gebhart/patrepeval huggingface dataset:
Fatty acid amide hydrolase as a potential therapeutic target for the treatment of pain and CNS disorders (2009)

BACKGROUND: Fatty acid amide hydrolase (FAAH) is an integral membrane enzyme that hydrolyzes the endocannabinoid anandamide and related amidated signaling lipids. Genetic or pharmacological inactivation of FAAH produces analgesic, anti-inflammatory, anxiolytic, and antidepressant phenotypes without showing the undesirable side effects of direct cannabinoid receptor agonists, indicating that FAAH may be a promising therapeutic target. OBJECTIVES: This review highlights advances in the development of FAAH inhibitors of different mechanistic classes and their in vivo efficacy. Also highlighted are advances in technology for the in vitro and in vivo selectivity assessment of FAAH inhibitors employing activity-based protein profiling (ABPP) and click chemistry-ABPP, respectively. Recent reports on structure-based drug design for human FAAH generated by protein engineering using interspecies active site conversion are also discussed. METHODS: The literature searches of Medline and SciFinder databases were used. CONCLUSIONS: There has been tremendous progress in our understanding in FAAH and development of FAAH inhibitors with in vivo efficacy, selectivity, and drug like pharmacokinetic properties.
Class 1 neural excitability, conventional synapses, weakly connected networks, and mathematical foundations of pulse-coupled models (1999)

Many scientists believe that all pulse-coupled neural networks are toy models that are far away from the biological reality. We show here, however, that a huge class of biophysically detailed and biologically plausible neural-network models can be transformed into a canonical pulse-coupled form by a piece-wise continuous, possibly noninvertible, change of variables. Such transformations exist when a network satisfies a number of conditions; e.g., it is weakly connected; the neurons are Class 1 excitable (i.e., they can generate action potentials with an arbitrary small frequency); and the synapses between neurons are conventional (i.e., axo-dendritic and axo-somatic). Thus, the difference between studying the pulse-coupled model and Hodgkin-Huxley-type neural networks is just a matter of a coordinate change. Therefore, any piece of information about the pulse-coupled model is valuable since it tells something about all weakly connected networks of Class 1 neurons. For example, we show that the pulse-coupled network of identical neurons does not synchronize in-phase. This confirms Ermentrout's result that weakly connected Class 1 neurons are difficult to synchronize, regardless of the equations that describe dynamics of each cell.
Is There a Relationship Between Patient-Reported Satisfaction and Persistence on Overactive Bladder Syndrome Pharmacotherapy? (2017)

Our study helps clarify the relationship between persistence on OAB medication and treatment satisfaction. We found that persistence could serve as a surrogate marker for patient satisfaction because those who reported being satisfied were more likely to persist on therapy at all study intervals.
Comparison of Ocular Wavefront Aberration Measurements Obtained Using Two Hartmann–Shack Wavefront Aberrometers (2022)

The Zernike coefficient values measured by the two aberrometers were well correlated in the control and KC groups. However, in eyes with KC, Aberrometer B tended to present greater values in several Zernike coefficients than Aberrometer A, suggesting that wavefront measurements obtained using the two aberrometers are not interchangeable in patients with KC.
Fast Evaluation of Retarded Electromagnetic Potentials for Quantum Calculations (2019)

A fast evaluation of retarded electromagnetic potentials is presented for quantum calculations on a uniform Cartesian grid. The induced potentials are incorporated into the quantum Hamiltonian of the time-dependent density functional theory (TDDFT) in real space. Both Lorentz and Coulomb gauge-fixed Hamiltonians are implemented using a real-time propagation scheme. The efficiency of the resulting formalism and implementation enables the evaluation of retardation effects on long carbon chains.
Abstract 3693: Small molecule microarray screens for inhibitors of oncogenic ETS factors (2010)

