gebhart/patrepeval huggingface dataset:
Reverse Engineering Digital Circuits Using Structural and Functional Analyses (2014)

Integrated circuits (ICs) are now designed and fabricated in a globalized multivendor environment making them vulnerable to malicious design changes, the insertion of hardware Trojans/malware, and intellectual property (IP) theft. Algorithmic reverse engineering of digital circuits can mitigate these concerns by enabling analysts to detect malicious hardware, verify the integrity of ICs, and detect IP violations. In this paper, we present a set of algorithms for the reverse engineering of digital circuits starting from an unstructured netlist and resulting in a high-level netlist with components such as register files, counters, adders, and subtractors. Our techniques require no manual intervention and experiments show that they determine the functionality of >45% and up to 93% of the gates in each of the test circuits that we examine. We also demonstrate that our algorithms are scalable to real designs by experimenting with a very large, highly-optimized system-on-chip (SOC) design with over 375000 combinational elements. Our inference algorithms cover 68% of the gates in this SOC. We also demonstrate that our algorithms are effective in aiding a human analyst to detect hardware Trojans in an unstructured netlist.
Evidence‐based options for treatment‐resistant adult bipolar disorder patients (2012)

Most studies identified were small, involved supplementation of typically complex ongoing treatments, varied in controls, randomization, and blinding, usually involved brief follow-up, and lacked replication. Clearer criteria for defining and predicting treatment resistance in BD are needed, as well as improved trial design with better controls, assessment of specific clinical subgroups, and longer follow-up.
Treatment with a γ-Ketoaldehyde Scavenger Prevents Working Memory Deficits in hApoE4 Mice (2011)

Both inflammation and oxidative injury are features of Alzheimer's disease (AD), but the contribution of these intertwined phenomena to the loss of working memory in this disease is unclear. We tested the hypothesis that highly reactive γ-ketoaldehydes that are formed both by non-enzymatic free radical catalyzed lipid peroxidation and by cyclooxygenases may be causally linked to the development of memory impairment in AD. We found that levels of γ-ketoaldehyde protein adducts were increased in the hippocampus of brains obtained postmortem from patients with AD compared to age-matched controls, but that levels of γ-ketoaldehyde protein adducts in the cerebellum were not different in the two groups. Moreover, immunohistochemistry revealed that adducts localized to hippocampal pyramidal neurons. We tested the effect of an orally available γ-ketoaldehyde scavenger, salicylamine, on the development of spatial working memory deficits in hApoE4 targeted replacement mice, a mouse model of dementia. Long-term salicylamine supplementation did not significantly alter body weight or survival, but protected against the development of age-related deficits in spatial working memory in 12-14 month old ApoE4 mice. These findings suggest that γ-ketoaldehyde adduct formation is associated with damage to hippocampal neurons in patients with AD and can contribute to the pathogenesis of spatial working memory deficits in hApoE4 mice. These data provide a rational basis for future studies exploring whether γ-ketoaldehyde scavengers may mitigate the development of cognitive dysfunction in patients with AD.
Overexpression of c-erbB-2 in epithelial ovarian cancer. Prognostic value and relationship with response to chemotherapy (1995)

c-erbB-2 overexpression in tumors from patients with ovarian cancer resulted in a poorer prognosis than for patients whose tumors did not have overexpression.
A statistical analysis of the correlation between large igneous provinces and lower mantle seismic structure (2014)

