gebhart/patrepeval huggingface dataset:
Spectral unmixing of multi-color tissue specific in vivo fluorescence in mice (2007)

Fluorescence Molecular Tomography (FMT) has emerged as a powerful tool for monitoring biological functions in vivo in small animals. It provides the means to determine volumetric images of fluorescent protein concentration by applying the principles of diffuse optical tomography. Using different probes tagged to different proteins or cells, different biological functions and pathways can be simultaneously imaged in the same subject. In this work we present a spectral unmixing algorithm capable of separating signal from different probes when combined with the tomographic imaging modality. We show results of two-color imaging when the algorithm is applied to separate fluorescence activity originating from phantoms containing two different fluorophores, namely CFSE and SNARF, with well separated emission spectra, as well as Dsred- and GFP-fused cells in F5-b10 transgenic mice in vivo. The same algorithm can furthermore be applied to tissue-specific spectroscopy data. Spectral analysis of a variety of organs from control, DsRed and GFP F5/B10 transgenic mice showed that fluorophore detection by optical systems is highly tissue-dependent. Spectral data collected from different organs can provide useful insight into experimental parameter optimisation (choice of filters, fluorophores, excitation wavelengths) and spectral unmixing can be applied to measure the tissue-dependency, thereby taking into account localized fluorophore efficiency. Summed up, tissue spectral unmixing can be used as criteria in choosing the most appropriate tissue targets as well as fluorescent markers for specific applications.
A novel receiver for Filp-OFDM in optical wireless communication (2015)

A unipolar orthogonal frequency division multi-plexing (OFDM) technique called flipped OFDM (Flip-OFDM), is suitable for intensity modulation and direct detection (IM/DD) channel which needs the transmitted signal to be real and positive. Flip-OFDM uses two consecutive OFDM subframes to transmit the positive and negative parts of the signal, respectively. In the conventional receiver, only the difference of the two subframes is used to recover the signal, leading to the under-utilization of the received power. This paper proposes a novel receiver characterizing temporal and spectral diversity combining to improve the performance of Flip-OFDM by extracting effective information from both the sum and the difference of the two subframes. Simulations show that the novel receiver provides a significant gain of about 2.3 dB at the BER of 10−4, compared with the conventional one in additive white gaussian noise (AWGN) channel. Moreover, the proposed receiver also simplifies computational complexity compared with the existing iterative receiver.
Nuclear Medicine Training: What Now? (2017)

Although the multidisciplinary nature of nuclear medicine (NM) and clinical molecular imaging is a key strength of the specialty, the breadth of disciplines involved in the practice of NM creates challenges for education and training. The evolution of NM science and technology-and the practice of clinical molecular imaging and theranostics-has created a need for changes in the approach to specialty training. The broader U.S. community of imaging physicians has been slow to accept this change, in good part due to historical divides between the NM and nuclear radiology (NR) communities. In this <i>Journal of Nuclear Medicine</i> Hot Topics discussion, we review the historical pathways to training; discuss the training needs for the modern practice of NM, clinical molecular imaging, and radionuclide therapy; and suggest a path forward for an approach to training that matches the needs of the evolving clinical specialty.
A Novel GH7 Endo-β-1,4-Glucanase from Neosartorya fischeri P1 with Good Thermostability, Broad Substrate Specificity and Potential Application in the Brewing Industry (2015)

An endo-β-1,4-glucanase gene, cel7A, was cloned from the thermophilic cellulase-producing fungus Neosartorya fischeri P1 and expressed in Pichia pastoris. The 1,410-bp full-length gene encodes a polypeptide of 469 amino acids consisting of a putative signal peptide at residues 1-20, a catalytic domain of glycoside hydrolase family 7 (GH7), a short Thr/Ser-rich linker and a family 1 carbohydrate-binding module (CBM 1). The purified recombinant Cel7A had pH and temperature optima of pH 5.0 and 60°C, respectively, and showed broad pH adaptability (pH 3.0-6.0) and excellent stability at pH3.0-8.0 and 60°C. Belonging to the group of nonspecific endoglucanases, Cel7A exhibited the highest activity on barley β-glucan (2020 ± 9 U mg-1), moderate on lichenan and CMC-Na, and weak on laminarin, locust bean galactomannan, Avicel, and filter paper. Under simulated mashing conditions, addition of Cel7A (99 μg) reduced the mash viscosity by 9.1% and filtration time by 24.6%. These favorable enzymatic properties make Cel7A as a good candidate for applications in the brewing industry.
Lettuce Soil Microbiome Modulated by an L-α-Amino Acid-Based Biostimulant (2023)

