gebhart/patrepeval huggingface dataset:
Three-dimensional photoacoustic tomography based on the focal-line concept (2011)

A full ring ultrasonic array-based photoacoustic tomography system was recently developed for small animal brain imaging. The 512-element array is cylindrically focused in the elevational direction, and can acquire a two-dimensional (2D) image in 1.6 s. In this letter, we demonstrate the three-dimensional (3D) imaging capability of this system. A novel 3D reconstruction algorithm was developed based on the focal-line concept. Compared to 3D images acquired simply by stacking a series of 2D images, the 3D focal-line reconstruction method renders images with much less artifacts, and improves the elevational resolution by 30% and the signal-to-noise ratio by two times. The effectiveness of the proposed algorithm was first validated by numerical simulations and then demonstrated with a hair phantom experiment and an ex vivo mouse embryo experiment.
Authentication and Secured Execution for the Infrastructure-as-a-Service Layer of the Cloud Computing Model (2013)

This paper presents a full system architecture allowing the authentication and secured execution of binary files using hardware-assisted on-the-fly memory encryption/decryption. In a context of general blurring of the physical relationship between a user and the computer which which it eventually interacts, this architecture has been thought so as to achieve a certain degree of robustness against corruptions in a cloud computing IaaS software stack, including when the corruptions may come from the lowest hyper vision layer.
Quantum Well Thermoelectric Devices (2005)

Fabrication development of high efficiency quantum well (QW) thermoelectric continues with the P-type B4C/B9C and N-type Si/SiGe films. Si/SiC is being developed to replace Si/SiGe for higher temperature operation. Both isothermal and gradient life testing are underway. One couple has achieved 700 hours at TH of 300°C and TC of 50°C with no degradation. Emphasis is now shifting towards couple and module design and fabrication. Preliminary design calculations regarding the development of actual quantum well modules will be presented for both power prediction and cooling applications. These modules can be used in future energy conversion system as well as air conditioning system designs.
Dual-reporter high-throughput screen for small-molecule in vivo inhibitors of plasminogen activator inhibitor type-1 yields a clinical lead candidate (2018)

Plasminogen activator inhibitor type-1 (PAI-1) is a <u>ser</u>ine <u>p</u>rotease <u>in</u>hibitor (serpin) implicated in numerous pathological processes, including coronary heart disease, arterial and venous thrombosis, and chronic fibrotic diseases. These associations have made PAI-1 an attractive pharmaceutical target. However, the complexity of the serpin inhibitory mechanism, the inherent metastability of serpins, and the high-affinity association of PAI-1 with vitronectin <i>in vivo</i> have made it difficult to identify pharmacologically effective small-molecule inhibitors. Moreover, the majority of current small-molecule PAI-1 inhibitors are poor pharmaceutical candidates. To this end and to find leads that can be efficiently applied to <i>in vivo</i> settings, we developed a dual-reporter high-throughput screen (HTS) that reduced the rate of nonspecific and promiscuous hits and identified leads that inhibit human PAI-1 in the high-protein environments present <i>in vivo</i> Using this system, we screened >152,000 pure compounds and 27,000 natural product extracts (NPEs), reducing the apparent hit rate by almost 10-fold compared with previous screening approaches. Furthermore, screening in a high-protein environment permitted the identification of compounds that retained activity in both <i>ex vivo</i> plasma and <i>in vivo</i> Following lead identification, subsequent medicinal chemistry and structure-activity relationship (SAR) studies identified a lead clinical candidate, MDI-2268, having excellent pharmacokinetics, potent activity against vitronectin-bound PAI-1 <i>in vivo</i>, and efficacy in a murine model of venous thrombosis. This rigorous HTS approach eliminates promiscuous candidate leads, significantly accelerates the process of identifying PAI-1 inhibitors that can be rapidly deployed <i>in vivo</i>, and has enabled identification of a potent lead compound.
DBPD: A Dynamic Birthmark-based Software Plagiarism Detection Tool (2017)

