gebhart/patrepeval huggingface dataset:
Solution Structure and Functional Ligand Screening of HI0719, a Highly Conserved Protein from Bacteria to Humans in the YjgF/YER057c/UK114 Family, (2002)

HI0719 belongs to a large family of highly conserved proteins with no definitive molecular function and is found in organisms ranging from bacteria to humans. We describe the NMR structure of HI0719, the first solution structure for a member of this family. The overall fold is similar to the crystal structures of two homologues, YabJ from Bacillus subtilis and YjgF from Escherichia coli, and all three structures are similar to that of chorismate mutase, although there is little sequence homology and no apparent functional connection. HI0719 is a homotrimer with a distinct cavity located at the subunit interface. Six of the seven invariant residues in the high identity group of proteins are located in this cavity, suggesting that this may be a binding site for small molecules. Using previously published observations about the biological role of HI0719 family members as a guide, over 100 naturally occurring small molecules or structural analogues were screened for ligand binding using NMR spectroscopy. The targeted screening approach identified six compounds that bind to HI0719 at the putative active site. Five of these compounds are either α-keto acids or α,β-unsaturated acids, while the sixth compound is structurally similar. Previous studies have proposed that some HI0719 homologues may act on small molecules in the isoleucine biosynthetic path and, if this is correct, the ligand screening results presented here suggest that the interaction most likely occurs with 2-ketobutyrate and/or its unstable enamine precursor.
Balancing bulk gas accumulation and gas output before and during lava fountaining episodes at Mt. Etna (2015)

We focus on a sequence of 9 lava fountains from Etna that occurred in 2011, separated by intervals of 5 to 10 days. Continuous measurements allowed to discover the occurrence of gravity decreases before the onset of most fountaining episodes. We propose that the gravity changes are due to the pre-fountaining accumulation of a foam layer at shallow levels in the plumbing system of the volcano. Relying on the relationship between amount of gas trapped in the foam and amount of gas emitted during each episode, we develop a conceptual model of the mechanism controlling the passage from Strombolian to lava fountaining activity. Gas leakage from the foam layer during the late stages of its accumulation increases the gas volume fraction at upper levels, thus inducing a decrease of the magma-static pressure in the trapping zone and a further growth of the foam. This feedback mechanism eventually leads to the collapse of the foam layer and to the onset of lava fountaining. The possibility to detect the development of a foam layer at depth and to set quantitative constraints on the amount of trapped gas is important because of the implications for forecasting explosive eruptions and predicting their intensity.
Abstract 1347: The CAPAC Platform maximizes therapeutic benefit and reduces systemic cytotoxic exposure in small and large animals (2021)

