gebhart/patrepeval huggingface dataset:
Expanded palette of Nano-lanterns for real-time multicolor luminescence imaging (2015)

Fluorescence live imaging has become an essential methodology in modern cell biology. However, fluorescence requires excitation light, which can sometimes cause potential problems, such as autofluorescence, phototoxicity, and photobleaching. Furthermore, combined with recent optogenetic tools, the light illumination can trigger their unintended activation. Because luminescence imaging does not require excitation light, it is a good candidate as an alternative imaging modality to circumvent these problems. The application of luminescence imaging, however, has been limited by the two drawbacks of existing luminescent protein probes, such as luciferases: namely, low brightness and poor color variants. Here, we report the development of bright cyan and orange luminescent proteins by extending our previous development of the bright yellowish-green luminescent protein Nano-lantern. The color change and the enhancement of brightness were both achieved by bioluminescence resonance energy transfer (BRET) from enhanced Renilla luciferase to a fluorescent protein. The brightness of these cyan and orange Nano-lanterns was ∼20 times brighter than wild-type Renilla luciferase, which allowed us to perform multicolor live imaging of intracellular submicron structures. The rapid dynamics of endosomes and peroxisomes were visualized at around 1-s temporal resolution, and the slow dynamics of focal adhesions were continuously imaged for longer than a few hours without photobleaching or photodamage. In addition, we extended the application of these multicolor Nano-lanterns to simultaneous monitoring of multiple gene expression or Ca(2+) dynamics in different cellular compartments in a single cell.
Fucosylation of Linear Alcohols: A Study of Parameters Influencing the Stereochemistry of Glycosylation (2001)

L-Fucose is a constituent of many glycoconjugates and often has a key role in the epitope involved in biological functions. The chemical synthesis of such compounds is necessary to generate sufficient material to explore the molecular details of their bioactivity. In this context, the development of practical and stereoselective α-fucosylation reactions is essential. Here are described several procedures for fucosylation of linear alcohols 9−16 with L-fucose (1) and a series of 2-O-benzyl-protected fucopyranosyl donors 3−8, together with parameters influencing the stereochemistry of glycosylation, such as protecting groups, catalysts, and dielectric constants of solvents. Although high α-selectivities have often been reported for fucosylation reactions with glycosyl acceptors, complete α-selectivity was never observed here, using linear spacer alcohols 9−16. Generally, the best α-selectivities were obtained in fucosylations of the alcohols under in situ anomerization conditions using tetrabutylammonium bromide (75−90% α-anomer), whereas promotion by NIS/TfOH(cat.) proceeded with poor stereoselectivity in treatment of the ethyl thiofucosides 3−5. No directing effects from the 4-O protecting groups were noted. For the 2-O-benzyl-protected 1-O-thioethyl fucopyranosyl donors 3−5, electronic effects of the fucosyl donor could not explain the observed stereoselectivity. The difference between the observed selectivities for α-fucosylations of glycosyl acceptors, in comparison with the linear spacer alcohols used here, is probably due to steric effects of the more bulky glycosyl acceptors.
The influence of surface chemistry on the kinetics and thermodynamics of bacterial adhesion (2018)

This work is concerned with investigating the effect of substrate hydrophobicity and zeta potential on the dynamics and kinetics of the initial stages of bacterial adhesion. For this purpose, bacterial pathogens Staphylococcus aureus and Escherichia coli O157:H7 were inoculated on the substrates coated with thin thiol layers (i.e., 1-octanethiol, 1-decanethiol, 1-octadecanethiol, 16-mercaptohexadecanoic acid, and 2-aminoethanethiol hydrochloride) with varying hydrophobicity and surface potential. The time-resolved adhesion data revealed a transformation from an exponential dependence to a square root dependence on time upon changing the substrate from hydrophobic or hydrophilic with a negative zeta potential value to hydrophilic with a negative zeta potential for both pathogens. The dewetting of extracellular polymeric substances (EPS) produced by E. coli O157:H7 was more noticeable on hydrophobic substrates, compared to that of S. aureus, which is attributed to the more amphiphilic nature of staphylococcal EPS. The interplay between the timescale of EPS dewetting and the inverse of the adhesion rate constant modulated the distribution of E. coli O157:H7 within microcolonies and the resultant microcolonial morphology on hydrophobic substrates. Observed trends in the formation of bacterial monolayers rather than multilayers and microcolonies rather than isolated and evenly spaced bacterial cells could be explained by a colloidal model considering van der Waals and electrostatic double-layer interactions only after introducing the contribution of elastic energy due to adhesion-induced deformations at intercellular and substrate-cell interfaces. The gained knowledge is significant in the context of identifying surfaces with greater risk of bacterial contamination and guiding the development of novel surfaces and coatings with superior bacterial antifouling characteristics.
Development of Novel Non-Viral Vectors for use in the Immunomodulation of Corneal Transplantation (2011)