With the burst of open source software, software plagiarism has been a serious threat to the software industry. In this paper, we present the demo tool DBPD: Dynamic Birthmark-based Software Plagiarism Detection. Major features of DBPD could be summarized as: 1) dynamic birthmark. The execution process of software is captured to generate the birthmark reflecting intrinsic properties of software; 2) high availability. It is available for crossplatform and binary executable’s plagiarism detection; 3) customizable. The birthmarks, similarity calculation metrics and detection criteria are configurable. The DBPD is implemented using C++ and Java, and currently can work under both Windows and Linux system. Three dynamic birthmarks are implemented in DBPD to identify the software according to its instruction, stack operation and system call.
Multimode interference devices with input-output ports on the sides (2006)

Multimode interference (MMI) devices are useful for power splitting and for the separation or combination of wavelengths or polarizations, usually in integrated optics. Input-output guides connect to the MMI region by ports. In all previously reported MMI devices, the input and output guides connect only to the ends of the MMI region; i.e., they are end ported. What is believed to be a novel arrangement of the input-output ports on MMI devices is described. By placing input-output ports either partially or entirely on the sides of the MMI region (i.e., side porting), a variety of benefits are achieved and a variety of new devices can be made.
Transductional Targeting with Recombinant Adenovirus Vectors (2002)

Replication-deficient adenoviruses are considered as gene delivery vectors for the genetic treatment of a variety of diseases. The ability of such vectors to mediate efficient expression of therapeutic genes in a broad spectrum of dividing and non-dividing cell types constitutes an advantage over alternative gene transfer vectors. However, this broad tissue tropism may also turn disadvantageous when genes encoding potentially harmful proteins (e.g. cytokines, toxic proteins) are expressed in surrounding normal tissues. Therefore, specific restrictions of the viral tropism would represent a significant technological advance towards safer and more efficient gene delivery vectors, in particular for cancer gene therapy applications. In this review, we summarize various strategies used to selectively modify the natural tropism of recombinant adenoviruses. The advantages, limitations and potential impact on gene therapy operations of such modified vectors are discussed.
A simple rolling mill model with linear quadratic optimal controller (2003)

The tandem rolling of metal is a complex engineering process whose optimization represents a challenging control problem. The current technology relies on complex nonlinear models that are used to develop control strategies to address the various control problems encountered. Such models however, necessitate extensive computational requirements for simulation. Also, in various instances, access to the detailed models may be unavailable, or computational capability may be limited, yet it is desired to obtain some rough indication of performance of specific control systems when coupled to the mill. Thus the need arises for a simplified model (which can be easily implemented on a PC) for testing of control concepts. This paper fulfills such a need by providing a simple linearized model of the mill. An example of the usefulness of the model is presented by coupling to a linear quadratic optimal controller with a simple method to mitigate disturbances in incoming metal thickness. Satisfactory results are demonstrated by a simulation.
Utilization of Filamentous Phage ϕRSM3 to Control Bacterial Wilt Caused by <i>Ralstonia solanacearum</i> (2012)

The wide host range of Ralstonia solanacearum, causal agent of bacterial wilt, and its ability to survive for long periods in the environment restrict the effectiveness of cultural and chemical control measures. The use of phages for disease control is a fast-expanding trend of plant protection with great potential to replace chemical measures. The filamentous phage ϕRSM3 that infects R. solanacearum strains and inactivates virulence on plants is a potential agent for controlling bacterial wilt in tomato. We demonstrated that inoculation of ϕRSM3-infected cells into tomato plants did not cause bacterial wilt. Instead, ϕRSM3-infected cells enhanced the expression of pathogenesis-related (PR) genes, including PR-1a, PR-2b, and PR7, in tomato plants. Moreover, pretreatment with ϕRSM-infected cells protect tomato plants from infection by virulent R. solanacearum strains. The effective dose of ϕRSM3-infected cells for disease prevention was determined to be approximately 10<sup>5</sup> CFU/ml. Because the ϕRSM3-infected cells can grow and continue to produce infectious phage particles under appropriate conditions, ϕRSM phages may serve as an efficient tool to control bacterial wilt in crops.
<title>Improved Dark-Field-Like Surface Inspection Technique Using Total Internal Reflection</title> (1980)

