidinones. The 4‐enol‐pyrimidin‐2‐one structure of the title compounds offers functional groups with the potential for Watson‐Crick hydrogen bonding.
Synthesis of 3,3‐dinitroazetidine from 1‐<i>t</i>‐butyl‐3,3‐dinitroazetidine (1992)

Abstract Treatment of 1‐ t ‐butyl‐3,3‐dinitroazetidine (1) with benzyl chloroformate resulted in a novel elimination of isobutylene to yield equimolar amounts of 1‐(benzyloxycarbonyl)‐3,3‐dinitroazetidine (3) and 1‐ t ‐butyl‐3,3‐dinitroazetidine hydrochloride. The carbamate 3 was effectively cleaved by trifluoromethanesulfonic acid to yield 3,3‐dinitroazetidinium trifluoromethanesulfonate (4) . Free 3,3‐dinitroazetidine (5) has also been isolated.
Cyclic Nucleotide-Gated Ion Channels (2002)

Cyclic nucleotide-gated (CNG) channels are nonselective cation channels first identified in retinal photoreceptors and olfactory sensory neurons (OSNs). They are opened by the direct binding of cyclic nucleotides, cAMP and cGMP. Although their activity shows very little voltage dependence, CNG channels belong to the superfamily of voltage-gated ion channels. Like their cousins the voltage-gated K+ channels, CNG channels form heterotetrameric complexes consisting of two or three different types of subunits. Six different genes encoding CNG channels, four A subunits (A1 to A4) and two B subunits (B1 and B3), give rise to three different channels in rod and cone photoreceptors and in OSNs. Important functional features of these channels, i.e., ligand sensitivity and selectivity, ion permeation, and gating, are determined by the subunit composition of the respective channel complex. The function of CNG channels has been firmly established in retinal photoreceptors and in OSNs. Studies on their presence in other sensory and nonsensory cells have produced mixed results, and their purported roles in neuronal pathfinding or synaptic plasticity are not as well understood as their role in sensory neurons. Similarly, the function of invertebrate homologs found in Caenorhabditis elegans, Drosophila, and Limulus is largely unknown, except for two subunits of C. elegans that play a role in chemosensation. CNG channels are nonselective cation channels that do not discriminate well between alkali ions and even pass divalent cations, in particular Ca2+. Ca2+ entry through CNG channels is important for both excitation and adaptation of sensory cells. CNG channel activity is modulated by Ca2+/calmodulin and by phosphorylation. Other factors may also be involved in channel regulation. Mutations in CNG channel genes give rise to retinal degeneration and color blindness. In particular, mutations in the A and B subunits of the CNG channel expressed in human cones cause various forms of complete and incomplete achromatopsia.
Partition-Aware Routing to Improve Network Isolation in Infiniband Based Multi-tenant Clusters (2015)

InfiniBand (IB) is a widely used network interconnect for modern high-performance computing systems. In large IB fabrics, isolation of nodes is provided through partitioning. The routing algorithm, however, is unaware of these partitions in the network, Traffic flows belonging to different partitions might share links inside the network fabric. This sharing of intermediate links creates interference, which is particularly critical to avoid in multi-tenant environments like a cloud. In such systems, each tenant should experience predictable network performance, unaffected by the workload of other tenants. In addition, using current routing schemes, routes crossing partition boundaries are considered when distributing routes onto links in the network, despite the fact that these routes will never be used. The result is degraded load-balancing. In this paper, we present a novel partition-aware fat-tree routing algorithm, pFTree. The pFTree algorithm utilizes several mechanisms to provide network-wide isolation of partitions belonging to different tenant groups. Given the available network resources, pFTree starts by isolating partitions at the physical link level, and then moves on to utilize virtual lanes, if needed. Our experiments and simulations show that pFTree is able to significantly reduce the affect of inter-partition interference without any additional functional overhead. Furthermore, pFTree also provides improved load-balancing over the de facto standard IB fat-tree routing algorithm.
Sensor‐mediated granular sludge reactor for nitrogen removal and reduced aeration demand using a dilute wastewater (2020)

