gebhart/patrepeval huggingface dataset:
Highly efficient FRET-based light-harvesting using nanocrystals (2009)

The use of nanocrystals in dye based applications has been increasing owing to the advantages of nanocrystals including small size, high efficiency, and tunable absorption and emission characteristics. Solubility and emission with high quantum yield in water is an issue for nanocrystals in biological applications. One of the best candidates is CdTe nanocrystals, which are highly efficient and soluble in water as synthesized. These make CdTe a highly preferable choice also for dye related biological applications. In this work, we employ CdTe nanocrystals as donors for nonradiative energy transfer to acceptor Rhodamine B dye molecules that are in their close proximity in solution. By varying the acceptor to donor concentration ratio (A/D) in solution, we show substantial modifications of the photoluminescence decay lifetimes of the donors from 25.3 ns to 7.2 ns as a result of efficient energy transfer and demonstrated enhanced emission of acceptor dyes. This leads to new possibilities for spectral multiplexing using dyes in conjunction with nanocrystals in biological applications.
Bariatric Orthopaedics: Total Knee Arthroplasty in Super-obese Patients (BMI > 50 kg/m2). Survivorship and Complications (2013)

With the numbers available, we could not identify what might have been modest differences in implant survivorship, however, complications were more frequent and functional outcomes were significantly lower in super-obese patients. Other studies similarly have found inferior outcomes in this challenging group of patients. Our data may be considered pilot data for future prospective studies with longer followup.
3-D Numerical Study of Turbulent Mixing of Intake Air and Exhaust Gas in a Low Pressure EGR System (2011)

A 3-D numerical study of turbulent mixing characteristics of air and exhaust gas in a low pressure EGR system (LP-EGR) has been performed under typical operating conditions. There are two objectives of this study. The first objective of the study is to understand and quantify the effects of following factors on mixing quality of exhaust gas and intake air: a) Rate of generation and dissipation of turbulence in the near mixing zone. b) Swirl induced due to formation of counter rotating vortex pairs (CVPs). c) Impingement of the EGR jet on the opposite wall of the intake manifold. The second objective of this study is to understand mixing quality with respect to pressure drop. Under typical conditions, on the low pressure side of the turbocharger, the pressure drop available to ensure required mass flow rate of EGR into the intake air is minimal. Hence, different EGR inlet configurations have been modeled to calculate the mixing quality along with the pressure drops. Some of configurations that have been studied are the effect of varying the diameter of EGR inlet tube, varying the insertion of EGR inlet tube into the intake air duct, angular injection, mixing elbow, multi-point EGR injection, EGR tube with multiple nozzles, venturi configuration, EGR flow control valve at EGR inlet etc. The above mixers have been compared by plotting respective mixing quality vs. EGR-side pressure drop and air-side pressure drop on a 3-D scatter plot at various operating conditions of the engine. One of the important conclusions of the study is that, in the range of operating conditions considered, a simple T-Junction like configuration, which generates maximum local turbulence and allows uninhibited formation and propagation of counter rotating vortex pairs, provides the best mixing quality with the least pressure drop.
Design of a solid catalyst for the synthesis of a molecule with blossom orange scent (2002)

The synthesis of 2-methyl-2-naphthyl-4-methyl-1,3-dioxolane, a compound with blossom orange scent, has been successfully carried out by acetalization reaction between methyl naphthyl ketone and propylene glycol using different acid solid catalysts. The size and polarity of reactants, intermediates and product determine the strong influence of the textural properties of the catalyst (crystal size, acidity and adsorption properties) with the large pore tridirectional zeolites (Y and Beta) being the most active. It has been found that the hydrophobicity of the catalyst can be more determinant than the number of active sites present in the catalyst. The results show an optimum in activity for Si/Al ratios in Y and Beta zeolites that correspond to 35 and 100, respectively.
Identification of ras/raf binding site and design of interfering peptide with potential clinical application (2016)

