gebhart/patrepeval huggingface dataset:
Activity of dianhydrogalactitol alone or with platinum drugs against non-small cell lung cancer cell lines. (2015)

e19145 Background: Non-small cell lung cancer (NSCLC) is usually treated with surgery followed by treatment with either tyrosine kinase inhibitors or platinum-based regimens, but long-term prognosis is poor. Dianhydrogalactitol (VAL-083) is a bi-functional alkylating agent with proven activity against NSCLC in preclinical and clinical trials. Here we aimed to investigate in vitro i) the role of p53 status in VAL-083 activity, ii) VAL-083 activity in comparison to cisplatin and oxaliplatin and iii) the combination of VAL-083 with cisplatin or oxaliplatin. Methods: Dependence on p53 status was investigated in isogenic HCT-116p53-/- and HCT-116p53+/+models. VAL-083 cytotoxicity was tested in a panel of 9 human NSCLC cell lines: 4 wild-type (wt), 4 mutant and 1 null for p53. The combination potential was investigated by determining superadditivity and synergy using the criteria of combination index (CI) < 1. Cytotoxicity was monitored on day 5 with the MTT assay. Results: Studies in HCT-116 models demonstrated that loss of p53 increased resistance to cisplatin and oxaliplatin by 3- and 6-fold, respectively, while resistance to VAL-083 was < 2-fold. As single agents, VAL-083, cisplatin and oxaliplatin showed good cytotoxicity in all NSCLC cell lines to varying degrees, with H460 as the most sensitive (IC50< 0.5 uM). The IC50 in the other cell lines ranged from 0.9-6.1 μM, 0.5-2.2 μM and 0.6-2.6 μM for VAL-083, cisplatin and oxaliplatin, respectively, and there was no overt difference in drug sensitivity between the wt and mutant/null p53 group. This suggests that either wt p53 is not activated and/or other genetic alterations reduce cytotoxic activities. The combination of VAL-083 with cisplatin or oxaliplatin in the A549 NSCLC model, demonstrated significant superadditivity (p < 0.05) and synergism (CI < 1) for both combinations. This strongly favors non-overlapping mode of action between the platinum drugs and VAL-083. Conclusions: VAL-083 is less dependent on p53 for activity than cisplatin and oxaliplatin. VAL-083 further demonstrates superadditivity/synergy against NSCLC cell lines when combined with cisplatin or oxaliplatin, suggesting a potential for VAL-083 as part of a combination treatment in NSCLC.
Searchable Symmetric Encryption: Improved Definitions and Efficient Constructions. (2006)

Searchable symmetric encryption (SSE) allows a party to outsource the storage of his data to another party in a private manner, while maintaining the ability to selectively search over it. This problem has been the focus of active research and several security definitions and constructions have been proposed. In this paper we begin by reviewing existing notions of security and propose new and stronger security definitions. We then present two constructions that we show secure under our new definitions. Interestingly, in addition to satisfying stronger security guarantees, our constructions are more efficient than all previous constructions. Further, prior work on SSE only considered the setting where only the owner of the data is capable of submitting search queries. We consider the natural extension where an arbitrary group of parties other than the owner can submit search queries. We formally define SSE in this multi-user setting, and present an efficient construction. 1
IMU/GPS System Provides Position and Attitude Data (2006)

A special navigation system is being developed to provide high-quality information on the position and attitude of a moving platform (an aircraft or spacecraft), for use in pointing and stabilization of a hyperspectral remote-sensing system carried aboard the platform. The system also serves to enable synchronization and interpretation of readouts of all onboard sensors. The heart of the system is a commercially available unit, small enough to be held in one hand, that contains an integral combination of an inertial measurement unit (IMU) of the microelectromechanical systems (MEMS) type, Global Positioning System (GPS) receivers, a differential GPS subsystem, and ancillary data-processing subsystems. The system utilizes GPS carrier-phase measurements to generate time data plus highly accurate and continuous data on the position, attitude, rotation, and acceleration of the platform. Relative to prior navigation systems based on IMU and GPS subsystems, this system is smaller, is less expensive, and performs better. Optionally, the system can easily be connected to a laptop computer for demonstration and evaluation. In addition to airborne and spaceborne remote-sensing applications, there are numerous potential terrestrial sensing, measurement, and navigation applications in diverse endeavors that include forestry, environmental monitoring, agriculture, mining, and robotics.
Quantifying Timed-Up-and-Go test: A smartphone implementation (2013)

