gebhart/patrepeval huggingface dataset:
Sum Frequency Generation from Langmuir−Blodgett Multilayer Films on Metal and Dielectric Substrates (2005)

Sum frequency generation (SFG) vibrational spectra of cadmium arachidate multilayer films adsorbed on a substrate with high nonresonant susceptibility, i.e., gold, and on a low nonresonant susceptibility substrate, i.e., fused quartz, have been investigated in the C-H stretching region in air. The films were formed by Langmuir-Blodgett (LB) deposition and their spectra recorded using SFG spectrometers employing both 532-nm nanosecond and 800-nm femtosecond lasers, with counter-propagating and co-propagating beam geometries, respectively. Both kinds of substrate were rendered hydrophobic by coating them with per-deuterated octadecanethiol (gold) or per-deuterated cadmium arachidate (fused quartz) monolayers. Single per-protonated arachidate layers in otherwise per-deuterated 10-layer films were used to show that the SFG resonances arise only from the topmost and lowermost layers in a LB film comprised of an even number of per-protonated layers, although the SFG spectra from the two hydrophobic substrates are different from each other. The differences in the spectra from the same ten-layer per-protonated films deposited on the two types of hydrophobic substrate have been explained in terms of a simple model that accounts for resonant and nonresonant contributions.
Kinetic [18F]-Fluoride of the Knee in Normal Volunteers (2019)

Quantitative [F]NaF PET is sensitive to variations in bone vascularization and metabolism in the knee joint.
Gene Editing of CCR5 in Hematopoietic Stem Cells in a Nonhuman Primate Model of HIV/AIDS (2014)

Abstract Background: Hematopoietic stem cell (HSC) transplantation remains the only clinically observed path to functional cure of HIV infection. To better understand the mechanism of HSC-driven HIV control, and apply this therapy to a greater number of patients, we have developed a model of combination antiretroviral therapy (cART)-suppressed HIV infection in the pigtailed macaque, applicable to both gene therapy- and allogeneic transplant-based cure strategies. Following transplantation of HIV-resistant, autologous cells into conditioned animals, we are evaluating the extent to which protected cell progeny impede infection by SIV/HIV (SHIV) chimeric virus in vivo. Methods: Animals are challenged with SHIV virus containing an HIV envelope, after which a 3-drug cART regimen is initiated. Autologous HSCs are engineered to resist infection through targeted disruption of the CCR5 genetic locus using Zinc Finger Nucleases (ZFNs). Engraftment, persistence, and SHIV response of these autologous stem cells, and stem cell-derived lymphoid and myeloid cells, are measured in vivo. Results: SHIV infection in the pigtailed macaque model results in sustained viremia with consequent reduction in CD4+ T cells. Moreover, administration of three-drug cART leads to rapid and durable suppression of plasma viremia to &lt;30 copies/mL plasma - suggesting that this model recapitulates key features of HIV infection and treatment in humans. CCR5 targeting experiments yield up to 60% gene disruption in CD34+ cells ex vivo, translating to approximately 5% disruption in vivo following transplant. Importantly, up to 10% of transplanted cells carry two disrupted alleles of CCR5; these cells should preferentially reconstitute CD4+ T-cell pools and other susceptible subsets following SHIV challenge. Consistent with this prediction, our preliminary data suggest that CCR5-deleted cells undergo positive selection following SHIV challenge in vivo. Conclusions: Our pigtailed macaque model of HIV infection and cART represents a promising platform for modeling functional cure strategies. Here we show that CCR5 deletion does not impair HSC engraftment or differentiation, and that CCR5-deleted cells can undergo SHIV-dependent positive selection even when present at low levels. Our model enables the evaluation of novel therapeutic approaches in the clinically relevant context of cART controlled SHIV infection - a setting of particular importance to approaches aimed at addressing the viral reservoir. Disclosures Wang: Sangamo Biosciences: Employment. Holmes:Sangamo Biosciences: Employment. Gregory:Sangamo Biosciences: Employment.
X-Ray Structural Analyses of Rare Earth Trifluoromethanesulfonate Complexes Bearing Urea Derivatives (1999)