Large igneous provinces (LIPs) lie approximately above the margins of the African and Pacific large low shear velocity provinces (LLSVPs) in the deep mantle. This spatial correlation has been used to argue that plumes are preferentially generated at the margins of LLSVPs. We perform a series of Monte Carlo–based statistical tests to assess the uniqueness of this conclusion. These tests indicate that (1) the reconstructed locations of LIPs are significantly correlated with both slower-than-average shear wave velocity regions, which contain LLSVPs, and the margins of these structures; and (2) these correlations cannot be statistically distinguished. That is, given current constraints, if plumes were generated randomly throughout regions of slower-than-average shear wave velocity in the deep mantle, then statistical tests are expected to show a significant correlation between the locations of LIPs and the margins of LLSVPs. We therefore conclude that it is premature to argue that the margins of LLSVPs represent preferred zones of plume generation. This conclusion is reinforced in our analysis by a demonstration that the expected mean distance of a set of points randomly placed in slower-than-average shear wave velocity regions is consistent with the observed mean distance between LIPs and the margins of LLSVPs. Finally, we also test the correlation between the reconstructed locations of LIPs and the horizontal gradient in deep mantle shear velocity perturbations. We find, given the uncertainty implied by different tomography models, that there is no statistically significant correlation and that being in a slow region (i.e. in the region of LLSVPs) is a stronger geographic requirement for plume generation than being at a specific (high) gradient.
Pictet–Spengler Reaction of Nitrones and Imines Catalyzed by Yb(OTf)3–TMSCl (2002)

Abstract The Pictet–Spengler reaction of nitrones and imines prepared from N-hydroxytryptamine and tryptamine gave the corresponding tetrahydro-β-carbolines in excellent yields in the presence of Yb(OTf)3–TMSCl in a mixture of CH2Cl2 and THF.
Design and implementation of a malware detection system based on network behavior (2014)

Abstract With the increasing of new malicious software attacks, the host‐based malware detection methods cannot always detect the latest unknown malware. Intrusion detection system does not focus on malware detection, whereas the behavior‐based detection methods still have some difficulties in being deployed in the network layer. This paper presents a malware detection method based on network behavior evidence chains. The proposed new method will detect the specific network behavior characteristics on three different stages as connection establishment, operating control, and connection maintenance. Then a final detection decision will be concluded according to the results detected in the different stages before. A system prototype is implemented to proof concept the proposed malware detection methods. Copyright © 2014 John Wiley & Sons, Ltd.
Terahertz Spectroscopy in Polymer Research: Assignment of Intermolecular Vibrational Modes and Structural Characterization of Poly(3-Hydroxybutyrate) (2013)

This paper reviews our recent spectroscopic study on poly(3-hydroxybutyrate) (PHB) for the terahertz (THz) frequency region. Clear differences are observed between the absorption spectra of crystalline and amorphous PHB, indicating that the higher order conformation of PHB determines the THz spectra. The THz polarization spectra are measured for a stretched PHB sample and the directions of the vibrational transition moments are determined. The spectra are found to have temperature dependences owing to which the peaks at lower frequencies shift with temperature, suggesting a large anharmonicity of the vibrational potential. To investigate low frequency vibrational modes more thoroughly, low-frequency Raman spectra are also measured for crystalline PHB. The observed vibrational modes in both THz and Raman spectra were successfully assigned by a quantum mechanical simulation of spectra with the Cartesian coordinate tensor transfer (CCT) method, which can provide realistic spectra of the PHB by considering the intermolecular interactions among polymer chains. The potential of CCT for the assignment of THz spectra is demonstrated. On the basis of these results, the structural change in PHB is studied. The isothermal crystallization of PHB is monitored with the help of THz absorption spectra. The observed spectra clearly show the crystal growth, and the crystallization rate is estimated by Avrami's model. Next, the isothermal crystallization spectra are analyzed using two-dimensional correlation spectroscopy (2DCOS). By using the synchronous and asynchronous data plots, the correlation between the absorption peaks and the temporal order of the changes in spectral intensity is determined.
SIMULATING ACCOMMODATION BY IMAGE AUTOCORRELATIONS (1972)

The integrated squared autocorrelation function of an image can be shown to represent a measure of pattern information or, more commonly, a measure of the amount, sharpness and complexity of contour and contrast in the image. The autocorrelation function can thus provide a relative measure of image focus inasmuch as contour and contrast information is lost as an image goes out of focus. It is argued that the autocorrelation of the retinal image could be used as a feedback signal for control of visual accommodation and that such a mechanism is consistent with many well known phenomena of accommodation. In addition it is shown that the autocorrelation model can simulate quantitative data obtained from experiments on human accommodative behavior.
A Theoretical Explanation for Perplexing Behaviors of Backpropagation-based Visualizations (2018)

