gebhart/patrepeval huggingface dataset:
Computationally Assisted Mechanistic Investigation and Development of Pd-Catalyzed Asymmetric Suzuki–Miyaura and Negishi Cross-Coupling Reactions for Tetra-ortho-Substituted Biaryl Synthesis (2018)

Metal-catalyzed cross-coupling reactions are extensively employed in both academia and industry for the synthesis of biaryl derivatives for applications to both medicine and material science. Application of these methods to prepare tetra-<i>ortho</i>-substituted biaryls leads to chiral atropisomeric products that introduces the opportunity to use catalyst-control to develop asymmetric cross-coupling procedures to access these important compounds. Asymmetric Pd-catalyzed Suzuki-Miyaura and Negishi cross-coupling reactions to form tetra-<i>ortho</i>-substituted biaryls were studied employing a collection of <i>P</i>-chiral dihydrobenzooxaphosphole (BOP) and dihydrobenzoazaphosphole (BAP) ligands. Enantioselectivities of up to 95:5 and 85:15 er were identified for the Suzuki-Miyaura and Negishi cross-coupling reactions, respectively. Unique ligands for the Suzuki-Miyaura reaction <i>vs</i> the Negishi reaction were identified. A computational study on these Suzuki-Miyaura and Negishi cross-coupling reactions enabled an understanding in the differences between the enantiodiscriminating events between these two cross-coupling reactions. These results support that enantioselectivity in the Negishi reaction results from the reductive elimination step, whereas all steps in the Suzuki-Miyaura catalytic cycle contribute to the overall enantioselection with transmetalation and reductive elimination providing the most contribution to the observed selectivities.
Trends in breast cancer during three decades in Denmark: Stage at diagnosis, surgical management and survival (2008)

During these three decades over-all survival of breast cancer improved. In the earlier periods we found survival differences according to residence, but in the late cohort there were no difference despite better stage distribution in the county with mammography-screening.
Formulation and Characterization of Echogenic Lipid−Pluronic Nanobubbles (2009)

The advent of microbubble contrast agents has enhanced the capabilities of ultrasound as a medical imaging modality and stimulated innovative strategies for ultrasound-mediated drug and gene delivery. While the utilization of microbubbles as carrier vehicles has shown encouraging results in cancer therapy, their applicability has been limited by a large size which typically confines them to the vasculature. To enhance their multifunctional contrast and delivery capacity, it is critical to reduce bubble size to the nanometer range without reducing echogenicity. In this work, we present a novel strategy for formulation of nanosized, echogenic lipid bubbles by incorporating the surfactant Pluronic, a triblock copolymer of ethylene oxide copropylene oxide coethylene oxide into the formulation. Five Pluronics (L31, L61, L81, L64 and P85) with a range of molecular weights (M(w): 1100 to 4600 Da) were incorporated into the lipid shell either before or after lipid film hydration and before addition of perfluorocarbon gas. Results demonstrate that Pluronic-lipid interactions lead to a significantly reduced bubble size. Among the tested formulations, bubbles made with Pluronic L61 were the smallest with a mean hydrodynamic diameter of 207.9 +/- 74.7 nm compared to the 880.9 +/- 127.6 nm control bubbles. Pluronic L81 also significantly reduced bubble size to 406.8 +/- 21.0 nm. We conclude that Pluronic is effective in lipid bubble size control, and Pluronic M(w), hydrophilic-lipophilic balance (HLB), and Pluronic/lipid ratio are critical determinants of the bubble size. Most importantly, our results have shown that although the bubbles are nanosized, their stability and in vitro and in vivo echogenicity are not compromised. The resulting nanobubbles may be better suited for contrast enhanced tumor imaging and subsequent therapeutic delivery.
Total Pancreatectomy and Islet Autotransplantation for Chronic Pancreatitis (2012)

TP can ameliorate pain and improve quality of life in otherwise refractory CP patients, even if narcotic withdrawal is delayed or incomplete because of earlier long-term use. IAT preserves meaningful islet function in most patients and substantial islet function in more than two thirds of patients, with insulin independence occurring in one quarter of adults and half the children.
GFP biofluorescence: imaging gene expression and protein dynamics in living cells. Design considerations for a fluorescence imaging laboratory. (1999)

Publisher Summary The fluorescence imaging laboratory best functions as a carefully planned system of tools for optimal image generation, display, analysis, and output. These systems are supported by the physical plant in which the lab exists. The interactions of these tools within the laboratory will largely determine the success of the facility. This chapter aims to raise the issues that need to be considered in creating such a facility. Any weak component will drive the quality of the final product and failure to attend to the details of the facility will lead to frustration on the part of the users. Only a few facilities exist that have every imaging tool. Fewer still are the facilities that have had the luxury of designing the laboratory at one time. Most facilities have evolved from a series of components that have been carefully assembled and fought for by the hard work of the facility director or manager. Because every component of the laboratory is expensive, each piece must be carefully considered and thought of in terms of its relationship to the other components in the lab and, even more important, in light of the scientific questions that need to be answered.
A Continuous Stirred Tank Reactor for the Systematic Control of Gold Nanoparticle Size. (2015)

