gebhart/patrepeval huggingface dataset:
Fructose Alters Intermediary Metabolism of Glucose in Human Adipocytes and Diverts Glucose to Serine Oxidation in the One–Carbon Cycle Energy Producing Pathway (2015)

Increased consumption of sugar and fructose as sweeteners has resulted in the utilization of fructose as an alternative metabolic fuel that may compete with glucose and alter its metabolism. To explore this, human Simpson-Golabi-Behmel Syndrome (SGBS) preadipocytes were differentiated to adipocytes in the presence of 0, 1, 2.5, 5 or 10 mM of fructose added to a medium containing 5 mM of glucose representing the normal blood glucose concentration. Targeted tracer [1,2-13C2]-d-glucose fate association approach was employed to examine the influence of fructose on the intermediary metabolism of glucose. Increasing concentrations of fructose robustly increased the oxidation of [1,2-13C2]-d-glucose to 13CO2 (p < 0.000001). However, glucose-derived 13CO2 negatively correlated with 13C labeled glutamate, 13C palmitate, and M+1 labeled lactate. These are strong markers of limited tricarboxylic acid (TCA) cycle, fatty acid synthesis, pentose cycle fluxes, substrate turnover and NAD+/NADP+ or ATP production from glucose via complete oxidation, indicating diminished mitochondrial energy metabolism. Contrarily, a positive correlation was observed between glucose-derived 13CO2 formed and 13C oleate and doses of fructose which indicate the elongation and desaturation of palmitate to oleate for storage. Collectively, these results suggest that fructose preferentially drives glucose through serine oxidation glycine cleavage (SOGC pathway) one-carbon cycle for NAD+/NADP+ production that is utilized in fructose-induced lipogenesis and storage in adipocytes.
Ultra-thin transition metal nitrides for tailorable plasmonic devices (Conference Presentation) (2018)

As a result of recent developments in nanofabrication techniques, the dimensions of metallic building blocks of plasmonic devices continue to shrink down to nanometer range thicknesses. The strong spatial confinement in atomically thin films is expected to lead to quantum and nonlocal effects, making ultra-thin films an ideal material platform to study light-matter interactions at the nanoscale. Most importantly, the optical and electronic properties of ultra-thin plasmonic films are expected to have a strong dependence on the film thickness, composition, strain, and local dielectric environment, as well as an increased sensitivity to external optical and electrical perturbations. Consequently, unlike their bulk counterparts which have properties that are challenging to tailor, the optical responses of atomically thin plasmonic materials can be engineered by precise control of their thickness, composition, and the electronic and structural properties of the substrate and superstrate. This unique tailorability establishes ultra-thin plasmonic films as an attractive material for the design of tailorable and dynamically switchable metasurfaces. While continuous ultra-thin films are very challenging to grow with noble metals, the epitaxial growth of TiN on lattice matched substrates such as MgO allows for the growth of smooth, continuous films down to 2 nm. In this study, we present both a theoretical and an experimental study of the dielectric function of ultrathin TiN films of varying thicknesses. The investigated ultrathin films remain highly metallic, with a carrier concentration on the order of 1022 /cm3 even in the thinnest film. Additionally, we demonstrate that the optical response can be engineered by controlling the thickness, strain, and oxidation. The observed plasmonic properties in combination with confinement effects introduce the potential of ultra-thin TiN films as a material platform for tailorable plasmonic metasurfaces.
A new method for parameter estimation in probabilistic models: Minimum probability flow (2020)

Fitting probabilistic models to data is often difficult, due to the general intractability of the partition function. We propose a new parameter fitting method, Minimum Probability Flow (MPF), which is applicable to any parametric model. We demonstrate parameter estimation using MPF in two cases: a continuous state space model, and an Ising spin glass. In the latter case it outperforms current techniques by at least an order of magnitude in convergence time with lower error in the recovered coupling parameters.
Role of 1-hydroxybenzotriazole in oxidation by laccase from Trametes versicolor. Kinetic analysis of the laccase-1-hydroxybenzotriazole couple (2006)

In the current studies, we used Lineweaver-Burke analysis to examine the role of 1-hydroxybenzotriazole (HBT) in the oxidation of various compounds by laccase from Trametes versicolor. At low concentrations, HBT was a competitive inhibitor of the oxidation, but at high concentrations, it was a noncompetitive inhibitor. Analysis of the oxidation of ferrocytochrome c by the laccase-HBT couple showed that increasing the concentration of ferrocytochrome c did not affect the V(max) but reduced the apparent K(m). In addition, in the manganese peroxidase-Mn(II) reaction, which is a typical oxidation system by mediator, the apparent K(m) and V(max) increased as the concentration of the substrate 2,6-dimethoxyphenol was increased. These results indicate that HBT is involved in the binding of laccase and substrates that laccase cannot oxidize alone.
Insights into the thermal and chemical stability of multilayered V2CTx MXene (2019)