Backpropagation-based visualizations have been proposed to interpret convolutional neural networks (CNNs), however a theory is missing to justify their behaviors: Guided backpropagation (GBP) and deconvolutional network (DeconvNet) generate more human-interpretable but less class-sensitive visualizations than saliency map. Motivated by this, we develop a theoretical explanation revealing that GBP and DeconvNet are essentially doing (partial) image recovery which is unrelated to the network decisions. Specifically, our analysis shows that the backward ReLU introduced by GBP and DeconvNet, and the local connections in CNNs are the two main causes of compelling visualizations. Extensive experiments are provided that support the theoretical analysis.
Downregulation of Myocardial Myocyte Enhancer Factor 2C and Myocyte Enhancer Factor 2C–Regulated Gene Expression in Diabetic Patients With Nonischemic Heart Failure (2002)

MEF2C and MEF2C-regulated genes are decreased in the failing hearts of diabetic patients. This transcriptional mechanism may contribute to the contractile dysfunction in heart failure patients with diabetes.
Atrophin Proteins Interact with the Fat1 Cadherin and Regulate Migration and Orientation in Vascular Smooth Muscle Cells (2009)

Fat1, an atypical cadherin induced robustly after arterial injury, has significant effects on mammalian vascular smooth muscle cell (VSMC) growth and migration. The related Drosophila protein Fat interacts genetically and physically with Atrophin, a protein essential for development and control of cell polarity. We hypothesized that interactions between Fat1 and mammalian Atrophin (Atr) proteins might contribute to Fat1 effects on VSMCs. Like Fat1, mammalian Atr expression increased after arterial injury and in VSMCs stimulated with growth and chemotactic factors including angiotensin II, basic fibroblast growth factor, and platelet-derived growth factor BB. Two distinct Atr2 transcripts, atr2L and atr2S, were identified by Northern analysis; in VSMCs, atr2S mRNA expression was more responsive to stimuli. By immunocytochemistry, Fat1 and Atrs colocalized at cell-cell junctions, in the perinuclear area, and in the nucleus. In coimmunoprecipitation studies, Fat1 interacted with both Atr1 and Atr2; these interactions required Fat1 amino acids 4300-4400 and an intact Atro-box in the Atrs. Knock-down of Atrs by small interfering RNA did not affect VSMC growth but had complex effects on migration, which was impaired by Atr1 knockdown, enhanced by Atr2L knockdown, and unchanged when both Atr2S and Atr2L were depleted. Enhanced migration caused by Atr2L knockdown required Fat1 expression. Similarly, orientation of cells after monolayer denudation was impaired in cells with Atr1 knockdown but enhanced in cells selectively depleted of Atr2L. Together these findings suggest that Fat1 and Atrs act in concert after vascular injury but show further that distinct Atr isoforms have disparate effects on VSMC directional migration.
Double-walled carbon nanotubes: Challenges and opportunities (2010)

Double-walled carbon nanotubes are coaxial nanostructures composed of exactly two single-walled carbon nanotubes, one nested in another. This unique structure offers advantages and opportunities for extending our knowledge and application of the carbon nanomaterials family. This review seeks to comprehensively discuss the synthesis, purification and characterization methods of this novel class of carbon nanomaterials. An emphasis is placed on the double wall physics that contributes to these structures' complex inter-wall coupling of electronic and optical properties. The debate over the inner-tube photoluminescence provides an interesting illustration of the rich photophysics and challenges associated with the myriad combinations of the inner and outerwall chiralities. Outerwall selective covalent chemistry will be discussed as a potential solution to the unattractive tradeoff between solubility and functionality that has limited some applications of single-walled carbon nanotubes. Finally, we will review the many different uses of double-walled carbon nanotubes and provide an overview of several promising research directions in this new and emerging field.
Ectopic expression of the minimal <i>whiE</i> polyketide synthase generates a library of aromatic polyketides of diverse sizes and shapes (1999)

