gebhart/patrepeval huggingface dataset:
3H-Pyrazolo[4,3-f]quinoline-Based Kinase Inhibitors Inhibit the Proliferation of Acute Myeloid Leukemia Cells In Vivo (2021)

The 3<i>H</i>-pyrazolo[4,3-<i>f</i>]quinoline moiety has been recently shown to be a privileged kinase inhibitor core with potent activities against acute myeloid leukemia (AML) cell lines in vitro. Herein, various 3<i>H</i>-pyrazolo[4,3-<i>f</i>]quinoline-containing compounds were rapidly assembled via the Doebner-Povarov multicomponent reaction from the readily available 5-aminoindazole, ketones, and heteroaromatic aldehydes in good yields. The most active compounds potently inhibit the recombinant FLT3 kinase and its mutant forms with nanomolar IC<sub>50</sub> values. Docking studies with the FLT3 kinase showed a type I binding mode, where the 3<i>H</i>-pyrazolo group interacts with Cys694 in the hinge region. The compounds blocked the proliferation of AML cell lines harboring oncogenic FLT3-ITD mutations with remarkable IC<sub>50</sub> values, which were comparable to the approved FLT3 inhibitor quizartinib. The compounds also inhibited the growth of leukemia in a mouse-disseminated AML model, and hence, the novel 3<i>H</i>-pyrazolo[4,3-<i>f</i>]quinoline-containing kinase inhibitors are potential lead compounds to develop into anticancer agents, especially for kinase-driven cancers.
Predicting CD137 upregulation on NK cells in patients receiving monoclonal antibody therapy (2015)

Meeting abstracts Monoclonal antibody (mAb) therapy-has changed the natural history of patients with B cell lymphomas, breast cancer, and head and neck cancers. However, response rates are suboptimal, highlighting the need to enhance mAb activity. Combining a tumor targeting mAb with a second
The Role of Soil Microbial Diversity in the Conservation of Native Seed Bacterial Microbiomes (2022)

Research into understanding the structure, composition and vertical transmission of crop seed microbiomes has intensified, although there is much less research into the seed microbiomes of crop wild relatives. Our previous study showed that the standard seed storage procedures (e.g., seed drying and storage temperature) can influence the seed microbiome of domesticated Glycine max. In this study, we characterized the seed microbiota of Glycine clandestina, a perennial wild relative of soybean (G. max (L.) Merr.) to expand our understanding about the effect of other storage procedures such as the periodic regeneration of seed stocks to bulk up seed numbers and secure viability on the seed microbiome of said seed. The G. clandestina microbiota was analysed from Generation 1 (G1) and Generation 2 (G2) seed and from mature plant organs grown in two different soil treatments T (treatment [native soil + potting mix]) and C (control [potting mix only]). Our dataset showed that soil microbiota had a strong influence on next generation seed microbiota, with an increased contribution of root microbiota by 90% and seed transmissibility by 36.3% in G2 (T) seed. Interestingly, the G2 seed microbiota primarily consisted of an initially low abundance of taxa present in G1 seed. Overall, our results indicate that seed regeneration can affect the seed microbiome composition and using native soil from the location of the source plant can enhance the conservation of the native seed microbiota.
Nanoscale assembly of silicon-like [Al(As1−xNx)]ySi5−2yalloys: Fundamental theoretical and experimental studies of structural and optical properties (2013)