Timed-Up-and-Go (TUG) is a simple, easy to administer, and frequently used test for assessing balance and mobility in elderly and people with Parkinson's disease. An instrumented version of the test (iTUG) has been recently introduced to better quantify subject's movements during the test. The subject is typically instrumented by a dedicated device designed to capture signals from inertial sensors that are later analyzed by healthcare professionals. In this paper we introduce a smartphone application called sTUG that completely automates the iTUG test so it can be performed at home. sTUG captures the subject's movements utilizing smartphone's built-in accelerometer and gyroscope sensors, determines the beginning and the end of the test and quantifies its individual phases, and optionally uploads test descriptors into a medical database. We describe the parameters used to quantify the iTUG test and algorithms to extract the parameters from signals captured by the smartphone sensors.
Use of the Escherichia coli gene for asparagine synthetase as a selective marker in a shuttle vector capable of dominant transfection and amplification in animal cells. (1987)

A new dominant amplifiable selective system for use in bacterium-animal cell shuttle vectors was developed by the insertion of a 2-kilobase genomic fragment containing the cloned Escherichia coli gene for asparagine synthetase (AS) into the pBR322-simian virus 40 recombinant vector pSV2 so as to place the translational initiator codon for the bacterial AS about 1,000 base pairs downstream from the simian virus 40 early promoter. This new construct, pSV2-AS, retains bacterial sequences for transcriptional and translational initiation and so can express AS in bacteria. The construct can also complement AS- mutants of mammalian cells, giving AS+ transfectants capable of growth in medium lacking asparagine, with relatively high efficiency (about 300 colonies per microgram of DNA per 10(6) cells exposed). The vector can be amplified up to 100-fold in such AS+ transfectants by selection in asparagine-free medium containing increasing concentrations of the AS inhibitor beta-aspartyl hydroxamate. AS+ transfectants were found to be much more resistant to a second AS inhibitor, Albizziin, than were normal AS+ animal cell lines. This difference, which may indicate a strong resistance of the bacterial AS enzyme to Albizziin, was exploited to develop an effective selection for bacterial AS transfectants of a number of wild-type AS+ cell lines of rat, Chinese hamster, mouse, and human origin. LR-73 cells, a Chinese hamster AS+ cell line, were transfected with pSV2-AS with an efficiency of about 1,000 colonies per 0.5 microgram of DNA per 10(6) cells. The integrated construct in these cells was amplified by incubation of the transfectants in increasing concentrations of beta-aspartyl hydroxamate. Advantages and disadvantages of this new dominant, selectable, and amplifiable marker over markers commonly used in shuttle vectors are discussed.
Nail Polish Try-On: Realtime Semantic Segmentation of Small Objects for\n Native and Browser Smartphone AR Applications (2019)

We provide a system for semantic segmentation of small objects that enables\nnail polish try-on AR applications to run client-side in realtime in native and\nweb mobile applications. By adjusting input resolution and neural network\ndepth, our model design enables a smooth trade-off of performance and runtime,\nwith the highest performance setting achieving~\\num{94.5} mIoU at 29.8ms\nruntime in native applications on an iPad Pro. We also provide a postprocessing\nand rendering algorithm for nail polish try-on, which integrates with our\nsemantic segmentation and fingernail base-tip direction predictions.\n
Genome-wide DNA methylation analysis during non-alcoholic steatohepatitis-related multistage hepatocarcinogenesis: comparison with hepatitis virus-related carcinogenesis (2017)

