gebhart/patrepeval huggingface dataset:
Molecular pharmacology and antitumor activity of palmarumycin-based inhibitors of thioredoxin reductase (2006)

The cytosolic thioredoxin redox system composed of thioredoxin-1 and the NADPH-dependent thioredoxin reductase-1 reductase is an important regulator of cell growth and survival. Thioredoxin-1 is overexpressed in many human tumors where it is associated with increased cell proliferation, decreased apoptosis, and decreased patient survival. We hypothesized that thioredoxin reductase-1 provides a target to inhibit the activity of overexpressed thioredoxin-1 for the development of novel anticancer agents. We found that the naphthoquinone spiroketal fungal metabolite palmarumycin CP1 is a potent inhibitor of thioredoxin reductase-1, but attempts to exploit the activity of palmarumycin CP1 analogues as antitumor agents in vivo were hampered by their insolubility. We have therefore developed PX-916, a water-soluble prodrug of a palmarumycin CP1 analogue. PX-916 rapidly releases the parent compound at physiologic pH and in plasma but is stable at acid pH, allowing its i.v. administration. PX-916 is a potent inhibitor of purified human thioredoxin reductase-1 and of thioredoxin reductase-1 activity in cells and tumor xenografts when given to mice and inhibits the downstream targets of thioredoxin-1 signaling, hypoxia-inducible factor-1alpha, and vascular endothelial growth factor in tumors. PX-916 showed excellent antitumor activity against several animal tumor models with some cures. Thus, the study shows that water-soluble inhibitors of thioredoxin reductase-1, such as PX-916, can block thioredoxin-1 signaling in tumors producing marked inhibition of tumor growth.
Revised Structure of Brevifoliol and Some Baccatin VI Derivatives (1993)

Brevifoliol and some baccatin VI derivatives have been shown to have a rearranged 11(15→1)abeo-taxane skeleton and not a taxane skeleton as originally reported, making abeo-taxanes an emerging major structural type of taxoids.
Portable high speed mid-IR spectrometer (2019)

The absorption spectra of mols. in the mid-IR (mid-IR) region are used for mol. anal., and the 5-15m wavelength range is sometimes called the fingerprint region, as it enables specific identification of mols. Mol. anal. using a mid-IR light source is typically performed using a Fourier-Transform IR Spectroscopy (FTIR) system. The delicate and complex optical alignment of such instruments limits the miniaturization of mid-IR spectrometers and increases the cost and size of the spectrometer. To solve this problem, we have developed a more robust spectrometer that combines a thermal imaging camera with a hyperspectral filter. This Fabry-Perot filter consists of two high-reflectivity Si/air mirrors that are assembled with a slight angle, so that the gradual change in the cavity gap between the two mirrors changes the resonant frequency of the filter. The variable filter disperses the broadband mid-IR light source to different frequencies, each assigned to a different pixel in the microbolometer array. The high refractive index contrast between silicon and air provides a large free spectral range, wide enough to cover a detection range of from 7 mm to 14 mm. By using a com.\nthermal imaging camera as detector and a Diesel engine glow plug as a source, we have demonstrated an inexpensive and robust spectrometer with no moving parts and rapid spectral acquisition. We present absorption spectra of various types of polymers, biomols. and drugs in the mid-IR region, obtained within 1 s, and compare these to spectra acquired with a conventional FTIR system.
Coumarin-derived discodermolide analogues possessing equivalent antiproliferative activity to the natural product—a further simplification of the lactone region (2007)

Analogues of discodermolide in which the complete C-1 to C-7 fragment is replaced with a coumarin moiety display equivalent potency to that of the natural product.
Two N-terminally truncated variants of human β-galactoside α2,6 sialyltransferase I with distinct properties for in vitro protein glycosylation (2016)