Ab initio theoretical simulations of Al(As${}_{1\ensuremath{-}x}$N${}_{x}$)Si${}_{3}$ alloys, a new class of optoelectronic materials, confirm that these compounds are likely to be disordered via a mechanism that preserves the integrity of the constituent III-V-Si${}_{3}$ tetrahedra but randomizes their orientation in the average diamond lattice of the compound. This type of disorder is consistent with experimental structural data and with the proposed growth mechanism for such alloys, according to which ``III:V(SiH${}_{3}$)${}_{3}$'' intermediate complexes are formed in the gas phase from reactions between group-III atomic beams and V(SiH${}_{3}$)${}_{3}$ molecules, delivering the entire III-V-Si${}_{3}$ tetrahedra to the growing film. Experimental optical studies of these Al(As${}_{1\ensuremath{-}x}$N${}_{x}$)Si${}_{3}$ alloys as well as more general [Al(As${}_{1\ensuremath{-}x}$N${}_{x}$)]${}_{y}$Si${}_{5\ensuremath{-}2y}$ compounds grown on Si substrates were carried out using spectroscopic ellipsometry. The resulting dielectric functions are found to be similar to broadened versions of their counterparts in pure Si. This broadening may have important practical applications, particularly in photovoltaics, because it dramatically enhances the optical absorption of Si in the visible range of the electromagnetic spectrum. A critical point analysis reveals the existence of direct optical transitions at energies as low as 2.5 eV, well below the lowest direct absorption edge of Si at 3.3 eV. Such transitions are predicted theoretically for perfectly ordered III-V-Si${}_{3}$ compounds, and the experimental results suggest that they are robust against tetrahedra orientational disorder.
Unconventional Nanotechnology-Based Tracers for Drilling and Completion Applications (2020)

Tracer technology is a very efficient diagnostic tool in the oil and gas industry to obtain valuable information about reservoirs. The interpretation of tracers that have traversed the reservoir reveals characteristics such as inter-well connections, heterogeneities, and water movements that can be used to improve hydrocarbon recovery efforts. A strong need exists for tracers that can withstand increasingly harsh reservoir conditions such as high pressure, high temperature, high salinity and sour environments. Recent progress in nanotechnology and developments in nanoparticle synthesis and engineering bring possibilities for tracer applications. This paper discusses a unique approach towards unconventional properties shown by nanoparticle tracers.
[Small bowel malignancies: why are they so rare?]. (2004)

Cancer of the small-bowel is rare and comprises 2.4% of gastrointestinal malignancies. This is despite of its large mucosal surface area and its location between the stomach and the large bowel, two of the most common cancer sites. Nevertheless, there is a similarity between the disease and colorectal cancer. Therefore, it is of great interest to study the protective mechanisms of this organ and how tumor arises when these protectors fail. Among the risk factors for small bowel malignancies are Inflammatory Bowel Disease (IBD), familial syndromes, and lifestyle parameters (alcohol consumption, smoking, and high fat and animal protein diet). Due to the unusual symptoms, the rarity of the disease, and the difficulty in small bowel imaging, a correct diagnosis is often delayed. The treatment of choice, which allows full recovery, as in other malignancies of the gastrointestinal tract, is surgical resection of the tumor.
Reliable energy-efficient spectrum management and optimization in cognitive radio networks: how often should we switch? (2013)

Spectrum handoff is a promising spectrum management approach that enables the secondary user to continue its transmission by switching to a sensed-as-idle channel when the current channel is re-occupied by the primary user. Periodic sensing is commonly employed to facilitate spectrum handoff by improving sensing accuracy so that the secondary user has a better opportunity to avoid transmission collision via switching to a truly idle channel. However, byproducts of spectrum handoff, such as extra energy cost on channel switch, switch delay, and collisions due to excessive switch, have been largely underestimated. These by-products which have significant impacts on the overall performance lead to the questions: Should we switch the channel? How often should we switch? In this article we first review several different periodic sensing and handoff mechanisms. Then we identify the trade-off between the secondary user's energy efficiency and transmission reliability. The proposed switch-stay model is elaborated and studied to balance the aforementioned trade-off in light of sensing accuracy, the probability of collision, throughput and delay constraints. Upper and lower bounds of the stay probability on the current channel are illustrated from these constraints. In addition, we discuss the implementation of an antenna-selection sensing mechanism in order to relax these bounds for a better energy-efficient spectrum management solution. Performance evaluation and some open issues are also discussed in this article.
A Unique Industrial – Academic Collaboration Towards the Next Generation of Schizophrenia Therapeutics (2014)

