gebhart/patrepeval huggingface dataset:
Figure S4 from An Orally Available Tubulin Inhibitor, VERU-111, Suppresses Triple-Negative Breast Cancer Tumor Growth and Metastasis and Bypasses Taxane Resistance (2023)

&lt;p&gt;Figure S4 shows that FACS analysis profiles of MDA-MB-231 and MDA-MB-468 TNBC cells following treatment with vehicle (Control), colchicine or paclitaxel, showing VERU-111 induces G2/M checkpoint arrest and apoptosis in TNBC cells. (A) Representative cell cycle distribution images after VERU-111 (10, 20, 50 and 100 nM), colchicine (100 nM) and paclitaxel (100 nM) treatment. Cells were treated for 24 h and stained with anti-phospho-histone H3 (Ser10) and propidium iodide (PI). (B) Representative FACS analysis profiles of apoptotic TNBC cells after 24 h treatment with VERU-111, colchicine or paclitaxel as detected by Annexin-V-FITC/PI staining. (C) Representative FACS analysis profiles of apoptotic TNBC cells after treating with 100 nM VERU-111 for 24, 48 or 72 h, cells were stained with Annexin-V-FITC and PI.&lt;/p&gt;
Elasticity reconstruction: Beyond the assumption of local homogeneity (2010)

Elasticity imaging is a novel domain which is currently gaining significant interest in the medical field. Most inversion techniques are based on the homogeneity assumption, i.e. the local spatial derivatives of the complex-shear modulus are ignored. This analysis presents an analytic approach in order to overcome this limitation, i.e. first order spatial derivatives of the real-part of the complex-shear modulus are taken into account. Resulting distributions in a gauged breast lesion phantom agree very well with the theoretical expectations. An in-vivo example of a cholangiocarcinoma demonstrates that the new approach provides maps of the viscoelastic properties which agree much better with expectations from anatomy.
Beaming light from a subwavelength metal slit surrounded by dielectric surface gratings (2006)

In this article, we demonstrate that a subwavelength metal slit surrounded by dielectric surface gratings possesses a directional beaming effect. We propose a surface plasmon diffraction scheme to explain the three kinds of beaming conditions. The numerical simulations of the illustrative structures undertaken used a Finite Difference Time Domain (FDTD) Method and a Rigorous Coupled Wave Analysis (RCWA) Method. Our simulations were found to be consistent and in agreement with the experimental results. In comparison with other metal structures, we find that dielectric metal structures offer better performance as well as the advantage of being able to be efficiently mass produced for large volume industrial applications.
Deep representation learning improves prediction of LacI-mediated transcriptional repression (2021)

Recent progress in DNA synthesis and sequencing technology has enabled systematic studies of protein function at a massive scale. We explore a deep mutational scanning study that measured the transcriptional repression function of 43,669 variants of the <i>Escherichia coli</i> LacI protein. We analyze structural and evolutionary aspects that relate to how the function of this protein is maintained, including an in-depth look at the C-terminal domain. We develop a deep neural network to predict transcriptional repression mediated by the lac repressor of <i>Escherichia coli</i> using experimental measurements of variant function. When measured across 10 separate training and validation splits using 5,009 single mutations of the lac repressor, our best-performing model achieved a median Pearson correlation of 0.79, exceeding any previous model. We demonstrate that deep representation learning approaches, first trained in an unsupervised manner across millions of diverse proteins, can be fine-tuned in a supervised fashion using lac repressor experimental datasets to more effectively predict a variant's effect on repression. These findings suggest a deep representation learning model may improve the prediction of other important properties of proteins.
The alkoxy radical, RCH2Ȯ, as a free radical product in x-irradiated single crystals of nucleosides and nucleotides (1977)