Sialic acid groups of protein N-glycans are important determinants of biological activity. Exposed at the end of the glycan chain, they are potential targets for glycan remodeling. Sialyltransferases (STs; EC 2.4.99) are the enzymes that catalyze the sialic acid transfer from a CMP-activated donor on to a carbohydrate acceptor in vivo. Recombinant expression of the full-length human β-galactoside α2,6 sialyltransferase I (ST6Gal-I) was hampered and therefore variants with truncated N-termini were investigated. We report on the distinct properties of two N-terminally truncated versions of ST6Gal-I, namely Δ89ST6Gal-I and Δ108ST6Gal-I, which were successfully expressed in human embryonic kidney cells. The different properties of these enzymes result most probably from the loss of interactions from helix α1 in the Δ108ST6Gal-I variant, which plays a role in acceptor substrate binding. The K<sub>m</sub> for N-acetyl-d-lactosamine was 10-fold increased for Δ108ST6Gal-I (84 mM) as compared to Δ89ST6Gal-I (8.3 mM). The two enzyme variants constitute a suitable tool box for the terminal modification of N-glycans. While the enzyme Δ89ST6Gal-I exhibited both ST (di-sialylation) and sialidase activity on a monoclonal antibody, the enzyme Δ108ST6Gal-I showed only ST activity with specificity for mono-sialylation.
Segmented multiple plane reconstruction: a novel approximate reconstruction scheme for multi-slice spiral CT (2002)

A new reconstruction scheme for multi-row spiral CT is described and results are presented. The spiral path is decomposed into small, overlapping segments which are used for a separate convolution and backprojection yielding a stack of segment images which contain only projection data of a partial scan (typically in the range of 20). These segment image stacks are, in a second step, reformatted to the requested image planes. In a third step, the reformatted segment images are added to obtain full images. The main benefit of the proposed algorithm is superior images quality. A 64-row dataset with a cone angle of 6.4 and a table feed of 80 mm per spiral turn has been reconstructed with excellent image quality. A filter direction for three-dimensional (3D) backprojection algorithms is suggested by investigating the limit where the partial scan size goes to zero.
Discovery of the First Histone Deacetylase 6/8 Dual Inhibitors (2013)

We disclose the first small molecule histone deacetylase (HDAC) inhibitor (3, BRD73954) capable of potently and selectively inhibiting both HDAC6 and HDAC8 despite the fact that these isoforms belong to distinct phylogenetic classes within the HDAC family of enzymes. Our data demonstrate that meta substituents of phenyl hydroxamic acids are readily accommodated upon binding to HDAC6 and, furthermore, are necessary for the potent inhibition of HDAC8.
A Re-examination of Tetrodotoxin for Prolonged Duration Local Anesthesia  (1998)

Combinations of epinephrine or bupivacaine with tetrodotoxin or with other high-potency toxins active on sodium channels should be examined for the potential to provide clinically useful, prolonged nerve blockade.
Prime-Boost Immunization with Adenoviral and Modified Vaccinia Virus Ankara Vectors Enhances the Durability and Polyfunctionality of Protective Malaria CD8 <sup>+</sup> T-Cell Responses (2009)

Protection against liver-stage malaria relies on the induction of high frequencies of antigen-specific CD8+ T cells. We have previously reported high protective levels against mouse malaria, albeit short-lived, by a single vaccination with adenoviral vectors coding for a liver-stage antigen (ME.TRAP). Here, we report that prime-boost regimens using modified vaccinia virus Ankara (MVA) and adenoviral vectors encoding ME.TRAP can enhance both short- and long-term sterile protection against malaria. Protection persisted for at least 6 months when simian adenoviruses AdCh63 and AdC9 were used as priming vectors. Kinetic analysis showed that the MVA boost made the adenoviral-primed T cells markedly more polyfunctional, with the number of gamma interferon (INF-gamma), tumor necrosis factor alpha (TNF-alpha), and interleukin-2 (IL-2) triple-positive and INF-gamma and TNF-alpha double-positive cells increasing over time, while INF-gamma single-positive cells declined with time. However, IFN-gamma production prevailed as the main immune correlate of protection, while neither an increase of polyfunctionality nor a high integrated mean fluorescence intensity (iMFI) correlated with protection. These data highlight the ability of optimized viral vector prime-boost regimens to generate more protective and sustained CD8+ T-cell responses, and our results encourage a more nuanced assessment of the importance of inducing polyfunctional CD8(+) T cells by vaccination.
Review on cochlear implant electrode array tip fold-over and scalar deviation (2019)

