gebhart/patrepeval huggingface dataset:
Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases (2015)

Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Crystal structures of several homomeric protein kinase complexes have a serine, threonine, or tyrosine autophosphorylation site of one kinase monomer located in the active site of another monomer, a structural complex that we call an "autophosphorylation complex." We developed and applied a structural bioinformatics method to identify all such autophosphorylation complexes in x-ray crystallographic structures in the Protein Data Bank (PDB). We identified 15 autophosphorylation complexes in the PDB, of which five complexes had not previously been described in the publications describing the crystal structures. These five complexes consist of tyrosine residues in the N-terminal juxtamembrane regions of colony-stimulating factor 1 receptor (CSF1R, Tyr(561)) and ephrin receptor A2 (EPHA2, Tyr(594)), tyrosine residues in the activation loops of the SRC kinase family member LCK (Tyr(394)) and insulin-like growth factor 1 receptor (IGF1R, Tyr(1166)), and a serine in a nuclear localization signal region of CDC-like kinase 2 (CLK2, Ser(142)). Mutations in the complex interface may alter autophosphorylation activity and contribute to disease; therefore, we mutated residues in the autophosphorylation complex interface of LCK and found that two mutations impaired autophosphorylation (T445V and N446A) and mutation of Pro(447) to Ala, Gly, or Leu increased autophosphorylation. The identified autophosphorylation sites are conserved in many kinases, suggesting that, by homology, these complexes may provide insight into autophosphorylation complex interfaces of kinases that are relevant drug targets.
Optimizing noise for defect analysis with through-focus scanning optical microscopy (2016)

Through-focus scanning optical microscopy (TSOM) shows promise for patterned defect analysis, but it is important to minimize total system noise. TSOM is a three-dimensional shape metrology method that can achieve sub-nanometer measurement sensitivity by analyzing sets of images acquired through-focus using a conventional optical microscope. Here we present a systematic noise-analysis study for optimizing data collection and data processing parameters for TSOM and then demonstrate how the optimized parameters affect defect analysis. We show that the best balance between signal-to-noise performance and acquisition time can be achieved by judicious spatial averaging. Correct background-signal subtraction of the imaging-system inhomogeneities is also critical, as well as careful alignment of the constituent images used in differential TSOM analysis.
Cocaine induces striatal c-fos-immunoreactive proteins via dopaminergic D1 receptors. (1991)

The protooncogene c-fos produces a phosphoprotein, Fos, which regulates gene transcription processes. In neuronal systems, Fos has been proposed to couple synaptic transmission to changes in gene expression by acting in the cell nucleus in concert with other proteins to form complexes in the promoter regions of target genes. We report here that the acute administration of a single dose of the indirect-acting dopaminergic agonist cocaine increases multiple Fos proteins in rat caudate nucleus. The increase is dose-dependent and is apparent immunocytochemically at 1 hr, maximal at 2 hr, and absent 48 hr after treatment. The increase seen immunocytochemically is composed of several molecular weight species as assessed by Western blotting of proteins from isolated striatal cell nuclei. Administration of the specific dopaminergic receptor antagonists sulpiride and SCH-23390 prior to cocaine support a significant role for D1 but not for D2 receptors in mediating this effect. These data indicate that D1 dopamine receptors are linked to a cellular immediate-early gene system(s) and suggest an action of cocaine at one or more levels of gene expression via modulation of transcriptional processes in activated cells.
Camera Motion-Based Analysis of User Generated Video (2009)

In this paper we propose a system for the analysis of user generated video (UGV). UGV often has a rich camera motion structure that is generated at the time the video is recorded by the person taking the video, i.e., the ¿camera person.¿ We exploit this structure by defining a new concept known as <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">camera view</i> for temporal segmentation of UGV. The segmentation provides a video summary with unique properties that is useful in applications such as video annotation. Camera motion is also a powerful feature for identification of keyframes and regions of interest (ROIs) since it is an indicator of the camera person's interests in the scene and can also attract the viewers' attention. We propose a new location-based saliency map which is generated based on camera motion parameters. This map is combined with other saliency maps generated using features such as color contrast, object motion and face detection to determine the ROIs. In order to evaluate our methods we conducted several user studies. A subjective evaluation indicated that our system produces results that is consistent with viewers' preferences. We also examined the effect of camera motion on human visual attention through an eye tracking experiment. The results showed a high dependency between the distribution of fixation points of the viewers and the direction of camera movement which is consistent with our location-based saliency map.
Degeneration of neurons, synapses, and neuropil and glial activation in a murine <i>Atm</i> knockout model of ataxia–telangiectasia (1997)