Despite intensive effort, no effective pharmacological inhibitors of the Ras oncoprotein have been reached the clinic given the impression that Ras proteins are undruggable. However, progresses have been made in several directions to manipulate Ras.
Solid‐Phase Chemistry: Cyclative Cleavage, a Versatile Concept in Solid‐Phase Organic Chemistry (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
The influence of dosage time of midazolam on its pharmacokinetics and effects in humans (1991)

The influence of dosage time of midazolam on its pharmacokinetics and effects on the central nervous system were investigated in six healthy volunteers, with pharmacokinetic-pharmacodynamic modeling. Each volunteer received single oral doses of 15 mg midazolam on four separate occasions: 8 AM, 2 PM, 8 PM, and 2 AM. An almost significant circadian variation was found in elimination half-life, shortest at 2 PM (1.26 +/- 0.47 hours, mean +/- SD) and longest at 2 AM (1.57 +/- 0.44 hours) (p = 0.05). Drug effects measured were alpha activity of the electroencepalograph and P100 latency of the visual-evoked response. The maximum drug effect (Emax) model described the concentration-effect relationship, extended with either a threshold drug concentration or a sigmoidicity parameter. A significant circadian variation was found in baseline alpha activity: highest at 8 AM (109% +/- 19% of the 24-hour mean) and lowest at 2 AM (80% +/- 12%). For alpha activity the drug concentration at half-maximum effect of both threshold Emax model and sigmoid Emax model showed lower values at 8 AM and 2 AM and higher values at 2 PM and 8 PM. However, these differences were either not significant (p = 0.10, threshold model) or on the verge of statistical significance (p = 0.05, sigmoid model). No circadian variation was found in the parameters describing the effect on the visual-evoked response. We conclude that the sensitivity of the central nervous system to midazolam, as reflected in alpha activity, possibly shows a circadian variation.
New organic chromophores for metal complexation: investigations into the synthesis and photophysics of thioindigo diimines, azaDIMEs, and their metal complexes (2018)

The synthesis and comprehensive characterization of diamine and diimine derivatives of thioindigo are reported. X-ray crystal structures demonstrate a planar structure for the diimine derivatives and a twisted conformation for the diamines. The diamine compounds absorb in the UV (λmax 324 nm - 328 nm), and exhibit moderate fluorescence (ΦF = 0.25, 0.045). A transient triplet state is observed in laser flash photolysis (LFP) experiments, with lifetimes an order of magnitude longer than those of the triplet state of thioindigo. The diimine compounds absorb at longer wavelengths than the diamines (λmax 495 nm - 510 nm), but are still slightly blue-shifted from thioindigo. The diimines have molar extinction coefficients 17 – 70% higher than thioindigo. The diimine compounds are not emissive, and LFP studies show transient species with microsecond lifetimes. The transient absorption spectra and quenching experiments of the diimines are consistent with trans-cis isomerisation about the central double bond.&#13;\n Mono- and diruthenium hexafluoroacetylacetonate (hfac) complexes of thioindigo-N,Nʹ-diphenyldiimine have been prepared. The monoruthenium complex was isolated as a racemic mixture and the diruthenium complexes were isolated as the meso (ΔΛ) and rac (ΔΔ and ΛΛ) diastereomers. Extensive structural characterization of the compounds revealed intrinsic diastereomeric differences in the X-ray crystal structures, cyclic voltammograms, and NMR spectra. Variable temperature NMR experiments demonstrated that the rac diastereomer undergoes conformational exchange with a rate constant of 8700 sec-1 at 298 K, a behavior that is not observed in the meso diastereomer. Ground state optical properties of the complexes were examined, showing that all the complexes possess metal-to-ligand charge transfer (MLCT) absorption bands in the near-infrared (λmax 689 nm – 783 nm). The compounds do not display photoluminescence in room temperature solution-phase experiments or in experiments at 77 K. Ultrafast transient absorption spectroscopy measurements revealed excited states with picosecond lifetimes. Unexpectedly, the transient absorption measurements revealed differences in the transient spectra and disparate time constants for the excited state decay of the diastereomers, which are linked to the conformational changes observed in the NMR experiments. &#13;\n\tInvestigations into the synthesis of azaDIMEs and azaDicarbazolyls are described. Examination of the Buchwald-Hartwig amination produced reaction conditions that enabled preparation of amino-diindoles. Oxidation of the amino-diindoles to azaDIMEs was complicated by concomitant oligomerization of the substrates. Substitution of the reactive positions of the amino-diindole afforded increased stability towards oxidative oligomerization. Scalable synthetic routes to azaDicarbazolyl precursors were identified and optimized, and preparation of amino and azaDicarbazolyl compounds was explored.
PET imaging of ischemic brain stroke necrosis with novel agent 18F-Fluoroglucaric Acid (2018)

