gebhart/patrepeval huggingface dataset:
Blue Phosphorescence from Iridium(III) Complexes at Room Temperature (2006)

We report a new family of homoleptic iridium(III) complexes that emit blue phosphorescence at room temperature. The iridium(III) complexes are comprised of phenyltriazole ligands and were easily prepared via short synthetic routes. The parent fac-tris(1-methyl-5-phenyl-3-propyl-[1,2,4]triazolyl)iridium(III) complex exhibits blue photoluminescence (PL) with emission peaks at 449 and 479 nm and has a solution PL quantum yield of 66%. The emission was sequentially blue-shifted by the attachment of one and two fluorine atoms to the ligand phenyl ring with the fac-tris{1-methyl-5-(4,6-difluorophenyl)-3-propyl-[1,2,4]triazolyl}iridium(III) complex having the 1931 Commission Internationale de l'Eclairage coordinates of (0.16, 0.12) at room temperature. In contrast, when the phenyl ring of the ligands was substituted by trifluoromethyl, the PL spectrum was red-shifted when compared to the parent compound whereas if the trifluoromethyl group was attached to the triazole ring, the emission was blue-shifted. The radiative rates of these new blue iridium(III) complexes were found to be in the range of 2−6 × 105 s-1, indicating that the emission had varying amounts of metal-to-ligand charge-transfer character. Molecular orbital calculations showed that for the fluorinated complexes the contribution of the ligand triplet character to the emissive energy state increased with the hypsochromic shift in emission. This was confirmed by time-resolved PL measurements, which showed that the complex with the deepest blue emission had the slowest radiative decay rate.
Kinetic Exclusion Assay Technology: Characterization of Molecular Interactions (2004)

Characterization of intermolecular interactions in terms of affinity, binding kinetics, stoichiometry, specificity, and thermodynamics can facilitate the selection of lead compounds in the discovery and development of protein therapeutics. KinExA (Sapidyne Instruments, Inc., Boise, ID) is a relatively new technology that is gaining use in characterizing molecular interactions, particularly with respect to antibody therapeutics. KinExA offers a platform that allows the measurement of true equilibrium binding affinity and kinetics using unmodified molecules in solution phase. This is accomplished by using a solid-phase immobilized molecule to probe for free concentration of one interaction component after allowing sufficient time to reach equilibrium (affinity measurements), or under pre-equilibrium conditions (kinetics). In this review, the theory behind KinExA technology is discussed, and examples of applying this technology to antibody characterization are provided. Finally, a comparison among KinExA, Biacore (surface plasmon resonance), and isothermal titration calorimetry is presented, and potential future improvements and applications of KinExA are discussed.
Models for Evaluating Agents Intended for the Prophylaxis, Mitigation and Treatment of Radiation Injuries Report of an NCI Workshop, December 3–4, 2003 (2004)

To develop approaches to prophylaxis/protection, mitigation and treatment of radiation injuries, appropriate models are needed that integrate the complex events that occur in the radiation-exposed organism. While the spectrum of agents in clinical use or preclinical development is limited, new research findings promise improvements in survival after whole-body irradiation and reductions in the risk of adverse effects of radiotherapy. Approaches include agents that act on the initial radiochemical events, agents that prevent or reduce progression of radiation damage, and agents that facilitate recovery from radiation injuries. While the mechanisms of action for most of the agents with known efficacy are yet to be fully determined, many seem to be operating at the tissue, organ or whole animal level as well as the cellular level. Thus research on prophylaxis/protection, mitigation and treatment of radiation injuries will require studies in whole animal models. Discovery, development and delivery of effective radiation modulators will also require collaboration among researchers in diverse fields such as radiation biology, inflammation, physiology, toxicology, immunology, tissue injury, drug development and radiation oncology. Additional investment in training more scientists in radiation biology and in the research portfolio addressing radiological and nuclear terrorism would benefit the general population in case of a radiological terrorism event or a large-scale accidental event as well as benefit patients treated with radiation.
The high‐risk benign tumor: Evidence from the two‐stage skin cancer model and relevance for human cancer (2007)