About 25% of corneal grafts will fail within five years (mainly due to T-cell-mediated rejection) and the ex-vivo delivery of immunomodulatory genes to the cornea is one attractive method to improve survival rates. Early efforts focused on the use of viral vectors, whose toxicity and immunogenicity remain formidable barriers. Here, we developed an arginine-rich oligopeptide featuring a novel tri-block design. Each block served a specific purpose – DNA binding, endosomal escape and cell membrane penetration – and was systematically optimised. The peptides could effectively bind and protect DNA from physical and enzymatic degradation. Since the corneal endothelium is an important target for therapy, mouse corneal endothelial cells (MCEC) were chosen for initial in-vitro testing. The peptides depended heavily on cell surface heparan sulfate and utilised multiple endocytosis pathways to gain entry into MCEC. Importantly, they mediated indolamine 2,3-dioxygenase (IDO) mRNA and protein expression efficiently in both MCEC and murine corneas. IDO catalyses the biodegradation of tryptophan which T-lymphocytes sensitively require for growth. Hence, IDO over-expression in the cornea can prolong allograft survival by locally suppressing T-cell activity. We demonstrated that the IDO expressed was biologically active and could suppress the growth of CD4 T-cells in a proliferation assay. Immunohistochemistry further determined that IDO expression was localised to the corneal endothelium and epithelium. Corneal transplantations were then performed using a fully MHC-mismatched mouse model. However, the survival of IDO-transfected grafts was only marginally prolonged relative to GFP-transfected corneas and was shortened compared to untreated corneas. Toxicity, as evidenced by propidium iodide staining, was suspected to shorten graft survival following peptide-mediated transfection. Efforts to modulate toxicity by reducing the transfection period in the presence of chloroquine also failed to prolong graft survival. Future work should therefore focus on reducing toxicity while improving the transfection efficiency of this peptide carrier.
Dysplastic Melanocytic Nevus Immunohistochemical Heterogeneity by Melanosomal Markers and S-100 (1991)

This study evaluates the expression of human melanosome specific antigen-1 and -2 (HMSA-1, -2) by dysplastic melanocytic nevus (DMN) and its significance by (a) immunostaining pattern, (b) other immunohistochemical markers (e.g., S-100), and (c) mesenchymal responses (e.g., lymphocytic infiltration). From 31 patients with DMN syndrome, 55 clinically characteristic and histologically (H&E) proven dysplastic nevi were assessed for HMSA expression. Approximately 70% of DMN lesions expressed the HMSA antigens; similar gross staining patterns were seen with both monoclonal antibodies (MoAbs). The expression of HMSA-2 was invariably associated with that of HMSA-1, but the converse did not apply. Two general staining patterns with MoAbs HMSA were appreciated: (a) uniform staining of the epidermal melanocytes in the DMN lesion (type I) and (b) nonuniform staining, with the epidermal melanocytes at the periphery of the DMN lesion reacting most intensely (type II). Although anti-S-100 antibody demonstrated a similar sensitivity (67%), it lacked specificity and did not distinguish different types of DMN, as compared with MoAbs HMSA. There was no correlation between these observed staining patterns and common histological features of DMN. There was a poor correlation between lymphocytic infiltrate (as judged by immunostaining for pan-T, Ti/h, Tc/s, and pan-B markers) and heterogeneity of immunostaining. We conclude that HMSA-1 and -2 are able to delineate two types of DMN and possibly bind different epitopes of the same antigen. Their potential usefulness in predicting malignant transformation of DMN has yet to be established.
Fifty Years of Diazeniumdiolate Research: A Tribute to Dr. Larry K. Keefer (2023)