Abstract The Click Activated Protodrugs Against Cancer (CAPACTM) platform aims to beat cancer without poisoning the body by activating powerful cancer therapies at the tumor site(s). CAPAC's mechanism of activation is based on click chemistry and is therefore agnostic to tumor characteristics, biomarker expression or other biological factors that vary across patients. This allows the CAPAC platform to be readily applicable to diverse tumor types. We describe the safety, pharmacokinetic and therapeutic benefits of SQ3370, the lead candidate of the CAPAC Platform, in small and large animals. SQ3370 consists of 2 components, SQL70 biopolymer and SQP33 protodrug. First, SQL70, a tetrazine-modified sodium hyaluronate biopolymer, is injected at the tumor site. Then, SQP33, a trans-cyclooctene (TCO)-modified protodrug of Doxorubicin (Dox) is given by IV infusion as 5 daily doses. The SQP33 protodrug has attenuated toxicity and is converted to active Dox by the SQL70 biopolymer at the tumor site through a highly efficient covalent reaction between tetrazine and TCO moieties. In mice, when administered in subcutaneous, intramuscular or intraperitoneal regions, around 50% of SQL70 was detectable after 2 weeks at the injection site. Biodistribution results suggested clearance of SQL70 by hepatic and renal routes. The MTD of SQ3370 in mice was nearly 20-times that of conventional Dox. Anti-tumor efficacy was evident even at 0.37x the MTD of SQ3370 suggesting that increasing the SQ3370 dosage to its MTD can maximize therapeutic benefit. Safety evaluation in 72 dogs that received either SQL70 biopolymer alone, SQP33 protodrug alone or both together (SQ3370) showed that all agents were well tolerated. The Highest Non-Severely Toxic Dose (HNSTD) of SQ3370 was 8.95 mg/kg/cycle in Dox Eq, at which dose there were minimal systemic adverse events and no evidence of cardiotoxicity. (The standard veterinary clinical dose for Dox in dogs is 1 mg/kg/cycle). The PK profiles in dogs demonstrated that SQL70 biopolymer efficiently captures the protodrug from circulation and releases active Dox. In conclusion, the CAPAC Platform represents a new therapeutic modality to treat solid tumors by using a drug with known efficacy, such as doxorubicin, and expanding its pharmacological capabilities. The CAPAC Platform enables higher concentrations of the active drug at the tumor site and minimizes systemic adverse effects associated with conventional chemotherapy. SQ3370 is currently being evaluated in a Phase I study in patients with advanced solid tumors (https://clinicaltrials.gov/ct2/show/NCT04106492). Citation Format: Sangeetha Srinivasan, Nathan A. Yee, Amir Mahmoodi, Michael Zakharian, M. Wayne Saville, Jose M. Mejia Oneto. The CAPAC Platform maximizes therapeutic benefit and reduces systemic cytotoxic exposure in small and large animals [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1347.
Transport-Limited Recombination of Photocarriers in Dye-Sensitized Nanocrystalline TiO2 Solar Cells (2003)

The effect of lithium intercalation on the transport dynamics and recombination kinetics in dye-sensitized nanoparticle TiO2 solar cells at lithium levels below 5 atom % was investigated by photocurrent and photovoltage transient and spectroelectrochemical techniques. Titanium dioxide films were doped electrochemically in the dark and under illumination. It was discovered that when Li+ is present in the electrolyte, lithium intercalates irreversibly into dye-sensitized TiO2 films at open circuit (ca. −0.7 V) under normal solar light intensities. Photocurrent transients of doped nonsensitized TiO2 films indicate that lithium doping decreases the diffusion coefficient of electrons through the nanoparticle network. Photocurrent and photovoltage transients of sensitized TiO2 films provide the first evidence that electron transport limits recombination with the redox electrolyte in working cells. As the Li density in the films increases, the diffusion and recombination times of photoelectrons increase proportionately, indicating a causal link between electron transport and recombination. The electron diffusion coefficient in dye-sensitized solar cells exhibits a power-law dependence on photocharge at all concentrations of inserted lithium in the TiO2 film. With increasing doping, the dependence of the electron diffusion coefficient on the photocharge becomes stronger, a phenomenon attributed to widening of the exponential conduction band tail resulting from disorder induced by randomly placed lithium defects in TiO2. The photovoltaic characteristics of dye-sensitized solar cells are largely unaffected by lithium intercalation, implying that intercalation has only a small effect on the charge collection efficiency and the rate of recombination. A simple model is presented that explains the observed transport-limited recombination. The results suggest that increasing the electron transport rate will not significantly improve the solar cell performance.
An on-demand shared tree with hybrid state for multicast routing in ad hoc mobile wireless networks (2003)

This paper describes the multicast shared tree protocol (MSTP) that has been designed to support the delivery of multicast packets in a mobile ad hoc network. MSTP uses a shared tree as its basic multicast infrastructure and, to maintain the tree against topology changes and network failures, it adopts the so called hybrid-state reliability mechanism, which combines the use of soft and hard state mechanisms applied to an on-demand scheme. It ensures fault tolerance and high group connectivity despite mobility, and provides a light-weight tree maintenance procedure.
Novel Approach to Minimizing Trocar Sites during Challenging Hand-Assisted Laparoscopic Surgery Utilizing the Gelport: Trans-Gel Instrument Insertion and Utilization (2003)

The Gelport permits simultaneous insertion of the surgeon's hand and a working laparoscopic instrument. This allows for maximally efficient utilization of the incision made for hand-assist device placement and may minimize the need for additional trocars during challenging laparoscopic cases.
Measurement and analysis of grip force during a golf shot (2008)