Maintenance of soil health is of foremost importance to sustain and increase crop productivity, while meeting the demand of a rising global population. Soil microbiome is gaining increasing attention as a modulator of soil health. Microbial communities confer traits to the soil as a living organism, which functions holistically and conforms part of the plant holobiont, reassembling the human-gut axis. Novel strategies in biostimulant development advocate for modulation of the native soil microbiome and the reinforcement of microbial networking to outpace pathogen inclusion. Consequently, we hypothesize that Terramin® Pro may promotes beneficial microorganisms, depending on the native microbiota of soil, which would lead to an improvement of crop performance indicators. We proposed a soil microbiome-based approach to characterize the effect of an L-α-amino acid based biostimulant (Terramin® Pro) on resulting plant phenotypes in lettuce cultivars (Lactuca sativa L.) to address our hypothesis. First, product application promoted Actinobacteria group in assorted soils with different track of agronomic practices. Secondly, biostimulant application improved chlorophyll content in particular soils deviating from standard conditions, i.e., sick or uncultivated ones. Specially, we observed that product application at 30 L ha−1 improved lettuce phenotype, while potentially promoted entomopathogenic fungi (Beauveria and Metarhizium spp.) and suppressed other lettuce disease-related fungi (Olpidium spp.) in nematode-infested soils. Further investigations could deepen into Terramin® Pro as a sustainable prebiotic strategy of soil indigenous microbiota, through in-house microbiome modulation, even in additional crops.
Insight into Adsorptive Desulfurization by Zeolites: A Machine Learning Exploration (2022)

Adsorptive desulfurization (ADS) of hydrocarbon fuels using zeolite-based adsorbents holds great promise due to the mild conditions required to remove sulfur, thus addressing the energy and environmental concerns. However, screening of the ever-increasing number of potential ADS zeolites for adsorptive capacity is increasingly intractable. Furthermore, there is no consensus on the parameters with a dominating influence; hence, adsorbent synthesis design has remained an art. Machine learning (ML) has gained popularity as a powerful tool for understanding the catalytic mechanism and providing insights into catalytic design. In this study, we used multiple linear regression (MLR) and random forest (RF) regression to explore the process of ADS by zeolites using data from the literature. We found better predictive performance under the RF model (R2 = 0.93) than the MLR model (R2 = 0.88), which violated the assumption of linearity. The initial adsorbate concentration showed the highest relative importance of the variables, followed by zeolite properties (metal ion, mesoporous volume, pore size, Si/Al ratio, and surface area) for ADS activity. Our RF prediction model may be used in place of experimental ADS zeolite screening, cutting down on time and resource requirements. This work demonstrates the utility of ML and literature survey data as an inexpensive alternative to experimentation when doing research to obtain mechanistic insight into the complex process of ADS.
Rare and Coding Region Genetic Variants Associated With Risk of Ischemic Stroke: The NHLBI Exome Sequence Project (2020)

Stroke is the second leading cause of death and the third leading cause of years of life lost. Genetic factors contribute to stroke prevalence, and candidate gene and genome-wide association studies (GWAS) have identified variants associated with ischemic stroke risk. These variants often have small effects without obvious biological significance. Exome sequencing may discover predicted protein-altering variants with a potentially large effect on ischemic stroke risk.
DRAVET ENGAGE. Parent caregivers of children with Dravet syndrome: Perspectives, needs, and opportunities for clinical research (2021)