A sensor-mediated strategy was applied to a laboratory-scale granular sludge reactor (GSR) to demonstrate that energy-efficient inorganic nitrogen removal is possible with a dilute mainstream wastewater. The GSR was fed a dilute wastewater designed to simulate an A-stage mainstream anaerobic treatment process. DO, pH, and ammonia/nitrate sensors measured water quality as part of a real-time control strategy that resulted in low-energy nitrogen removal. At a low COD (0.2 kg m<sup>-3</sup> day<sup>-1</sup> ) and ammonia (0.1 kg-N m<sup>-3</sup> day<sup>-1</sup> ) load, the average degree of ammonia oxidation was 86.2 ± 3.2% and total inorganic nitrogen removal was 56.7 ± 2.9% over the entire reactor operation. Aeration was controlled using a DO setpoint, with and without residual ammonia control. Under both strategies, maintaining a low bulk oxygen level (0.5 mg/L) and alternating aerobic/anoxic cycles resulted in a higher level of nitrite accumulation and supported shortcut inorganic nitrogen removal by suppressing nitrite oxidizing bacteria. Furthermore, coupling a DO setpoint aeration strategy with residual ammonia control resulted in more stable nitritation and improved aeration efficiency. The results show that sensor-mediated controls, especially coupled with a DO setpoint and residual ammonia controls, are beneficial for maintaining stable aerobic granular sludge. PRACTITIONER POINTS: Tight sensor-mediated aeration control is need for better PN/A. Low DO intermittent aeration with minimum ammonium residual results in a stable N removal. Low DO aeration results in a stable NOB suppression. Using sensor-mediated aeration control in a granular sludge reactor reduces aeration cost.
Experimental study on the effect of porosity on the elastic properties of methane hydrate formation (2023)

Summary Methane gas hydrate is usually distributed in loose sediment formation and high porosity consolidated formation, the porosity of different formations varies greatly. Understanding the effects of porosity on elastic properties might be helpful for better hydrate seismic exploration. In this study, synthetic rock samples with a mineral composition similar to the formation in the South China Sea were used in laboratory study of simulating the gas hydrate formation. The gas hydrate simulation and acoustic testing system was used to conduct the hydrate formation experiments on three rock samples with different porosity. The experimental results indicate that the P- wave and S- wave velocities significantly decrease with the increasing porosity, and Vp/Vs significantly increase. The samples with high porosity are more sensitive to the hydrate saturation. The velocity variation of rock samples with higher porosity is more significant. S- wave velocity is more significantly affected by natural gas hydrate saturation than P- wave velocity.
MRI-based glomerular morphology and pathology in whole human kidneys (2014)

Nephron number (N(glom)) and size (V(glom)) are correlated with risk for chronic cardiovascular and kidney disease and may be predictive of renal allograft viability. Unfortunately, there are no techniques to assess N(glom) and V(glom) in intact kidneys. This work demonstrates the use of cationized ferritin (CF) as a magnetic resonance imaging (MRI) contrast agent to measure N(glom) and V(glom) in viable human kidneys donated to science. The kidneys were obtained from patients with varying levels of cardiovascular and renal disease. CF was intravenously injected into three viable human kidneys. A fourth control kidney was perfused with saline. After fixation, immunofluorescence and electron microscopy confirmed binding of CF to the glomerulus. The intact kidneys were imaged with three-dimensional MRI and CF-labeled glomeruli appeared as punctate spots. Custom software identified, counted, and measured the apparent volumes of CF-labeled glomeruli, with an ~6% false positive rate. These measurements were comparable to stereological estimates. The MRI-based technique yielded a novel whole kidney distribution of glomerular volumes. Histopathology demonstrated that the distribution of CF-labeled glomeruli may be predictive of glomerular and vascular disease. Variations in CF distribution were quantified using image texture analyses, which be a useful marker of glomerular sclerosis. This is the first report of direct measurement of glomerular number and volume in intact human kidneys.
Novel Biomolecular Finger Printing with an Active Dual-Band Antenna Biosensor (2006)