Benign tumors that form following chemical initiation and promotion in the mouse skin can be grouped into two classes. The majority of papillomas do not progress to squamous cell carcinoma (SCC), and these are designated as low-risk or terminally benign papillomas. In contrast, a much smaller group forms the true precursor to the SCC, and these have a significantly higher frequency and rate of malignant conversion than the bulk of low-risk papillomas. In standard two-stage carcinogenesis studies both tumor types are present, but grossly indistinguishable. Here we describe properties and potential origins of high-risk papillomas and discuss the relevance of this model for certain human cancers with defined premalignant states.
Serum neurofilament light chain levels as a marker of upper motor neuron degeneration in patients with Amyotrophic Lateral Sclerosis (2018)

Altogether, these findings suggest that elevated serum NfL levels in ALS are driven by UMN degeneration and the disease progression rate and are independently associated with survival at time of diagnosis.
52.2: A Low‐Cost Stable Amorphous Silicon AMOLED Display with Full V T ‐ and V OLED Shift Compensation (2007)

Abstract We present a new simple and low cost pixel circuit and driving scheme for the a‐Si AMOLED displays using conventional AMLCD drivers. Measurement results show significant stability and high immunity to temperature and mobility variations which makes the pixel circuit and driving scheme attractive for implementation in different technologies. A 9‐inch a‐Si AMOLED display fabricated based on this driving scheme shows high uniformity and long lifetime.
Identification of optimal classification functions for biological sample and state discrimination from metabolic profiling data (2004)

The proposed discrimination methodology was applied to plasma and tissue (liver) metabolic profiling data describing the time progression of liver dysfunction in a rat model of acute hepatic failure generated by d-galactosamine (GalN) injection. From the plasma data, our methodology identified seven (out of a total of 23) metabolites, and the corresponding transform functions, as the best inputs to the optimal diagnostic index. This index showed better time resolution and increased noise robustness compared with an existing metabolic index, Fischer's BCAA/AAA molar ratio, as well as indexes generated using other commonly used discriminant analysis tools. Comparison of plasma and liver indexes found two consensus metabolites, lactate and glucose, which implicate glycolysis and/or gluconeogenesis in mediating the metabolic effects of GalN.
Design of Peptide-Based Prodrug Chemistry and Its Application to Glucagon-like Peptide I (2007)

Peptide-based drugs are highly effective medicines with relatively short duration of action and of variable therapeutic index. Glucagon-like peptide 1 is a hormone that offers promise in the treatment of Type II diabetes. However, the biggest problem in the therapeutic use of GLP-1 is its extremely short half-life in plasma (~2&#13;\nmin). A prodrug of GLP-1 should extend and improve the pharmacodynamics of this&#13;\npeptide hormone. We have designed prodrugs that slowly convert to the parent drug at&#13;\nphysiological conditions of 37C and pH 7.2 driven by their inherent chemical instability&#13;\nwithout the need of any enzymatic cleavage. We observed that amide prodrugs could not&#13;\nconvert to the active peptides under physiological conditions. Consequently, we decided to synthesize peptide drugs which had a hydroxy-terminal extension instead of a Nterminal amine. Ester prodrugs were prepared using these hydroxy-peptides as the&#13;\nscaffold. We explored the diketopiperazine and diketomorpholine (DKP and DMP) strategy for the chemical flexibility that it offers to develop prodrugs with variable time&#13;\nactions. The esters proved to be more labile than the corresponding amides and the&#13;\ndynamic range in rate of cleavage ranged from an hour to almost half a week. We found&#13;\nthat the rate of cleavage depends on the structure and stereochemistry of the dipeptide pro-moiety and also on the strength of the nucleophile. The careful selection of appropriate functionality that balances chemical, biological and immunological features under physiological conditions has also been reported.
Comparison of Hypotonic and Isotonic Solutions Containing Sodium Hyaluronate on the Symptomatic Treatment of Dry Eye Patients (2001)

This study was designed to compare the efficacy of two artificial tears both containing hyaluronic acid but differing in their osmolarity. A multicentric double-masked, crossover clinical trial was performed in which 158 subjects were randomized to receive either hypotonic or isotonic artificial tears up to 6 times a day. Both treatments were effective in improving signs and symptoms to a similar extent. No adverse events were reported. It was concluded that hypotonic and isotonic eye drops are comparable for the symptomatic treatment of patients suffering from dry eye syndrome.
An efficient system for selectively altering genetic information within mRNAs (2016)