Dravet syndrome (DS) is an intractable developmental and epileptic encephalopathy significantly impacting affected children and their families. A novel, one-time, adeno-associated virus (AAV)-mediated gene regulation therapy was designed to treat the underlying cause of DS, potentially improving the full spectrum of DS manifestations. To ensure the first-in-human clinical trial addresses meaningful outcomes for patients and families, we examined their perspectives, priorities, goals, and desired outcomes in the design phase through a mixed methods approach (quantitative and qualitative). We conducted a non-identifiable parent caregiver survey, shared through a patient advocacy organization (n = 36 parents; children age ≤6 years). Parents were also engaged via three group discussions (n = 10; children age 2-20 years) and optional follow-up in-depth individual interviews (n = 6). Qualitative data analysis followed an inductive interpretive process, and qualitative researchers conducted a thematic analysis with a narrative approach. Survey results revealed most children (94%) were diagnosed by age 1, with onset of seizures at mean age 6.2 months and other DS manifestations before 2 years. The most desired disease aspects to address with potential new disease-modifying therapies were severe seizures (ranked by 92% of caregivers) and communication issues (development, expressive, receptive; 72-83%). Qualitative results showed the need for trial outcomes that recognize the impact of DS on the whole family. Parents eventually hope for trials including children of all ages and were both excited about the potential positive impact of a one-time disease-modifying therapy and mindful of potential long-term implications. Participants reflected on the details and risks of a clinical trial design (e.g., sham procedures) and described the different factors that relate to their decision to participate in a trial. Their main aspirations were to stop neurodevelopmental stagnation, to reduce seizures, and to reduce the impact on their families' wellbeing. To our knowledge, this is the first study within a patient-oriented research framework that specifically explored parents' needs and perceptions regarding clinical trials of a potential disease-modifying therapy for children with a severe, developmental disease, such as DS.
Generalized equations for rectified diffusion (1982)

There are at least four different equations present in the literature for the threshold for growth of gas bubbles by rectified diffusion. These various equations have limited regions of applicability and also give significantly different predictions in common regions of applicability. In this paper, a set of general equations are obtained for the growth rate and the threshold for rectified diffusion that apply over a wider range of interest. It is shown that under certain restrictions the previous equations agree with the more general ones given here. Finally, graphical representations of the equations are given showing the degree of approximation and the range of applicability of the specialized equations.
Chemistry of new particle growth in mixed urban and biogenic emissions – insights from CARES (2014)

Abstract. Regional new particle formation and growth events (NPEs) were observed on most days over the Sacramento and western Sierra foothills area of California in June 2010 during the Carbonaceous Aerosols and Radiative Effect Study (CARES). Simultaneous particle measurements at both the T0 (Sacramento, urban site) and the T1 (Cool, rural site located ~40 km northeast of Sacramento) sites of CARES indicate that the NPEs usually occurred in the morning with the appearance of an ultrafine mode at ~15 nm (in mobility diameter, Dm, measured by a mobility particle size spectrometer operating in the range 10-858 nm) followed by the growth of this modal diameter to ~50 nm in the afternoon. These events were generally associated with southwesterly winds bringing urban plumes from Sacramento to the T1 site. The growth rate was on average higher at T0 (7.1 ± 2.7 nm h−1) than at T1 (6.2 ± 2.5 nm h−1), likely due to stronger anthropogenic influences at T0. Using a high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS), we investigated the evolution of the size-resolved chemical composition of new particles at T1. Our results indicate that the growth of new particles was driven primarily by the condensation of oxygenated organic species and, to a lesser extent, ammonium sulfate. New particles appear to be fully neutralized during growth, consistent with high NH3 concentration in the region. Nitrogen-containing organic ions (i.e., CHN+, CH4N+, C2H3N+, and C2H4N+) that are indicative of the presence of alkyl-amine species in submicrometer particles enhanced significantly during the NPE days, suggesting that amines might have played a role in these events. Our results also indicate that the bulk composition of the ultrafine mode organics during NPEs was very similar to that of anthropogenically influenced secondary organic aerosol (SOA) observed in transported urban plumes. In addition, the concentrations of species representative of urban emissions (e.g., black carbon, CO, NOx, and toluene) were significantly higher whereas the photo-oxidation products of biogenic VOCs (volatile organic compounds) and the biogenically influenced SOA also increased moderately during the NPE days compared to the non-event days. These results indicate that the frequently occurring NPEs over the Sacramento and Sierra Nevada regions were mainly driven by urban plumes from Sacramento and the San Francisco Bay Area, and that the interaction of regional biogenic emissions with the urban plumes has enhanced the new particle growth. This finding has important implications for quantifying the climate impacts of NPEs on global scale.
Effect of Oral Sebacic Acid on Postprandial Glycemia, Insulinemia, and Glucose Rate of Appearance in Type 2 Diabetes (2010)