Abstract not provided.
Molecular Weight Determination of Polymers by Matrix Assisted Laser Desorption Ionization in Mass Spectrometry (1995)

Matrix assisted laser desorption ionization in mass spectrometry is a fast and accurate method to determine the molecular weight of natural and synthetic polymers. Unknown peptides such as elastase inhibitor and D-hydantoinase were analyzed using sinapinic acid as matrix and their molecular weights were compared with the results from protein sequencer and gel filtration chomatography, respectively. Synthetic polymers such as polyethyleneglycol, polypropyleneglycol, polydimethylsiloxane, and polystyrene were analyzed using matrices such as 2,5-dihydroxybenzoic acid, 4-hdroxyazobenzenecarboxylic acid, and 2-nitrophenyl octyl ether. Average molecular weights of polystyrene were compared with molecular weights by gel permeation chromatography. 
Keywords MALDI, Matrix, Peptide, Protein, Synthetic Polymer, Average Molecular Weight, Gel Permeation Chromatography.
Technology and Information Fusion Needs to Address the Food, Energy, Water Systems (FEWS) Nexus Challenges (2015)

In response to the Food, Energy, Water Systems (FEWS) Nexus Challenge grant awarded by NSF, the team of investigators led by David Ebert, along with Christian Butzke, Melba Crawford, Phillip Owens, and Dimitrios Peroulis conducted a two-day workshop in Napa, California on November 5th and 6th, 2015. The workshop addressed the emerging issues in the food/energy/water systems throughout the diverse geography of the United States and over various crops and environmental conditions to better understand and model and ultimately devise a solution for the challenges to the FEWS nexus. One of the intended outcomes of the workshop was to generate a report that will chart the research challenges and opportunities for solving these challenges and have an impact on scientific fields including, sensing technology, hydrology, soil science, climate, data fusion, analysis, visualization, and data driven decision 2 making, as well as agricultural production, local and regional economies, sustainability and planning. The information contained in this post-workshop report serves as that foundation.In response to the Food, Energy, Water Systems (FEWS) Nexus Challenge grant awarded by NSF, the team of investigators led by David Ebert, along with Christian Butzke, Melba Crawford, Phillip Owens, and Dimitrios Peroulis conducted a two-day workshop in Napa, California on November 5th and 6th, 2015. The workshop addressed the emerging issues in the food/energy/water systems throughout the diverse geography of the United States and over various crops and environmental conditions to better understand and model and ultimately devise a solution for the challenges to the FEWS nexus. One of the intended outcomes of the workshop was to generate a report that will chart the research challenges and opportunities for solving these challenges and have an impact on scientific fields including, sensing technology, hydrology, soil science, climate, data fusion, analysis, visualization, and data driven decision 2 making, as well as agricultural production, local and regional economies, sustainability and planning. The information contained in this post-workshop report serves as that foundation.
Persistent polyamorphism in the chiton tooth: From a new biomineral to inks for additive manufacturing (2021)

Engineering structures that bridge between elements with disparate mechanical properties are a significant challenge. Organisms reap synergy by creating complex shapes that are intricately graded. For instance, the wear-resistant cusp of the chiton radula tooth works in concert with progressively softer microarchitectural units as the mollusk grazes on and erodes rock. Herein, we focus on the stylus that connects the ultrahard and stiff tooth head to the flexible radula membrane. Using techniques that are especially suited to probe the rich chemistry of iron at high spatial resolution, in particular synchrotron Mössbauer and X-ray absorption spectroscopy, we find that the upper stylus of <i>Cryptochiton stelleri</i> is in fact a mineralized tissue. Remarkably, the inorganic phase is nano disperse santabarbaraite, an amorphous ferric hydroxyphosphate that has not been observed as a biomineral. The presence of two persistent polyamorphic phases, amorphous ferric phosphate and santabarbaraite, in close proximity, is a unique aspect that demonstrates the level of control over phase transformations in <i>C. stelleri</i> dentition. The stylus is a highly graded material in that its mineral content and mechanical properties vary by a factor of 3 to 8 over distances of a few hundred micrometers, seamlessly bridging between the soft radula and the hard tooth head. The use of amorphous phases that are low in iron and high in water content may be key to increasing the specific strength of the stylus. Finally, we show that we can distill these insights into design criteria for inks for additive manufacturing of highly tunable chitosan-based composites.
Experimental measurements of multi-carrier based Doppler heartrate tracker (2016)