Site-directed RNA editing (SDRE) is a strategy to precisely alter genetic information within mRNAs. By linking the catalytic domain of the RNA editing enzyme ADAR to an antisense guide RNA, specific adenosines can be converted to inosines, biological mimics for guanosine. Previously, we showed that a genetically encoded iteration of SDRE could target adenosines expressed in human cells, but not efficiently. Here we developed a reporter assay to quantify editing, and used it to improve our strategy. By enhancing the linkage between ADAR's catalytic domain and the guide RNA, and by introducing a mutation in the catalytic domain, the efficiency of converting a U A: G premature termination codon (PTC) to tryptophan (U G: G) was improved from ∼11 % to ∼70 %. Other PTCs were edited, but less efficiently. Numerous off-target edits were identified in the targeted mRNA, but not in randomly selected endogenous messages. Off-target edits could be eliminated by reducing the amount of guide RNA with a reduction in on-target editing. The catalytic rate of SDRE was compared with those for human ADARs on various substrates and found to be within an order of magnitude of most. These data underscore the promise of site-directed RNA editing as a therapeutic or experimental tool.
Enzymes containing porous polymersomes as nano reaction vessels for cascade reactions (2008)

Polystyrene(40)-b-poly(isocyanoalanine(2-thiophen-3-yl-ethyl)amide)(50) (PS-PIAT) polymersomes have the unique property of being sufficiently porous to allow diffusion of small (organic) substrates while retaining large biomolecules such as enzymes inside. Herein we report on the encapsulation and protection of glucose oxidase (GOx) and horse radish peroxidase (HRP) in PS-PIAT polymersomes and the successful employment of these functionalised nanoreactors in a cascade reaction. The demonstrated concept allows for further application in other enzymatic cascade reactions, bio-organic hybrid systems and biosensing devices.
Peptide Cross-Links in Bacterial Cell Wall Peptidoglycans Studied with Specific Endopeptidases from Streptomyces albus G (1966)

peer reviewed
The C Terminus of SNAP25 Is Essential for Ca2+-dependent Binding of Synaptotagmin to SNARE Complexes (2000)

The plasma membrane soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins syntaxin and synaptosome-associated protein of 25 kDa (SNAP25) and the vesicle SNARE protein vesicle-associated membrane protein (VAMP) are essential for a late Ca(2+)-dependent step in regulated exocytosis, but their precise roles and regulation by Ca(2+) are poorly understood. Botulinum neurotoxin (BoNT) E, a protease that cleaves SNAP25 at Arg(180)-Ile(181), completely inhibits this late step in PC12 cell membranes, whereas BoNT A, which cleaves SNAP25 at Gln(197)-Arg(198), is only partially inhibitory. The difference in toxin effectiveness was found to result from a reversal of BoNT A but not BoNT E inhibition by elevated Ca(2+) concentrations. BoNT A treatment essentially increased the Ca(2+) concentration required to activate exocytosis, which suggested a role for the C terminus of SNAP25 in the Ca(2+) regulation of exocytosis. Synaptotagmin, a proposed Ca(2+) sensor for exocytosis, was found to bind SNAP25 in a Ca(2+)-stimulated manner. Ca(2+)-dependent binding was abolished by BoNT E treatment, whereas BoNT A treatment increased the Ca(2+) concentration required for binding. The C terminus of SNAP25 was also essential for Ca(2+)-dependent synaptotagmin binding to SNAP25. syntaxin and SNAP25.syntaxin.VAMP SNARE complexes. These results clarify classical observations on the Ca(2+) reversal of BoNT A inhibition of neurosecretion, and they suggest that an essential role for the C terminus of SNAP25 in regulated exocytosis is to mediate Ca(2+)-dependent interactions between synaptotagmin and SNARE protein complexes.
Orientation and Microenvironment of Naphthalene Guest in the Host Nanoporous Phase of Syndiotactic Polystyrene (2005)