We report on the thermal stability of multilayered V2CTx MXenes under different atmospheres by combining in situ Raman spectroscopy with ex situ X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and scanning electron microscopy (SEM) in order to elucidate and monitor the molecular, electronic, and structural changes of both the surface and bulk of the V2CTx MXene which has recently received much attention. The MXene samples were heated up to 600 °C in inert (N2), oxidative (CO2, air), and reductive (H2) environments under similar conditions. In situ Raman showed that the V[double bond, length as m-dash]O vibration for two-dimensional vanadia is preserved up to 600 °C under N2, while its intensity reduces under H2. When heated above 300 °C under either CO2 or air, V2CTx slightly oxidizes or transforms into V2O5, respectively. Furthermore, SEM revealed the presence of an accordion-like layered structure for the MXene under N2 and H2, while under CO2 and air the layered structure collapses and forms VO2 (V4+) and V2O5 (V5+) crystals, respectively. XPS reveals that, regardless of the gas, surface V species oxidize above 300 °C during the dehydration process. Finally, we demonstrated that the partial dehydration of V2CTx results in the partial oxidation of the material, and the total dehydration is achieved once 700 °C is reached. We believe that our methodology is a unique alternative to tune the dehydration, oxidation, and properties of V2CTx, which allows for the expansion of applications of MXenes.
Solid‐State Lithium/Selenium–Sulfur Chemistry Enabled via a Robust Solid‐Electrolyte Interphase (2018)

Abstract Lithium/selenium‐sulfur batteries have recently received considerable attention due to their relatively high specific capacities and high electronic conductivity. Different from the traditional encapsulation strategy for suppressing the shuttle effect, an alternative approach to directly bypass polysulfide/polyselenide formation via rational solid‐electrolyte interphase (SEI) design is demonstrated. It is found that the robust SEI layer that in situ forms during charge/discharge via interplay between rational cathode design and optimal electrolytes could enable solid‐state (de)lithiation chemistry for selenium‐sulfur cathodes. Hence, Se‐doped S 22.2 Se/Ketjenblack cathodes can attain a high reversible capacity with minimal shuttle effects during long‐term and high rate cycling. Moreover, the underlying solid‐state (de)lithiation mechanism, as evidenced by in situ 7 Li NMR and in operando synchrotron X‐ray probes, further extends the optimal sulfur confinement pore size to large mesopores and even macropores that have been long considered as inferior sulfur or selenium host materials, which play a crucial role in developing high volumetric energy density batteries. It is expected that the findings in this study will ignite more efforts to tailor the compositional/structure characteristics of the SEI layers and the related ionic transport across the interface by electrode structure, electrolyte solvent, and electrolyte additive screening.
Metalloporphyrin Hosts for Supramolecular Chemistry of Fullerenes (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
ChemInform Abstract: A Most User‐Friendly Protocol for Ring Closing Metathesis Reactions. (1999)

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.
Ganciclovir Inhibits Human Adenovirus Replication and Pathogenicity in Permissive Immunosuppressed Syrian Hamsters (2014)

Adenovirus infections of immunocompromised patients can develop into deadly multiorgan or systemic disease. The virus is especially threatening for pediatric allogeneic hematopoietic stem cell transplant recipients; according to some studies, 10% or more of these patients succumb to disease resulting from adenovirus infection. At present, there is no drug approved for the treatment or prevention of adenovirus infections. Compounds that are approved to treat other virus infections are used off-label to combat adenovirus, but only anecdotal evidence of the efficacy of these drugs exists. Ganciclovir, a drug approved for the treatment of herpesvirus infection, was previously reported to be effective against human adenoviruses in vitro. To model adenovirus infections in immunocompromised humans, we examined ganciclovir's efficacy in immunosuppressed Syrian hamsters intravenously infected with type 5 human adenovirus (Ad5). This animal model is permissive for Ad5 replication, and the animals develop symptoms similar to those seen in humans. We demonstrate that ganciclovir suppresses Ad5 replication in the liver of infected hamsters and that it mitigates the consequences of Ad5 infections in these animals when administered prophylactically or therapeutically. We show that ganciclovir inhibits Ad5 DNA synthesis and late gene expression. The mechanism of action for the drug is not clear; preliminary data suggest that it exerts its antiadenoviral effect by directly inhibiting the adenoviral DNA polymerase. While more extensive studies are required, we believe that ganciclovir is a promising drug candidate to treat adenovirus infections. Brincidofovir, a drug with proven activity against Ad5, was used as a positive control in the prophylactic experiment.
Capability of LiTaO3/Quartz HAL SAW Resonators Confirmed by Simulation and Measurement (2019)

