gebhart/patrepeval huggingface dataset:
Mad1 Function in Cell Proliferation and Transcriptional Repression Is Antagonized by Cyclin E/CDK2 (2005)

The transcription factors of the Myc/Max/Mad network play essential roles in the regulation of cellular behavior. Mad1 inhibits cell proliferation by recruiting an mSin3-corepressor complex that contains histone deacetylase activity. Here we demonstrate that Mad1 is a potent inhibitor of the G(1) to S phase transition, a function that requires Mad1 to heterodimerize with Max and to bind to the corepressor complex. Cyclin E/CDK2, but not cyclin D and cyclin A complexes, fully restored S phase progression. In addition inhibition of colony formation and gene repression by Mad1 were also efficiently antagonized by cyclin E/CDK2. This was the result of cyclin E/CDK2 interfering with the interaction of Mad1 with HDAC1 and reducing HDAC activity. Our findings define a novel interplay between the cell cycle regulator cyclin E/CDK2 and Mad1 and its associated repressor complex and suggests an additional mechanism how cyclin E/CDK2 affects the G(1) to S phase transition.
Increased Synaptic Strength and mGlu2/3 Receptor Plasticity on Mouse Prefrontal Cortex Intratelencephalic Pyramidal Cells Following Intermittent Access to Ethanol (2021)

Together, these studies provide insight into the specific PFC neurocircuits altered by voluntary drinking. In addition, the findings provide an additional rationale for developing compounds that potentiate mGlu<sub>2</sub> and/or mGlu<sub>3</sub> receptor function as potential treatments for AUD.
Self-passivated copper gates for amorphous silicon thin-film transistors (1997)

A solution to the amorphous silicon transistor gate metallization problem in active matrix liquid crystal displays (AMLCD's) is demonstrated, in the form of a self-passivated copper (Cu) process. Cu is passivated by a self-aligned chromium (Cr) oxide encapsulation formed by surface segregation of Cr in dilute Cu-10-30 at.%Cr alloys at 400/spl deg/C, solving the problems of chemical reactivity during the plasma deposition, diffusion, poor adhesion to the substrate, and oxidation. The performance of self-passivated Cu bottom-gate thin-film transistors (TFT's) and their stability during thermal bias stress testing is comparable to that of Cr-gate reference TFT's. The gate line resistivity (including encapsulation) is 4.5 μ/spl Omega//spl middot/cm at present.
Improvements in Complex Mixture Analysis by NMR:  DQF-COSY iDOSY (2007)

Diffusion-ordered NMR spectroscopy (DOSY NMR) is a highly useful tool for the study of complex mixtures via NMR. Often, spectral overlap limits the ability of obtaining cleanly separated subspectra of the components due to inherently instable multiexponential fits or data inversion procedures. Three-dimensional DOSY variants offer the advantage of separating individual peaks in an additional dimension, such that robust monoexponential fits to cross-peaks may be used to determine the diffusion coefficients with higher accuracy. For sensitivity reasons, methods based on proton nuclei are preferable. We show that a double-quantum-filtered COSY-DOSY experiment provides advantages over COSY-DOSY, while high signal-to-noise ratios are maintained. We demonstrate the viability of the technique by applying it to a solution of single-stranded DNA oligomers and to a mixture of unprocessed beeswax and decanol.
AI Descartes: Combining Data and Theory for Derivable Scientific Discovery (2021)

Scientists have long aimed to discover meaningful formulae which accurately describe experimental data. One common approach is to manually create mathematical models of natural phenomena using domain knowledge, then fit these models to data. In contrast, machine-learning algorithms automate the construction of accurate data-driven models while consuming large amounts of data. Ensuring that such models are consistent with existing knowledge is an open problem. We develop a method for combining logical reasoning with symbolic regression, enabling principled derivations of models of natural phenomena. We demonstrate these concepts for Kepler's third law of planetary motion, Einstein's relativistic time-dilation law, and Langmuir's theory of adsorption, automatically connecting experimental data with background theory in each case. We show that laws can be discovered from few data points when using formal logical reasoning to distinguish the correct formula from a set of plausible formulas that have similar error on the data. The combination of reasoning with machine learning provides generalizable insights into key aspects of natural phenomena. We envision that this combination will enable derivable discovery of fundamental laws of science. We believe that this is a crucial first step for connecting the missing links in automating the scientific method.
Fluorescence Enhancement From Single DNA Molecules Confined In Si/SiO2 Nanochannels (2010)