Abstract X-Ray structural analyses of the rare earth(III) trifluoromethanesulfonates (triflates) with urea derivatives are described. The reactions of anhydrous rare earth triflates with 8 equiv of tetrahydro-2-pyrimidinone (trimethyleneurea (PU)) in methanol give [M(pu)8](OTf)3 (OTf = triflate) (M = Sm: 1a; M = Y: 1b; M = Nd: 1c; M = Eu: 1d; M = Gd: 1e; M = Tb: 1f; M = Dy: 1g; M = Ho: 1h; M = Yb: 1i), and [Sc(pu)6](OTf)3 (2). X-Ray crystallographic analyses of these complexes indicate that a pair of PU ligands are interacting with each other through the hydrogen bonds. The reaction of anhydrous samarium(III) triflate with 6 equiv of 1,3-dimethyl-3,4,5,6-tetrahydro-2(1H)-pyrimidinone (1,3-dimethyltrimethyleneurea (DMPU)) in tetrahydrofuran (THF) affords [Sm(dmpu)6](OTf)3 (3) which has a hexa-coordinated octahedral structure. Anhydrous samarium(III) triflate reacts with 5 equiv of 1,3-dimethyl-2-imidazolidinone (DMI) to give [Sm(Otf)2(dmi)5]OTf (4) which has a hepta-coordinated pentagonal bipyramidal structure. Five DMI ligands in 4 coordinate to the samarium atom in a propeller-like fashion.
Flavonoids syntheses. II. Synthesis of flavones with a 2',3',6'-trioxygenated ring B. (1985)

3', 5, 6', 7-Tetrahydroxy-2', 8-dimethoxyflavone (1) and its isomers (2, 3 and 4) were synthesized to confirm the proposed structure for a flavone isolated from Scutellaria baicalensis and S. rehderiana.
Supplementary Figure 2 from Functional Identification of Cancer-Specific Methylation of <i>CDO1</i>, <i>HOXA9</i>, and <i>TAC1</i> for the Diagnosis of Lung Cancer (2023)

&lt;p&gt;PDF file - 100KB, DNA Methylation of CDO1, HOXA9, and TAC1 is Highly Sensitive for Stage I NSCLC in the Cancer Genome Atlas.&lt;/p&gt;
Influence of Nonstoichiometry on Extrinsic Electrical Conduction and Microwave Dielectric Loss of BaCo 1/3 Nb 2/3 O 3 Ceramics (2010)

The microwave (MW) dielectric loss (or quality factor, Q ) of BaCo 1/3 Nb 2/3 O 3 (BCN) ceramics exhibits a strong dependence on sample‐processing conditions and is not always consistent with the degree of 1:2 B‐site cation ordering. Impedance spectroscopy results reveal that these BCN ceramics exhibit remarkably different electrical properties due to low levels of nonstoichiometry induced during ceramic processing. These compositional changes are difficult to detect by common chemical techniques but can have a significant influence on the electrical properties, and in particular on the extrinsic electrical conduction and Q . The influence of extrinsic conduction induced by ceramic processing should therefore be considered when optimizing Q in MW dielectric ceramics.
A β‐Hairpin‐Binding Protein for Three Different Disease‐Related Amyloidogenic Proteins (2014)

Amyloidogenic proteins share a propensity to convert to the β-structure-rich amyloid state that is associated with the progression of several protein-misfolding disorders. Here we show that a single engineered β-hairpin-binding protein, the β-wrapin AS10, binds monomers of three different amyloidogenic proteins, that is, amyloid-β peptide, α-synuclein, and islet amyloid polypeptide, with sub-micromolar affinity. AS10 binding inhibits the aggregation and toxicity of all three proteins. The results demonstrate common conformational preferences and related binding sites in a subset of the amyloidogenic proteins. These commonalities enable the generation of multispecific monomer-binding agents.
Direct Observation of a Defect-Mediated Viscoelastic Transition in a Hydrogel of Lipid Membranes and Polymer Lipids (1997)

We present the first direct imaging of a new hydrogel of lipid membranes containing polymer lipids. Freeze-fracture electron microscopy shows unambiguously that the hydrogel's surprisingly large viscoelasticity is explained by a novel defect topology of interconnections between defects. The defects are spherulites with high membrane curvatures which are either isotropic or cylinderlike. A lower concentration of dislocation-type defects was also observed. The interconnections between the defects distinguish the hydrogel from simple ``onion'' phases of multilamellar vesicles with a smaller viscoelasticity.
Immunological Therapeutic and Imaging Approaches for Prion Disease (2003)