This literature review revealing the fact of higher rate of electrode insertion trauma associated with pre-curved electrode type irrespective of CI brand is one step closer to obsolete it from the clinical practice in the interest of patient's cochlear health.
Continuous wave 16 µm CF&lt;inf&gt;4&lt;/inf&gt;laser (1983)

A 16 μm CF <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</inf> laser oscillator has operated continuous wave in a cooled static cell. Pump powers required from the low-pressure continuous wave CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> laser were approximately 3 W. The laser cavity was a multiple-pass off-axis-path two-mirror ring resonator. Unidirectional CF <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</inf> laser power at 615 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> exceeded 2 mW. Rate equations were used to estimate scaling of this laser source. For modest pump powers (40 W) approximately 1 W of emission power is predicted from this small and simple system.
Detection and Quantification of Engineered Proanthocyanidins in Transgenic Plants (2007)

Proanthocyanidins (PAs) are oligomeric plant natural products mostly derived from epicatechin and/or catechin monomers. In studies aimed at engineering PAs into plant tissues that do not naturally make these compounds, we have expressed PA biosynthetic and regulatory genes in tobacco, alfalfa ( Medicago sativa) and the model legume Medicago truncatula. Because engineered tannins may be produced in small quantities and it is often necessary to screen many independent plant lines, we have developed an improved, highly sensitive method to quantify and determine the composition of oligomeric PAs in plant extracts. The method involves normal-phase HPLC separation of semi-purified PAs followed by post-column reaction with the PA-specific reagent DMACA (dimethylaminocinnamaldehyde). This procedure allows for accurate and sensitive quantification of individual oligomeric PAs and, unlike currently used methods, does not require exhaustive sample preparation and clean-up. Compositional data are shown for genetically engineered PAs in tobacco and alfalfa.
Design and Development of a Smart Exercise Bike for Motor Rehabilitation in Individuals With Parkinson's Disease (2015)

Recent studies in rehabilitation of Parkinson's disease (PD) have shown that cycling on a tandem bike at a high pedaling rate can reduce the symptoms of the disease. In this research, a smart motorized bicycle has been designed and built for assisting Parkinson's patients with exercise to improve motor function. The exercise bike can accurately control the rider's experience at an accelerated pedaling rate while capturing real-time test data. Here, the design and development of the electronics and hardware as well as the software and control algorithms are presented. Two control algorithms have been developed for the bike; one that implements an inertia load (static mode) and one that implements a speed reference (dynamic mode). In static mode the bike operates as a regular exercise bike with programmable resistance (load) that captures and records the required signals such as heart rate, cadence and power. In dynamic mode the bike operates at a user-selected speed (cadence) with programmable variability in speed that has been shown to be essential to achieving the desired motor performance benefits for PD patients. In addition, the flexible and extensible design of the bike permits readily changing the control algorithm and incorporating additional I/O as needed to provide a wide range of riding experiences. Furthermore, the network-enabled controller provides remote access to bike data during a riding session.
Cooperative Concatenated Coding for Wireless Systems (2007)

Cooperative transmission has been of growing interest recently where users take advantage of each other's resources for better overall performance. In this paper, coded cooperation for wireless networks is considered and a novel cooperative concatenated coding strategy is proposed. In contrast to previous works, this scheme features additional coding benefits other than spatial diversity. Specifically, we show that remarkable error rate reduction can be achieved even when the receive SNR of all cooperating users is maintained at a specific level. The idea of interleaver gain of concatenated codes is exploited and it is shown that the error rate decreases dramatically with the number of cooperating nodes. Multiple cooperating users with unequal message sizes can also be supported easily and a reduced-complexity cooperative encoding structure is provided for good inter-user channels. Code design criteria are also investigated, as well as, the performance under various data-block sizes and number of cooperating users.
Mitochondrial Imaging with Combined Fluorescence and Stimulated Raman Scattering Microscopy Using a Probe of the Aggregation-Induced Emission Characteristic (2017)