The RCH2Ȯ radical is formed in x-irradiated 3′-cytidylic acid (3′CMP), 5-chlorodeoxyuridine (ClUdR), 5-bromodeoxyuridine (BUdR), adenosine⋅HCl (AR⋅HCl), and deoxyadenosine monohydrate (AdR⋅H2O) owing to the net loss of hydrogen from O5′ of the primary hydroxylic group. ESR measurements were made between 78 and 100 K on single crystals of 3′CMP, ClUdR, BUdR, and AR⋅HCl and on polycrystalline AdR⋅H2O. The range of principal g values is gmax=2.054–2.093, gint=2.005–2.009, gmin =1.995–2.000. The range of sum of the isotropic β-hydrogen hyperfine couplings is Aβ1iso +Aβ2iso=141–156 G. The g tensors and Aβiso values are used to determine which oxygen nonbonding orbital contains the bulk of the unpaired electron density. The unpaired electron 2p orbital symmetry axis is perpendicular to a plane determined by X(H) ⋅⋅⋅Ȯ–C. Of the two relevant hydrogen bonds in the undamaged molecule, the X–H⋅⋅⋅O bond remains intact whereas the hydrogen in the O–H⋅⋅⋅Y bond is displaced. The equation Aβiso=B0+B2 cos2ϑ, with B0 =0 and B2=101±13 G describes the dependency of the β-hydrogen hyperfine coupling on the torsion angle ϑ, between the unpaired electron symmetry axis and the C–Hβ bond of the RCH2Ȯ radical. Mechanisms of formation, factors in stabilization, and reactions of decay are discussed.
Efficient replacement of nonuniform objects in Web caches (2002)

Cache performance depends heavily on replacement algorithms, which dynamically select a suitable subset of objects for caching in a finite space. Developing such algorithms for wide-area distributed environments is challenging because, unlike traditional paging systems, retrieval costs and object sizes are not necessarily uniform. In a uniform caching environment, a replacement algorithm generally seeks to reduce cache misses, usually by replacing an object with the least likelihood of re-reference. In contrast, reducing total cost incurred due to cache misses is more important in nonuniform caching environments. The authors present the least-unified value algorithm, which performs better than existing algorithms for replacing nonuniform data objects in wide-area distributed environments.
Multi-View Camera Pose Estimation for Robotic Arm Manipulation (2020)

This article proposes a novel approach aimed at estimating the pose of a camera, affixed to a robotic manipulator, against a target object. Our approach provides a way to exploit the redundancy of the robotic arm kinematics by directly considering manipulator poses in the model formulation for camera pose estimation. We adopt a single camera multi-shot technique that minimizes the reprojection error over all the rigid poses. The results of the proposed method are compared to four other studies employing either monocular or stereo setup. The experimental results on synthetic and real data show that the proposed monocular approach achieves better and in some cases comparable results to the stereo approach. Moreover, the proposed approach is significantly more robust and precise compared to other methods.
Furnace and Acid Tower Refractory Lining Integrity Monitoring by Acoustic Techniques (2017)

Process vessels such as smelting furnaces and acid towers are lined by refractory bricks. Degradation of the refractory lining in smelting furnaces begins since the start of the operation. For acid towers, the failure of castable refractory or the mortar between the refractories can cause high concentration acid leaks. Eventually the lining degradation becomes crucial and requires replacement. Since shutdowns are prohibitively expensive, it is desirable to identify the damaged areas and schedule maintenance shutdowns at the optimal frequency so as to reduce the cost of repair and shutdown periods. For this reason, non-destructive testing (NDT) techniques are developed to determine the lining condition while the vessels are still on-line. In this paper, we discuss the application of discrete Acousto Ultrasonic-Echo (AU-E) measurements and real-time continuous Acoustic Emission (AE) monitoring for the determination of refractory lining integrity in smelting furnaces and acid towers.
Experimental realization of Bloch oscillations in a parity-time synthetic silicon photonic lattice (2016)

As an important electron transportation phenomenon, Bloch oscillations have been extensively studied in condensed matter. Due to the similarity in wave properties between electrons and other quantum particles, Bloch oscillations have been observed in atom lattices, photonic lattices, and so on. One of the many distinct advantages for choosing these systems over the regular electronic systems is the versatility in engineering artificial potentials. Here by utilizing dissipative elements in a CMOS-compatible photonic platform to create a periodic complex potential and by exploiting the emerging concept of parity-time synthetic photonics, we experimentally realize spatial Bloch oscillations in a non-Hermitian photonic system on a chip level. Our demonstration may have significant impact in the field of quantum simulation by following the recent trend of moving complicated table-top quantum optics experiments onto the fully integrated CMOS-compatible silicon platform.
Pharmacological reduction of mucosal but not neuronal serotonin opposes inflammation in mouse intestine (2013)