A large challenge in biophysics when studying single molecules using fluorescence microscopy is to obtain a signal that is clearly detectable above the background noise. Ways to improve or optimize the fluorescence signal is therefore of great interest. We here study DNA extended in 320 nm deep funnel-shaped SiO2 nanochannels with a width ranging from 40nm to 600nm. The DNA is stained with a fluorescent dye (YOYO-1) and we show that the total emission from the DNA varies significantly with the dimensions of the channels (Figure) and has a peak intensity at half the wavelength of the emitted light. Measurements at varying salt concentrations, where the same confinement leads to different extension of the DNA, confirm that it is solely the geometry of the channel that governs the enhancement effect, ruling out alternative explanations, such as self-quenching. By using polarizers on the emission side we can investigate the light polarized parallel and perpendicular to the channel separately and we see that they show vastly different behavior with the peak in emission only detected in the light polarized parallel to the channels. We will discuss how our data may be explained by cavity-resonance effects when the lateral dimensions of the channels coincide with half the wavelength of the emitted light. Our results suggest that it is possible to fine-tune the size and shape of the nanochannels to maximize the number of photons collected from the molecule under study, for example when studying DNA interacting with single DNA-binding proteins where maximizing the photon budget is paramount.
Heparan Sulfate Separation, Sequencing, and Isomeric Differentiation: Ion Mobility Spectrometry Reveals Specific Iduronic and Glucuronic Acid-Containing Hexasaccharides (2009)

We describe the resolution of heparan sulfate (HS) isomers by chromatographic methods and their subsequent differentiation by mass spectrometry (MS), ion mobility, and (1)H nuclear magnetic resonance (NMR) analysis. The two purified hexasaccharide isomers produced nearly identical MS spectra, quantitative disaccharide profiles, and partial enzymatic digestions. However, both tandem spectrometry (MS(2)) and ion mobility spectrometry (IMS) indicated structural differences existed. All data suggested the distinction between the two hexasaccharides resided in their uronic acid stereochemistries. Glucuronic (GlcA) and iduronic acids (IdoA) were subsequently defined by (1)H NMR analysis completing the structural analysis and verifying the unique structures initially indicated by MS(2) and IMS. Our results suggest that IMS may be a powerful tool in the rapid differentiation of GlcA and IdoA containing isomers in the absence of prior structural knowledge.
Designs For High Power, Single Mode Operation In Broad Stripe Semiconductor Lasers (1988)

TWo methods are describrd in this paper to obtain high power in a single lateral mode operation in a broad stripe semiconductor laser. (1) Antiguiding index profile-solution to the wave equation for a one-dimensional, quadratic variation in the complex refractive index profile are used to calculate the optical gain and the intensity profile of the lateral modes of broad-stripe semiconductor lasers. A large gain difference between the fundamental mode and higher order modes is obtained in profiles with strong real-index antiguiding and weak gain-guiding. A criterion for comparing the tendency for single mode operation is introduced and applied to quadratic, step, and array profiles. (2) Variable facet reflectance-the reflectance at the facets of a wide stripe laser is made to vary spatially across the width of the stripe. It is found that the gain differences between the fundamental mode and higher order modes can be greatly increased. Several reflectance profiles are examined and the results are campared using the same criterion as in method (1).
Qualitative and Quantitative Expression Profile of Muscarinic Receptors in Human Urothelium and Detrusor (2006)

We identified all 5 existing muscarinic receptor subtypes in detrusor and urothelium, and transcripts levels of M2 and M3 were comparable in detrusor. These results support an alternative site of action in urothelium for anti-muscarinic drugs. Urothelial receptors should be considered in the design of future drugs for overactive bladder.
Characterization of recombinant cat albumin (2003)