In vivo quantitative measurement of biodistribution plays a critical role in the drug/probe development and diagnosis/treatment process monitoring. In this work, we report a probe, named AIE-SRS-Mito, for imaging mitochondria in live cells via fluorescence (FL) and stimulated Raman scattering (SRS) imaging. The probe features an aggregation-induced emission (AIE) characteristic and possesses an enhanced alkyne Raman peak at 2223 cm<sup>-1</sup>. The dual-mode imaging of AIE-SRS-Mito for selective mitochondrion-targeting was examined on a homemade FL-SRS microscope system. The detection limit of the probe in the SRS imaging was estimated to be 8.5 μM. Due to the linear concentration dependence of SRS and inertness of the alkyne Raman signal to environmental changes, the intracellular distribution of the probe was studied, showing a local concentration of >2.0 mM in the mitochondria matrix, which was >100-fold higher than the incubation concentration. To the best of our knowledge, this is the first time that the local concentration of AIE molecules inside cells has been measured noninvasively and directly. Also, the nonquenching effect of such AIE molecules in cell imaging has been verified by the positive correlation of FL and SRS signals. Our work will encourage the utilization of SRS microscopy for quantitative characterization of FL probes or other nonfluorescent compounds in living biological systems and the development of FL-SRS dual-mode probes for specific biotargets.
Density-independent functions for on-line microwave moisture meters: a general discussion (1998)

Density-independent calibration functions are a suitable solution for problems involving variation of bulk density in on-line determination of the moisture content in particulate materials by microwave techniques. Foundations of three of these functions are briefly reviewed and their frequency and temperature dependences are shown for wheat. Their effectivenesses for prediction of the moisture content are compared and optimum conditions for a cost-effective moisture meter are discussed.
Rejuvenating senescent and centenarian human cells by reprogramming through the pluripotent state (2011)

Direct reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) provides a unique opportunity to derive patient-specific stem cells with potential applications in tissue replacement therapies and without the ethical concerns of human embryonic stem cells (hESCs). However, cellular senescence, which contributes to aging and restricted longevity, has been described as a barrier to the derivation of iPSCs. Here we demonstrate, using an optimized protocol, that cellular senescence is not a limit to reprogramming and that age-related cellular physiology is reversible. Thus, we show that our iPSCs generated from senescent and centenarian cells have reset telomere size, gene expression profiles, oxidative stress, and mitochondrial metabolism, and are indistinguishable from hESCs. Finally, we show that senescent and centenarian-derived pluripotent stem cells are able to redifferentiate into fully rejuvenated cells. These results provide new insights into iPSC technology and pave the way for regenerative medicine for aged patients.
An Alternate Geometry for a Piezoelectric MEMS Microphone, Part I: Design and Analysis (2007)

Microphones fabricated using microelectromechanical systems (MEMS) technology are one of the fastest growing applications of MEMS. While most commercial MEMS microphones are sensed capacitively, piezoelectric MEMS microphones require less accompanying electronics and offer increased linearity. Currently, piezoelectric MEMS microphones suffer from high noise levels, limiting their applicability. This paper presents an alternative sensor geometry consisting of a cantilever beam electrostatically clamped to the center of a diaphragm that both favorably concentrates stress from the applied acoustic load and eliminates the deleterious effects of residual stress in the piezoelectric material. A complete analysis of the sensitivity and noise characteristics of the electromechanical design (including the amplifying electronics) is performed and compared to a design employing a piezoelectric layer on a diaphragm. The analysis has shown that the proposed geometry can be used to build microphones sensed via aluminum nitride with noise levels around 48 dBA while similar materials and sizes result in noise levels around 57 dBA using the standard geometry.
Chemical Interaction-Guided, Metal-Free Growth of Large-Area Hexagonal Boron Nitride on Silicon-Based Substrates (2017)