The single recombinant expressing the Streptomyces coelicolor minimal whiE (spore pigment) polyketide synthase (PKS) is uniquely capable of generating a large array of well more than 30 polyketides, many of which, so far, are novel to this recombinant. The characterized polyketides represent a diverse set of molecules that differ in size (chain length) and shape (cyclization pattern). This combinatorial biosynthetic library is, by far, the largest and most complex of its kind described to date and indicates that the minimal whiE PKS does not independently control polyketide chain length nor dictate the first cyclization event. Rather, the minimal PKS enzyme complex must rely on the stabilizing effects of additional subunits (i.e., the cyclase whiE-ORFVI) to ensure that the chain reaches the full 24 carbons and cyclizes correctly. This dramatic loss of control implies that the growing polyketide chain does not remain enzyme bound, resulting in the spontaneous cyclization of the methyl terminus. Among the six characterized dodecaketides, four different first-ring cyclization regiochemistries are represented, including C7/C12, C8/C13, C10/C15, and C13/C15. The dodecaketide TW93h possesses a unique 2,4-dioxaadamantane ring system and represents a new structural class of polyketides with no related structures isolated from natural or engineered organisms, thus supporting the claim that engineered biosynthesis is capable of producing novel chemotypes.
Molecular computation: RNA solutions to chess problems (2000)

We have expanded the field of "DNA computers" to RNA and present a general approach for the solution of satisfiability problems. As an example, we consider a variant of the "Knight problem," which asks generally what configurations of knights can one place on an n x n chess board such that no knight is attacking any other knight on the board. Using specific ribonuclease digestion to manipulate strands of a 10-bit binary RNA library, we developed a molecular algorithm and applied it to a 3 x 3 chessboard as a 9-bit instance of this problem. Here, the nine spaces on the board correspond to nine "bits" or placeholders in a combinatorial RNA library. We recovered a set of "winning" molecules that describe solutions to this problem.
Production and Stimulation Analysis of Multiple Hydraulic Fracturing of a 2,000-ft Horizontal Well (1989)

Abstract The performance of multiple hydraulic fracturing treatments along a 2000-foot horizontal well bore was completed in a gas bearing, naturally-fractured shale gas reservoir in Wayne County, West Virginia. Pre-frac flow and pressure data, hydraulic fracturing treatments, and post-stimulation flow and pressure data form the basis from which a comprehensive analysis was performed. Average field production from 72 wells was used as baseline data for the analysis. Such data was used to show the significance of enhanced production from a horizontal well in a field that was partially depleted. The post-frac stabilized flow rate was 95,000 cubic feet per day (mcf/d) from 2000 feet of horizontal borehole. Under current reservoir pressure conditions, the horizontal well produced at a rate 7 times greater than the field current average of 13 mcfd for stimulated vertical wells. This increase in gas production suggests that horizontal wells, in strategically placed locations within partially depleted fields, could significantly increase reserves.
Neutralized Coupling Elements for MIMO Operation in 4G Mobile Terminals (2014)

A novel multiple-input-multiple-output (MIMO) dual-antenna system covering the low LTE700 and GSM850/900 communication standards is proposed for mobile terminals. The two-port antenna system is composed of two 3-D coupling elements, placed on the vertices of the short corner of a rectangular FR4 substrate. This rectangular shape emulates the printed circuit board of a modern mobile terminal. To achieve high port-to-port isolation, the neutralization technique is applied. Simulated reflection coefficients, total efficiencies, and envelope coefficient correlation are compared to measured data showing good agreement and competitive performance.
Upregulation of microrna‐451 increases the sensitivity of <scp>A</scp>549 cells to radiotherapy through enhancement of apoptosis (2015)

Upregulation of miR-451 sensitized radioresistant NSCLC A549 cells to irradiation through the enhancement of apoptosis. The activation of PTEN post-irradiation was possibly correlated with the radiosensitization of A549 cells induced by miR-451 overexpression.
A Survey on High Efficiency Wireless Local Area Networks: Next Generation WiFi (2016)