347 Objectives: Brain stroke is the second most common cause of death worldwide, with considerable disability among survivors. Greater than 80% of brain strokes are due to cerebrovascular occlusion, particularly middle cerebral artery occlusion. Current management of stroke patients is aimed at preventing the progression of at-risk cerebral tissue towards infarction by restoring blood supply to ischemic but viable tissue (a.k.a. penumbra). The timing of treatment with respect to the type and stage of evolution of stroke critically determines the treatment success. By providing valuable information about the presence, size, and growth of infarct (umbra) and surrounding ischemia (penumbra), imaging contributes greatly to clinical decision making. While the gold standard for determining the penumbra is F-18-FMISO/PET, the agent is unavailable in most medical centers. The objective of this research was to investigate the utility of a new PET agent F-18-Fluoroglucaric acid (FGA) to delineate infarct in a mouse brain stroke model of middle cerebral artery occlusion (MCAO).
 Methods: Radiopharmaceutical FGA was synthesized in one-pot by a 5 min controlled oxidation of commercially available F-18-Fluorodeoxyglucose. Quality control of FGA was performed by radio-TLC. Brain stroke was induced in the left cerebral hemisphere of male CD-1 mice (20-25 g) by occluding middle cerebral artery and allowing reperfusion after 1 h of occlusion. After 24 h of reperfusion, mice were subjected to imaging with Tc-99m-HMPAO (92.5 MBq) and F-18-FGA (92.5 MBq) for perfusion and infarct assessment, respectively. Helical SPECT was acquired after 1 h of Tc-99m-HMPAO injection, whereas PET was acquired after 1-2 h of F-18-FGA injection. PET was also acquired ex vivo after separating skull from whole body. In addition, radioactivity associated with left (ipsilateral) and right (contralateral) cerebral hemispheres was determined in a well counter. The brains were sectioned for TTC staining. Results: Gamma counting of the brain hemispheres showed an almost three-fold increase in FGA accumulation in the ipsilateral hemisphere as compared to the contralateral hemisphere. Ex vivo PET of intact skull clearly demonstrated differential FGA accumulation in the stroke area. However, in vivo resolution of stroke was noticeably affected by normal nasal accumulation of FGA. Corresponding HMPAO/SPECT also showed a perfusion defect in the ipsilateral hemisphere, which was corroborated with TTC staining. Conclusions: Results show that FGA has a potential to enable extremely sensitive and high resolution neuroimaging of brain infarcts. F-18-labeled FGA can be rapidly synthesized from ubiquitously available F-18-FDG in a simple reaction.
Four-wave mixing of Nd 3+ impurities in glasses and crystals (1990)

Degenerate four-wave mixing measurements have been performed on a wide variety of Nd3+ doped oxide and fluoride glasses and crystals. Crossed beams from a cw argon-ion laser were used to excite directly the Nd3+ ions and establish population gratings. We have found that an absorptive type grating cannot account for the magnitude of our four-wave mixing signals, but instead, that the nonresonant contribution from a phase grating predominates.
A decentralized, prospective, observational study to collect real-world data from patients with myasthenia gravis using smartphones (2023)

While these symptom signatures require further study and validation, our results suggest that digital phenotyping, characterized by increased multidimensionality and frequency of the data collection, holds promise for furthering our understanding of clinically significant exacerbations and reimagining the approach to treating MG as a heterogeneous condition.
Comparative affects of plasmid‐encoded interleukin 12 and interleukin 18 on the protective efficacy of DNA vaccination against Mycobacterium tuberculosis (2002)