The aim of this study was to clarify the significance of DNA methylation alterations during non-alcoholic steatohepatitis (NASH)-related hepatocarcinogenesis. Single-CpG-resolution genome-wide DNA methylation analysis was performed on 264 liver tissue samples using the Illumina Infinium HumanMethylation450 BeadChip. After Bonferroni correction, 3331 probes showed significant DNA methylation alterations in 113 samples of non-cancerous liver tissue showing NASH (NASH-N) as compared with 55 samples of normal liver tissue (NLT). Principal component analysis using the 3331 probes revealed distinct DNA methylation profiles of NASH-N samples that were different from those of NLT samples and 37 samples of non-cancerous liver tissue showing chronic hepatitis or cirrhosis associated with hepatitis B virus (HBV) or hepatitis C virus (HCV) infection (viral-N). Receiver operating characteristic curve analysis identified 194 probes that were able to discriminate NASH-N samples from viral-N samples with area under the curve values of more than 0.95. Jonckheere-Terptsra trend test revealed that DNA methylation alterations in NASH-N samples from patients without hepatocellular carcinoma (HCC) were inherited by or strengthened in NASH-N samples from patients with HCC, and then inherited by or further strengthened in 22 samples of NASH-related HCC (NASH-T) themselves. NASH- and NASH-related HCC-specific DNA methylation alterations, which were not evident in viral-N samples and 37 samples of HCC associated with HBV or HCV infection, were observed in tumor-related genes, such as WHSC1, and were frequently associated with mRNA expression abnormalities. These data suggested that NASH-specific DNA methylation alterations may participate in NASH-related multistage hepatocarcinogenesis.
Encoded Self-Assembling Chemical Libraries (2005)

The display of chemical moieties at the extremity of synthetic oligonucleotides allows the self-assembly of large chemical libraries in which every chemical moiety is associated to a unique DNA sequence, serving as an 'identification bar code'. In this article, we describe the principles, the potential, and the challenges of this novel technology, which promises to facilitate the isolation of high-affinity binders to protein targets of biological and pharmaceutical interest.
Two Dimensional Unsteady Aerodynamics of Miniature Trailing Edge Effectors (2006)

Miniature trailing edge effectors (MiTEs) are small flaps, typically around 1% chord, actuated with deflection angles up to 90 degrees. Their small size, combined with low required power and good control authority, enables the devices to be used for high bandwidth control as well as conventional attitude control. However, some of the aerodynamic characteristics of these devices are complex and poorly understood. This paper describes time accurate computations that were performed using the INS2D flow solver to resolve unsteady characteristics including transient response and vortex shedding phenomena. The frequency response was studied to identify the dynamics of moving MiTEs, an important aspect of these new control devices.
An Extensible Compiler for Implementing Software Design Patterns as Concise Language Constructs (2021)

Design patterns are generic solutions to common programming problems. Design patterns represent a typical example of design reuse. However, implementing design patterns can lead to several problems, such as programming overhead and traceability. Existing research introduced several approaches to alleviate the implementation issues of design patterns. Nevertheless, existing approaches pose different implementation restrictions and require programmers to be aware of how design patterns should be implemented. Such approaches make the source code more prone to faults and defects. In addition, existing design pattern implementation approaches limit programmers to apply specific scenarios of design patterns (e.g. class-level), while other approaches require scattering implementation code snippets throughout the program. Such restrictions negatively impact understanding, tracing, or reusing design patterns. In this paper, we propose a novel approach to support the implementation of software design patterns as an extensible Java compiler. Our approach allows developers to use concise, easy-to-use language constructs to apply design patterns in their code. In addition, our approach allows the application of design patterns in different scenarios. We illustrate our approach using three commonly used design patterns, namely Singleton, Observer and Decorator. We show, through illustrative examples, how our design pattern constructs can significantly simplify implementing design patterns in a flexible, reusable and traceable manner. Moreover, our design pattern constructs allow class-level and instance-level implementations of design patterns.
Design and analysis of an axial flux magnetically geared generator (2015)