Sebacic acid significantly reduced hyperglycemia after a meal in type 2 diabetic subjects. This beneficial effect was associated with a reduction in glucose Ra, probably due to lowered hepatic glucose output and increased peripheral glucose disposal.
A Predictive Model for Cochlear Implant Outcome in Children with Cochlear Nerve Deficiency (2019)

The outcome of cochlear implantation (CI) in patients with cochlear nerve deficiency (CND) is variable, resulting in a wide range of speech perception performance, from degrees of environmental sound perception to conversation without lip-reading. Twenty-five cochlear implantees with CND were enrolled retrospectively to determine the factors correlated with CI outcome in patients with CND and to develop a predictive model for CI outcome. CI outcome was evaluated using the Categories of Auditory Performance (CAP) score at 2 years after CI. Patients with negative auditory brainstem response (ABR) showed a significantly lower CAP score than those with positive ABR (2.5 ± 1.7, 4.8 ± 0.7; p = 0.001). The area ratio of vestibulocochlear nerve (VCN) to facial nerve (FN) at the cerebellopontine angle on magnetic resonance images was positively correlated with CI outcome (p < 0.001). With multiple regression analysis, a predictive equation accounting for 66% of variance of CAP score at 2 years after CI was [Formula: see text]. We found that preoperative ABR and area ratio of VCN to FN at the cerebellopontine angle could predict CI outcome in patients with CND. Preoperative counselling based on our predictive model might be helpful to determine treatment modality for auditory rehabilitation and which ear to implant.
Quasi‐biennial oscillation and tracer distributions in a coupled chemistry‐climate model (2006)

We have used a fully coupled chemistry‐climate model (CCM), which generates its own wind and temperature quasi‐biennial oscillation (QBO), to study the effect of coupling on the QBO and to examine the QBO signals in stratospheric trace gases, particularly ozone. Radiative coupling of the interactive chemistry to the underlying general circulation model tends to prolong the QBO period and to increase the QBO amplitude in the equatorial zonal wind in the lower and middle stratosphere. The model ozone QBO agrees well with Stratospheric Aerosol and Gas Experiment II and Total Ozone Mapping Spectrometer satellite observations in terms of vertical and latitudinal structure. The model captures the ozone QBO phase change near 28 km over the equator and the column phase change near ±15° latitude. Diagnosis of the model chemical terms shows that variations in NO x are the main chemical driver of the O 3 QBO around 35 km, i.e., above the O 3 phase change.
Degradable gold core–mesoporous organosilica shell nanoparticles for two-photon imaging and gemcitabine monophosphate delivery (2017)

The synthesis of degradable gold core–mesoporous organosilica shell nanoparticles is described.
Multi-rank processing for passive ranging in underwater acoustic environments subject to spatial coherence loss (2011)

In this work we derive the maximum likelihood estimator for passive wavefront curvature ranging systems operating in environments subject to a spatial coherence loss. As a consequence of the spatial coherence loss, the optimum processor is no longer a rank-1 matched filter and now instead involves a multi-rank weighted combination of the data based on the coherence matrix eigenvectors and eigenvalues. We also establish an interesting connection of our proposed multi-rank processor to the conventional rank-1 processor, and to the non-coherence sub-array processor, under different operating conditions. A comparative study is carried out in evaluating the performance of the proposed processors.
Effects of nanotube alignment and measurement direction on percolation resistivity in single-walled carbon nanotube films (2007)