Neural degeneration is one of the clinical manifestations of ataxia-telangiectasia, a disorder caused by mutations in the Atm protein kinase gene. However, neural degeneration was not detected with general purpose light microscopic methods in previous studies using several different lines of mice with disrupted Atm genes. Here, we show electron microscopic evidence of degeneration of several different types of neurons in the cerebellar cortex of 2-month-old Atm knockout mice, which is accompanied by glial activation, deterioration of neuropil structure, and both pre- and postsynaptic degeneration. These findings are similar to those in patients with ataxia-telangiectasia, indicating that Atm knockout mice are a useful model to elucidate the mechanisms underlying neurodegeneration in this condition and to develop and test strategies to palliate and prevent the disease.
Effective dosing of L-carnitine in the secondary prevention of cardiovascular disease: a systematic review and meta-analysis (2014)

There appears to be no significant marginal benefit in terms of all-cause mortality, heart failure, unstable angina, or myocardial reinfarction in the setting of acute MI for oral L-carnitine maintenance doses of greater or less than 3 g per day.
Potential for a unified topological approach to electromagnetic effects protection (1992)

An approach to the potential unification technology for a wide spectrum of electromagnetic environments (EMEs) is presented. Of particular interest is the protection of complex electronic systems. An electromagnetic topological approach is utilized to develop a consistent shielding protection method. Applicable electromagnetic topological techniques are presented. The varying characteristics of the various EMEs, for electromagnetic sources both internal and external to the system, are described. The EMEs considered include: electromagnetic interference/compatibility (EMI/EMC), lightning electromagnetic pulse (LEMP), nuclear EMP (NEMP), and high-power microwaves (HPMs). Existing protection practices, incompatibilities, and suggested remedies are discussed. A quantitative and generalized topological protection approach and the basic technological means for applying it are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Application Driven SCM and NAND Flash Hybrid SSD Design for Data-Centric Computing System (2015)

In order to efficiently store, retrieve and process big data, the data-centric computing paradigm is adopted and an application-driven storage class memory (SCM)/NAND flash hybrid solid-state drive (SSD) is designed. SSD data management algorithms minimize data movement inside the storage system and the SSD system design parameter, SCM/NAND capacity ratio, is chosen depending on the application. Design guidelines are proposed, based on the evaluation of three SCM/NAND flash hybrid SSDs with: (1) write-back (WB) cache, (2) write-optimized data management (WO-DM) and (3) read-write balanced data management (RWB-DM) algorithms. The WO-DM algorithm achieves the highest SSD performance for write-intensive applications, whereas RWB-DM is most appropriate for read-hot (frequently accessed)-random workloads. As long as the workload is not read-cold-sequential or write-cold-sequential, adding SCM to the NAND SSD system is cost-effective to boost performance. Less than 10% SCM/NAND capacity ratios provides 10x speed, compared to the NAND flash-only SSD.
Monomer Sequence Distribution in Ethylene—Propylene Rubber Measured by 13C NMR. 3. Use of Reaction Probability Model (1978)