Observations suggest that that peripheral TPH inhibitors uncouple the positive linkage of enterochromaffin cell-derived 5-HT to intestinal inflammation. Because peripheral TPH inhibitors evidently do not enter the murine ENS, they lack deleterious effects on constitutive intestinal motility in mice.
Chemical Synthesis of ZnO Nanocrystals (2006)

Nano-crystalline ZnO particles were synthesized using alcoholic solutions of zinc acetate dihydrate through a colloidal process. Five types of capping agents: 3-aminopropyl trimethoxysilane (Am), tetraethyl orthosilicate (TEOS), mercaptosuccinic acid (Ms), 3-mercaptopropyl trimethoxysilane (Mp) and polyvinylpyrrolidone (Pv) were added at the first ZnO precipitation time (1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> PPT) to limit the particle growth. The first three capping agents effectively capped the ZnO nanoparticles and limited the growth of the particles, while the last two capping agents caused agglomeration or larger clusters in the solutions. Particles synthesized were in the size range of 10nm to 30nm after capping, and grew to 60nm and 100nm in 3 weeks and 6 weeks respectively during storage at ambient conditions. Refluxing time was found to only affect the 1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> PPT time. Washing by methanol and water and slow drying are very important in converting Zn(OH) <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> into ZnO. XRD analyses revealed that single crystal ZnO nanoparticles were achieved with crystal size 53-55nm. Photoluminescence (PL) spectra showed high intensity in UV emission and very low intensity in the visible emission, which indicates a good surface morphology of the ZnO nanoparticles with little surface defect. Optical absorption spectra showed absorption at wavelength of 380nm from the uncapped ZnO, corresponding to the band-gap of bulk ZnO. While capped ZnO absorbed at shorter wavelength (350nm) indicating a much smaller particle size.
Synthesis of Atomically Precise Silver Clusters by Using the Miscibility Principle (2014)

Abstract Invited for the cover of this issue is Thalappil Pradeep at the Indian Institute of Technology Madras, India. The cover image shows a schematic phase diagram of the three‐component solvent system used for preparing monolayer‐protected silver clusters. The different clusters obtained by keeping the reactants the same but adjusting the solvent system by moving to different regions of the phase diagram are shown in different colors.
Extracting the Beat: An Experience-dependent Complex Integration of Multisensory Information Involving Multiple Levels of the Nervous System (2009)

In a series of studies we have shown that movement (or vestibular stimulation) that is synchronized to every second or every third beat of a metrically ambiguous rhythm pattern biases people to perceive the meter as a march or as a waltz, respectively. Riggle (this volume) claims that we postulate an "innate", "specialized brain unit" for beat perception that is "directly" influenced by vestibular input. In fact, to the contrary, we argue that experience likely plays a large role in the development of rhythmic auditory-movement interactions, and that rhythmic processing in the brain is widely distributed and includes subcortical and cortical areas involved in sound processing and movement. Further, we argue that vestibular and auditory information are integrated at various subcortical and cortical levels along with input from other sensory modalities, and it is not clear which levels are most important for rhythm processing or, indeed, what a "direct" influence of vestibular input would mean. Finally, we argue that vestibular input to sound location mechanisms may be involved, but likely cannot explain the influence of vestibular input on the perception of auditory rhythm. This remains an empirical question for future research.
Nanoarchitecturing of Natural Melanin Nanospheres by Layer-by-Layer Assembly: Macroscale Anti-inflammatory Conductive Coatings with Optoelectronic Tunability (2017)

Natural melanins are biocompatible conductors with versatile functionalities. Here, we report fabrication of multifunctional poly(vinyl alcohol)/melanin nanocomposites by layer-by-layer (LBL) assembly using melanin nanoparticles (MNPs) directly extracted from sepia officinalis inks. The LBL assembly offers facile manipulation of nanotextures as well as nm-thickness control of the macroscale film by varying solvent qualities. The time-resolved absorption was monitored during the process and quantitatively studied by fractal dimension and lacunarity analysis. The capability of nanoarchitecturing provides confirmation of complete monolayer formation and leads to tunable iridescent reflective colors of the MNP films. In addition, the MNP films have durable electrochemical conductivities as evidenced by enhanced charge storage capacities for 1000 cycles. Moreover, the MNP covered ITO (indium tin oxide) substrates significantly reduced secretion of inflammatory cytokines, TNF-α, by raw 264.7 macrophage cells compared to bare ITO, by a factor of 5 and 1.8 with and without lipopolysaccharide endotoxins, respectively. These results highlight the optoelectronic device-level tunability along with the anti-inflammatory biocompatibility of the MNP LBL film. This combination of performance should make these films particularly interesting for bioelectronic device applications such as electroceuticals, artificial bionic organs, biosensors, and implantable devices.
Electric-field molecular fingerprinting of blood: new prospects for probing human health (2021)