This article describes the unique industrial-academic collaboration that has been running for four years between Janssen Pharmaceutica NV and the Vanderbilt Center for Neuroscience Drug Discovery (VCNDD) towards identifying the next generation of schizophrenia therapeutics. This was a true collaboration, with both entities engaged in chemistry, In vitro pharmacology, DMPK and In vivo behavioral pharmacology, and aligned to deliver a first-in-class clinical candidate (NME) and additional back-up molecules. Notably, a first NME was delivered in a rapid timeframe and targeted the novel mechanism of mGlu5 positive allosteric modulation. As with any true collaboration, both sides brought unique skills to the table--Janssen leveraged deep drug discovery expertise and infrastructure, while Vanderbilt brought deep knowledge of the chemistry and pharmacology of the target in addition to the ability to provide deep scientific insight into the mechanism behind target modulation. In this article, we will discuss the science which drove our collaboration as well as some key lessons learned.
Liprin &alpha;1 interacts with PP2A B56&gamma; (2008)

Inhibition of the protein phosphatase 2A (PP2A) family of serine-threonine phosphatases contributes to human cell transformation. Depletion of PP2A complexes containing the PP2A B56gamma regulatory subunit in immortalized human cells induces cell transformation in vitro. To examine the function of PP2A B56gamma complexes, we applied tandem affinity purification and mass spectrometry to detect proteins that bind to PP2A B56gamma. We identified liprin alpha1 as a novel PP2A B56gamma interacting protein. B56gamma-liprin alpha1 complexes are distinct from PP2A complexes containing B56gamma. Consistent with this finding, liprin alpha1 does not directly contribute to cell transformation. However, suppression of liprin alpha1 by RNA interference alters cell morphology. These findings suggest a novel role for PP2A B56gamma independent of its regulation of PP2A activity.
Organotypic culture in three dimensions prevents radiation-induced transformation in human lung epithelial cells (2016)

The effects of radiation in two-dimensional (2D) cell culture conditions may not recapitulate tissue responses as modeled in three-dimensional (3D) organotypic culture. In this study, we determined if the frequency of radiation-induced transformation and cancer progression differed in 3D compared to 2D culture. Telomerase immortalized human bronchial epithelial cells (HBECs) with shTP53 and mutant KRas expression were exposed to various types of radiation (gamma, (+)H, (56)Fe) in either 2D or 3D culture. After irradiation, 3D structures were dissociated and passaged as a monolayer followed by measurement of transformation, cell growth and expression analysis. Cells irradiated in 3D produced significantly fewer and smaller colonies in soft agar than their 2D-irradiated counterparts (gamma P = 0.0004; (+)H P = 0.049; (56)Fe P < 0.0001). The cell culture conditions did not affect cell killing, the ability of cells to survive in a colony formation assay, and proliferation rates after radiation-implying there was no selection against cells in or dissociated from 3D conditions. However, DNA damage repair and apoptosis markers were increased in 2D cells compared to 3D cells after radiation. Ideally, expanding the utility of 3D culture will allow for a better understanding of the biological consequences of radiation exposure.
From Meta I to Meta II (2006)

Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text A. Z. Genack and V. Shalaev, "From Meta I to Meta II," in Photonic Metamaterials: From Random to Periodic, Technical Dgest (CD) (Optical Society of America, 2006), paper ThE4. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Conformations and Photophysics of a Stilbene Dimer (2003)

Photophysical studies of pseudo-p-distyryl[2.2]paracyclophane, a model molecule of a stilbene dimer arranged in a brick-wall geometry, in tetrahydrofurane solution indicate the existence of at least two conformers in the ground state. The conformer A with the smallest optical gap of 3 eV has a short radiative lifetime of 3.3 ns, while the conformer B with an optical gap about 0.3 eV larger is much more abundant in solution and its radiative lifetime is about 10 times longer. Ab initio calculations show that the ground-state energy has a shallow minimum with respect to the torsional angle between the styryl side group and the paracyclophane core around the zero position, with the lowest energy conformation at a torsional angle of −21°. On this basis, A and B are assigned to flat and twisted conformations, respectively. Conformer B shows a partial decay of excited-state absorption and fluorescence with a time constant ranging from 5 to 30 ps, depending on excitation photon energy. We attribute this to isomerization of the stilbene moiety, which initially keeps conjugation in the ground state. The isomerization product is long-lived and tends to accumulate in solution.
Association of Variants in BAG3 With Cardiomyopathy Outcomes in African American Individuals (2018)