The pioneering studies of Dr. Larry Keefer and colleagues with diazeniumdiolates or NONOates as a platform have unraveled the chemical biology of many nitric oxides and have led to the design of a variety of promising therapeutic agents in oncology, gastroenterology, antimicrobials, wound healing, and the like. This dedication to Dr. Larry Keefer briefly highlights some of his studies using the diazeniumdiolate platform in the cancer arena.
Improving Sensitivity in Ultrasound Molecular Imaging by Tailoring Contrast Agent Size Distribution: In Vivo Studies (2010)

Molecular imaging with ultrasound relies on microbubble contrast agents (MCAs) selectively adhering to a ligand-specific target. Prior studies have shown that only small quantities of microbubbles are retained at their target sites, therefore, enhancing contrast sensitivity to low concentrations of microbubbles is essential to improve molecular imaging techniques. In order to assess the effect of MCA diameter on imaging sensitivity, perfusion and molecular imaging studies were performed with microbubbles of varying size distributions. To assess signal improvement and MCA circulation time as a function of size and concentration, blood perfusion was imaged in rat kidneys using nontargeted size-sorted MCAs with a Siemens Sequoia ultrasound system (Siemans, Mountain View, CA) in cadence pulse sequencing (CPS) mode. Molecular imaging sensitivity improvements were studied with size-sorted alphavbeta3-targeted bubbles in both fibrosarcoma and R3230 rat tumor models. In perfusion imaging studies, video intensity and contrast persistence was approximately 8 times and approximately 3 times greater respectively, for "sorted 3-micron" MCAs (diameter, 3.3 +/- 1.95 microm) when compared to "unsorted" MCAs (diameter, 0.9 +/- 0.45 microm) at low concentrations. In targeted experiments, application of sorted 3-micron MCAs resulted in a approximately 20 times video intensity increase over unsorted populations. Tailoring size-distributions results in substantial imaging sensitivity improvement over unsorted populations, which is essential in maximizing sensitivity to small numbers of MCAs for molecular imaging.
Hepatitis C Virus Dynamics In Vivo And the Antiviral Efficacy of Interferon Alfa Therapy (1999)

To better understand the dynamics of hepatitis C virus and the antiviral effect of interferon--2b (IFN), viral decline in 23 patients during therapy was analyzed with a mathematical model. The analysis indicates that the major initial effect of IFN is to block virion production or release, with blocking efficacies of 81, 95, and 96% for daily doses of 5, 10, and 15 million international units, respectively. The estimated virion half-live (t 1/2 ) was, on average, 2.7 hours, with pretreatment production and clearance of 10 12 virions per day. The estimated infected cell death rates exhibited large interpatient variation (corresponding t 1/2 1.7 to 70 days), was inversely correlated with baseline viral load, and was positively correlated with alanine aminotransferase levels. Fast death rates were predictive of virus being undetectable by polymerase chain reaction at 3 months. These findings show that infection with hepatitis C virus is highly dynamic and that early monitoring of viral load can help guide therapy.
Effect of B-factor and its analogues on rifamycin biosynthesis in Nocardia sp. (1988)

B-Factor, 3'-(1-butylphosphoryl)adenosine, which was isolated from yeast extract, is an inducer of rifamycin production in a rifamycin non-producing Nocardia mutant. Feeding of B-factor to the mutant culture demonstrated that the induction process was triggered during early stationary phase. Rifamycin production in the mutant was also induced by an exogenous supply of 3-amino-5-hydroxybenzoic acid, an intermediate of the antibiotic pathway, suggesting that a step upstream from the intermediate is regulated by B-factor. B-Factor analogues, i.e., alkylesters of 3'-AMP with alkyl side chains of C(2) approximately C(12) and n-butyl esters of 3'-GMP and 2'-AMP all showed the B-factor activity. Among these n-octyl ester of 3'-AMP showed the lowest effective concentration of approximately 3 x 10(-10) M. An intrinsic substance of the Nocardia sp. with potent B-factor activity and a UV absorption maximum at 260 nm was isolated from the cells of the parental strain.
Human Tumor Immunology at the Molecular Divide (2007)