Axial flux magnetically geared machines offer the potential to achieve exceptional torque densities at high diameters. This work proposes a topology for an axial flux magnetically geared machine, in which the electric machine is placed in the bore of the axial flux magnetic gear. This new topology offers the advantage of correctly matching the size of the electric machine to its required torque without increasing the volume of the system beyond that of the magnetic gear. A proof of concept prototype with a torque density of 7.8 kNm/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> was designed, fabricated, and tested to evaluate the novel topology. A less conservative alternate design capable of achieving 60.6 kNm/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> was also simulated to demonstrate the topology's potential for high torque densities, and even higher torque densities can be reached at larger scale designs.
A low profile compact reconfigurable MIMO antenna for cognitive radio applications (2015)

A novel meandered line, multi-band, planar inverted F shape frequency agile multiple-input multiple-output (MIMO) antenna is presented. The proposed dual-element MIMO antenna is compact with frequency tuning capability over a wide-band. The frequency reconfigurability was achieved using a unique combination of PIN and varactor diodes. PIN diodes are used for mode selection while the varactor diode is used to sweep the frequency over a wide band especially below 1 GHz. The proposed single substrate design is compact with small form factor and suitable for small wireless handheld devices for cognitive radio applications. Good MIMO performance metrics were achieved with reasonable isolation. The antenna system is developed on a single substrate area of dimensions 65×120×1.56 mm3.
Low-voltage electro-optic polymer modulators (2006)

Electro-optic (EO) polymer modulators have demonstrated high speed external modulation of optical signals. Additionally, EO polymers have closely matched refractive indices at optical and microwave wavelengths, which enables high bandwidth operation. An EO polymer includes a polymer matrix and an organic "push-pull" chromophore that can be modified to give poled polymers with high EO activity. This high EO activity and optical-microwave velocity match offer the promise of accomplishing broadband, high speed optical modulation with low drive voltage. Such optical signal modulation is critical for applications in phased array radar and RF photonics. However, practical fabrication of optical modulators that realize the potential of EO polymers requires clad materials with optimized properties such as conductivity, dielectric constant, optical loss, and refractive index. In addition, other practical issues such as electrode design, optical fiber coupling, and hermetic packaging are critical in final device performance. We report on high-speed electrode parameters as well as electro-optic performance versus frequency of modulators fabricated on 6" silicon wafers. The r<sub>33</sub> values measured on single layer thin films are compared with those resulting from V<sub>π</sub> measurements on devices. We compare the effect of EO polymer morphology on device fabrication and optical loss for different EO polymers.
Serotypes and Polyacrylamide Gel Electrophoresis Types among Disease-Associated Isolates of Group B Neisseria meningitidis in Spain, 1976-1979 (1983)

A high annual incidence of meningococcal meningitis and septicemia occurred in Spain from 1976 through 1980 with a peak of 19 cases per 100,000 population in 1979. Approximately 80% were caused by group B Neisseria meningitidis. Studies were undertaken to determine the distribution of groups, outer membrane protein serotypes and polyacrylamide gel electrophoresis (PAGE) types among 338 disease-associated group B isolates from six regions of Spain. The related serotypes 1, 8, and 15 accounted for 38% (129 of 338) of the isolates. Serotype 2, the major disease type in the United States, was responsible for 14% (48 of 338) of the disease in Spain and was prevalent in only one region. Forty-three percent (146 of 338) were nonserotypable. The predominant PAGE type among the nonserotypable strains was PAGE type IV (79%). These studies demonstrate the necessity of surveillance for selection of suitable serotypes to be included in protective group B meningococcal vaccines.
A Kalman Filtering Framework for Physiological Detection of Anxiety-Related Arousal in Children With Autism Spectrum Disorder (2014)