This study presents experimental results of multi-carrier based Doppler radar signal processing for vital signs tracking. When small motion-transients exist, it is expected that a disturbance at a carrier frequency is different from other carrier frequencies. The multi-carrier based Doppler radar shows the possibility to overcome the motion-transient effect in some situations. Six tests are performed to measure multi-carrier Doppler signals. Their heartrate tracking results show that the mean values of the tracked heartrates are within plus/minus 3% of the ground truth R-R interval frequency of their electrocardiogram measurements. It is also shown that the variance values of the tracked heartrates are all within 0.0062 Hz. The proposed signal processing scheme seems to have potential to track vital signs while small motion-transients exist.
Fabrication and Characterization of Hybrid Stealth Liposomes (2018)

Next-generation liposome systems for anticancer and therapeutic delivery require the precise insertion of stabilizing polymers and targeting ligands. Many of these functional macromolecules may be lost to micellization as a competing self-assembly landscape. Here, hybrid stealth liposomes, which utilize novel cholesteryl-functionalized block copolymers as the molecular stabilizer, are explored as a scalable platform to address this limitation. The employed block copolymers offer resistance to micellization through multiple liposome insertion moieties per molecule. A combination of thermodynamic and structural investigations for a series of hybrid stealth liposome systems suggests that a critical number of cholesteryl moieties per molecule defines whether the copolymer will or will not insert into the liposome bilayer. Colloidal stability of formed hybrid stealth liposomes further corroborates the critical copolymer architecture value.
Texture synthesis‐by‐analysis method based on a multiscale early‐vision model (1996)

A new texture synthesis-by-analysis method, applying a visually based approach that has some important advantages over more traditional texture modeling and synthesis techniques is introduced. The basis of the method is to encode the textural information by sampling both the power spectrum and the histogram of homogeneously textured images. The spectrum is sampled in a log-polar grid using a pyramid Gabor scheme. The input image is split into a set of 16 Gabor channels (using four spatial frequency levels and four orientations), plus a lowpass residual (LPR). The energy and equivalent bandwidths of each channel, as well as the LPR power spectrum and the histogram, are measured and the latter two are compressed. The synthesis process consists of generating 16 Gabor filtered independent noise signals with spectral centers equal to those of the Gabor filters, whose energy and equivalent bandwidths are calculated to reproduce the measured values. These bandpass signals are mixed into a single image, whose LPR power spectrum and histogram are modified to match the original features. Despite the coarse sampling scheme used, very good results have been achieved with nonstructured textures as well as with some quasiperiodic textures. Besides being applicable to a wide range of textures, the method is robust (stable, fully automatic, linear, and with a fixed code length) and compact (it uses only 69 parameters).
Defining NAD(P)(H) Catabolism (2023)

Dietary vitamin B3 components, such as nicotinamide and nicotinic acid, are precursors to the ubiquitous redox cofactor nicotinamide adenine dinucleotide (NAD<sup>+</sup>). NAD<sup>+</sup> levels are thought to decline with age and disease. While the drivers of this decline remain under intense investigation, strategies have emerged seeking to functionally maintain NAD<sup>+</sup> levels through supplementation with NAD<sup>+</sup> biosynthetic intermediates. These include marketed products, such as nicotinamide riboside (NR) and its phosphorylated form (NMN). More recent developments have shown that NRH (the reduced form of NR) and its phosphorylated form NMNH also increases NAD<sup>+</sup> levels upon administration, although they initially generate NADH (the reduced form of NAD<sup>+</sup>). Other means to increase the combined levels of NAD<sup>+</sup> and NADH, NAD(H), include the inhibition of NAD<sup>+</sup>-consuming enzymes or activation of biosynthetic pathways. Multiple studies have shown that supplementation with an NAD(H) precursor changes the profile of NAD(H) catabolism. Yet, the pharmacological significance of NAD(H) catabolites is rarely considered although the distribution and abundance of these catabolites differ depending on the NAD(H) precursor used, the species in which the study is conducted, and the tissues used for the quantification. Significantly, some of these metabolites have emerged as biomarkers in physiological disorders and might not be innocuous. Herein, we review the known and emerging catabolites of the NAD(H) metabolome and highlight their biochemical and physiological function as well as key chemical and biochemical reactions leading to their formation. Furthermore, we emphasize the need for analytical methods that inform on the full NAD(H) metabolome since the relative abundance of NAD(H) catabolites informs how NAD(H) precursors are used, recycled, and eliminated.
Windows Phone 7 from a Digital Forensics’ Perspective (2012)