Protective immunity against Mycobacterium tuberculosis infection requires the induction and maintenance of mycobacteria-specific, IFN-gamma-secreting CD4+ and CD8+ T lymphocytes. The development of Th1-like T cells is promoted by the early secretion and synergistic action of interleukin (IL)-12 and IL-18. This study compares the effects of plasmid-encoded IL-12 and IL-18 on the immunogenicity and protective efficacy of a DNA vaccine expressing the M. tuberculosis-secreted protein antigen 85B (DNA-85B). Co-immunization with either IL-12- or IL-18-expressing plasmids augmented the IFN-gamma-secreting T-cell response, and the maximum effect was observed with plasmids encoding both cytokines. Further the IL-12, but not the IL-18-expressing plasmid, significantly increased the protective efficacy of DNA-85B against pulmonary M. tuberculosis infection. Therefore co-administration of plasmid-encoded cytokines provides a potential method for optimizing the protective efficacy of DNA vaccination against tuberculosis.
Optical Properties Of A Silver Layer In ZnO/Ag/ZnO and TiO 2 /Ag/TiO 2 Systems (1989)

Effective dielectric constants of the silver layers in three ZnO/Ag/ZnO and two Ti0<sub>2</sub>/Ag/Ti0<sub>2</sub> coatings are determined using spectroscopic ellipsometry assuming a three-layer model for the coatings. Drude analysis of the data shows that the effective dielectric constants of silver in the red and near infrared regions are close to that of bulk silver, and both, bulk plasmon energy and core polarizability, depend on the layer thickness. Three peaks, at 3.8-3.9, 3.5-3.7 and 2.9-3.3 eV, are observed in the spectra of the imaginary part of the effective dielectric constant. Generation of surface plasmons, indicated by these peaks, is considered as a consequence of surface roughness which is not included in the original three-layer model. Analysis of data on transmittance and reflectance, measured at incidence angles of 45&deg; and 60&deg; , confirms surface plasmon generation.
Biocatalysis at Work: Applications in the Development of Sagopilone (2015)

For the antitumour agent sagopilone, an epothilone analogue, a large-scale synthesis was developed to synthesise the active pharmaceutical ingredient for clinical trials, exploring enzymatic and microbial methods to produce chiral building blocks on a multi-kilogram scale. The three building blocks were identified as key intermediates in the synthesis and needed to be produced with high optical purity in yields higher than those previously published. The improved syntheses of two of these building blocks are detailed herein. For building block A, the chemical research synthesis was abandoned, and a novel chemical route was developed leading to building block A via an enzymatic hydrolysis process. For building blocks C, replacement of a chemical catalytic procedure by a microbial process meant that the development of a new starting material could be avoided, thereby accelerating the development process. For the clinical development process, a human metabolite of sagopilone was required as a reference. To accelerate the synthesis of the metabolite, no chemical synthesis was investigated; rather, we relied solely on oxidoreductases. The human metabolite of sagopilone was synthesised on a multi-gram scale in a single-step process using genetically engineered E. coli expressing human cytochrome P450 enzyme 2C19. The integration of enzymatic and microbial processes provided tools that enable the synthesis of highly functionalised intermediates and metabolites.
Progress in Adenoviral Capsid-Display Vaccines (2018)

Adenoviral vectored vaccines against infectious diseases are currently in clinical trials due to their capacity to induce potent antigen-specific B- and T-cell immune responses. Heterologous prime-boost vaccination with adenoviral vector and, for example, adjuvanted protein-based vaccines can further enhance antigen-specific immune responses. Although leading to potent immune responses, these heterologous prime-boost regimens may be complex and impact manufacturing costs limiting efficient implementation. Typically, adenoviral vectors are engineered to genetically encode a transgene in the E1 region and utilize the host cell machinery to express the encoded antigen and thereby induce immune responses. Similarly, adenoviral vectors can be engineered to display foreign immunogenic peptides on the capsid-surface by insertion of antigens in capsid proteins hexon, fiber and protein IX. The ability to use adenoviral vectors as antigen-display particles, with or without using the genetic vaccine function, greatly increases the versatility of the adenoviral vector for vaccine development. This review describes the application of adenoviral capsid antigen-display vaccine vectors by focusing on their distinct advantages and possible limitations in vaccine development.
Prognostic value of gain of chromosome 5q in localized renal cell carcinoma. (2019)