Our results show that the proposed method can detect physiological arousal associated with anxiety with high accuracy, providing support for technical feasibility of augmenting anxiety treatments with automatic detection techniques. This approach can ultimately lead to more effective anxiety treatment for a larger and more diverse population.
Link Structure Graphs for Representing and Analyzing Web Sites (2006)

Standard Web graph representation fails to capture topic association and functional groupings of links and their occurrence across pages in the site. That limits its applicability and usefulness. In this paper we introduce a novel method for representing hypertext organization of Web sites in the form of Link Structure Graphs (LSGs). The LSG captures both the organization of links at the page level and the overall hyperlink structure of the collection of pages. It comprises vertices that correspond to link blocks of several types and edges that describe reuse of such blocks across pages. Identification of link blocks is approximated by the analysis of the HTML Document Object Model (DOM). Further differentiation of blocks into types is based on the recurrence of block elements across pages. The method gives rise to a compact representation of all the hyperlinks on the site and enables novel analysis of the site organization. Our approach is supported by the findings of an exploratory user study that reveals how the hyperlink structure is generally perceived by the users. We apply the algorithm to a sample of Web sites and discuss their link structure properties. Furthermore, we demonstrate that selective crawling strategies can be applied to generate key elements of the LSG incrementally. This further broadens the scope of LSG applicability.
A small-molecule antivirulence agent for treating <i>Clostridium difficile</i> infection (2015)

Clostridium difficile infection (CDI) is a worldwide health threat that is typically triggered by the use of broad-spectrum antibiotics, which disrupt the natural gut microbiota and allow this Gram-positive anaerobic pathogen to thrive. The increased incidence and severity of disease coupled with decreased response, high recurrence rates, and emergence of multiple antibiotic-resistant strains have created an urgent need for new therapies. We describe pharmacological targeting of the cysteine protease domain (CPD) within the C. difficile major virulence factor toxin B (TcdB). Through a targeted screen with an activity-based probe for this protease domain, we identified a number of potent CPD inhibitors, including one bioactive compound, ebselen, which is currently in human clinical trials for a clinically unrelated indication. This drug showed activity against both major virulence factors, TcdA and TcdB, in biochemical and cell-based studies. Treatment in a mouse model of CDI that closely resembles the human infection confirmed a therapeutic benefit in the form of reduced disease pathology in host tissues that correlated with inhibition of the release of the toxic glucosyltransferase domain (GTD). Our results show that this non-antibiotic drug can modulate the pathology of disease and therefore could potentially be developed as a therapeutic for the treatment of CDI.
Recognition of viral hemagglutinins by NKp44 but not by NKp30 (2001)

Natural killer (NK) cells destroy virus-infected and tumor cells without prior antigen stimulation. The NK cell cytotoxicity is regulated in large part by the expression of NK cell receptors that are able to bind major histocompatibility complex (MHC) class I glycoproteins. NK cells also express lysis triggering receptors specific for non-MHC ligands, including NKp30, NKp44, NKp46 and CD16. However, the nature of their ligands, recognized on target cells, is undefined. We have recently shown that the NKp46 protein, but not the CD16 protein, recognizes the hemagglutinin (HA) of influenza virus (IV) and the hemagglutinin-neuraminidase (HN) of Sendai virus (SV), and that the recognition of HA from IV requires the sialylation of NKp46 oligosaccharides. We have also demonstrated that binding of NKp46 to HA of IV is required for lysis of cells expressing the corresponding glycoproteins by a substantial subset of NK clones. Here we show that NKp44, but not NKp30, can also recognize the HA of both IV and SV and that the recognition of IV HA requires the sialylation of the NKp44 receptor in a similar way to that of NKp46. SV infection of 721.221 cells expressing MHC class I proteinsresulted in the abrogation of the inhibition by NK clones expressing high levels of NKp44. In addition, the binding of NKp44 to HA improves the ability of some NK clones to lyse IV infected cells.