This paper reports hetero acoustic layer (HAL) surface acoustic wave (SAW) resonators using a thin LiTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> (LT) plate with negative TCF and a quartz substrate with positive TCF. In the previous study, a high impedance (Z) ratio (82 dB), an excellent temperature coefficient of frequency (TCF: 2 ppm/°C), and spurious-free characteristic up to 14 GHz were demonstrated. In this study, two kinds of LT/ quartz HAL SAW resonators with different wavelengths of interdigital transducer (IDT) were fabricated, and measured results were compared with simulated ones. The measured bandwidths (BWs) roughly agreed with the simulated ones. Although many measured values of Z ratios are lower than the simulated ones, the best Z ratios among them are similar to the simulated ones. This result is reasonable taking account of the imperfectness of laboratory-level fabrication, and suggests that the simulation in this study well predicts the performance of real devices.
Preoperative assessment of ureteropelvic junction obstruction with endoluminal sonography and helical CT. (1997)

Our objective was to compare the value of endoluminal sonography with the value of helical CT in the preoperative assessment of crossing vessels in patients with ureteropelvic junction (UPJ) obstruction.Thirteen patients with UPJ obstruction underwent contrast-enhanced helical CT with multiplanar reformations and endoluminal sonography. Imaging preceded surgery for UPJ repair. On imaging, vessels were considered significant if greater than or equal to 2 mm in diameter and within 1 cm of the UPJ.Three patients had no crossing vessels revealed by either study. On sonography, another patient had a vessel revealed with a diameter that varied between 1.3 and 2.2 mm; on CT no correlate was detected. The remaining nine patients had vessels revealed by both techniques. On CT, four patients had two vessels revealed and five patients had single vessels revealed for a total of 13 vessels revealed by CT. On sonography, five patients had two vessels revealed and five patients had single vessels revealed. Thus, 15 vessels were revealed by sonography. Both arteries and veins were revealed anterior, posterior, and medial to the UPJ; no lateral vessels were seen. Four patients underwent laparoscopy, during which the absence, presence, and location of vessels were found to correlate with sonography and helical CT.Endoluminal sonography and helical CT were similar in revealing crossing vessels in patients with UPJ obstruction.
B Cell Recognition of the Conserved HIV-1 Co-Receptor Binding Site Is Altered by Endogenous Primate CD4 (2008)

The surface HIV-1 exterior envelope glycoprotein, gp120, binds to CD4 on the target cell surface to induce the co-receptor binding site on gp120 as the initial step in the entry process. The binding site is comprised of a highly conserved region on the gp120 core, as well as elements of the third variable region (V3). Antibodies against the co-receptor binding site are abundantly elicited during natural infection of humans, but the mechanism of elicitation has remained undefined. In this study, we investigate the requirements for elicitation of co-receptor binding site antibodies by inoculating rabbits, monkeys and human-CD4 transgenic (huCD4) rabbits with envelope glycoprotein (Env) trimers possessing high affinity for primate CD4. A cross-species comparison of the antibody responses showed that similar HIV-1 neutralization breadth was elicited by Env trimers in monkeys relative to wild-type (WT) rabbits. In contrast, antibodies against the co-receptor site on gp120 were elicited only in monkeys and huCD4 rabbits, but not in the WT rabbits. This was supported by the detection of high-titer co-receptor antibodies in all sera from a set derived from human volunteers inoculated with recombinant gp120. These findings strongly suggest that complexes between Env and (high-affinity) primate CD4 formed in vivo are responsible for the elicitation of the co-receptor-site-directed antibodies. They also imply that the naïve B cell receptor repertoire does not recognize the gp120 co-receptor site in the absence of CD4 and illustrate that conformational stabilization, imparted by primary receptor interaction, can alter the immunogenicity of a type 1 viral membrane protein.
Genome-wide association and functional studies identify the DOT1L gene to be involved in cartilage thickness and hip osteoarthritis (2012)

Hip osteoarthritis (HOA) is one of the most disabling and common joint disorders with a large genetic component that is, however, still ill-defined. To date, genome-wide association studies (GWAS) in osteoarthritis (OA) and specifically in HOA have yielded only few loci, which is partly explained by heterogeneity in the OA definition. Therefore, we here focused on radiographically measured joint-space width (JSW), a proxy for cartilage thickness and an important underlying intermediate trait for HOA. In a GWAS of 6,523 individuals on hip-JSW, we identified the G allele of rs12982744 on chromosome 19p13.3 to be associated with a 5% larger JSW (P = 4.8 × 10(-10)). The association was replicated in 4,442 individuals from three United Kingdom cohorts with an overall meta-analysis P value of 1.1 × 10(-11). The SNP was also strongly associated with a 12% reduced risk for HOA (P = 1 × 10(-4)). The SNP is located in the DOT1L gene, which is an evolutionarily conserved histone methyltransferase, recently identified as a potentially dedicated enzyme for Wnt target-gene activation in leukemia. Immunohistochemical staining of the DOT1L protein in mouse limbs supports a role for DOT1L in chondrogenic differentiation and adult articular cartilage. DOT1L is also expressed in OA articular chondrocytes. Silencing of Dot1l inhibited chondrogenesis in vitro. Dot1l knockdown reduces proteoglycan and collagen content, and mineralization during chondrogenesis. In the ATDC5 chondrogenesis model system, DOT1L interacts with TCF and Wnt signaling. These data are a further step to better understand the role of Wnt-signaling during chondrogenesis and cartilage homeostasis. DOT1L may represent a therapeutic target for OA.
Improving Interpretability of Deep Neural Networks with Semantic Information (2017)

