gebhart/patrepeval huggingface dataset:
Designer spin systems via inverse statistical mechanics. II. Ground-state enumeration and classification (2013)

In the first paper of this series [DiStasio, Jr., Marcotte, Car, Stillinger, and Torquato, Phys. Rev. B 88, 134104 (2013)], we applied inverse statistical-mechanical techniques to study the extent to which targeted spin configurations on the square lattice can be ground states of finite-ranged radial spin-spin interactions. In this sequel, we enumerate all of the spin configurations within a unit cell on the one-dimensional integer lattice and the two-dimensional square lattice up to some modest size under periodic boundary conditions. We then classify these spin configurations into those that can or cannot be unique classical ground states of the aforementioned radial pair spin interactions and found the relative occurrences of these ground-state solution classes for different system sizes. As a result, we also determined the minimal radial extent of the spin-spin interaction potentials required to stabilize those configurations whose ground states are either unique or degenerate (i.e., those sharing the same radial spin-spin correlation function). This enumeration study has established that unique ground states are not limited to simple target configurations. However, we also found that many simple target spin configurations cannot be unique ground states.
Ashwagandha Derived Withanone Targets TPX2-Aurora A Complex: Computational and Experimental Evidence to its Anticancer Activity (2012)

Cancer is largely marked by genetic instability. Specific inhibition of individual proteins or signalling pathways that regulate genetic stability during cell division thus hold a great potential for cancer therapy. The Aurora A kinase is a Ser/Thr kinase that plays a critical role during mitosis and cytokinesis and is found upregulated in several cancer types. It is functionally regulated by its interactions with TPX2, a candidate oncogene. Aurora A inhibitors have been proposed as anticancer drugs that work by blocking its ATP binding site. This site is common to other kinases and hence these inhibitors lack specificity for Aurora A inhibition in particular, thus advocating the need of some alternative inhibition route. Previously, we identified TPX2 as a cellular target for withanone that selectively kill cancer cells. By computational approach, we found here that withanone binds to TPX2-Aurora A complex. In experiment, withanone treatment to cancer cells indeed resulted in dissociation of TPX2-Aurora A complex and disruption of mitotic spindle apparatus proposing this as a mechanism of the anticancer activity of withanone. From docking analysis, non-formation/disruption of the active TPX2-Aurora A association complex could be discerned. Our MD simulation results suggesting the thermodynamic and structural stability of TPX2-Aurora A in complex with withanone further substantiates the binding. We report a computational rationale of the ability of naturally occurring withanone to alter the kinase signalling pathway in an ATP-independent manner and experimental evidence in which withanone cause inactivation of the TPX2-Aurora A complex. The study demonstrated that TPX2-Aurora A complex is a target of withanone, a potential natural anticancer drug.
Photoinduced Luminescence Blinking and Bleaching in Individual Single‐Walled Carbon Nanotubes (2008)

The temporal evolution of photoluminescence in individual single-walled carbon nanotubes (SWNT) under strong laser irradiation is studied and pronounced blinking and bleaching is observed, caused by photoinduced oxidation that subsequently quenches mobile excitons. The nanotubes are isolated with sodium cholate and spun onto either a glass or mica surface. Their bleaching behavior is investigated for variable laser intensities in air and argon atmosphere. The decay rate for luminescence bleaching generally increases with higher laser intensity, however saturating on mica substrates, which is attributed to limited availability of oxygen in the vicinity of the nanotubes. Step-like events in the luminescence time traces corresponding to single oxidation events are analyzed regarding relative step height and suggest an exciton diffusion range of about 105 nm.
Pyotr Ivanovich Astrakhantsev: first post-war Director of the Leningrad Pharmaceutical Institute (2021)