In the mid-1980s, as a young investigator at Duke University running a human immunology laboratory with interest in T cell allograft rejection, I was becoming very confident in my ability to grow human alloreactive T cell lines from small biopsies of kidney allografts and use them to define their Ag
Predicting Hearing Aid Microphone Preference in Everyday Listening (2004)

Seventeen hearing-impaired adults were fit with omnidirectional/directional hearing aids, which they wore during a four-week trial. For each listening situation encountered in daily living during a total of seven days, participants selected the preferred microphone mode and described the listening situation in terms of five environmental variables, using a paper and pencil form. Results indicated that hearing-impaired adults typically spend the majority of their active listening time in situations with background noise present and surrounding the listener, and the signal source located in front and relatively near. Microphone preferences were fairly evenly distributed across listening situations but differed depending on the characteristics of the listening environment. The omnidirectional mode tended to be preferred in relatively quiet listening situations or, in the presence of background noise, when the signal source was relatively far away. The directional mode tended to be preferred when background noise was present and the signal source was located in front of and relatively near the listener. Results suggest that knowing only signal location and distance and whether background noise is present or absent, omnidirectional/directional hearing aids can be set in the preferred mode in most everyday listening situations. These findings have relevance for counseling patients when to set manually switchable omnidirectional/directional hearing aids in each microphone mode, as well as for the development of automatic algorithms for selecting omnidirectional versus directional microphone processing.
36‐1: Invited Paper: Liquid‐Crystal Lasers: Recent Advances and Future Opportunities (2022)

Liquid crystal (LC) lasers use a layer of chiral nematic liquid crystal to form a self‐organising resonant cavity. When doped with fluorescent dye and suitably excited, they form versatile micro‐lasers with high efficiencies, low thresholds, and selective wavelength emission across a continuous range of the visible spectrum. This, combined with their scalable fabrication, makes them attractive candidates for a wide variety of photonic applications, including laser displays. This paper includes a review of the principles of operation, of recent enhancements that are advancing the technology closer to market, and concludes with demonstrations of LC lasers used for medical imaging and low‐speckle holography.
Comparative efficacy of different herbicides in summer pearlmillet (2013)

Among the different chemical weed management practices atrazine 1000 g/ha PE fb HW at 30 DAS recorded minimum number of monocot and dicot weed. Pendimethalin treated plots showed poor germination which might be due to the phytotoxic effect of herbicide. Further, interculturing fb HW at 20 and 40 DAS registered higher grain (7.82 t/ha) and stover yields (19.44 t/ha) which was closely followed by atrazine 1000 g/ha PE fb HW at 30 DAS
Validation and Evaluation of Memorial Symptom Assessment Scale Short-Form (Msas-Sf)In a Romanian Cohort of Hemodialysis Patients (2015)

The aim of this study was to validate the MSAS-SF in a Romanian hemodialysis (HD) population and to assess the prevalence and severity of physical and psychological symptoms of patients. Materials and methods: 102 stable patients (41 males, 61 females, mean age 52.51 ± 12.02 years), who were treated with hemodialysis (HD) three times weekly completed questionnaires on prevalence and severity of symptoms. To determine symptoms prevalence and severity for HD patients MSAS-SF was used. Cronbach`s alpha reliability test was performed to assess internal consistency of the MSAS-SF. Results: The Cronbach’s alpha reliability score for the total number of items of the MSAS-SF was 0.838, while for the subscales of MSAS-SF the reliability scores  ranged  from acceptable to very good. The top three symptoms experienced by hemodialysis patients were lack of energy, followed by pain, and worrying. The most frequently reported physical symptoms included lack of energy (69.6%), pain (68.6%), and numbness /tingling in hands/feet (64.7%), difficulty sleeping (63.7%), dry mouth (61.8%), dizziness (58.8%), and problems with sexual interest or activity (52%). The most frequent psychological symptoms included worrying (65.7%), feeling sad (59.8%), feeling nervous (50%), and feeling irritable (40.2%). Conclusions: These results support the validity of the MSAS-SF in the assessment of Romanian patients undergoing hemodialysis. Hemodialysis patients have important psychological and physical symptoms burden.
On effective virtual networks interconnection (2016)