This study demonstrates that genetic variants in BAG3 found almost exclusively in individuals of African ancestry were not causative of disease but were associated with a negative outcome in patients with a dilated cardiomyopathy through modulation of the function of BAG3. The results emphasize the importance of biological differences in causing phenotypic variance across diverse patient populations, the need to include diverse populations in genetic cohorts, and the importance of determining the pathogenicity of genetic variants.
Optimized flow allocation for anonymous communication in multipath wireless networks (2012)

In anonymous networks, a subset of nodes is chosen to act as covert relays to hide timing information from unauthorized observers. While such covert relays increase anonymity, they cause performance degradation by delaying or dropping packets. In this paper, we propose flow allocation methods that maximize anonymity for multipath wireless networks with predetermined covert relay nodes, while taking into account packet-loss as a constraint. Using a rate-distortion framework, we show how to assign probabilities which split the flows from source to destination among all possible routes and show that selecting routes according to the assigned probabilities achieves maximum anonymity given the packet-loss constraint.
An Opportunistic Promoter Sharing Regulatory Sequences with either a Muscle-Specific or a Ubiquitous Promoter in the Human Aldolase A Gene (1993)

The human aldolase A gene is transcribed from three different promoters, pN, pM, and pH, all of which are clustered within a small 1.6-kbp DNA domain. pM, which is highly specific to adult skeletal muscle, lies in between pN and pH, which are ubiquitous but particularly active in heart and skeletal muscle. A ubiquitous enhancer, located just upstream of pH start sites, is necessary for the activity of both pH and pN in transient transfection assays. Using transgenic mice, we studied the sequence controlling the muscle-specific promoter pM and the relations between the three promoters and the ubiquitous enhancer. A 4.3-kbp fragment containing the three promoters and the ubiquitous enhancer showed an expression pattern consistent with that known in humans. In addition, while pH was active in both fast and slow skeletal muscles, pM was active only in fast muscle. pM activity was unaltered by the deletion of a 1.8-kbp region containing the ubiquitous enhancer and the pH promoter, whereas pN remained active only in fast skeletal muscle. These findings suggest that in fast skeletal muscle, a tissue-specific enhancer was acting on both pN and pM, whereas in other tissues, the ubiquitous enhancer was necessary for pN activity. Finally, a 2.6-kbp region containing the ubiquitous enhancer and only the pH promoter was sufficient to bring about high-level expression of pH in cardiac and skeletal muscle. Thus, while pH and pM function independently of each other, pN, remarkably, shares regulatory elements with each of them, depending on the tissue. Importantly, expression of the transgenes was independent of the integration site, as originally described for transgenes containing the beta-globin locus control region.
Understanding Human Behaviors in Crowds by Imitating the Decision-Making Process (2018)

Crowd behavior understanding is crucial yet challenging across a wide range of applications, since crowd behavior is inherently determined by a sequential decision-making process based on various factors, such as the pedestrians' own destinations, interaction with nearby pedestrians and anticipation of upcoming events. In this paper, we propose a novel framework of Social-Aware Generative Adversarial Imitation Learning (SA-GAIL) to mimic the underlying decision-making process of pedestrians in crowds. Specifically, we infer the latent factors of human decision-making process in an unsupervised manner by extending the Generative Adversarial Imitation Learning framework to anticipate future paths of pedestrians. Different factors of human decision making are disentangled with mutual information maximization, with the process modeled by collision avoidance regularization and Social-Aware LSTMs. Experimental results demonstrate the potential of our framework in disentangling the latent decision-making factors of pedestrians and stronger abilities in predicting future trajectories.
Low loss multilayer frequency selective surface NIMs for the Mid-IR: Modeling, synthesis and characterization (2010)