Recent advances in ultrafast laser science have opened new prospects in probing living systems. Suddenly-excited molecular vibrations emit picosecond-duration coherent infrared light characteristic of the sample’s composition. Given the capacity of this electric-field molecular fingerprint (EMF) to cross-molecularly probe organic samples, we evaluate the feasibility of EMF for biomedical diagnostics. We report high stability of EMF over time and show that several cancer entities leave their signatures in the EMF of serum. Leveraging on the advances of stability, reproducibility and sensitivity of EMF, we provide foundation for applications of infrared molecular profiles in the preventive care model of health monitoring.
Fat grafting exclusively for whole breast reconstruction (2020)

The ability to create a whole breast purely from a process of repeat fat grafting is a huge advance in breast reconstruction. Nonetheless, despite impressive outcomes from several prominent surgeons, others have struggled to achieve satisfactory results, and this topic of exclusive fat grafting remains controversial. Despite refinements of clinical technique, objective measurements of fat resorption approach 50% in large volume fat grafting for breast reconstruction. Focus has shifted to cellular manipulation of adipose tissue and its components in order to improve fat survival and feasibility of clinical translation. Stromal vascular fraction-enriched fat grafting has been used clinically with reported success in cosmetic augmentation3 and in reconstruction following breast-conserving oncological resections. Fat grafting used exclusively for whole breast reconstruction is a great advance in restoring tissues with minimally invasive approaches. Reduced donor site morbidity and ability to achieve a complete breast mound with only minimal incisions and autologous tissue moves the field of breast reconstruction forward in a dramatic way.
The HOL-OCL book (2006)

inline like fn x => 2 * x or in display style: datatype OclType = Integer | Real | String | Boolean | OclAny | Set of OclType (* ...
The Diagnosis of Syndromes by Use of a Dysmorphology Database (1991)

A dysmorphology data base can be useful for the clinician in the task of diagnosing multiple malformation syndromes in children. In this article the database POSSUM is described. Four patients with multiple anomalies referred for diagnostic syndrome evaluation are presented. They serve as examples on how POSSUM efficiently can be applied to obtain a short list of appropriate alternative syndromes, subsequently followed by a discussion on the differential diagnosis in each case. A specific, rare syndrome was diagnosed with the aid of POSSUM in all four cases. POSSUM appears to be useful for the diagnosis of dysmorphic syndromes.
Analysis of the Effects of Conductivity on Small Antenna Characteristics (2020)

In this paper, the impact of metallic material conductivity used to build an Inverted F Antenna (IFA) is studied using both an improved antenna model described in our previous works [1], [2] and 3D electromagnetism simulation tool. The metal conductivity effect is shown on antenna efficiency and input impedance (quality factor) to evaluate the compliance of the realized model with fundamental limits of compact antennas. On the other hand, the model makes it possible to provide an interpretation to the observations made on the properties of the antenna.
[Inhibitors of isoprenylation of ras p21]. (1997)

Posttranslational modification and membrane localization are critical for the function of products of ras oncogenes which are frequently founded to be mutated in human tumors. Farnesylation by farnesyltransferase (FTase) is the first and obligatory step in the processing of ras p21, and FTase has attracted attention as a new target of anticancer agents. Many FTase inhibitors have been identified or synthesized in random screening, and studies on FPP analogs, CAAX analogs, and bisubstrate analogs. These inhibitors induced flat reversion and inhibited the anchorage-independent growth of ras transformant and ras-mutated human tumor cells through the inhibition of posttranslational modification of ras p21. B1086, L-739,749, L-744,832 and FTI-276, which are CAAX analogs, were reported to show inhibition of tumor growth in ras-mutated human tumor xenograft models and to induce regression of mammary and salivary carcinoma in ras transgenic mouse model. FTase inhibitors have the potential to be developed as therapy for ras-mutated human tumors. On the other hand, it has been reported that K-ras 4B p21 could be modified by geranylgeranyltransferase (GGTase). Therefore, GGTase inhibitors have also been evaluated in addition to FTase inhibitors.
Electrochemical energy storage in a sustainable modern society (2013)