The network services today require extremely agile and mobile, however, the traditional IP infrastructures are so rigid that cannot fit services well. A way should be put forward to automate the network to improve responsiveness to change. SDN and network virtualization (NV) are two hottest approaches to make networking more automated and scalable to support virtualized and cloud environments. Network virtualization combines hardware and software network resources and network functionality into a single virtual network. SDN is created to simplify traffic management and achieve operational efficiencies by establish and exercising central control over packet forwarding. In this paper, we focus on the situation where SDN controller needs to connect two virtual networks temporarily. We put forward three algorithms to try to make this connection more effective and evaluate these three algorithms.
Laser, ultrasonic and manual measurements of citrus tree canopy volume (2001)

Tools that rapidly quantify tree canopy volumes would be valuable to citrus industry.This study was conducted to compare ultrasonic and laser measurements of citrus canopyvolumes with manual measurement methods. Fifteen trees with different canopy heights andvolumes were selected for the study. The manual and ultrasonic measurements were used tocompute a canopy volume in cubic meters whereas laser measurements were used to computelaser canopy volume index. The three approaches were statistically compared. It was foundthat ultrasonic and laser methods have good correlations to the manual methods (R2 >0.85,RMSE<2.15 m3). Laser showed better prediction of canopy volume than the ultrasonic becauseof the higher resolution. Therefore, ultrasonic or laser sensors can be used for automaticmapping and quantification of the canopy volumes of citrus trees.
Fertilization and early embryology: Use of lasers in assisted fertilization and hatching (1994)

The erbium-yttrium-aluminium-garnet (Er:YAG) laser has been applied to micromanipulation in humans. It was used in the fertilization process for both subzonal insemination (SUZI) and for partial zona dissection (PZD). Laser-assisted micromanipulation achieved significantly higher fertilization rates (34.8%) when compared to mechanical SUZI (16.1%), but use of the laser did not improve the PZD results (laser 14.8% versus mechanical 14%). The Er:YAG laser was used to assist hatching. In the mouse it significantly improved the hatching rate (80 versus 29.3%) 110 h after administration of human chorionic gonadotrophin. This technique was applied in two different centres to patients with previous in vitro fertilization (IVF) failures. the implantation rate per embryo (14.4% laser-assisted hatching versus 6% control group) and the pregnancy rate per transfer (40 versus 16.2%) were improved.
Observation of latent reliability degradation in ultrathin oxides after heavy-ion irradiation (2002)

Constant voltage time-dependent-dielectric-breakdown distributions were obtained for both unirradiated and irradiated 3.0 and 3.2 nm thick SiO2 films subjected to Co60 gamma irradiation and heavy ions of 823 MeV Xe129 (linear energy transfer=59 MeV-cm2/mg). The gamma irradiation had no effect on oxide lifetime. The heavy ion irradiation substantially reduced oxide life even though the devices were biased at 0.0 V during irradiation. The reduction of oxide lifetime under constant-voltage stress conditions was a strong function of the heavy ion fluence.
Characterization a Bending Fatigue Mini‐Specimen Technique (Krause Type) of Nuclear Materials (2015)

This chapter contains sections titled: Introduction Specimens Experimental Procedure FEA Model Results and Discussion Conclusion
Classification and investigation of artifacts in magnetic resonance imaging. (1987)

Many MR artifacts are not understandable in terms of previous imaging experience. A variety of artifacts is presented here; their origins and elimination are discussed.
Multiphase Flows with Droplets and Particles (2011)

Since the publication of the first edition of Multiphase Flow with Droplets and Particles, there have been significant advances in science and engineering applications of multiphase fluid flow. Maintaining the pedagogical approach that made the first edition so popular, this second edition provides a background in this important area of fluid mecha
Energy Exchangers: Run-Around Membrane (2014)

The run-around membrane energy exchanger (RAMEE) is a novel passive energy recovery system currently under development and research. It applies a closed-loop liquid desiccant to transfer heat and moisture between two adjacent or nonadjacent air streams with temperature and water vapor concentration differences. This entry discusses the construction and operation of RAMEEs, as well as their effectiveness in transferring heat and moisture between air streams. They have high effectiveness values and low pressure drops, as well as negligible contaminant transfer between air streams. These features make RAMEEs both economical and environmentally friendly for use in building heating, ventilation, and air-conditioning (HVAC) systems, especially for retrofit applications and health-care facilities.