Over the last few years there has been increasing interest in metamaterials research because of the exciting applications made possible by refractive index engineering. Negative index materials (NIMs) were first theorized in 1968 by Veselago, who predicted that a material possessing simultaneously negative permittivity ε and permeability μ would exhibit novel properties, including backward-propagating waves, near-field focusing, and a modified Snell's law. Pendry's more recent recognition that a flat slab of material with n = -1 could be used as a "perfect lens", started a drive to experimentally demonstrate NIMs from the RF regime through optical wavelengths. However, many NIM experiments have suffered from high absorption and impedance mismatch losses, and most optical NIMs have been very thin with respect to the wavelength, reducing their utility in practical devices. We have previously reported our use of a flexible architecture based on periodic arrays of subwavelength metallo-dielectric structures coupled with genetic algorithm (GA) optimization to minimize the losses inherent in NIMs. We have also investigated optimizing larger metallo-dielectric stacks in order to realize practical, volumetric NIMs. In this paper, we describe our progress in modeling the response of two-layer metallo-dielectric NIMs as well as designing, fabricating and characterizing two-layer metallo-dielectric NIMs for the mid-IR.
ChemInform Abstract: Hydrophobic, Regiospecific Guest Binding by Transition‐Metal Host Complexes Having Permanent Voids as Revealed by FT‐NMR Relaxation Studies. (1986)

Abstract Adetailed study of the host‐guest complexation behaviour of the vaulted cyclidene Complexes (I) is presented.
Accounting for the effects of widespread discrete clutter in subsurface EMI remote sensing of metallic objects (2005)

In practice, most signal processing strategies for discrimination of buried objects are clutter limited. This applies even to discrimination of shallow sizable metallic objects, such as unexploded ordnance (UXO), which are to be found predominantly in the top meter of soil. The environment typically features widespread metallic clutter from detonated ordnance or other sources. Such fragments can be numerous and are often shallower than the objects of interest. Currently, the preeminent remote sensing mode for buried UXO is ultrawideband electromagnetic induction (EMI), operating over part or all of the band from some tens of hertz up to perhaps hundreds of kilohertz. Particularly because EMI fields fall off sharply with range, signals from shallow clutter may be relatively strong and can easily obscure essential scatterer signatures. To treat this, a rational theory of EMI scattering from widespread metallic clutter is formulated and tested. For dense, well-distributed clutter, analytical rules are derived for dependence of signal strength on sensor elevation, under various fundamental excitation types. For more erratic, sparse clutter distributions, signal statistics from Monte Carlo simulations show patterns like those from the analytical rules. The dependence of clutter signal magnitude on antenna elevation is determined for both thin surface layers and for volume layers of widespread small items, and for both dense and sparse clutter distributions. These are contrasted with the patterns expected from single, larger, discrete objects of interest, and the contrast is exploited in discrimination exercises for the screening problem. For sparse clutter distributions, results from inversion processing formulations that account for the patterns of clutter statistics are compared to simple least squares treatments.
Serum antibodies against peripheral nervous system antigens in leprosy. (1991)

Since antibodies against peripheral nervous system (PNS) antigens may play a pathogenetic role in the mechanism of nerve damage in leprosy, sera from leprosy patients and contacts were investigated for anti-PNS antibodies by ELISA and immunoblot. In ELISA, elevated anti-PNS antibody levels were detected in 4 of 98 (4.1%) leprosy patients (4 of 52, 7.7%, lepromatous leprosy patients), in 1 of 28 (3.6%) contacts, and in 1 of 18 (5.6%) normal controls. There was no correlation between anti-PNS antibody levels and the bacterial index or neuropathy in leprosy. Immunoblot with a sample of six leprosy and five control sera showed that the antigenic binding pattern (mainly within the 100-200-kDa region) was very similar in patients and controls. Staining intensity, however, appeared to be higher with the leprosy sera than with the control sera. IgM and IgG were found to contribute to the staining pattern: IgM in the 150-200-kDa range, IgG with multiple bands between 25 kDa and 200 kDa. Thus, the presence and levels of serum anti-PNS antibodies in leprosy appear to be unrelated to parameters of disease activity, neuropathy in particular, and do not seem to be critically involved in the pathogenesis of nerve damage.