Currently there is no effective treatment or prophylaxis against prion diseases. Although sporadic forms of this disease are relatively rare, the incidence of the transmissible prionoses is rising as a result of the exposure of Western European populations to bovine spongiform encephalopathy. It has been recently demonstrated in animal models that active or passive immunization may delay the onset of disease or even protect from the occurrence of symptoms if started prior to prion replication involving the central nervous system. Results of these animal studies suggest that development a vaccination approach for humans is feasible within the near future. Another aspect of prion diseases, potentially limiting the practical use of the vaccine, is lack of diagnostic tests detecting infected, non-symptomatic subjects. This can partially be overcome using high field magnetic resonance imaging (MRI), which in animal models is capable of detecting signal alterations in the brain before the onset of symptoms. Another potential way to improve the sensitivity and specificity for prion infection diagnosis is using ligands specifically targeting the β-sheet structure of PrPSc or anti-PrP antibodies. These can be coupled either with paramagnetic agents or radioisotopes making PrPSc detectable using MRI or scintigraphy respectively. Successful development of such ligands has been demonstrated for Alzheimers disease and is currently being studied for prionoses.
ChemInform Abstract: Opioid Agonists and Antagonists. Peptides Containing N‐Terminal Allyl Groups and/or a Thiomethylene Linkage in Place of a Peptide Bond. (1988)

Abstract Peptides (III), (IV), (IX)‐(XV) containing N‐allyl or N,N‐diallyl groups are synthesized as potential opioid antagonists.
Supplementary Methods, Figures 1-3, Table 1 from Optical Imaging with Her2-Targeted Affibody Molecules Can Monitor Hsp90 Treatment Response in a Breast Cancer Xenograft Mouse Model (2023)

&lt;p&gt;PDF file - 232K&lt;/p&gt;
Low-energy Collisions of Methane Ions at a Fluoroalkyl Monolayer Surface (1996)

Reactive scattering of low-energy (<100 eV) CHn+ (n = 0–4) ions with a fluorinated self-assembled monolayer (F-SAM) surface produces fluorine-containing scattered ions, including CF+, C2HF2+ and C3F3+. Evidence is provided that these ion–surface reactions occur by surface-induced dissociation (SID) prior to new bond formation. Chemical sputtering of the ion-beam modified surface is consistent with the modification of the fluorinated SAM surface by the methane derived ions occurring at the terminal CF3 group. Studies with 13C-labeled ions show the formation of 12CF+ and 13CF+ in nearly equal abundance. The participation of carbon atoms arising from both the surface and the projectile suggests the intermediacy of a symmetrical fluoronium collision complex, such as [F13CF12CF]+, involving the SID fragments of the projectile and the terminal CF3 group of the surface. A 20% translational to vibrational (T → V) energy conversion is estimated from the inelastic collisions which lead to SID, a result which is consistent with previous studies using other ions on the same surface.
Irradiance enhancement and increased laser damage threshold in As_2S_3 moth-eye antireflective structures (2015)

It has been experimentally observed that moth-eye antireflective microstructures at the end of As2S3 fibers have an increased laser damage threshold relative to thin-film antireflective coatings. In this work, we computationally study the irradiance enhancement in As2S3 moth-eye antireflective microstructures in order to explain the increased damage threshold. We show that the irradiance enhancement occurs mostly on the air side of the interfaces and is minimal in the As2S3 material. We give a physical explanation for this behavior.
Magnetic suspension and vibration control of beams for non-contact processing (2003)

This paper presents an integrated approach to magnetic suspension of a tubular beam for noncontact processing. We describe noncontact sensors and actuators, structure modelling/identification, and control methods for such systems. We have also designed an experiment that uses 8 sensors and 8 actuators to suspend a 3 m long, 6.35 mm diameter steel tube. Results from this experiment are presented herein. To facilitate the experiment, we designed a novel two-dimensional position sensor by utilizing the concept of an x-y variable differential transformer. We also designed two types of actuators that apply magnetic force on the tube in two axes. The system dynamics are modelled theoretically, and identified experimentally from within the closed-loop system. In order to control the system under varying boundary conditions, we propose a slow roll-up lead compensator. We also introduce sensor interpolation and sensor averaging methods to make the control loop more robust. Our proposed ideas are verified in the experimental results.
The rat β3‐adrenergic receptor gene contains an intron (1993)