There were several periods in the history connected with the rebuilding of the Saint Petersburg State Chemical and Pharmaceutical University, which is over a century old, due to certain events related to the fate of Russia. One of these periods came after the Great Patriotic War. Some students and teachers were evacuated, some joined front line troops, others stayed in besieged Leningrad to live and work. Part of the facilities was evacuated. Another part was destroyed and lost. It was necessary to start all over again.&#x0D; Based on unpublished documents from Saint Petersburg archives, this paper reconstructs the biography of P.I. Astrakhantsev (19051961), a university graduate, chemist, the first post-war director of the Leningrad Institute of Pharmacy. His life path was connected with Alma Mater, as well as with the work in the leading chemical institution of the USSR the State Institute of Applied Chemistry (at present the Russian Scientific Center of Applied Chemistry) he also taught chemistry in the 1st Leningrad Medical Institute, Molotov Pharmaceutical Institute, All-Union Correspondence Forest Engineering Institute.
In situ characterization of sputtered thin films using a normal incidence laser reflectometer (1992)

We will demonstrate the implementation and the use of a normal incidence semiconductor laser reflectometer as an in situ monitoring tool in a computer automated system for reactive sputter deposition of Si/SiOx/SiNx dielectric films. An anode with a viewing hole that was designed specifically for this purpose enables the introduction of both the sputtering gases and the collimated laser beam into the vacuum chamber normal to the processed wafer surface. We will discuss the reflectometer design considerations and the automated data acquisition. We will also demonstrate the use of a normal incidence reflectivity measurement system for in situ determination of the optical deposition rate and material properties such as the refractive index and the absorption loss.
Modification of Rat Thymocyte Membrane Properties by Hyperthermia and Ionizing Radiation (1978)

Thymocytes are one the most widely used cell models for the study of radiation-induced interphase death. This cell-type was chosen for the study of hyperthermic and radiation effects on two membrane-related processes implicated in the interphase death of cells: Na+-dependent 2-aminoisobutyric acid (AIB) transport and cyclic 3'-5' adenosine monophsophate formation. The response of AIB transport to heat is dose-dependent, but the biphasic thermal response curve (AIB uptake versus time) differs fom the sigmoidal radiation response curve. Heating thymocytes for 20-30 min at 43 degrees C stimulates AIB uptake. Additional heating at 43 degrees C, however, markedly reduces AIB uptake. Despite the immediate stimulating effect of heat (30 min at 43 degrees C), the thymocyte has already developed irrepairable impairments, as demonstrated by the fractionated heating experiments. The heat-induced impairment of AIB uptake is mainly on the Na+-dependent component of neutral amino-acid transport, affecting primarily the maximal rate of uptake, i.e. Vmax. Additional evidence for heat-induced plasma membrane damage is the alteration in cAMP levels. Heating thymocytes for 30 min or longer at 43 degrees C causes a massive rise in cAMP level within the cell. This differs from thymocytes exposed to radiation where no rise in cAMP is observed.
A cluster of familial Creutzfeldt–Jakob disease mutations recapitulate conserved residues in Doppel: a case of molecular mimicry? (2002)

Intrachromosomal deletions linking Dpl expression to the PrP promoter produce cerebellar degeneration that can be abrogated by the introduction of wild-type PrP transgenes. Since Dpl-like truncated forms of PrP are neuropathogenic in mice and likewise counterbalanced by expression of PrP(C) we asked whether naturally occurring mutant forms of human PrP have Dpl-like attributes. Five PRNP missense mutations causing familial Creutzfeldt-Jakob disease (F-CJD) map to a helical region found in both PrP(C) and Dpl and result in amino acids identical to conserved residues in Dpl. These F-CJD alleles may cause mutant PrP to become a weak mimetic of Dpl structure and/or function.
Transdiagnostic Associations between Anger Hostility and Chemokine Interferon-gamma Inducible Protein 10 (2023)

Our analyses revealed a significant positive association between the symptom cluster anger hostility in SCL-90-R and the chemokine IP-10 in the subgroup of patients using psychotropic medications.
Monitoring cutting tool operation and condition with a magnetoelastic rate of change of torque sensor (2008)

Application of a magnetoelastic rate of change of torque sensor to monitor the condition of milling cutters and operating parameters is described. Cutting tools naturally degrade with use by wear, chipping, or fracture, and the efficiency and quality of the product are highly dependent on the tool condition. The theoretical analysis is compared to experimental data in detecting changes in torque during each cutting event, and the rate of change of torque signal is investigated for a variety of cutting tool conditions.
Firefly luciferin-luciferase luminescence by milligauss ultra-low frequency pulsed magnetic field applied pure water without ATP (2005)