Abstract Members of the ETS transcription factors family are involved in many cancers and are often targeted by translocation events that result in oncogenic gene fusions or dysregulated ETS factor expression. For example, the vast majority of prostate cancers harbor translocations involving the ETS factors ERG, ETV1 and ETV4 (most commonly, these are fused to the TMPRSS2 androgen-regulated gene or other house keeping genes). Overexpression of ETS factor gene fusions can induce or sustain malignant characteristics of cancer cells such as survival or invasiveness. However transcription factors have often been deemed “undruggable” by conventional approaches. The focus of this project is to employ novel screening approaches to identify and characterize small molecules that are able to bind and modulate the biological function of oncogenic ETS factors. Toward this end, we have performed Small Molecule Microarray (SMM) screens that involve a total of 80,000 distinct small molecules spanning several categories, including diversity-oriented synthesis (DOS) products, natural products, and other biologically active chemotypes. The SMM screens identified six compound that selectively bind the ETS factor ETV1 with a stringent Zscore. Two of these compounds have shown inhibitory activity in an ETV1-specific promoter-induced luciferase system. Surface Plasmon Resonance analysis has confirmed that each of the two lead compounds binds ETV1 directly, with one compound showing submicromolar binding kinetics. This compound in particular was able to reduce the expression of several ETV1 downstream targets such as MMP1 and MMP7. These efforts suggest that we have identified novel small molecule “perturbagens” of ETV1, an oncogenic ETS transcription factor. More generally, our results suggest that SMM-based screens may offer a robust approach to identify novel compounds that bind and perturb the function of cancer-associated proteins deemed poorly “druggable” by conventional methods. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3693.
Genetic Causes of Familial Pituitary Adenomas (2011)

Pituitary adenomas are benign intracranial neoplasms and clinically apparent pituitary adenomas have a prevalence of approximately 1:1,000 individuals. They usually arise sporadically, but familial pituitary adenomas comprise about 5% of all cases, more than half of which include multiple endocrine neoplasia type 1 (MEN1) and Carney complex (CNC). The other half is represented by familial isolated pituitary adenomas (FIPA), a clinical entity described in the late 1990s. Recently, interest has been focused on the genetic pathophysiology of familial pituitary adenomas. MEN1 is due to mutations in MEN1 gene. CNC is related to PRKAR1A mutations and still unknown disruptions on 2p16. Mutations of CDKN1B in MEN1-like patients without MEN1 mutations allowed the differentiation of the condition as MEN4. About 15% of FIPA kindreds are associated with aryl hydrocarbon receptor-interacting protein (AIP) gene mutations, which suggests that this is a genetically heterogeneous condition. Overall, familial pituitary adenomas represent a small proportion of pituitary tumors, but are particularly significant as affected individuals may be younger, and adenomas may be relatively difficult to treat.
Evaluation of Insecticides for Control of Potato Leafhopper on Raspberry, 1989 (1990)

Abstract The experiment was conducted at the Rock Springs Research Farm. The study was laid out as a completely randomized design with 7 treatments each replicated 4 times. Treatments consisted of 5 plants, spaced 3 feet apart. Data were obtained from samples taken from the center section of plots. Each plot was rated for potato leafhopper damage on leaves. A toxicity index to assess damage was created on a scale of 0-3: 0 = no visible damage; 1 = 2% of leaves curled; 2 = 50%-75% of leaves curled; 3 = &amp;gt;75% of leaves curled. On 16 Jun, treatments were applied using a CO2 Precision Boom Sprayer that delivered 72 gal/acre at 35 psi. The spray boom was equipped with twin fan nozzles (T.J. 60-1104 vs). On 18 Jul treatments were applied using a Meyers Boom Sprayer that was adjusted to deliver 72 gal/acre traveling 3 mph. Treatments in parentheses were applied previously on 25 May.
An osteoconductive PLGA scaffold with bioactive β-TCP and anti-inflammatory Mg(OH)2 to improve in vivo bone regeneration (2019)