We report that the rat beta 3-adrenergic receptor (beta 3-AR) gene has an intron. The intron starts with an in-frame stop codon with the result that unspliced transcripts will encode a C-terminal truncated protein. The reported protein sequences of mouse and human beta 3-AR were both deduced from genomic DNA sequences. Given the heterogeneity at the C-termini of the otherwise highly similar rat, mouse and human sequences, we discuss the intriguing possibility that the beta 3-AR gene of the latter two species also contain an intron near the extremity of the open reading frame. A beta-adrenergic receptor (beta-AR) cDNA we have cloned from rat colonic tissue which has a sequence essentially identical to that previously reported for the rat adipose beta 3-AR cDNA [(1991) J. Chem. 266, 24053], encodes the spliced version of the beta 3-AR.
Estimation of the Static Young's Modulus for Sandstone Reservoirs Using Support Vector Regression (2022)

Abstract The static Young's Modulus (Estatic) is an important parameter affecting the design of different aspects related to oil and gas producing wells. It is significantly changing based on the type of the formation, and hence, an accurate method of identifying Estatic is required. This study evaluates the performance of support vector regression (SVR) for prediction of the Estatic. The SVR model was learned to evaluate the Estatic from the well logs of the bulk formation density in addition to compressional and shear transit time. It was learned and tested on 592 training datasets of the inputs and their corresponding Estatic, these datasets were obtained from a sandstone formation in Well-A. The learned SVR model was then validated on 38 data points from Well-B, the performance of the optimized SVR on predicting the Estatic for the validation data was also compared with these of the early optimized artificial neural networks (ANN) and functional neural networks (FNN). As a result, all machine learning models showed high precision in predicting the Estatic for the validation data where Estatic was estimated with average absolute percentage errors of 3.80%, 2.54, and 2.03% and correlation coefficients of 0.991, 0.997, and 0.999 using the optimized ANN, FNN, and SVR models, respectively. This result shows the high accuracy of the SVR on predicting the Estatic.
Head Impact Exposure in Practices Correlates With Exposure in Games for Youth Football Players (2018)

This study aimed to compare head impact exposures between practices and games in football players ages 9 to 14 years, who account for approximately 70% of all football players in the United States. Over a period of 2 seasons, 136 players were enrolled from 3 youth programs, and 49,847 head impacts were recorded from 345 practices and 137 games. During the study, individual players sustained a median of 211 impacts per season, with a maximum of 1226 impacts. Players sustained 50th (95th) percentile peak linear acceleration of 18.3 (46.9) g, peak rotational acceleration of 1305.4 (3316.6) rad·s<sup>-2</sup>, and Head Impact Technology Severity Profile of 13.7 (24.3), respectively. Overall, players with a higher frequency of head impacts at practices recorded a higher frequency of head impacts at games (P < .001, r<sup>2</sup> = .52), and players who sustained a greater average magnitude of head impacts during practice also recorded a greater average magnitude of head impacts during games (P < .001). The youth football head impact data quantified in this study provide valuable insight into the player exposure profile, which should serve as a key baseline in efforts to reduce injury.
Data from Reversal of NK-Cell Exhaustion in Advanced Melanoma by Tim-3 Blockade (2023)

&lt;div&gt;Abstract&lt;p&gt;The immunoregulatory protein T-cell immunoglobulin- and mucin-domain–containing molecule-3 (Tim-3) mediates T-cell exhaustion and contributes to the suppression of immune responses in both viral infections and tumors. Tim-3 blockade reverses the exhausted phenotype of CD4&lt;sup&gt;+&lt;/sup&gt; and CD8&lt;sup&gt;+&lt;/sup&gt; T cells in several chronic diseases, including melanoma. Interestingly, natural killer (NK) cells constitutively express Tim-3; however, the role of Tim-3 in modulating the function of these innate effector cells remains unclear, particularly in human diseases. In this study, we compared the function of Tim-3 in NK cells from healthy donors and patients with metastatic melanoma. NK cells from the latter were functionally impaired/exhausted, and Tim-3 blockade reversed this exhausted phenotype. Moreover, Tim-3 expression levels were correlated with the stage of the disease and poor prognostic factors. These data indicate that Tim-3 can function as an NK-cell exhaustion marker in advanced melanoma and support the development of Tim-3–targeted therapies to restore antitumor immunity. &lt;i&gt;Cancer Immunol Res; 2(5); 410–22. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Development of a 4-valent genotyping assay for direct identification of the most frequent Pseudomonas aeruginosa serotypes from respiratory specimens of pneumonia patients (2014)