Abstract One can measure r 1 r 2 for an ethylene—propylene rubber by determining composition and χ, the ratio of contiguous to isolated propylene units. Our previous determination of χ depended on measuring methine carbon resonances in a 13 C NMR spectrum. The χ method based solely on methine peak area measurements is inaccurate. This is not because the χ method is theoretically unsound, but because it is impossible to accurately extract the methine areas, necessary to calculate χ from the complex 13 C NMR spectra of ethylene—propylene rubbers. The presence of inverted propylene produces ambiguity in a portion of the methine region. This means the methine areas can be used only to calculate a maximum and minimum boundary for r 1 r 2 . Another difficulty in using only methine areas to determine χ arises at propylene levels less than 35 wt%, because the methine areas for contiguous propylene triads become very small and are overlapped by strong resonances from long methylene sequences. We have developed a reaction probability method which accurately accounts for all the resonance areas in a 13 C NMR spectrum of an ethylene—propylene rubber instead of restricting the analysis to the tertiary carbon areas. The reaction probability method produces a complete calculated 13 C NMR spectrum as a best fit to the observed spectrum. The deduced probabilities provide the following derived quantities: (1) “ r 1 r 2 ”, a measure of monomer sequence randomness, (2) the distribution of methylene sequence lengths, (3) composition, (4) amount of propylene inversion. The probabilities can be used to directly calculate “ r 1 r 2 ”. Or alternatively, the probabilities can be used to calculate the methine carbon areas including the separation of the ambiguous methine area into contiguous and isolated contributions. These areas calculated from the probabilities can then be used to determine χ and the resultant r 1 r 2 . The two values for r 1 r 2 are in good agreement, lending credence to the probability analysis. The composition derived from probabilities agrees with other analytical methods such as proton NMR and infrared. The limitation of the method is that we cannot accurately determine the percent propylene inversion. We can only conclude that in the majority of the copolymers of 20 to 60 wt% propylene that we have studied, the concentration of inverted propylene is significant and is between 10 and 40% of the total propylene present. Propylene enriched in carbon-13 could be used to prepare copolymers and perhaps resolve this uncertainty.
Interleukin 4 receptor on human lung cancer: a molecular target for cytotoxin therapy. (2002)

Previous studies have demonstrated that human lung tumor cell lines express interleukin 4 (IL-4) receptors, and IL-4 can mediate modest to moderate antiproliferative activity in vitro and in vivo in animal models of human lung tumors. On the basis of these studies, IL-4 was tested in clinical trials; however, it showed little antitumor activity in lung cancer patients. In the present study, we examined the expression of IL-4 receptors (IL-4Rs) in lung tumor samples and normal lung tissues and tested whether an IL-4R targeted agent will have better antitumor activity in vitro and in vivo compared with IL-4. IL-4R expression was tested by immunohistochemistry in 54 lung tumor samples and normal lung tissues in a tissue array, by reverse-transcription PCR and Northern blot analyses in lung tumor cell lines. Cytotoxic activity of IL-4 cytotoxin [IL-4(38-37)-PE38KDEL], composed of a circular permuted IL-4 and a mutated form of Pseudomonas exotoxin (PE38KDEL) was tested by protein synthesis inhibition and clonogenic assays in seven lung tumor cell lines. Antitumor activity of IL-4 cytotoxin was tested in vitro and in immunodeficient animal models of human lung tumors. We observed that IL-4Rs are expressed at higher levels in situ in lung tumor samples compared with normal lung tissues and IL-4 cytotoxin is highly and specifically cytotoxic to lung tumor cell lines in vitro. Intratumoral and i.p. administration of IL-4 cytotoxin to immunodeficient mice with s.c. established human lung H358 non-small cell lung cancer tumors mediated considerable antitumor activity in a dose-dependent manner with the higher dose producing durable complete responses. On the other hand, H460 non-small cell lung cancer tumors expressing low levels of IL-4R did not respond to IL-4 cytotoxin therapy. Because IL-4 cytotoxin mediates its antitumor activity through IL-4R, and a variety of lung tumors expressed high levels of IL-4R, we propose testing the safety of this agent in patients with lung cancer.
Inherent Tradeoffs in the Fair Determination of Risk Scores (2023)

chapter Share on Inherent Tradeoffs in the Fair Determination of Risk Scores Author: Manish Raghavan Massachusetts Institute of Technology, Sloan School of Management and Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology, Sloan School of Management and Department of Electrical Engineering and Computer ScienceView Profile Authors Info & Claims The Societal Impacts of Algorithmic Decision-MakingSeptember 2023https://doi.org/10.1145/3603195.3603197Published:08 September 2023Publication History 0citation0DownloadsMetricsTotal Citations0Total Downloads0Last 12 Months0Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Publisher SiteGet Access
Inhibition of type 1 diabetes in filaria‐infected non‐obese diabetic mice is associated with a T helper type 2 shift and induction of FoxP3<sup>+</sup> regulatory T cells (2008)