Poly(lactic-co-glycolic acid) (PLGA) has been widely used as a biomaterial for pharmaceutical and medical applications. However, the decomposition products of PLGA are known to acidify the surrounding tissue of the implanted site, causing an inflammatory response. Previously, we developed PLGA/inorganic nanocomposites and optimized the amounts of inorganic compounds, β-tricalcium phosphate (β-TCP) and magnesium hydroxide [Mg(OH)2], in terms of osteogenesis of normal human osteoblasts and anti-inflammatory responses of preosteoclastic cells in vitro. In this study, the potential of the optimized PLGA/β-TCP/Mg(OH)2 nanocomposite (TCP/MH) to promote bone repair through osteoinductive, osteoconductive, and anti-inflammatory abilities was assessed using a bone defect in a rat humeral defect model. PLGA nanocomposites with or without inorganic compounds, PLGA, β-TCP, MH, and TCP/MH were prepared through one-step bulk modification using a twin-screw extruder. The resulting TCP/MH nanocomposite successfully enhanced the bone regeneration rate for allowing complete bone defect healing with significantly suppressed inflammatory responses. Taken together, the organic and inorganic bioactive nanocomposite developed in this study, TCP/MH, is a promising material in orthopedic implantation.
Quantum-chemical modeling of smectite clays (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuantum-chemical modeling of smectite claysS. Aronowitz, L. Coyne, J. Lawless, and J. RishponCite this: Inorg. Chem. 1982, 21, 10, 3589–3593Publication Date (Print):October 1, 1982Publication History Published online1 May 2002Published inissue 1 October 1982https://pubs.acs.org/doi/10.1021/ic00140a003https://doi.org/10.1021/ic00140a003research-articleACS PublicationsRequest reuse permissionsArticle Views101Altmetric-Citations41LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Human Dynamics Modeling: The Digital Biomechanics Lab. (1998)

Abstract : Report developed under SBIR contract. This Phase I SBIR demonstrated a novel technique for physics-based simulation of realistic human behavior. The technique combines a control system that uses life-like motion recorded from live humans with versatile and rigorous physics-based simulation. The project demonstrated use of the technique in the context of human running at different speeds, with varying backpack loads and over varying terrain.
Modeling the impact of manufacturing imperfections on photonic crystal device performance: design of perturbation-tolerant PBG components (2004)

Standard perturbation theory (PT) and coupled mode theory (CMT) formulations fail or exhibit very slow convergence when applied to the analysis of geometrical variations in high index-contrast optical components such as Bragg fibers and photonic crystals waveguides. By formulating Maxwell's equations in perturbation matched curvilinear coordinates, we have derived several rigorous PT and CMT expansions that are applicable in the case of generic non-uniform dielectric profile perturbations in high index-contrast waveguides. In strong fiber tapers and fiber Bragg gratings we demonstrate that our formulation is accurate and rapidly converges to an exact result when used in a CMT framework even in the high index-contrast regime. We then apply our method to investigate the impact of hollow Bragg fiber ellipticity on its Polarization Mode Dispersion (PMD) characteristics for telecom applications. Correct PT expansions allowed us to design an efficient optimization code which we successfully applied to the design of dispersion compensating hollow Bragg fiber with optimized low PMD and very large dispersion parameter. We have also successfully extended this methodology to treat radiation scattering due to common geometric variations in generic photonic crystals. As an example, scattering analysis in strong 2D photonic crystal tapers is demonstrated.
Sampling schemes for reconstruction of multidimensional signals from multiple level threshold crossing (2003)

Two intermediate sampling schemes are developed which bridge the gap between Nyquist sampling and one-level crossing representation by enabling signals to be recovered from multiple-level threshold crossings. To this end, semi-implicit and implicit sampling strategies and their corresponding reconstruction algorithms are derived. A preliminary investigation of the quantization characteristics of some of the proposed sampling and reconstruction schemes, is included.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Optical data exchange of 100-Gbit/s DQPSK signals (2010)

We experimentally demonstrate the phase-transparent optical data exchange between two differential quadrature phase-shift keying (DQPSK) signals by exploiting the signal depletion effect of non-degenerate four-wave mixing (FWM) in a highly nonlinear fiber (HNLF). Identical phase modulation is applied to the two pumps to suppress the stimulated Brillouin scattering (SBS) effect and enable the pump phase cancellation in the exchanged signals. Optical data exchange of 100-Gbit/s return-to-zero DQPSK (RZ-DQPSK) signals is implemented with a power penalty of less than 5 dB at a bit-error rate (BER) of 10(-9). Moreover, we investigate the impact of the temporal pump phase misalignment on the exchange performance and the dynamic range of the input signal power for the 100-Gbit/s RZ-DQPSK data exchange. The tolerance of the temporal pump phase misalignment is assessed to be +/-2 ps. An approximate 20-dB dynamic range of the input signal power is achieved.
Use of Genetically Modified Phages to Deliver Suicidal Genes to Target Bacteria (2009)