This paper reports on the biological activities of milligauss magnetic field (mG) applied PBS and also of mG-applied highly purified water on biological systems including CHO cells and luciferin-luciferase system. PBS and highly purified water were exposed to ultra low frequency magnetic field (mg-ULF) which was generated by an Helmholtz coil under visible light . When mG/light-applied pure water or PBS was added to the medium, CHO cells which have UTP receptor on the cell surface and which responds to exogenous ATP which in turn causes an increase of intracellular Ca/sup 2+/ level were found to elevate intracellular Ca/sup 2+/ level and suramin, an antagonist for the receptor, blocked the mG/light-applied PBS or water activity on the cells. When magnetic field was applied on pure water under visible light, for more than 12 hours at 40/spl deg/C, the pure water caused the luminescence of luciferin in the presence of luciferase. This reaction did not require ATP nor Mg/sup 2+/ in the reaction mixture at all. However, without luciferase in the reaction mixture no luminescence was observed. This mG/light-applied water did not scavenge luciferin-luciferase luminescence by the water. This is the first report that luciferin-luciferase luminescence without ATP and Mg/sup 2+/ and this raises the question of what kind of molecular species play stable energy donor in place of ATP. One hypothesis is that the magnetic energy applied onto pure water was stored in certain water (cluster) molecule: H/sub 3/O/sup +/(H2O)/sub n/, as a form with stable hydrogen bond resonance, and transferred to the enzyme protein molecule resulting to form oxy-luciferin with luminescence.
Lasers incorporating two-dimensional photonic crystal mirrors (2005)

Wavelength (nm)CFQl Fig. 3 Transmission spectra along several propagation directions, 0, defined in Fig. lb, for a = 0.28 km.The solid (dotted) curves are as in Fig. 2. that a polar plot of the attenuation positions seen in Fig. 3 reproduces the geometry of the Brillouin zones (depicted in Fig. 1).This has been confirmed experimentally, both in the near-infrared' and in the visible!Our low-index-contrast nanochannelglass-based photonic crystals can allow the fabrication of devices, such as filters, tunable by adjusting the propagation direction and polarization.Unlike materials used in previous work, the present photonic crystals are easily scaled to very large physical dimensions, exceeding 2 inches on a side.1.
Some aspects of the unimolecular decarbonylation reaction of C/sub 7/H/sub 7/O/sup +/ cations (1979)

This study investigated the unimolecular reaction chemistry of a number of C/sub 7/H/sub 7/O/sup +/ ions generated from a variety of precursor molecules, e.g., the cresols, substituted benzyl alcohols, and substituted alkyl phenyl ethers. As a model for the heteroatom tropylium ion, the C/sub 7/H/sub 7/O/sup +/ ion was generated via hydrogen atom loss from the molecular ion of 3,5-cycloheptadienone. The results for metastable kinetic energy release measurements are consistent with different structures for the decomposing C/sub 7/H/sub 7/O/sup +/ ions.
High-speed electro-optical silicon modulators based on photonic crystal waveguides (2007)

An ultra-compact silicon Mach-Zehnder interferometer (MZI) modulator featuring p-i-n-diode-embedded photonic crystal waveguides has been fabricated. As carrier injection is the only practical option for optical modulation in silicon, a lower limit of current density (~10<sup>4</sup>A/cm<sup>2</sup>) exists for achieving gigahertz modulation in the widely employed p-i-n diode configuration. Electrical simulations have been performed to design and analyze the device. The device interaction length was reduced by one order of magnitude compared to the conventional waveguide based MZI modulators by taking advantage of the slow group velocity exhibited by photonic crystal waveguides (PCWs). A maximum modulation depth of 93% has been obtained under an injected current of 7.1 mA. High-speed optical modulation at 1 Gbit s<sup>-1</sup> in the 1.55 micron wavelength region was experimentally demonstrated. To our knowledge, this is the fastest speed ever achieved for a p-i-n diode based integrated silicon MZI modulator.
Signal Processing for Time-of-Flight Imaging Sensors: An introduction to inverse problems in computational 3-D imaging (2016)