Hexagonal boron nitride (h-BN) is an ideal platform for interfacing with two-dimensional (2D) nanomaterials to reduce carrier scattering for high-quality 2D electronics. However, scalable, transfer-free growth of hexagonal boron nitride (h-BN) remains a challenge. Currently, h-BN-based 2D heterostructures require exfoliation or chemical transfer of h-BN grown on metals resulting in small areas or significant interfacial impurities. Here, we demonstrate a surface-chemistry-influenced transfer-free growth of large-area, uniform, and smooth h-BN directly on silicon (Si)-based substrates, including Si, silicon nitride (Si<sub>3</sub>N<sub>4</sub>), and silicon dioxide (SiO<sub>2</sub>), via low-pressure chemical vapor deposition. The growth rates increase with substrate electronegativity, Si < Si<sub>3</sub>N<sub>4</sub> < SiO<sub>2</sub>, consistent with the adsorption rates calculated for the precursor molecules via atomistic molecular dynamics simulations. Under graphene with high grain density, this h-BN film acts as a polymer-free, planar-dielectric interface increasing carrier mobility by 3.5-fold attributed to reduced surface roughness and charged impurities. This single-step, chemical interaction guided, metal-free growth mechanism of h-BN for graphene heterostructures establishes a potential pathway for the design of complex and integrated 2D-heterostructured circuitry.
<title>Combined ellipsometer, reflectometer, scatterometer, and Kerr effect microscope for thin film disk characterization</title> (2000)

A new instrument has recently been developed for characterizing various properties of thin film magnetic disks. Since defects on thin film disks can take many forms, it is useful to combine many different optical detection techniques into a single tool. This greatly improves the chances of detecting a wide variety of defects, both topographic and non- topographic. The ellipsometer part of the instrument is used to measure the lubricant, carbon layers and organic contamination on thin film disks. The reflectometer is used to detect scratches, pits, particles, and texture angle. The scatterometer is used to detect particles, corrosion, and surface roughness. The Kerr effect microscope detects magnetic patterns on thin film disks and can be used as a replacement for ferrofluid marking of magnetic defects. The instrument also incorporates a built-in precision diamond scribe for marking defects. The theory of operation and the design of this instrument will be discussed. Examples will be given of the different types of defects and thin films that can be detected on thin film disks.
Proteomic Identification of Salivary Biomarkers of Type-2 Diabetes (2009)

The identification of biomarkers to noninvasively detect prediabetes/diabetes will facilitate interventions designed to prevent or delay progression to frank diabetes and its attendant complications. The purpose of this study was to characterize the human salivary proteome in type-2 diabetes to identify potential biomarkers of diabetes. Whole saliva from control and type-2 diabetic individuals was characterized by multidimensional liquid chromatography/tandem mass spectrometry (2D-LC-MS/MS). Label-free quantification was used to identify differentially abundant protein biomarkers. Selected potential biomarkers were then independently validated in saliva from control, diabetic, and prediabetic subjects by Western immunoblotting and ELISA. Characterization of the salivary proteome identified a total of 487 unique proteins. Approximately 33% of these have not been previously reported in human saliva. Of these, 65 demonstrated a greater than 2-fold difference in abundance between control and type-2 diabetes samples. A majority of the differentially abundant proteins belong to pathways regulating metabolism and immune response. Independent validation of a subset of potential biomarkers utilizing immunodetection confirmed their differential expression in type-2 diabetes, and analysis of prediabetic samples demonstrated a trend of relative increase in their abundance with progression from the prediabetic to the diabetic state. This comprehensive proteomic analysis of the human salivary proteome in type-2 diabetes provides the first global view of potential mechanisms perturbed in diabetic saliva and their utility in detection and monitoring of diabetes. Further characterization of these markers in a larger cohort of subjects may provide the basis for new, noninvasive tests for diabetes screening, detection, and monitoring.
Fast Lithium‐Ion Conducting Thin‐Film Electrolytes Integrated Directly on Flexible Substrates for High‐Power Solid‐State Batteries (2011)

By utilizing an equilibrium processing strategy that enables co-firing of oxides and base metals, a means to integrate the lithium-stable fast lithium-ion conductor lanthanum lithium tantalate directly with a thin copper foil current collector appropriate for a solid-state battery is presented. This resulting thin-film electrolyte possesses a room temperature lithium-ion conductivity of 1.5 × 10(-5) S cm(-1) , which has the potential to increase the power of a solid-state battery over current state of the art.