The emerging paradigm of the Internet of Everything, along with the increasing demand of Internet services everywhere, results in a remarkable and continuous growth of the global Internet traffic. As a cost-effective Internet access solution, WiFi networks currently generate a major portion of the global Internet traffic. Furthermore, the number of WiFi public hotspots worldwide is expected to increase by more than sevenfold by 2018. To face this huge increase in the number of densely deployed WiFi networks, and the massive amount of data to be supported by these networks in indoor and outdoor environments, it is necessary to improve the current WiFi standard and define specifications for high efficiency wireless local area networks (HEWs). This paper presents potential techniques that can be applied for HEWs, in order to achieve the required performance in dense HEW deployment scenarios, as expected in the near future. The HEW solutions under consideration includes physical layer techniques, medium access control layer strategies, spatial frequency reuse schemes, and power saving mechanisms. To accurately assess a newly proposed HEW scheme, we discuss suitable evaluation methodologies, by defining simulation scenarios that represent future HEW usage models, performance metrics that reflect HEW user experience, traffic models for dominant HEW applications, and channel models for indoor and outdoor HEW deployments. Finally, we highlight open issues for future HEW research and development.
Segmenting Brain Tumors using Alignment-Based Features (2006)

Detecting and segmenting brain tumors in magnetic resonance images (MRI) is an important but time-consuming task performed by medical experts. Automating this process is a challenging task due to the often high degree of intensity and textural similarity between normal areas and tumor areas. Several recent projects have explored ways to use an aligned spatial 'template' image to incorporate spatial anatomic information about the brain, but it is not obvious what types of aligned information should be used. This work quantitatively evaluates the performance of 4 different types of alignment-based (AB) features encoding spatial anatomic information for use in supervised pixel classification. This is the first work to (1) compare several types of AB features, (2) explore ways to combine different types of AB features, and (3) explore combining AB features with textural features in a learning framework. We considered situations where existing methods perform poorly, and found that combining textural and AB features allows a substantial performance increase, achieving segmentations that very closely resemble expert annotations.
Use of lithium (alpha-methylbenzyl)allylamide for a formal asymmetric synthesis of thienamycin (1997)

The highly stereoselective conjugate addition of lithium (αR)-(α-methylbenzyl)allylamide 3 to (E)-tert-butyl penta-2,4-dienoate 4, followed by a stereoselective aldol reaction with acetaldehyde, are the key steps in the synthesis of the known β-lactam intermediate, (3S,4R)-3-E(R)-1-(tert-butyldimethylsilyloxy)ethyl]-4-vinylazetidin-2-one 2, for elaboration to thienamycin and its derivatives.
The immune modulatory effects of umbilical cord-derived mesenchymal stromal cells in severe COVID-19 pneumonia (2021)

Coronavirus disease 2019 (COVID-19) may result in a life-threatening condition due to a hyperactive immune reaction to severe acute respiratory syndrome-coronavirus-2 infection, for which no effective treatment is available. Based on the potent immunomodulatory properties of mesenchymal stromal cells (MSCs), a growing number of trials are ongoing. This prompted us to carry out a thorough immunological study in a patient treated with umbilical cord-derived MSCs and admitted to the Intensive Care Unit for COVID-19-related pneumonia. The exploratory analyses were assessed on both peripheral blood and bronchoalveolar fluid lavage samples at baseline and after cellular infusion by means of single-cell RNA sequencing, flow cytometry, ELISA, and functional assays. Remarkably, a normalization of circulating T lymphocytes count paralleled by a reduction of inflammatory myeloid cells, and a decrease in serum levels of pro-inflammatory cytokines, mostly of interleukin-6 and tumor necrosis factor-α, were observed. In addition, a drop of plasma levels of those chemokines essential for neutrophil recruitment became evident that paralleled the decrease of lung-infiltrating inflammatory neutrophils. Finally, circulating monocytes and low-density gradient neutrophils acquired immunosuppressive function. This scenario was accompanied by an amelioration of respiratory, renal, inflammatory, and pro-thrombotic indexes. Our results provide the first immunological data possibly related to the use of umbilical cord-derived MSCs in severe COVID-19 context.