We sought to determine whether Litomosoides sigmodontis, a filarial infection of rodents, protects against type 1 diabetes in non-obese diabetic (NOD) mice. Six-week-old NOD mice were sham-infected or infected with either L3 larvae, adult male worms, or adult female worms. Whereas 82% of uninfected NOD mice developed diabetes by 25 weeks of age, no L. sigmodontis-infected mice developed disease. Although all mice had evidence of ongoing islet cell inflammation by histology, L. sigmodontis-infected mice had greater numbers of total islets and non-infiltrated islets than control mice. Protection against diabetes was associated with a T helper type 2 (Th2) shift, as interleukin-4 (IL-4) and IL-5 release from alpha-CD3/alpha-CD28-stimulated splenocytes was greater in L. sigmodontis-infected mice than in uninfected mice. Increased circulating levels of insulin-specific immunoglobulin G1, showed that this Th2 shift occurs in response to one of the main autoantigens in diabetes. Multicolour flow cytometry studies demonstrated that protection against diabetes in L. sigmodontis-infected NOD mice was associated with significantly increased numbers of splenic CD4(+) CD25(+) FoxP3(+) regulatory T cells. Interestingly, injection of crude worm antigen into NOD mice also resulted in protection against type 1 diabetes, though to a lesser degree than infection with live L. sigmodontis worms. In conclusion, these studies demonstrate that filarial worms can protect against the onset of type 1 diabetes in NOD mice. This protection is associated with a Th2 shift, as demonstrated by cytokine and antibody production, and with an increase in CD4(+) CD25(+) FoxP3(+) regulatory T cells.
Presidential Attention Focusing in the Global Arena: The Impact of International Travel on Foreign Publics (2016)

Presidents increasingly engage in public diplomacy, especially traveling to other nations. Often presidents target the public in the visited nation, with the aim of improving the opinion climate there and then using that improved opinion climate to further U.S. policy goals in the visited nation. To a degree, then, foreign travel resembles presidential domestic going public. This article tests one important linkage in the process from a presidential trip to foreign public opinion, whether trips can focus public opinion in the visited nation on the president. Analysis uses a pooled cross‐sectional time series analysis of weekly Google Trends data for forty‐two nations during Barack Obama's first term in office. Results suggest that presidential trips lead to impressive increases in searches on the president, an indication of increased attention to the president. The conclusion places the findings into two literatures, presidential going public and public diplomacy, and suggests directions for future research.
QoS control via robust envelope-based MBAC (2002)

Measurement-based admission control (MBAC) offers an attractive means for satisfying the quality-of-service (QoS) requirements of delay-sensitive multimedia applications, without requiring an advanced and detailed traffic characterization of each individual traffic flow. In this paper, we argue that measured maximal rate envelopes of the aggregate traffic flow can be used to design an MBAC algorithm that successfully controls the admissible region subject to the applications' QoS constraints, for the case of heterogeneous and highly bursty traffic flows, buffered multiplexers, and both moderate and large numbers of traffic flows.
ChemInform Abstract: Reactions of Coordinated Ligands. Part 14. Synthesis of a Tetradentate Phosphorus Macrocycle in a Palladium(II) Template. (1986)

Abstract Die Cyclisierung des disek, Diphosphins MePH(CH 2 ) 2 PHMe mit o‐Xylylendichlorid im Pd(II)‐Templat liefert den Pd(II)‐Komplex (II) des vierzähnigen makrocyclischen Liganden (III) als Gemisch dreier Stereoisomeren.
Contractual Limitations on Reverse Engineering (2011)