This chapter contains sections titled: Introduction Lethal Agent Delivery Systems (LADS) Labeled Phages as Therapeutic Agents Avoiding the Host Immune Response Conclusion References
Single Amino Acid Substitutions in κ-Conotoxin PVIIA Disrupt Interaction with the Shaker K+ Channel (2000)

kappa-Conotoxin PVIIA (kappa-PVIIA), a 27-amino acid peptide with three disulfide cross-links, isolated from the venom of Conus purpurascens, is the first conopeptide shown to inhibit the Shaker K(+) channel (Terlau, H., Shon, K., Grilley, M., Stocker, M., Stühmer, W., and Olivera, B. M. (1996) Nature 381, 148-151). Recently, two groups independently determined the solution structure for kappa-PVIIA using NMR; although the structures reported were similar, two mutually exclusive models for the interaction of the peptide with the Shaker channel were proposed. We carried out a structure/function analysis of kappa-PVIIA, with alanine substitutions for all amino acids postulated to be key residues by both groups. Our data are consistent with the critical dyad model developed by Ménez and co-workers (Dauplais, M., Lecoq, A., Song, J. , Cotton, J., Jamin, N., Gilquin, B., Roumestand, C., Vita, C., de Medeiros, C., Rowan, E. G., Harvey, A. L., and Ménez, A. (1997) J. Biol. Chem. 272, 4802-4809) for polypeptide antagonists of K(+) channels. In the case of kappa-PVIIA, Lys(7) and Phe(9) are essential for activity as predicted by Savarin et al. (Savarin, P., Guenneugues, M., Gilquin, B., Lamthanh, H., Gasparini, S., Zinn-Justin, S., and Ménez, A. (1998) Biochemistry 37, 5407-5416); these workers also correctly predicted an important role for Lys(25). Thus, although kappa-conotoxin PVIIA has no obvious sequence homology to polypeptide toxins from other venomous animals that interact with voltage-gated K(+) channels, there may be convergent functional features in diverse K(+) channel polypeptide antagonists.
ChemInform Abstract: Elemental Fluorine. Part 22. Fluorination of 3β‐Acetoxy‐5α‐androstan‐17‐one Using Fluorine and Selectfluor®. (2009)

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 of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Adaptive motion coordination: Using velocity feedback to achieve parameter convergence (2008)

We study a coordination problem where the objective is to steer a group of agents to a formation that translates with a prescribed reference velocity. In [1] we considered the situation where the information of reference velocity is available only to a leader, and developed a decentralized adaptive design with which the other agents reconstruct the reference velocity. Although [1] guaranteed that the desired formation is achieved, it did not ensure parameter convergence. We now propose a new adaptive redesign, which incorporates relative velocity feedback in addition to relative position feedback, to guarantee parameter convergence.
Real-time face-priority auto focus for digital and cell-phone cameras (2008)

Auto-focus (AF) has been a key feature in consumer level digital and cell-phone cameras allowing users to focus automatically on a particular plane in a scene in order to get a sharp image. Face priority AF has become of interest lately due to the fact that most pictures captured by consumers are of human faces. In face-priority AF, the focusing decision is made based on a detected face area in the image, thus capturing a sharp picture of the face. While many face detection algorithms exist in the literature, very few of them are actually suitable for real-time software deployment on resource limited digital or cell-phone camera processors. In this paper, a fast face-detection algorithm is introduced by combining a skin color model cluster with a computationally efficient shape processing scheme. Comparison results with a standard algorithm in terms of robustness, speed and accuracy are provided. This face detection algorithm is incorporated into our previously developed rule-based AF method to achieve real-time face-priority AF on an actual digital camera platform.
Evidence for two electronic phases inY1−xLaxTiO3from thermoelectric and magnetic susceptibility measurements (2005)