We have used Monte Carlo simulations to study the effects of nanotube alignment and measurement direction on the resistivity in single-walled carbon nanotube films. These films consist of multiple layers of conductive nanotube networks with percolative transport as the dominant conduction mechanism. We find that minimum resistivity occurs for a partially aligned rather than a perfectly aligned nanotube film. When nanotubes are strongly aligned, the film resistivity becomes highly dependent on the measurement direction. We also find that aligning the nanotubes too strongly or measuring the resistivity in a direction which is very different from the alignment direction causes the film to approach the percolation threshold, as evidenced by the inverse power law increase in resistivity. Furthermore, the location of the resistivity minimum and the values of the inverse power law critical exponents are not universal, but depend strongly on other nanotube and device parameters. To illustrate this explicitly, we have studied the effect of three parameters, namely, nanotube length, nanotube density per layer, and device length on the scaling of nanotube film resistivity with nanotube alignment and measurement direction. We find that longer nanotubes, denser films, and shorter device lengths decrease the alignment critical exponent and the alignment angle at which minimum resistivity occurs, but increase the measurement direction critical exponent. However, the amount of increase or decrease in the critical exponents or the minima locations is different for each parameter. We explain these results by simple physical and geometrical arguments. Characterizing and understanding the effects of alignment and measurement direction on the percolation resistivity in films and composites made up of one-dimensional conductors, such as nanotubes, give valuable insights into the optimal way to arrange these nanomaterials for potential applications in optoelectronics, sensors, and flexible microelectronics.
The Aldosteronoma Resolution Score (2008)

The ARS accurately identifies individuals at low (ARS < or =1) or high (ARS > or =4) likelihood of complete resolution of hypertension without further need of lifelong antihypertensive medications after adrenalectomy for aldosteronoma. This scoring system can help clinicians objectively inform patients of likely clinical outcomes before surgical intervention.
MARTINDALE: ‘Martindale — the Extra Pharmacopoeia’ (30th ed), edited by J. E. F. Reynolds (1993)

MARTINDALE: 'Martindale — the Extra Pharmacopoeia' (30th ed), edited by J. E. F. Reynolds Arthur G Lipman Arthur G Lipman Professor of Clinical Pharmacy College of Pharmacy, University of Utah, Salt Lake City, USA Search for other works by this author on: Oxford Academic Google Scholar International Journal of Pharmacy Practice, Volume 2, Issue 2, July 1993, Page 124, https://doi.org/10.1111/j.2042-7174.1993.tb00740.x Published: 22 February 2011
Graphene surpasses GaAs/AlGaAs for the application of the quantum Hall effect in metrology (2015)

The quantum Hall effect (QHE) theoretically provides a universal standard of electrical resistance in terms of the Planck constant $h$ and the electron charge $e$. In graphene, the spacing between the lowest discrete energy levels occupied by the charge carriers under magnetic field is exceptionally large. This is promising for a quantum Hall resistance standard more practical in graphene than in the GaAs/AlGaAs devices currently used in national metrology institutes. Here, we demonstrate that large QHE devices, made of high quality graphene grown by propane/hydrogen chemical vapour deposition on SiC substrates, can surpass state-of-the-art GaAs/AlGaAs devices by considerable margins in their required operational conditions. In particular, in the device presented here, the Hall resistance is accurately quantized within $1\times 10^{-9}$ over a 10-T wide range of magnetic field with a remarkable lower bound at 3.5 T, temperatures as high as 10 K, or measurement currents as high as 0.5 mA. These significantly enlarged and relaxed operational conditions, with a very convenient compromise of 5 T, 5.1 K and 50 $μ$A, set the superiority of graphene for this application and for the new generation of versatile and user-friendly quantum standards, compatible with a broader industrial use. We also measured an agreement of the quantized Hall resistance in graphene and GaAs/AlGaAs with an ultimate relative uncertainty of $8.2\times 10^{-11}$. This supports the universality of the QHE and its theoretical relation to $h$ and $e$, essential for the application in metrology, particularly in view of the forthcoming Système International d'unités (SI) based on fundamental constants of physics, including the redefinition of the kilogram in terms of $h$.