Windows Phone 7 is a new smartphone operating system with the potential to become one of the major smartphone platforms in the near future. Phones based on Windows Phone 7 are only available since a few months, so digital forensics of the new system is still in its infancy. This paper is a first look at Windows Phone 7 from a forensics’ perspective. It explains the main characteristics of the platform, the problems that forensic investigators face, methods to circumvent those problems and a set of tools to get data from the phone. Data that can be acquired include the file system, the registry, and active tasks. Based on the file system, further information like SMSs, Emails and Facebook data can be extracted.
Pulmonary haemorrhage in Oriental patients with systemic lupus erythematosus (1997)

We reviewed the case records of 10 Oriental patients with systemic lupus erythematosus (SLE) who developed pulmonary haemorrhage (PH) between 1987 and 1996 to determine their clinical presentation and outcome. All the patients had clinical evidence of PH including a sudden onset of dyspnoea, tachycardia, fall in haemoglobin (at least 1.5 gm%) and bilateral diffuse alveolar infiltrates on chest radiographs. At the time of PH, nine patients had a disease duration of 2 years or less and all the patients had clinical and/or laboratory evidence of active lupus disease. Fever and lung crepitations were present in 90% of patients while haemoptysis and chest pain occurred in only three and two patients, respectively. All the patients were treated with high dose intravenous corticosteroids and in addition seven had a combination of pulse methylprednisolone and cyclophosphamide, and four had received plasmapheresis. Four patients died as a result of PH. One patient died of pneumonia three years after recovering from PH while the remaining five had no recurrence of PH after a median follow-up of 22 months. Our study suggests that PH in Oriental lupus patients often occurs early in the disease, rarely presents with haemoptysis and has a high mortality despite aggressive immunosuppressive therapy.
Characterization of nodular and thermal defects in hafnia/silica multilayer coatings using optical, photothermal, and atomic force microscopy (1998)

Multilayer coatings manufactured from metallic hafnium and silica sources by reactive electron beam deposition, are being developed for high fluence optics in a fusion lasers with a wavelength of 1053 nm and a 3 ns pulse length. Damage threshold studies have revealed a correlation between laser damage and nodular defects, but interestingly laser damage is also present in nodule-free regions. Photothermal studies of optical coatings reveal the existence of defects with strong optical absorption in nodule-free regions of the coating. A variety of microscopic techniques were employed to characterize the defects for a better understanding of the thermal properties of nodular defects and role of thermal defects in laser damage. Photothermal microscopy, utilizing the surface thermal lensing technique, was used to map the thermal characteristics of 3 mm X 3 mm areas of the coatings. High resolution subaperture scans, with a 1 micrometers step size and a 3 micrometers pump beam diameter, were conducted on the defects to characterize their photothermal properties. Optical and atomic force microscopy was used to visually identify defects and characterize their topography. The defects were then irradiated to determine the role of nodular and thermal defects in limiting the damage threshold of the multilayer.
ChemInform Abstract: β‐Diketo Building Blocks for MCRs‐Based Syntheses of Heterocycles (2011)

Abstract Review: 169 refs.
Hydroperoxides as pseudohalides: oxidation, oxidative alkylation, acylation and arylation of acrylonitrile (1995)

New general syntheses, based on free-radical oxidative alkylation, acylation and arylation of acrylonitrile, in the presence of ButO2H, are reported; the concept of the peroxy group as a pseudohalide is suggested to explain these new reactions.
A Portable Computational Cluster for Modeling and Simulation (2009)

In the present paper we are describing the development of a portable computational cluster infrastructure based on Apple’s MacMini systems. The objective of this effort is to initiate the exploration of the feasibility for building and evaluating a low cost computational cluster system that could be portable due to the small form factor of the individual units while it could still provide considerable computational scalability. Here we outline our experiences in the form of a how-to methodology for setting up a MAC OS X 10.4 cluster for Xgrid and three popular versions of Message Passing Interface (MPI), i.e., OpenMPI, LAM-MPI, and MPICH2. Subsequently, we describe some performance measurements through the utilization of the Fire Dynamic Simulator (FDS) for two cases of reactive flow topologies. Finally, Xgrid with OpenMPI throughput and latency performance results are presented and discussed.
Cryopreservation of dehydrated Caenorhabditis elegans with multiple recoveries using a granular medium (2021)

Ultracold storage is widely used to preserve genetic stocks. Standard cryopreservation methods for the nematode <i>C. elegans</i> are vulnerable to refrigeration failures, which can result in the loss of stock viability due to freeze-thaw damage. In previous work our laboratory developed a method for cryopreserving worms in a dehydrated form that remains viable after multiple freeze-thaw cycles. However, strains preserved in this manner can be recovered only once from each cryopreservation tube. Here we describe a cryopreservation method in which <i>C. elegans</i> are dehydrated in a granular medium (cornmeal) prior to freezing. To recover worms, a small fraction (~1%) of the medium may be removed with the remainder returned to cold storage. Our improved cryopreservation method is not only resistant to refrigeration failures but also greatly increases the number of recoveries per tube compared to current methods.