Structural, transport, and magnetic measurements on nearly oxygen stoichiometric samples of the system ${\mathrm{Y}}_{1\ensuremath{-}x}{\mathrm{La}}_{x}{\mathrm{TiO}}_{3}$ and ${\mathrm{LuTiO}}_{3}$ have revealed that antiferromagnetic ${\mathrm{LaTiO}}_{3}$ is a $p$-type conductor with holes spread over more than 10 Ti-atom centers in itinerant-electron clusters having a motional enthalpy $\ensuremath{\Delta}{H}_{m}=0.035\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$. With the substitution of Y for La, short-range orbital-order fluctuations introduce ferromagnetic interatomic spin-spin interactions that increasingly reduce the magnitude of the Weiss constant $\ensuremath{\theta}$ and suppress ${T}_{\mathrm{N}}$ as $x$ decreases. The volume fraction of a localized-electron, orbitally ordered second phase containing small-polaron holes increases with decreasing $x&lt;0.6$ until it becomes the majority phase for $x\ensuremath{\leqslant}0.3$ with static orbital ordering below a temperature ${T\phantom{\rule{0.1em}{0ex}}}^{*}$ that increases as $x$ decreases. The volume fraction of the ferromagnetic phase does not reach unity at $x=0$, but it approaches unity in ${\mathrm{LuTiO}}_{3}$. Antiferromagnetic interactions across orbital-order antiphase interfaces lowers to zero the remanence of the ferromagnetic phase. The data appear to distinguish an itinerant-electron antiferromagnetism in the La-rich samples from a localized-electron ferromagnetic phase with a cooperative Jahn-Teller distortion.
A short water-filled pulse tube for the measurement of the acoustic properties of materials at low frequencies (1998)

A method of measuring the acoustic properties of materials at low frequencies in a water-filled pulse tube, which was a fraction of a wavelength long, was investigated. The method employed active sound cancellation at the end of the tube opposite from the sample, and signal processing of two hydrophone signals to separate the signal incident on the sample from its reflection. Two analytical models were developed and an experimental tube was built to examine the feasibility of such measurements. The results from the simulation and experiment suggest that the short water-filled pulse tube would be useful for measuring compliant materials at moderately low frequencies (down to 300 Hz), but not for measuring high impedance materials or for making measurements at very low frequencies. The simulation and experiment showed that the thicker the sample, relative to a wavelength, the lower the sensitivity to experimental errors. Fortunately, many of the materials of interest in underwater acoustics are compliant materials with relatively slow phase velocities and consequently shorter wavelengths. The impedance of the backing behind the sample also influences the sensitivity of results to errors in the measurements. [Work supported by ONR and NSF.]
Supplementary Table 1 from Genome-Wide CpG Island Profiling of Intraductal Papillary Mucinous Neoplasms of the Pancreas (2023)

&lt;p&gt;XLS file - 27K&lt;/p&gt;
SMCHD1 Promotes ATM-dependent DNA Damage Signaling and Repair of Uncapped Telomeres (2019)

Abstract SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing protein 1) has been implicated in X-chromosome inactivation, imprinting and DNA damage repair. Mutations in SMCHD1 can also cause facioscapulohumoral muscular dystrophy. More recently, SMCHD1 has also been detected as component of telomeric chromatin. Here, we identify requirements of SMCHD1 for DNA damage signaling and non-homologous end joining (NHEJ) at unprotected telomeres. Co-depletion of SMCHD1 with TRF2 reduced the rate of 3’ overhang removal in time course experiments and the number of telomere end fusions. In SMCHD1 deficient cells, the formation of ATM pS1981, γH2AX and 53BP1 containing telomere dysfunction induced foci (TIFs) were diminished indicating defects in checkpoint signaling. Strikingly, removal of TPP1 and subsequent activation of ATR signaling rescued telomere fusion events in TRF2-depleted SMCHD1 knockout cells. Together, these data indicate that SMCHD1 depletion reduces telomere fusions in TRF2-depleted cells due to defects in ATM-dependent DNA checkpoint signaling. SMCHD1 mediates DNA damage signaling activation upstream of ATM phosphorylation at uncapped telomeres.