The storage of electrical energy in a rechargeable battery is subject to the limitations of reversible chemical reactions in an electrochemical cell. The limiting constraints on the design of a rechargeable battery also depend on the application of the battery. Of particular interest for a sustainable modern society are (1) powering electric vehicles that can compete with cars powered by the internal combustion engine and (2) stationary storage of electrical energy from renewable energy sources that can compete with energy stored in fossil fuels. Existing design strategies for the rechargeable battery have enabled the wireless revolution and the plug-in hybrid electric car, but they show little promise of providing safe, adequate capacity with an acceptable shelf and cycle life to compete in cost and convenience with the chemical energy stored in fossil fuels. Electric vehicles that are charged overnight (plug-in vehicles) offer a distributed energy storage, but larger battery packs are needed for stationary storage of electrical energy generated from wind or solar farms and for stand-by power. This paper outlines the limitations of existing commercial strategies and some developing strategies that may overcome these limitations.
Characterization of indolinones which preferentially inhibit VEGF-C- and VEGF-D-induced activation of VEGFR-3 rather than VEGFR-2 (2001)

1VEGF-C and VEGF-D are lymphangiogenic factors that bind to and activate VEGFR-3, a fms-like tyrosine kinase receptor whose expression is limited almost exclusively to lymphatic endothelium in the adult. Processed forms of VEGF-C and VEGF-D can also activate VEGFR-2, a key player in the regulation of angiogenesis. There is increasing evidence to show that these receptor–ligand interactions play a pivotal role in a number of pathological situations. Inhibition of receptor activation by VEGF-C and VEGF-D could therefore be pharmaceutically useful. Furthermore, to understand the different roles of VEGF-C, VEGF-D, VEGFR-2 and VEGFR-3 in pathological situations it will be necessary to dissect the complex interactions of these ligands and their receptors. To facilitate such studies we cloned, sequenced and characterized the expression of rat VEGF-C and VEGF-D. We showed that Cys152→Ser mutants of processed rat VEGF-C can activate VEGFR-3 but not VEGFR-2, while the corresponding mutation in rat VEGF-D inhibits its ability to activate both VEGFR-2 and VEGFR-3. We also synthesized and characterized indolinones that differentially block VEGF-C- and VEGF-D-induced VEGFR-3 kinase activity compared to that of VEGFR-2. These tools should be useful in analysing the different activities and roles of VEGF-C, VEGF-D and their ligands, and in blocking VEGFR-3-mediated lymphangiogenesis.
New Ways to Treat Tuberculosis Using Dendrimers as Nanocarriers (2018)

Tuberculosis (TB) is a contagious infection that usually attacks not only the lungs, but also brain and spine. More than twenty drugs have been developed for the treatment of TB, but most of them were developed some years ago. They are used in different combinations. Isoniazid and Rifampicin are examples of the five first line TB drugs, whereas, for instance, Levofloxacin, Kanamycin and Linezolid belong to the second line drugs that are used for the treatment of drug resistant TB. Several new bicyclic nitroimidazoles (e.g., Delamanid) without mutagenic effects were developed. New TB drugs need to provide several main issues such as more effective, less toxic, and less expensive for drug resistant TB. Besides polymeric, metal-based nanoparticles, polymeric micelles and polymers, dendrimer nanostructures represent ideal delivery vehicles and offer high hopes for the future of nanomedicine. In this original review, we present and analyze the development of anti-TB drugs in combination with dendrimers. Few articles have highlighted the encapsulation of anti-TB drugs with dendrimers. Due to their unique structure, dendrimers represent attractive candidates for the encapsulation and conjugation of other anti-TB drugs presenting important drawbacks (e.g., solubility, toxicity, low bioavailability) that hinder their development, including clinic trials.