Abstract This chapter considers various issues that may have more impact on interoperability in the future. These include open-source software, software patents and statutory requirements. This chapter explains that while copyright law has evolved in a manner that prevents its use to exercise control of interface specifications, Microsoft and other companies continue to pursue proprietary business strategies, with great success. It also argues that even if copyright does not protect a program's interface specifications, a patent that applies to the program's interface or basic functionality can frustrate interoperability with that program.
An Approach to the High-level Maintenance Planning for EMU Trains Based on Simulated Annealing (2017)

A high-speed train needs high-level maintenance when its accumulated running mileage or time reaches predefined threshold. The date of delivering an Electric Multiple Unit (EMU) train to maintenance ranges within a time window rather than be a fixed date. Obviously, changing the delivering date always means a different impact on the supply of EMU trains and operation cost. Therefore, the delivering plan has the potential to be optimized. This paper formulates the EMU train high-level maintenance planning problem as a non-linear 0-1 programming model. The model aims at minimizing the mileage loss of all EMU trains with the consideration of the maintenance capacity of the workshop and maintenance ratio at different times. The number of trains under maintenance not only depends on the current maintenance plan, but also influenced by the trains whose maintenance time span from the last planning horizon to current horizon. A state function is established to describe whether a train is under maintenance. By using this function the constraint of restricting the total number of trains that are under maintenance can be formulated reasonably well. Finally, a simulated annealing algorithm is proposed for solving the problem.
Extracellular matrix assembly of cell‐derived and plasma‐derived fibronectins by substrate‐attached fibroblasts (1988)

Using a previously described model system for the incorporation of plasma fibronectin into the extracellular matrix (McKeown-Longo, P.J. and Mosher, D.F., 1985. J. Cell Biol., 100:364-374), we compared the binding of cell-derived and plasma-derived fibronectins to human fibroblast cell layers. Binding was measured in time course experiments using metabolically labeled cell-derived, iodinated cell-derived, and iodinated plasma-derived fibronectins. The kinetics of matrix assembly of cell- and plasma-derived fibronectins were the same. Competitive binding curves using intact fibronectin or the 70-kD amino-terminal fragment of fibronectin suggested that cell surface binding sites have equal affinity for cell- and plasma-derived fibronectins. Iodinated fibronectins did not bind to isolated matrices containing collagen type I, fibronectin, and thrombospondin. These results suggest that fibroblasts do not distinguish between cell-derived and plasma-derived fibronectins when assembling exogenous fibronectin into extracellular matrix.
Dependence of Shell Mix on Feedthrough in Direct Drive Inertial Confinement Fusion (2004)

The mixing of cold, high-density shell plasma with the low-density, hot spot plasma by the Rayleigh-Taylor instability in inertial confinement fusion is experimentally shown to correlate with the calculated perturbation feedthrough from the ablation surface to the inner shell surface. A fourfold decrease in the density of shell material in the mix region of direct drive implosions of gas filled spherical plastic shells having predicted convergence ratios approximately 15 was observed when laser imprint levels were reduced and the initial shell was thicker, corresponding to a reduction in the feedthrough rms level by a factor of 6. Shell mix is also shown to limit the spherical compression of the implosion.
Numerical Investigation on Gas-solid Flow in a Circumfluent Cyclone Separator (2019)

The efficient removal of fine dust from exhaust gas reduces the harm to human health and minimizes material waste. A circumfluent cyclone (CFC) was designed to perform with increased gas-solid separation efficiency and decreased pressure drop compared to conventional cyclone separators, and its flow pattern and velocity distribution were investigated. Commercial computational fluid dynamics software was used to simulate the 3D-gas-flow field using the Reynolds stress model (RSM). The simulation results (e.g., for the velocity profile, pressure drop, and separation efficiency) were in good agreement with the experimental results and indicated that about 78% of the gas flows directly out of the CFC through the inner cylinder and then the vortex finder, which significantly shortens the cleaned gas flow path and thereby reduces friction loss. The CFC also decreases the shortcut flow rate near the vortex finder entrance, reducing particle escape. Finally, the discrete particle model (DPM) was used to predict the flow pattern of particles of different sizes.