In this study, grip force was measured during a standard golf tee shot using two different measurement techniques. The first utilized a matrix-type thin-film sensor applied to a golf grip, from which total grip force could be readily determined. The second method involved 31 individual thin-film force sensors strategically placed on two golf gloves, allowing the force output of specific regions of the hands to be measured. Twenty golfers of varying ability participated in each test. The discovery of a unique grip force ‘signature’ for each golfer emerged from these data. That is, each golfer had a very repeatable total grip force trace, but these traces varied considerably between golfers. High-speed video was also recorded for many of the golfers tested so that key phases in the swing could be identified on the force traces.
Reduced-complexity wrap-around Viterbi algorithm for decoding tail-biting convolutional codes (2008)

Tail-biting convolutional codes (TBCC) are simple and powerful forward error correction (FEC) codes. They have been adopted as the FEC scheme for data and/or overhead channels in many wireless communications systems, including IS-54, EDGE, WiMAX and LTE. A convolutional code is called tail-biting (or circular) if the beginning state of its encoding trellis is always equal to the ending state after encoding. However, the circular state information is not available to the receiver. One important task in decoding TBCC is to estimate the circular state based on the received soft bit values. Many efficient algorithms have been proposed for decoding TBCC. Among them the wrap-around Viterbi algorithm (WAVA) provides near-ML (maximum likelihood) performances with the lowest complexity. In this paper, we propose several algorithms to further reduce the average number of decoding iterations and the memory usage in WAVA. Simulation results show that the complexity reduction from our proposed algorithms comes with no or almost negligible performance degradation.
Handwritten chinese character recognition using kernel active handwriting model (2004)

This paper describes a kernel active handwriting model (K-AHM) and its application to handwritten Chinese character recognition. In the model, the kernel principal component analysis is applied to capture nonlinear variations caused by handwriting, and a fitness function on the basis of a chamfer distance transform is introduced to search for optimal shape parameters using genetic algorithms (GAs). The K-AHM is applied to handwritten Chinese character recognition, which converts the complex pattern recognition problem into recognizing a small set of primitive structures called radicals. By treating Chinese character composition as a discrete-time Markov process, character composition is carried out with the Viterbi algorithm. The proposed methodology has been successfully implemented in an experimental recognition system.
Spatiotemporal computed tomography of dynamic processes (2011)

Modern computed tomography (CT) equipment allowing fast 3-D imaging also makes it possible to monitor dynamic processes by 4-D imaging. Because the acquisition time of various 3-D-CT systems is still in the range of at least milliseconds or even hours, depending on the detector system and the source, the balance of the desired temporal and spatial resolution must be adjusted. Furthermore, motion artifacts will occur, especially at high spatial resolution and longer measuring times. We propose two approaches based on nonsequential projection angle sequences allowing a convenient postacquisition balance of temporal and spatial resolution. Both strategies are compatible with existing instruments, needing only a simple reprograming of the angle list used for projection acquisition and care with the projection order list. Both approaches will reduce the impact of artifacts due to motion. The strategies are applied and validated with cold neutron imaging of water desorption from originally saturated particles during natural air-drying experiments and with x-ray tomography of a polymer blend heated during imaging.
ECCS/CIB Joint Committee on Sandwich Constructions: Recent European Recommendations on Design and Testing (2010)

Light-weight sandwich panels, made of two metal faces separated by an insulating core material, are modern pre-fabricated construction components. The design, manufacture and use of these composite structural elements have required continuous development of regulations and standards. The Joint Committee is the combination of two working groups; CIB W056 Lightweight constructions and ECCS TWG 7.9 Sandwich panels and related structures. It therefore provides a powerful forum for the consideration of international research and development of the design, testing and end-use of sandwich panels. This paper introduces the Joint Committee and its work by outlining its history and its most important publication, European Recommendation for sandwich panels. The significant influence of the Committee on the recently published European Product Standard EN 14509 is also described. Focus is then directed to the latest publications of the Joint Committee, namely the Preliminary European Recommendations for Testing and Design of fastenings for sandwich panels and the State of the art report for Design of Sandwich Panels with Openings. The latter is still under preparation and will probably be published in 2010.
Investigation of an Amide-Pseudo Amide Hydrogen Bonding Motif within a Series of Theophylline:Amide Cocrystals (2015)