Recombinant cat albumin may be used as a paradigmatic tool to analyse mechanisms of allergen-triggered exacerbation of AD, for diagnostic and, perhaps for therapeutic purposes.
Thermodynamic Properties of Trialkali (Li, Na, K) Hexa-alanates: A Combined DFT and Experimental Study (2008)

The present work combines periodic density functional theory (DFT) calculations of thermodynamic properties and experimental synthesis to explore the ternary (Li, Na, K) phase diagram of LixNayK3−x−yAlH6 hexa-alanates. About 70 virtual phases, of various possible structures and different alkali metal compositions are investigated by DFT simulations. The thermodynamic stability of each of the 10 phases found to exhibit relative low formation energies is tested versus the decomposition into mixtures of monoalkali hexa-alanates. Three potentially stable candidate phases are revealed. Among them, only LiNaKAlH6 may compete with the stability of the mixture of bialkali hexa-Alanate and monoalkali tetra-alanate phases according to DFT calculation. We attempt to synthesize different trialkali hexa-alanates by ball milling of NaH, LiH, KH, Al, and 2 mol % TiCl3 under hydrogen pressure of 10 MPa near room temperature. For the various tested compositions, the X-ray diffraction (XRD) analysis reveals only the formation of monoalkali hydrides and bialkali hexa-alanates mixed with the tetra-alanate KAlH4 phase. As a consequence of the experimental and theoretical investigations, the alternative furnished by trialkali hexa-alanates is seriously questioned. The LiNaKAlH6 phase, the best potential candidate according to DFT calculations, was not successfully formed by ball milling synthesis. Finally, we propose a general interpretation of the relative difference of Van’t Hoff plots of the first and the second dehydrogenation steps, which gives out the thermodynamic limit of alkali alanates as potential materials for on board reversible hydrogen storage.
Current Control of Interleaved DC-DC Converter in Continuous and Discontinuous Mode (2018)

The following topics are dealt with: machine control; aircraft power systems; power convertors; electric vehicles; permanent magnet motors; DC-DC power convertors; invertors; synchronous motors; battery powered vehicles; electric current control.
What affects pedestrian crossing difficulty at urban intersections in a developing country? (2022)

In developing countries, road traffic crashes involving pedestrians have become a foremost concern. At present, road safety assessment plans and selection of interventions are primarily restricted to traditional approaches that depend on the investigations of historical crash data. However, in developing countries such as India, the availability, consistency, and accuracy of crash data are major concerns. In contrast, proactive approaches such as studying road users' risk perception have emerged as a substitute method of examining potential risk factors. An individual's risk perception offers vital information on probable crash risk, which may be beneficial in detecting high-risk locations and major causes of crashes. Since the pedestrian fatality risk is not uniform across the urban road network level, it may be expected that pedestrians' perceived risk measured in terms of “crossing difficulty” would also vary across the sites. In this perspective, the present paper establishes a mathematical association between the pedestrians' perceived “crossing difficulty” and actual crashes. The model outcome confirms that pedestrians' perceived crossing difficulty is a good surrogate of fatal pedestrian crashes at the intersection level in Kolkata City, India. Subsequently, to examine the impact of traffic exposures, road infrastructure, land use, spatial factors, and pedestrian-level attributes on pedestrians' “crossing difficulty”; a set of Ordered Logit models are developed. The model outcomes show that high vehicle and pedestrian volume, vehicular speed, absence of designated bus stop, the presence of inaccessible pedestrian crosswalk, on-street parking, lack of signalized control (for both vehicle and pedestrian), inadequate sight distance, land use pattern, slum population, pedestrian-vehicular post encroachment time, waiting time before crossing, road width, and absence of police enforcement at an intersection significantly and positively increase pedestrian's crossing difficulty at urban intersections. To end, the model findings are advantageously utilized to develop a set of countermeasures across 3E's of road safety.
Renal Cell Osteopontin Production is Stimulated by Calcium Oxalate Monohydrate Crystals (1998)