Time-of-flight (ToF) sensors offer a cost-effective and realtime solution to the problem of three-dimensional (3-D) imaging-a theme that has revolutionized our sceneunderstanding capabilities and is a topic of contemporary interest across many areas of science and engineering. The goal of this tutorial-style article is to provide a thorough understanding of ToF imaging systems from a signal processing perspective that is useful to all application areas. Starting with a brief history of the ToF principle, we describe the mathematical basics of the ToF image-formation process, for both time- and frequency-domain, present an overview of important results within the topic, and discuss contemporary challenges where this emerging area can benefit from the signal processing community. In particular, we examine case studies where inverse problems in ToF imaging are coupled with signal processing theory and methods, such as sampling theory, system identification, and spectral estimation, among others. Through this exposition, we hope to establish that ToF sensors are more than just depth sensors; depth information may be used to encode other forms of physical parameters, such as, the fluorescence lifetime of a biosample or the diffusion coefficient of turbid/scattering medium. The MATLAB scripts and ToF sensor data used for reproducing figures in this article are available via the author?s webpage: http://www.mit.edu/~ayush/Code.
The Role of Fecal Microbiota Transplantation in Neurological Diseases (2019)

The therapeutic use of human feces to promote host health and ameliorate disease has been sporadically reported in the annals of medicine for centuries. In the last half century, fecal microbiota transplantation (FMT), the therapeutic infusion of healthy donor fecal microbiome into an individual with disease, has gained widespread acceptance by the medical profession. This is largely due to FMT’s remarkable therapeutic efficacy in treating Clostridium difficile infection (CDI). Scientists are now exploring the therapeutic application of FMT to other gastrointestinal (e.g., inflammatory bowel disease and irritable bowel syndrome) and non-gastrointestinal disorders (e.g., autism, chronic fatigue syndrome, multiple sclerosis, Parkinson’s disease) in which a dysbiotic microbiome is thought to play a role in disease progression. The advent of advanced molecular techniques and their application to the gut microbiome has allowed us to begin unraveling the complexity of the gut microbiome. This deeper understanding has, in turn, helped us appreciate the gut microbiome’s crucial role in virtually every aspect of host functioning, including its central role in the development, structure, and functioning of the nervous system. This relationship, commonly referred to as the ‘microbiome–gut–brain axis’ (MGBA), describes the bidirectional communication, by way of biochemical signaling, that exists between the microbiome and the central nervous system. To date, most of the research on the role of the gut microbiome in the MGBA has been performed using animal studies. In this chapter, we review the wealth of experimental data supporting the role of the gut microbiome in the functioning of the nervous system, before exploring the scientific rationale for the clinical application of FMT, and its clinical use, in treating neurological diseases. Although preliminary, the promising results realized in managing these neurological conditions thus far, which represent a significant unmet need, warrant further research in this area.
Percutaneous Multielectrode Endocardial Mapping During Ventricular Tachycardia in the Swine Model (1996)

The multielectrode catheter enables rapid and safe percutaneous endocardial mapping of ventricular tachycardia in the swine model. Exploration of the clinical potential of the multielectrode catheter seems warranted.
Onboard Locomotive Exhaust Emissions Measurement (2007)

Limiting harmful locomotive exhaust emissions is important to the Nation’s health and safety. The Environmental Protection Agency (EPA) has comprehensive gaseous exhaust emissions (or referred to as emissions hereto) testing requirements in place. All current tests are conducted on stationary locomotives. This paper discusses the development of an efficient stationary emissions measurement system that is compact, portable, easy to use, and applicable to onboard locomotives for in-use, over-the-road testing. More efficient locomotive emissions testing and better understanding of in-use emissions would be beneficial to all stakeholders. Sharma &amp; Associates, Inc., (SA) adapted an off-the-shelf, portable, on-road, heavy-duty diesel truck emissions analyzer for locomotive use. This process included development of the necessary peripheral equipment and a computer program to take the raw emissions and report them as brake-specific emissions rates and duty cycle emissions. This paper describes the use of this system on a stationary locomotive. The system is currently being fitted and tested for over-the-road use. The measurement of particulate matter and smoke opacity were out of scope of the phase of the project that this paper is based on and not addressed hereto.
Senolytic elimination of senescent macrophages restores muscle stem cell function in severely dystrophic muscle (2022)