This paper describes a method of illuminating the region at and near the surface of a transparent sample or of a film on a transparent substrate. The features then observed, using ordinary microscopic magnification, are a speckle pattern due to surface roughness and discrete points of light due to localized point scattering sites both on and just within the surface. While the technique is similar to dark-field microscopy, here the region just within the surface is highly illuminated, and additional information concerning the size and position of scattering sites can be learned. In this technique the surface is illuminated from within the sample with a well-collimated polarized laser beam at an angle of incidence equal to or greater than the critical angle. When using an s-polarized beam, a standing wave pattern is set up just within the surface of the sample. Since the incident beam is totally reflected, the antinodes have four times the incident beam intensity and the nodes have zero intensity. This standing wave pattern may be translated and the nodal spacing may be changed by changing the angle of incidence and/or changing the laser wave-length. This allows selective illumination of various surface features. Additionally, by the use of a film of matching fluid on the surface under inspection, the roughness-caused speckle pattern may be eliminated leaving only the light coming from point scattering sites. We will describe methods of using this technique to determine certain size and positional features of the discrete scattering sites. Examples of various surfaces as viewed by this technique and other standard techniques are compared. This inspection technique has been used to study surface cleaning methods, laser damage nucleation sites, and ion milling of optical surfaces.
Majorana-like Photons from Vector Vortex Beams of Classically Entangled Photons Propagating through Brain (2019)

Majorana like photons are introduced from class of classically entangled Cylindrical Vector Vortex Beams. An enhanced transmission is observed in mouse brain from Majorana vector photons with orbital angular momentum due to their non-separability.
Abstract 1762: Keratin 17 identifies prognostic subtypes of pancreatic ductal adenocarcinoma (2017)

Abstract Recent RNA sequencing (RNASeq) studies from Bailey et al., 2016, Moffitt et al., 2015 and Collisson et al., 2011 reported that mRNA expression from bulk tumor defines molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) that are highly correlated with patient survival. These studies independently identified Keratin 17 (K17) mRNA overexpression as one of over 20 upregulated transcripts that define the RNA signature of the most lethal PDACs. Studies in our lab determined that neither K17 gene missense mutations nor copy-number alterations explain the upregulation of K17 mRNA expression by malignant cells. In addition, we found that K17 expression, measured at the protein level by immunohistochemistry or at the level of mRNA by RNASeq, is sufficient to stratify patients by short- vs long- term survival at baseline after resection. These retrospective survival analyses were performed in four independent patient cohorts using a uniform threshold to define low- vs high- K17 patients (total n= 558). High-K17 cases were twice as likely to die from this disease compared to stage-matched low-K17 cases (P values &lt; 0.05). Furthermore, we determined that K17 expression is associated with outcome after Gemcitabine treatment using the Bailey et al., 2016 patient cohort (n= 94). This is the first study to show that the expression of a single gene, K17, can accurately subtype PDAC at initial diagnosis. In conclusion, K17 was identified as a robust and independent, clinically relevant, prognostic and predictive biomarker to stratify clinical outcome at the time of initial diagnosis and to potentially inform clinical decisions regarding chemotherapeutic intervention. Citation Format: Luisa F. Escobar-Hoyos, Cindy Leiton, Elizabeth Vanner, Lucia Roa-Pena, Jinyu Li, Scott Powers, Ali Akalin, Jela Bandovic, Peter Bailey, David Chang, Richard Moffitt, Jen Jen Yeh, Andrew Biankin, Kenneth Shroyer. Keratin 17 identifies prognostic subtypes of pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1762. doi:10.1158/1538-7445.AM2017-1762
Time-Regulated Actuation Signal for Enhancement of Droplet Transportation in Digital Microfluidics, (2014)