No AccessJournal of UrologyUrological Survey: Abstracts: Urolithiasis, Endourology and Laparoscopic Surgery1 May 1998Renal Cell Osteopontin Production is Stimulated by Calcium Oxalate Monohydrate Crystals J.C. Lieske, M.S. Hammes, J.R. Hoyer, and F.G. Toback J.C. LieskeJ.C. Lieske More articles by this author , M.S. HammesM.S. Hammes More articles by this author , J.R. HoyerJ.R. Hoyer More articles by this author , and F.G. TobackF.G. Toback More articles by this author View All Author Informationhttps://doi.org/10.1097/00005392-199805000-00136AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Renal Cell Osteopontin Production is Stimulated by Calcium Oxalate Monohydrate Crystals." The Journal of Urology, 159(5), pp. 1779–1780 Department of Medicine, University of Chicago, Chicago, Illinois, and Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania.© 1998 by American Urological Association, Inc.FiguresReferencesRelatedDetails Volume 159Issue 5May 1998Page: 1779-1780 Advertisement Copyright & Permissions© 1998 by American Urological Association, Inc.MetricsAuthor Information J.C. Lieske More articles by this author M.S. Hammes More articles by this author J.R. Hoyer More articles by this author F.G. Toback More articles by this author Expand All Advertisement PDF DownloadLoading ...
Data from Targeting CD73 with AB680 (Quemliclustat), a Novel and Potent Small-Molecule CD73 Inhibitor, Restores Immune Functionality and Facilitates Antitumor Immunity (2023)

&lt;div&gt;Abstract&lt;p&gt;T cells play a critical role in the control of cancer. The development of immune checkpoint blockers (ICB) aimed at enhancing antitumor T-cell responses has revolutionized cancer treatment. However, durable clinical benefit is observed in only a subset of patients, prompting research efforts to focus on strategies that target multiple inhibitory signals within the tumor microenvironment (TME) to limit tumor evasion and improve patient outcomes. Adenosine has emerged as a potent immune suppressant within the TME, and CD73 is the major enzyme responsible for its extracellular production. CD73 can be co-opted within the TME to impair T-cell–mediated antitumor immunity and promote tumor growth. To target this pathway and block the formation of adenosine, we designed a novel, selective, and potent class of small-molecule inhibitors of CD73, including AB680 (quemliclustat), which is currently being tested in patients with cancer. AB680 effectively restored T-cell proliferation, cytokine secretion, and cytotoxicity that were dampened by the formation of immunosuppressive adenosine by CD73. Furthermore, in an allogeneic mixed lymphocyte reaction where CD73-derived adenosine had a dominant suppressive effect in the presence of PD-1 blockade, AB680 restored T-cell activation and function. Finally, in a preclinical mouse model of melanoma, AB680 inhibited CD73 in the TME and increased the antitumor activity of PD-1 blockade. Collectively, these data provide a rationale for the inhibition of CD73 with AB680 in combination with ICB, such as anti–PD-1, to improve cancer patient outcomes.&lt;/p&gt;&lt;/div&gt;
Nanoscale potential distribution across multiquantum well structures: Kelvin probe force microscopy and secondary electron imaging (2005)

Ultrahigh vacuum cross-sectional Kelvin probe force microscopy has been used to characterize In0.17GaAs∕GaAsP0.06 multiquantum well structures, together with secondary electron microscopy. Individual 8nm quantum wells were well resolved in both methods, and were found to be in a good agreement with numerical simulations of the work function profile. It is shown that the surface potential contrast in the Kelvin probe force microscopy measurements is greatly enhanced using deconvolution algorithms, and the reasons for the different contrast in the electron microscopy images are discussed.
Nanofluidic rocking Brownian motors for multi-channel separation of spherical nanoparticles with nanometer scale resolution (2021)

Rocking Brownian motors achieve directional motion in highly diffusive environments by combining an inherently asymmetric static potential energy landscape and an oscillating “rocking” force [1, 2]. Our nanofluidic imple- mentation [3] features a confining wall with a ratchet-type nano-topography and AC electric fields as driving force. The potential energy landscape is due to electrostatic interactions between the charged particles and wall surfaces in close proximity. Based on this scheme, we have developed a nanoparticle size-separation device [4]. Along the particle transport direction, one of the confining walls features a sawtooth-like topography with a superimposed slope. In turn, we obtain a ratchet-shaped potential with increasing potential energy barrier heights caused by the decreasing nanofluidic gap. A sharp drop in particle current occurs as the potential barriers increase. The drop happens the later, the smaller the particle size. This allows for a sequential separation of the particle suspension into multiple sub-populations. The device was modeled by solving the Fokker-Planck equation. We show that the physics of the separation mechanism is governed by the energy landscape under forward tilt of the ratchet. The separation resolution is thus only dependent on the applied force. Experimentally, we demonstrate the separation of spherical gold particles of nominal 80 and 100 nm diameters with an applied voltage of 3.5 V and a sorting time of 20 s. We achieve a resolution of 2 nm, in accordance with our simulation results.
VMShadow (2014)