The pharmaceutically active compound theophylline (T) was cocrystallized with the amides formamide (1), acetamide (2), N-methylformamide (3), N,N-dimethylformamide (4), benzamide (5), and pyrazinamide (6), with systems T:1, T:5, and T:6 displaying polymorphic behavior. The cocrystals with formamide (T:1), acetamide (T:2), and benzamide (T:5), and one polymorph of the cocrystal with pyrazinamide (T:6-I), contain an R22(9) hydrogen bonding motif between the amide cocrystal formers and the HN–C–C═O moiety of the theophylline molecule (an amide-pseudo amide synthon). This motif was, however, absent from the other polymorph of the pyrazinamide cocrystal (T:6-II) and also from the N-methylformamide cocrystal (T:3) (and is not possible in the N,N-dimethylformamide cocrystal (T:4)). These observations are rationalized using hydrogen bond propensity calculations, although limitations of using such calculations for predicting cocrystallization are noted. The amide-pseudo amide synthon is favored when theophylline cocrystallizes with both primary amides and with secondary amides which are locked in a cis configuration. On heating, all cocrystals were found to dissociate before melting due to loss of the amide, making stability to dissociation a more meaningful measure of cocrystal stability than melting point for these systems. On dissociation of the cocrystals, theophylline typically crystallizes as the commonly observed polymorph Form II. In the case of the acetamide cocrystal (T:2), however, the rarely observed metastable polymorph, Form V, crystallizes concomitantly with Form II suggesting that cocrystal dissociation on heating could be a strategy for identifying novel polymorphic forms of compounds.
Transgenic mice with green fluorescent protein-labeled pancreatic β-cells (2003)

We have generated transgenic mice that express green fluorescent protein (GFP) under the control of the mouse insulin I gene promoter (MIP). The MIP-GFP mice develop normally and are indistinguishable from control animals with respect to glucose tolerance and pancreatic insulin content. Histological studies showed that the MIP-GFP mice had normal islet architecture with coexpression of insulin and GFP in the beta-cells of all islets. We observed GFP expression in islets from embryonic day E13.5 through adulthood. Studies of beta-cell function revealed no difference in glucose-induced intracellular calcium mobilization between islets from transgenic and control animals. We prepared single-cell suspensions from both isolated islets and whole pancreas from MIP-GFP-transgenic mice and sorted the beta-cells by fluorescence-activated cell sorting based on their green fluorescence. These studies showed that 2.4 +/- 0.2% (n = 6) of the cells in the pancreas of newborn (P1) and 0.9 +/- 0.1% (n = 5) of 8-wk-old mice were beta-cells. The MIP-GFP-transgenic mouse may be a useful tool for studying beta-cell biology in normal and diabetic animals.
Electronic marking and identification techniques to discourage document copying (1995)

Modern computer networks make it possible to distribute documents quickly and economically by electronic means rather than by conventional paper means. However, the widespread adoption of electronic distribution of copyrighted material is currently impeded by the ease of unauthorized copying and dissemination. In this paper we propose techniques that discourage unauthorized distribution by embedding each document with a unique codeword. Our encoding techniques are indiscernible by readers, yet enable us to identify the sanctioned recipient of a document by examination of a recovered document. We propose three coding methods, describe one in detail, and present experimental results showing that our identification techniques are highly reliable, even after documents have been photocopied.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Petrol approach to high-level power estimation (2002)

High-level power estimation is essential for designing complex low-power ICs. However, the lack of flexibility, or restriction to synthesizable code of previously presented high-level power estimation approaches limits their use. In this paper we present a novel, more general and flexible high-level power estimation approach, that avoids these limitations. Petrol, as we call it, is not limited to specialized application domains, synthesizable VHDL, or data path parts of a design. We show that glitches can be usefully modeled at higher levels of abstraction. The Petrol approach shows good correlation with gate-level power estimates. It is currently used for commercial designs.
Immunohistochemical Investigations on Cerebellar Purkinje Cells of Menkes' Kinky Hair Disease: Disappearance of Inositol 1, 4, 5‐Triphosphate Receptor Protein, and Expression of Phosphorylated Neurofilament Proteins, αB‐Crystallin and Stress‐response Proteins (1993)