Digital Microfluidics (DMF) is an attractive technology for biological/chemical micro-reactions due to its distinct droplet manageability via electronic automation. However, the limited velocity of droplet transportation has hindered DMF from being utilized in high throughput applications. Here we introduce two novel control-engaged electrode-driving techniques: Natural Discharge after Pulse (NDAP) and Cooperative Electrodes (CE). NDAP is based on a series of DC pulses and multi-cycle natural discharging coordinated with the droplet dynamic motions, facilitating real-time droplet position sensing. CE is an early-charging of the target electrode before discharging the current one to avoid droplet deformation and local vibration at the gaps between two electrodes. By combining NDAP with CE, we have for the first time increased the droplet transportation efficiency without compromising the lifetime of electrodes in DMF. This work, together with our previous publications, should be valuable for scientists and engineers working on enhancing the throughput and the reliability of control-engaged DMF systems for automated applications.
Novel Monoclonal Antibodies Against the Proximal (Carboxy-Terminal) Portions of MUC16 (2010)

The CA125 antigen, recognized by the OC125 antibody, is a tissue-specific circulating antigen expressed in ovarian cancer. The CA125 antigen is encoded by the MUC16 gene cloned by Yin and Lloyd. The full-length gene describes a complex tethered mucin protein present primarily in a variety of gynecologic tissues, especially neoplasms. OC125 and other related antibodies react with glycosylation-dependent antigens present exclusively in the cleaved portion of the molecule. These antibodies are not useful as screening tools, nor can they detect the proximal residual MUC16 protein fragment after cleavage. This has limited its diagnostic and therapeutic applications. Using synthetic peptides, we raised novel-specific antibodies to the carboxy-terminal portion of MUC16 retained by the cell proximal to the putative cleavage site. These antibodies were characterized using fluorescence-activated cell-sorting analysis, enzyme-linked immunoassay, Western blot analysis, and immunohistochemistry. Each of the selected monoclonal antibodies was reactive against recombinant GST-ΔMUC16 protein and the MUC16-transfected SKOV3 cell line. Three antibodies, 4H11, 9C9, and 4A5 antibodies showed high affinities by Western blot analysis and saturation-binding studies of transfected-SKOV3 cells and displayed antibody internalization. Immunohistochemical positivity with novel antibody 4H11 was similar to OC125 but with important differences, including diffuse positivity in lobular breast cancer and a small percentage of OC125-negative ovarian carcinomas that showed intense and diffuse 4H11. Development of such antibodies may be useful for the characterization of MUC16 biology and allow for future studies in targeted therapy and diagnostics.
A functionally graded shape memory polymer (2010)

In this article we describe the preparation and characterization of a functionally graded shape memory polymer (SMP) that, unlike conventional SMPs, has a range of transition temperatures that are spatially distributed in a gradient fashion within one single article. This is achieved by post-curing a pre-cured glassy SMP in a linear temperature gradient that imposes different vitrification temperature limits at different positions along the gradient. Utilizing indentation-based surface shape memory coupled with optical measurements of photoelastic response, the capability of this material to respond over a wide range of thermal triggers is examined and correlated with the graded glass transition behavior. The shape recovery response of the gradient SMP under a condition of continuous heating is demonstrated. This new class of SMP offers great potential for such applications as passive temperature sensing and precise control of shape evolution during a thermally triggered shape recovery.
Production of hydrocarbon gases from oil shale. [low molecular weight paraffinic hydrocarbon gases formed from preheated and prehydrogenated organic hydrocarbon portion of oil shale] (1975)

The oil shale is gradually preheated in a preheat and prehydrogenation zone to a temperature of about 700/sup 0/ to about 950/sup 0/F in the presence of hydrogen-rich gas without substantial production of liquid or gas in the preheat and prehydrogenation zone. Then the preheated and prehydrogenated oil shale is treated in a hydrogasification zone at a temperature of about 1,200/sup 0/ to about 1,500/sup 0/F in the presence of hydrogen-rich gas to form predominately low molecular weight paraffinic hydrocarbon gases from the preheated and prehydrogenated organic hydrocarbon portion of the oil shale. The hydrogen-rich gas may be passed countercurrent in thermal exchange relation to the spent shale to recover heat from the spent shale heating the hydrogen-rich gas for passage countercurrent and in thermal exchange relation to fresh oil shale in the preheat and prehydrogenation zone. The improvement of this process lies in the exceptionally high conversion of the organic component of oil shale to products of high value having high content of low molecular weight paraffinic hydrocarbon gases. (auth)
Community enhanced tutorials (2013)