The aging of the immune system, or immunosenescence, was recently verified to have a causal role in driving the aging of solid organs, while the senolytic elimination of senescent immune cells was found to effectively delay systemic aging. Our recent study also showed that immune cells in severely dystrophic muscles develop senescence-like phenotypes, including the increased expression of senescence-associated secretory phenotype (SASP) factors and senescence markers. Here we further investigated whether the specific clearance of senescent immune cells in dystrophic muscle may effectively improve the function of muscle stem cells and the phenotypes of dystrophic muscle. We observed increased percentage of senescent cells in macrophages from <i>mdx</i>/utro(-/-) mice (a murine model for muscular dystrophy disease, dystrophin-/-; utrophin-/-), while the treatment of <i>mdx</i>/utro(-/-) macrophages with senolytic drug fisetin resulted in reduced number of senescent cells. We administrated fisetin to <i>mdx</i>/utro(-/-) mice for 4 weeks, and observed obviously reduced number of senescent immune cells, restored number of muscle cells, and improve muscle phenotypes. In conclusion, our results reveal that senescent immune cells, such as macrophages, are greatly involved in the development of muscle dystrophy by impacting the function of muscle stem cells, and the senolytic ablation of these senescent cells with fisetin can be an effective therapeutic strategy for improving function of muscle stem cells and phenotypes of dystrophic muscles.
Classification -based method in optimal image interpolation (1998)

In this thesis, we introduce two new approaches to optimal image interpolation which are based on the idea that image data falls into different categories or classes, such as edges of different orientation and smoother gradients. Both these methods work by first classifying the image data in a window around the pixel being interpolated, and then using an interpolation filter designed for the selected class. The first method, which we call Resolution Synthesis (RS), performs the classification by computing probabilities of class membership in a Gaussian mixture model. The second method, which we call Tree-based Resolution Synthesis (TRS), uses a regression tree. Both of these methods are based on stochastic models for image data whose parameters must have been estimated beforehand, by training on sample images. We demonstrate that under some assumptions, both of these methods are actually optimal in the sense that they yield minimum mean-squared error (MMSE) estimates of the target-resolution image, given the source image. We also introduce Enhanced Tree-based RS, which consists of TRS interpolation followed by an enhancement stage. During the enhancement stage, we recursively add adjustments to the pixels in the interpolated image. This has the dual effect of reducing interpolation artifacts while imparting additional sharpening. We present results of the above methods for interpolating images which are free of artifacts. In addition, we present results which demonstrate that RS can be trained for high-quality interpolation of images which exhibit certain characteristic artifacts, such as JPEG images and digital camera images. We also present results of a new interpolative image coding method which uses RS along with the well-known JPEG compression scheme. These results demonstrate that for relatively low bit rates, the RS-based compression scheme can improve upon JPEG compression used alone, in terms of subjective image quality (for an approximately fixed bit-rate), and in terms of better rate-distortion tradeoff.
Supplementary Tables from Preclinical Evidence That 3′-Deoxy-3′-[<sup>18</sup>F]Fluorothymidine PET Can Visualize Recovery of Hematopoiesis after Gemcitabine Chemotherapy (2023)

&lt;p&gt;Supplementary Table S1. Mean values [plus minus] standard deviations of different PET quantification approaches and number of samples analyzed. Supplementary Table S2. Mean values [plus minus] standard deviations of the figures presented in the results section and number of samples analyzed. Supplementary Table S3. Mean values [plus minus] standard deviation of peripheral blood counts measured at various time points after gemcitabine administration.&lt;/p&gt;
Cathodoluminescence of Ga2(S0.73Te0.27)3 (1985)

Intense and stable orange cathodoluminescence emission is discovered in Ga 2 (S 0.73 Te 0.27 ) 3 at room temperature. Solid solutions of the Ga-S-Te system were grown by the closed tube chemical transport method using GaI 3 as a transporting agent. Intensity of the cathodoluminescence increases linearly with an incident electron beam current, and with an accelerating voltage. The line-shape of the spectrum is broad and independent of the condition of the incident beam. The peak wavelength is 6900Å and corresponds to the energy gap, 1.80 eV, obtained from the optical transmission measurement.