623 Background: While gain of chromosome 5q is a frequently seen cytogenetic abnormality noted to occur in patients with renal cell carcinoma (RCC), little is known about its prognostic significance. We investigated the association of gain of 5q with disease-free survival (DFS) in patients with localized (non-metastatic T1-2) RCC. Methods: All patients from UCLA with primary tumor stage T1-2 RCC who had tumor cytogenetic analysis on tumor specimen were included. Alterations in chromosome 5q was specifically reviewed in this study. Logistic regression analyses were used to assess association of gain of 5q with final histopathology, ISUP grading, and T-stage. Cox proportional hazard modeling and Kaplan-Meier analyses were used to assess the impact of gain of 5q on DFS. Recurrence was defined as any local recurrence or development of new metastasis. Results: A total of 676 patients were included in this study. Gain of 5q occurred in 108 (16%) patients and was more commonly seen in clear cell versus non-clear cell tumors (19% vs. 9%, p = .002). Gain of 5q was associated with low grade ISUP (1 or 2) of clear-cell RCC (p = 0.011). On survival analysis, there was a 67% decreased risk of RCC recurrence for patients with gain of 5q (HR = 0.33, p = 0.018). The 5- and 10-year risk of recurrence was 2% vs. 16% and 14% vs. 28% for patients with and without gain of 5q, respectively (p = 0.013). In multivariable Cox analysis, the gain of 5q was an independent prognostic factor (p = .026 with ISUP grade and p = .025 with T-stage). These findings were confirmed among clear-cell RCC subgroup. Conclusions: Gain of chromosome 5q is an independent prognostic factor associated with decreased risk of recurrence in patients with localized T1-2 renal cell carcinoma. Identifying patients with a gain of 5q will improve the stratification of the risk of recurrence, could allow to adapt the follow-up protocols and avoid adjuvant treatment.
Correction to: Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls (2018)

Upon publication of the original article [1], the authors had flagged that Fig. 1 had been published twice, as both Fig. 1 and Additional file 3.
Formal Models and Hybrid Approaches for Efficient Manual Image Annotation and Retrieval (2011)

Although important in practice, manual image annotation and retrieval has rarely been studied by means of formal modeling methods. In this chapter, the authors propose a set of formal models to characterize the annotation times for two commonly-used manual annotation approaches, that is, tagging and browsing. Based on the complementary properties of these models, the authors design new hybrid approaches, called frequency-based annotation and learning-based annotation, to improve the efficiency of manual image annotation as well as retrieval. Both our simulation and experimental results show that the proposed algorithms can achieve up to a 50% reduction in annotation time over baseline methods for manual image annotation, and produce significantly better annotation and retrieval results in the same amount of time.
Loss of centromere function drives karyotype evolution in closely related Malassezia species (2020)

Genomic rearrangements associated with speciation often result in variation in chromosome number among closely related species. <i>Malassezia</i> species show variable karyotypes ranging between six and nine chromosomes. Here, we experimentally identified all eight centromeres in <i>M. sympodialis</i> as 3-5-kb long kinetochore-bound regions that span an AT-rich core and are depleted of the canonical histone H3. Centromeres of similar sequence features were identified as CENP-A-rich regions in <i>Malassezia furfur</i>, which has seven chromosomes, and histone H3 depleted regions in <i>Malassezia slooffiae</i> and <i>Malassezia globosa</i> with nine chromosomes each. Analysis of synteny conservation across centromeres with newly generated chromosome-level genome assemblies suggests two distinct mechanisms of chromosome number reduction from an inferred nine-chromosome ancestral state: (a) chromosome breakage followed by loss of centromere DNA and (b) centromere inactivation accompanied by changes in DNA sequence following chromosome-chromosome fusion. We propose that AT-rich centromeres drive karyotype diversity in the <i>Malassezia</i> species complex through breakage and inactivation.