Interpretability of deep neural networks (DNNs) is essential since it enables users to understand the overall strengths and weaknesses of the models, conveys an understanding of how the models will behave in the future, and how to diagnose and correct potential problems. However, it is challenging to reason about what a DNN actually does due to its opaque or black-box nature. To address this issue, we propose a novel technique to improve the interpretability of DNNs by leveraging the rich semantic information embedded in human descriptions. By concentrating on the video captioning task, we first extract a set of semantically meaningful topics from the human descriptions that cover a wide range of visual concepts, and integrate them into the model with an interpretive loss. We then propose a prediction difference maximization algorithm to interpret the learned features of each neuron. Experimental results demonstrate its effectiveness in video captioning using the interpretable features, which can also be transferred to video action recognition. By clearly understanding the learned features, users can easily revise false predictions via a human-in-the-loop procedure.
Surface characterization of tyrosine‐derived polycarbonates (1997)

The surfaces of five biodegradable tyrosine-derived polycarbonates were studied using contact angle measurements, ESCA, and static SIMS. The wettability, critical surface tension, and polarity of these polymers decreased with increasing chain length of the pendent alkyl groups. Surface elemental composition, as determined by ESCA, was consistent with the stoichiometry of the repeat unit of the polymers. High-resolution C1s, O1s, and N1s ESCA spectra also showed results consistent with the different bonding states of these elements in the polymer repeat unit. In both positive and negative ion spectra, SIMS experiments showed fragment ions characteristic of the polymer backbone. Fragment ions characteristic of the pendent groups were identified in the negative ion SIMS spectra only, while the positive SIMS spectra provided a characteristic fingerprint for each polymer. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 63: 1467–1479, 1997
Electronic approaches to restoration of sight (2016)

Retinal prostheses are a promising means for restoring sight to patients blinded by the gradual atrophy of photoreceptors due to retinal degeneration. They are designed to reintroduce information into the visual system by electrically stimulating surviving neurons in the retina. This review outlines the concepts and technologies behind two major approaches to retinal prosthetics: epiretinal and subretinal. We describe how the visual system responds to electrical stimulation. We highlight major differences between direct encoding of the retinal output with epiretinal stimulation, and network-mediated response with subretinal stimulation. We summarize results of pre-clinical evaluation of prosthetic visual functions in- and ex vivo, as well as the outcomes of current clinical trials of various retinal implants. We also briefly review alternative, non-electronic, approaches to restoration of sight to the blind, and conclude by suggesting some perspectives for future advancement in the field.
The Relation of Physical Activity to Cardiovascular Disease Risk Factors in Mauritians (1991)

The authors investigated the relation between physical activity and cardiovascular disease risk factors in a random sample of 4,658 Asian Indian, Creole, and Chinese adults aged 25-74 years from the island nation of Mauritius. Subjects known to have diabetes were excluded from analyses. Subjects were divided into "active" and "inactive" groups on the basis of a combined leisure and occupational physical activity score determined at interview (April 1987). Two-hour plasma glucose concentration and fasting and 2-hour serum insulin concentrations were significantly lower and high density lipoprotein (HDL) cholesterol was significantly higher in active subjects of both sexes. Plasma uric acid and fasting triglyceride levels were also lower among active subjects, but significantly so only in females. Systolic and diastolic blood pressure levels, body mass index (weight (kg)/height (m)2), and waist:hip ratio varied little between the two activity groups. In multiple linear regression analyses, physical activity made an independent negative contribution to the models for 2-hour glucose and insulin in both males and females, as well as for fasting insulin in males. When glucose and insulin were not included, physical activity also made an independent contribution to the models for plasma triglycerides (inversely) in females and HDL cholesterol and HDL cholesterol as a proportion of total cholesterol (positively) in males. The authors have demonstrated improved cardiovascular disease profiles associated with physical activity in Mauritians. The data suggest that much of the effect is modulated via an effect on insulin-glucose metabolism. Promotion of exercise should become an important strategy in the prevention of cardiovascular disease and glucose intolerance in this population.