Syndiotactic polystyrene (s-PS) films including a fluorescent guest (naphthalene, NP) in their nanoporous δ crystalline phase have been prepared and characterized by X-ray diffraction, infrared linear dichroism, molecular modeling, and fluorescence depolarization techniques. A nearly perpendicular orientation of the fused rings of NP guest molecules with respect to the chain axis of the δ crystalline structure has been established by molecular mechanics and by evaluation of directions of transition moment vectors of infrared vibrational modes. The fluorescence depolarization is more efficient for NP guest molecules into the host phase than for NP molecules simply absorbed in the amorphous phase. This could be due to a more efficient resonance energy transfer between guest molecules, possibly associated with their ordered positioning and orientation into the host nanoporous polymeric crystallites.
[Inhibition of human laryngeal cancer Hep-2 cells by taxol]. (2003)

Taxol can block Hep-2 cells in G2/M, The induction of apoptosis Hep-2 cells by taxol was closely associated with mitotic arrest of cell cycle.
Chemical and Biological Investigation of the Polar Constituents of the Starfish Luidia clathrata, Collected in the Gulf of Mexico (1995)

Ten new [1-10] and three known [11-13] polyhydroxysteroids were isolated, along with four known asterosaponins [14-17], from the starfish Luidia clathrata, collected from the offshore waters of the northern Gulf of Mexico. The EtOH extracts of this starfish showed feeding-deterrent properties against marine fish, and inhibited the settlement of larvae of barnacles and bryozoans, as well as the growth of several bacteria. The structures of the new compounds were determined by interpretation of their nmr spectral data and by comparison with the spectral data of known compounds. The assignment of the configurations of the side-chain stereogenic centers of compounds 1 and 3-10 were based on the comparison of their nmr data with those of the stereoisomeric model compounds after derivatization with the chiral auxiliary MTPA reagent. Larval settlement assays conducted on ten isolated compounds revealed they are all potent inhibitors of settlement. Two of these isolated compounds inhibited the growth of several bacteria.
Experimental demonstration of ultra-low-power single polarization 56 Gb/s QAM-16 generation without DAC using CMOS photonics (2014)

We experimentally demonstrate back-to-back transmission of QAM-16 at 56 Gb/s over a single polarization, representing a dual polarization system link of 112 Gb/s, without using an electrical DAC, on a CMOS Photonics platform.
Physically-based mesh generation: automated triangulation of surfaces and volumes via bubble packing (1993)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1993.
Immunogenicity and Toxicity Testing of an Experimental HIV-1 Vaccine in Nonhuman Primates (1992)

A highly purified saponin from Q. saponaria (QS-21) was tested in juvenile rhesus macaques for adjuvant activity and toxicity. The QS-21 was tested alone or as part of an experimental subunit HIV-1 vaccine containing a truncated recombinant HIV-1 envelope protein (gp160D) adsorbed to alum. Antibody responses were measured using ELISA and cell-mediated immunity was measured using cellular proliferation assays. Potential toxicity was monitored by standard clinical pathology testing using peripheral blood and urine samples. No toxic effects were observed, even after the administration of the experimental vaccines three times at monthly intervals. The QS-21 saponin adjuvant enhanced total antibody production levels by greater than 100-fold and broadened the specificity of the response so that additional epitopes were recognized, when compared with alum-adsorbed HIV-1 gp160D formulation. Low-level, antigen-specific proliferative responses to HIV-1 recombinant gp160 were induced by either vaccine formulation. Proliferative responses were induced by a sham challenge with soluble recombinant HIV-1 gp160 for all of the animals that had been vaccinated. However, those that received the HIV-complete vaccine formulation containing QS-21 responded significantly better. These data demonstrated that the QS-21 adjuvant augmented both antibody responses and cell-mediated immunity and established immunological memory. The potent adjuvant activity and lack of toxicity suggest that this adjuvant should be safe and effective for use in HIV-1 vaccines.
Exploration on the mechanism of DNA adsorption on graphene and graphene oxide via molecular simulations (2015)