Immunohistochemical investigations were carried out on cerebellar Purkinje cells in patients with Menkes' kinky hair disease (MD) and normal control subjects (ages: 1–65 years). Six antibodies were used. They were specific to inositol 1,4,5‐triphosphate receptor protein regarded as P 400 (P 400 /IP 3 R), phosphorylated neurofilament proteins (pNFP), αB‐crystallin, stress‐response protein (srp) 72, srp 27 and ubiquitin, respectively. In normal brains, all Purkinje cell bodies, axons, and dendrites including the spiny branchlets of dendrites were positive for anti‐P 400 /IP 3 R antibody. In comparison, not every Purkinje cells in MD cases had P 400 /IP 3 R immunoreactivity. And some of the cells were more intensely stained than others. The immunoreaction products of P 400 /IP 3 R were frequently detected in cell bodies and proximal portions of the dendrites, but not in the peripheral dendrites including spiny branchlets. Most of the Purkinje cell bodies in MD reacted with anti‐pNFP antibody, while only a small fraction of the cells was positive with anti‐αB‐crystallin and srp 72 and srp 27. Ubiquitin immunoreactivity was not detected. In contrast, Purkinje cell bodies from normal subjects were not recognized by antibody to pNFP, αB‐crystallin, srp 72 and srp 27. Our results indicate that MD is associated with the loss of inositol 1,4,5‐triphosphate receptor in Purkinje cells, and an aberrant phosphorylation of neurofilament proteins or aberrant distribution of normal phosphorylated neurofilament proteins. These impairments may lead to the expression of stress response proteins or αB‐crystallin in some cells.
Stimuli‐Responsive Macromolecular Architecture by Butler Cyclopolymerizations: Synthesis and Applications (2022)

This article reviews the synthesis of polyzwitterions (PZs) (poly-carboxybetaines, -phosphonobetaines, and -sulfobetaines) having multiple pH-responsive centers. The synthesis follows the Butler cyclopolymerization protocol involving a multitude of diallylammonium salts and their copolymerization with SO<sub>2</sub> and maleic acid. The PZs have been transformed into cationic-, anionic-polyelectrolytes, and polyampholytes under the influence of pH. Particular attention is given to the application of these polymers as antiscalants, mild steel corrosion inhibitors, components in constructing Aqueous Two-Phase Systems (ATPSs), and membrane modifiers. The ATPSs could be used to separate various biomolecules, including proteins. Many amphiphilic polymers incorporating a few mol % hydrophobic monomers have shown enhanced viscosities and could be suitable for applications in oil fields. The progress of applying Butler cyclopolymerization in reversible addition-fragmentation chain transfer (RAFT) chemistry has been discussed. Future works are expected to focus on RAFT cyclopolymerization to construct block copolymers.
HOW COMPETITION DRIVES BUSINESS TO DISARRAY?? (2017)

This cannot be substituted with disruptive approach for the very reason of it being unsustainable.
Fiber Characterization Using Whispering Gallery Modes(Invited) (2019)

Fiber whispering gallery modes (WGMs) are surface waves that propagate azimuthally along the outer surface of the fiber cladding. Those waves that are in phase every turn give rise to narrow resonances defined by the resonant wavelength and a high Q factor. The actual values of the resonant wavelengths depend on the radius and the refractive index of the fiber cladding, enabling the development of several fiber characterization techniques. In addition, the typical high Q factor of these resonances (Q > 106) provides the characterization techniques with a low detection limit. Here, we report the development of a technique for measuring temperature profiles along the optical fiber, which enables the characterization of UV-induced absorption loss in photosensitive fibers, and a technique for the measurement of the elasto-optic coefficients and the anisotropy generated by the axial strain in standard fibers.