Pseudomonas aeruginosa is a common cause of nosocomial infections and is associated with high rates of mortality. In order to facilitate rapid and sensitive identification of the most prevalent serotypes of P. aeruginosa, we have developed a 4-valent real-time PCR-based assay using oligonucleotides specific for open-reading frames constituting the O-antigen-specific lipopolysaccharide loci of P. aeruginosa. The assay simultaneously detects and differentiates between each of the four serotypes IATS-O1, -O6, -O11 and serogroup 2 (IATS-O2, -O5, and -O16) with high sensitivity and specificity in a single-tube reaction. No cross-reactivity was observed with other serotypes of P. aeruginosa or other microbial species, and reproducibility was demonstrated regardless of template, i.e. purified DNA, bacterial culture and clinical specimens (broncho-alveolar lavage). The limit of detection of the assay was approximately 100 copies per reaction for IATS-O1, -O2 and -O11, and 50 copies per reaction for IATS-O6. Comparison of the assay specificity with a commercially available slide agglutination kit showed consistent results; however, the number of non-typable isolates was reduced by 15 % using the genotyping assay. Use of the 4-valent genotyping assay in the context of a clinical trial resulted in identification of pneumonia patients positive for the IATS-O11 serotype, and hence eligible for therapy with panobacumab (an investigational monoclonal antibody against the O-polysaccharide of serotype IATS-O11).
mRNA COVID‐19 vaccine effectiveness against SARS‐CoV‐2 infection in a prospective community cohort, rural Wisconsin, November 2020 to December 2021 (2022)

Reduced COVID-19 vaccine effectiveness (VE) has been observed with increasing predominance of SARS-CoV-2 Delta (B.1.617.2) variant. Two-dose VE against laboratory-confirmed SARS-CoV-2 infection (symptomatic and asymptomatic) was estimated using Cox proportional hazards models with time-varying vaccination status in a prospective rural community cohort of 1266 participants aged ≥12 years. Between November 3, 2020 and December 7, 2021, VE was 56% for mRNA COVID-19 vaccines overall, 65% for Moderna, and 50% for Pfizer-BioNTech. VE when Delta predominated (June to December 2021) was 54% for mRNA COVID-19 vaccines overall, 59% for Moderna, and 52% for Pfizer-BioNTech.
Digital health during COVID-19: lessons from operationalising new models of care in ophthalmology (2021)

The COVID-19 pandemic has resulted in massive disruptions within health care, both directly as a result of the infectious disease outbreak, and indirectly because of public health measures to mitigate against transmission. This disruption has caused rapid dynamic fluctuations in demand, capacity, and even contextual aspects of health care. Therefore, the traditional face-to-face patient-physician care model has had to be re-examined in many countries, with digital technology and new models of care being rapidly deployed to meet the various challenges of the pandemic. This Viewpoint highlights new models in ophthalmology that have adapted to incorporate digital health solutions such as telehealth, artificial intelligence decision support for triaging and clinical care, and home monitoring. These models can be operationalised for different clinical applications based on the technology, clinical need, demand from patients, and manpower availability, ranging from out-of-hospital models including the hub-andspoke pre-hospital model, to front-line models such as the inflow funnel model and monitoring models such as the so-called lighthouse model for provider-led monitoring. Lessons learnt from operationalising these models for ophthalmology in the context of COVID-19 are discussed, along with their relevance for other specialty domains.
ChemInform Abstract: Stereoselective Synthesis of F‐Alkyl α,β‐Unsaturated Esters and Their Epoxidation. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Empirical performance assessment using soft-core processors on reconfigurable hardware (2007)

Simulation has been the de facto standard method for performance evaluation of newly proposed ideas in computer architecture for many years. While simulation allows for theoretically arbitrary fidelity (at least to the level of cycle accuracy) as well as the ability to monitor the architecture without perturbing the execution itself, it suffers from low effective fidelity and long execution times.