Several studies have shown that the fundamental principle of biosensors for DNA detection based on graphene oxide (GO) is the preferential adsorption of single-stranded DNA (ssDNA) over double-stranded DNA (dsDNA) on GO. However, the interactions between DNA and GO at the atomic level are poorly understood, and molecular dynamics (MD) simulation can be used to further explore these interactions. In the current study, we performed MD simulations to investigate the dynamic process of both ssDNA and dsDNA adsorption onto GO and pristine graphene (PG). We found that ssDNA was firmly adsorbed and lay flat on the surface of PG and GO, whereas dsDNA was preferentially oriented upright on both surfaces, resulting in weaker adsorption energies. Exploration of the mechanism of DNA segments binding to PG and GO indicated that π–π stacking interaction was the dominant force in the adsorption of DNA segments on PG, while both π–π stacking and hydrogen bonding contributed to the binding affinity between DNA segments and GO. These findings are of significant importance to the understanding of the interactions between DNA and GO, and the optimization of DNA and GO-based biosensors.
RASSF1A in maternal plasma as a molecular marker of preeclampsia (2013)

The study demonstrates potential use of cfDNA and cffDNA in maternal plasma as markers for the early prediction of women at risk for PE.
Drug Resistance and the Role of Combination Chemotherapy in Improving Patient Outcomes (2013)

Resistance to cancer chemotherapy is a common phenomenon especially in metastatic breast cancer (MBC), a setting in which patients typically have had exposure to multiple lines of prior therapy. The subsequent development of drug resistance can result in rapid disease progression during or shortly after completion of treatment. Moreover, cross-class multidrug resistance limits patient treatment choices, particularly in a setting where treatments options are few. One attempt to minimize the impact of drug resistance has been the concurrent use of two or more chemotherapy agents with unrelated mechanisms of action and differing modes of drug resistance, with the intent of blocking the development of multiple intracellular escape pathways essential for tumor survival. Within the past decade, an array of mechanistically diverse agents has augmented the list of combination regimens that may be both synergistic and efficacious in pretreated MBC. The aim of this paper is to review mechanisms of resistance to common chemotherapy agents and to consider current combination treatment options for heavily pretreated and/or drug-resistant patients with MBC.
Redesigning check‐processing operations using animated computer simulation (2000)

This paper describes the steps taken by a major commercial bank in the USA to redesign a critical function within its check‐processing operation. Animated simulation models of the current and new process were developed to understand the relationship between process parameters, waiting times, and productivity measures. We describe the animated simulation modeling approach in detail, present sample results and provide directions for further use of such an approach in banking.
Studies on the acid formation and deprotection reaction by novel sulfonates in a chemical amplification positive photoresist. (1990)

The novel photo-acid-generator tri(methanesulfonyloxy)benzene was investigated in a positive deep-UV resist, containing bisphenol A protected with t-butoxycarbonyl groups as inhibitor compound in a novolak matrix polymer. The deprotection reaction by the generated methanesulfonic acid was studied using UVspectroscopy and IR-spectroscopy. The amount of generated acid was determined by comparison with model films containing known amounts of methanesulfonic acid. The deprotection degree, the catalytic chain length of the deprotection reaction, and the quantum yield of the acid generation were determined. The amount of photogenerated acid was unexpectedly high, and the quantum yield was much higher than the theoretical maximum. No photosensitivity was observed in control experiments with model films in which the acid generator was mixed in cellulose acetate as a non-absorbing matrix polymer, whereas the addition of a phenol-type model compound to this formulation resulted in formation of acid after exposure to deep-UV light. This shows that the acid generator is sensitized by a phenolic resin. The sensitivity of the resist as a function of exposure wavelength was in good correlation with the absorption spectrum of the resist.
Learning and 1-bit Compressed Sensing under Asymmetric Noise (2016)

We study the approximate recovery problem: Given corrupted 1-bit measurements of the form sign(w^*⋅x_i), recover a vector w that is a good approximation to w^* ∈ R^d. This problem has been studied by both the learning theory and signal processing communities. In learning theory, this is known as the problem of learning halfspaces with noise, and in signal processing, as 1-bit compressed sensing, in which there is an additional assumption that w^* is t-sparse. The challenge in both cases is to design computationally efficient algorithms that are tolerant to large amounts of noise under realistic noise models. Furthermore, in the case of 1-bit compressed sensing, we require the number of measurements x_i to scale polynomially in t and only polylogarithmically in d, the ambient dimension. In this work, we introduce algorithms with nearly optimal guarantees for both problems under two realistic noise models, bounded (Massart) noise and adversarial (agnostic) noise, when the measurements x_i’s are drawn from any isotropic log-concave distribution. In bounded (Massart) noise, an adversary can flip the measurement of each point x with probability η(x)≤η