In the paper, we report a novel biomolecular finger printing method with an active dual-band micro-coplanar inverted F antenna biosensor (DMCPIFA-Bio) on printed circuit board. The purpose of this research is to use the frequency band of microwave to characterize the responses of different biomolecules and concentrations. We used a dual-band antenna of 3 and 7 GHz frequency band as the active source and the spectral responses of probed molecules can be used for finger printing purpose. The preliminary result shows the relationship between conditions of biomolecules and the parameter of impedance, dB(S(l,l)) and phase. From analysis result, we found that the change of the concentration and total impedance value have better linear relationship. In additions, there are other parameters like initial analysis dB(S(l,l)) and change of frequency which may have high correlation to biomolecular weight size.
A tetrameric perylene diimide non-fullerene acceptor <i>via</i> unprecedented direct (hetero)arylation cross-coupling reactions (2018)

This study reports on the synthesis of an indancenodithiophene perylene diimide tetramer via unique direct (hetero)arylation reactivity. The thiophene based core structure is shown to be easily functionalized with four perylene diimides at the four active C-H positions. This new reactivity provides a simple synthetic pathway towards tetrameric perylene diimides which have emerged as one of the best classes of electron acceptors for organic solar cells.
Use of a microarray to assess the distribution of plasmid and chromosomal virulence genes in strains of enteroaggregative Escherichia coli (2005)

A DNA microarray was used to analyze the distribution of plasmid and chromosomal genes among strains of enteroaggregative Escherichia coli (EAEC) isolated from a prospective diarrhoea surveillance study in the United Kingdom. Target genes were extracted from existing databases and from the genome sequence of prototype EAEC strain 042. We found that strains exhibiting the aggregative adherence (AA) phenotype could be broadly divided into two groups depending upon whether they harboured genes from the EAEC virulence plasmid (pAA) and a set of chromosomal genes found in EAEC strain 042. Several chromosomal loci were inherited en bloc, and were more common in strains which we designated Group 1; genes at the pheU locus were particularly conserved. Genes encoded on the pAA plasmid and those under control of the master regulator AggR were also concentrated in the Group 1 EAEC. A gene encoding a type 1 pilin allele was detected more frequently in Group 2 EAEC. Our data suggest that strains previously designated as typical EAEC harbour a large number of conserved plasmid and chromosomal loci, further illuminating a package of virulence genes common to the most important EAEC.
β-Sarcoglycan Gene Transfer Leads to Functional Improvement in a Model of LGMD2E (S61.002) (2014)

Objective: The goal of this study is to demonstrate efficacy of AAV-mediated β-sarcoglycan gene transfer in β-SG knock-out mice to provide proof-of-principle for gene replacement therapy for limb-girdle muscular dystrophy type 2E Background: Limb-girdle muscular dystrophy (LGMD) type 2E results from mutations in the gene encoding β-sarcoglycan causing loss of functional protein. The sarcoglycans (α, β, γ, and δ-SG) are structural proteins localized at the cell membrane of muscle fibers that together with dystrophin and other proteins make up the dystrophin-associated protein complex (DAPC). Loss of functional protein in this complex results in an unstable sarcolemma leading to myofiber death and eventual muscle weakness. Methods: We generated a self-complementary AAVrh74 vector containing a codon optimized human β-Sarcoglycan gene (hSGCB) driven by the muscle specific tMCK promoter. To demonstrate efficacy of vector delivery we injected two doses (3x1010 and 1x1011 vg) by direct injection to the tibialis anterior muscle of β-SG KO mice. We have also treated β-SG KO mice using a clinically relevant vascular delivery model to deliver AAV.tMCK.hSGCB to the lower limb muscles. Results: Following direct intramuscular gene transfer in β-SG KO mice, we had clear demonstration of hSGCB expression and improvement in dystrophic pathology. We also showed hSGCB expression in lower limb muscles following vascular delivery. Functional outcome measures performed in the extensor digitorum longus muscle following vascular delivery showed an improvement in specific force generation in treated muscles. Conclusions: Delivery of a normal copy of the β-SG gene to diseased muscle will allow for the production of functional wild-type protein, resulting in restoration of the DAPC and an improvement in muscle function. This pre-clinical study is pivotal for establishing proof-of-principle for translation of AAV.βSG gene transfer in LGMD2E patients.