Distributed clouds offer a choice of data center locations to application providers to host their applications. In this paper we consider distributed clouds that host virtual desktops(VDs) which are then accessed by their users through remote desktop protocols. VDs have different sensitivities to latency, primarily determined by the types of applications running (games or video players are more sensitive to latency) and the end users' locations. We design VMShadow, a system to automatically optimize the location and performance of latency-sensitive VDs in the cloud. VMShadow performs black-box fingerprinting of a VM's network traffic to infer its latency-sensitivity and employs a greedy heuristic based algorithm to move highly latency-sensitive VMs to cloud sites that are closer to their end users. VMShadow employs WAN-based live migration and a new network connection migration protocol to ensure that the VM migration and subsequent changes to the VM's network address are transparent to end-users. We implement a prototype of VMShadow in a nested hypervisor and demonstrate its effectiveness for optimizing the performance of VM-based desktops in the cloud. Our experiments on a private and the public EC2 cloud show that VMShadow is able to discriminate between latency-sensitive and insensitive desktop applications and judiciously move only those VMs that will benefit the most. For desktop VMs with video activity, VMShadow improves VNC's refresh rate by 90%. Further our connection migration proxy, which utilizes dynamic rewriting of packet headers, imposes a rewriting overhead of only 13μs per packet. Trans-continental VM migrations take about 4 minutes.
Impact of obesity on outcomes after definitive dose‐escalated intensity‐modulated radiotherapy for localized prostate cancer (2015)

For patients with CaP receiving dose-escalated intensity-modulated RT with daily image-guidance, increasing BMI appears to be associated with an increased risk of BF, DM, CSM, and overall mortality.
An extrapolation method for the determination of Cliff‐Lorimer kAB factors at zero foil thickness (1986)

SUMMARY An extrapolation method is proposed to be useful for the determination of the Cliff‐Lorimer k AB factor at zero foil thickness. The method consists of measuring k AB factors as a function of the measured foil thickness, t M , and extrapolating the relationship toward t M =0. The intersection between the extrapolated line and the ordinate of t M =0 gives ( k AB ) 0 which is free from the effect of absorption. The straight line extrapolation that can be achieved by a linear‐least squares method is particularly developed to eliminate arbitrariness introduced in the extrapolation process. The extrapolation method is applied to data available in the literature. It is shown that the method yields the ( k AB ) 0 factors compatible with those predicted from the theoretical calculation. It is also shown that this method can circumvent several problems which make it complex and difficult to determine accurate values of the absorption‐free k AB factors. Using the straight line extrapolatioin, it is possible to estimate the degree of the thickness overestimation which arises when the foil thickness is measured by the contamination spot separation (CSS) method. Validity of the straight line extrapolation is further discussed.
Zero-Shot Learning of Continuous 3D Refractive Index Maps from Discrete Intensity-Only Measurements (2021)

Intensity diffraction tomography (IDT) refers to a class of optical microscopy techniques for imaging the 3D refractive index (RI) distribution of a sample from a set of 2D intensity-only measurements. The reconstruction of artifact-free RI maps is a fundamental challenge in IDT due to the loss of phase information and the missing cone problem. Neural fields (NF) has recently emerged as a new deep learning (DL) paradigm for learning continuous representations of complex 3D scenes without external training datasets. We present DeCAF as the first NF-based IDT method that can learn a high-quality continuous representation of a RI volume directly from its intensity-only and limited-angle measurements. We show on three different IDT modalities and multiple biological samples that DeCAF can generate high-contrast and artifact-free RI maps.