Web-based tutorials are a popular help resource for learning how to perform unfamiliar tasks in complex software. However, in their current form, web tutorials are isolated from the applications that they support. In this paper we present FollowUs, a web-tutorial system that integrates a fully-featured application into a web-based tutorial. This novel architecture enables community enhanced tutorials, which continuously improve as more users work with them. FollowUs captures video demonstrations of users as they perform a tutorial. Subsequent users can use the original tutorial, or choose from a library of captured community demonstrations of each tutorial step. We conducted a user study to test the benefits of making multiple demonstrations available to users, and found that users perform significantly better using our system with a library of multiple demonstrations in comparison to its equivalent baseline system with only the original authored content.
Tricyclic Pyrazoles. 4. Synthesis and Biological Evaluation of Analogues of the Robust and Selective CB<sub>2</sub>Cannabinoid Ligand 1-(2‘,4‘-Dichlorophenyl)-6-methyl-<i>N</i>-piperidin-1-yl- 1,4-dihydroindeno[1,2-<i>c</i>]pyrazole-3-carboxamide (2006)

New analogues (2a-p) of the previously reported CB(2) ligands 6-methyl- and 6-chloro-1-(2',4'-dichlorophenyl)-N-piperidin-1-yl-1,4-dihydroindeno[1,2-c]pyrazole-3-carboxamides (1a,b) have been synthesized and evaluated for cannabinoid receptor affinity. One example, 1-(2',4'-dichlorophenyl)-6-methyl-N-cyclohexyilamine-1,4-dihydroindeno[1,2-c] pyrazole-3-carboxamide (2a) was shown to have single digit nanomolar affinity for cannabinoid CB(2) receptors. Furthermore, compounds 2a and 2b, as well as lead structures 1a,b, were also shown to be agonist in an in vitro model based on human promyelocytic leukemia HL-60 cells.
Production and Characterization of Saratin, an Inhibitor of von Willebrand Factor-Dependent Platelet Adhesion to Collagen (2001)

Platelets tether to collagen in both a von Willebrand factor (vWF)-dependent and a vWF-independent manner. We have recently characterized a recombinant protein, saratin, isolated from the saliva of the leech Hirudo medicinalis, expressed it in Hansenula polymorpha, and studied its effect on direct and indirect platelet-collagen interactions. Saratin dose dependently inhibited the binding of purified human vWF to human type I and III collagens (IC(50)= 0.23 +/- 0.004 and 0.81 +/- 0.04 microg mL(-1), respectively) and to calf skin collagen (IC(50)= 0.44 +/- 0.008 microg mL(-1)). Furthermore, saratin showed a similar inhibitory potency against the binding of human, rodent, and porcine plasma vWF to these collagens. In a flow chamber under conditions of elevated shear (2700 s(-1)), saratin dose dependently and potently inhibited platelet aggregate formation on a collagen-coated surface (IC(50)= 0.96 +/- 0.25 microg mL(-1)), but at reduced shear (1300 s(-1)) a rightward shift in the dose-response curve was noted (IC(50)= 5.2 +/- 1.4 microg mL(-1)). Surface plasmon resonance analysis revealed both high and low affinity binding sites for saratin on human collagen type III (K(d) 5 x 10(-8) M and 2 x 10(-6) M, respectively). Although low concentrations of saratin, which inhibited platelet adhesion under increased shear (i.e., saturation of high-affinity binding sites), had no effect on vWF-independent collagen-induced platelet aggregation, high concentrations (i.e., saturation of low-affinity binding sites) were found to inhibit platelet aggregation. These data demonstrate that saratin is a potent inhibitor of vWF-dependent platelet adhesion to collagen and hence may have therapeutic potential as an antithrombotic agent.
Interband cascade laser emitting at λ=3.75μm in continuous wave above room temperature (2008)

We report a five-stage interband cascade laser that operates at λ=3.75μm in cw mode up to a maximum temperature of 319K. With gold electroplating, epitaxial-side-up mounting, and one facet coated for high reflectivity, a 3mm×9.2μm ridge emits over 10mW of cw power at 300K.