gebhart/patrepeval huggingface dataset:
Colon cancer specific nuclear matrix protein alterations in human colonic adenomatous polyps (2003)

Most colon cancers arise within preexisting adenomatous polyps or adenomas. The slow evolution from the non-invasive premalignant lesion, the adenomatous polyp, to invasive cancer supports a strategy of early detection. Recently, we identified unique nuclear matrix proteins (NMPs) specific for colon cancer (CC2, CC3, CC4, CC5). Most of the NMPs identified are common to all cell types, but several identified NMPs are tissue and cell line specific. The objective of this study is to describe and characterize the NMP profile of premalignant adenomatous colon polyps. Specifically when in the adenoma-carcinoma sequence four specific colon cancer NMPs, previously described, appear. Using two-dimensional (2-D) gel analysis 20 colon polyps (one juvenile polyp, six tubular adenoma (TA), seven tubulovillous adenoma (TVA), six TVA with focal high-grade dysplasia (HGD), were analyzed for the presence of four (CC2, CC3, CC4, CC5) specific NMPs. CC2 was not seen in any of the premalignant polyps. CC5 was present in only two premalignant TVA with HGD and in one TA. CC3 and CC4 were present in most adenomas. None of the NMPs were seen in the juvenile polyp, which is not considered to be a precursor of colon cancer. CC2 and CC5 are NMPs expressed at the junction of an advanced adenoma and invasive colorectal cancer. CC3 and CC4 are expressed earlier in the evolution of adenomatous polyps. Development of an assay to these proteins may serve as a new method for early detection of colorectal cancer.
Improved coagulation and haemostasis in haemophilia with inhibitors by combinations of superFactor Va and Factor VIIa (2015)

Bypassing inhibitors in haemophilia patients is limited to activated (a) Factor(F)VII products. We introduced "FVa activity augmentation" as another bypassing strategy and studied effects of an engineered FVa variant designated superFVa. Procoagulant and clot stabilising properties of superFVa and recombinant human (rh)FVIIa, either alone or in combination, were studied in thrombin generation and clot lysis assays in normal human plasma (NHP) with or without anti-FVIII inhibitors, in haemophilia plasma, and in FVIII-deficient mice or in wild-type mice with anti-FVIII inhibitors. SuperFVa was as effective as rhFVIIa to improve thrombin generation or clot lysis. Furthermore, procoagulant effects were significantly enhanced when these compounds were combined. RhFVIIa at 40 nM (a therapeutic concentration) improved thrombin generation mildly, but markedly improved thrombin generation when combined with a low concentration (e. g. 3 nM) of superFVa. In clot lysis studies, the concentration of rhFVIIa to normalise clot lysis times could be reduced by 100-fold (e. g. from 40 nM to 0.4 nM) when combined with a low concentration (0.37 nM) of superFVa. In haemostasis studies of FVIII-deficient mice, blood loss was dose-dependently reduced by either superFVa or rhFVIIa. SuperFVa (200 U/kg) corrected mean blood loss indistinguishably from rhFVIII. Blood loss correction by rhFVIIa was greatly improved when combined with superFVa. Similar blood loss correction results were observed for therapies in wild-type mice after infusion with anti-FVIII inhibitors. Thus, superFVa may be an effective procoagulant agent in the setting of haemophilia with inhibitors and it merits further evaluation for new bypassing strategies.
Nanoscale Subsurface Imaging of Nanocomposites via Resonant Difference-Frequency Atomic Force Ultrasonic Microscopy (2007)

A scanning probe microscope methodology, called resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM), has been developed. The method employs an ultrasonic wave launched from the bottom of a sample while the cantilever of an atomic force microscope engages the sample top surface. The cantilever is driven at a frequency differing from the ultrasonic frequency by one of the contact resonance frequencies of the cantilever. The nonlinear mixing of the oscillating cantilever and the ultrasonic wave at the sample surface generates difference-frequency oscillations at the cantilever contact resonance. The resonance-enhanced difference-frequency signals are used to create amplitude and phase-generated images of nanoscale near-surface and subsurface features. RDF-AFUM phase images of LaRC-CP2 polyimide polymer containing embedded nanostructures are presented. A RDF-AFUM micrograph of a 12.7 micrometer thick film of LaRC-CP2 containing a monolayer of gold nanoparticles embedded 7 micrometers below the specimen surface reveals the occurrence of contiguous amorphous and crystalline phases within the bulk of the polymer and a preferential growth of the crystalline phase in the vicinity of the gold nanoparticles. A RDF-AFUM micrograph of LaRC-CP2 film containing randomly dispersed carbon nanotubes reveals the growth of an interphase region at certain nanotube-polymer interfaces.
Multitrack Power Conversion Architecture (2016)

This paper introduces a MultiTrack power conversion architecture that represents a new way of combining switched capacitor circuits and magnetics. The MultiTrack architecture takes advantages of the distributed power processing concept and a hybrid switched-capacitor/magnetics circuit structure. It reduces the voltage ratings on devices, reduces the voltage regulation stress of the system, improves the component utilization, and reduces the sizes of passive components. This architecture is suitable to dc- dc and grid-interface applications that require both isolation and wide voltage conversion range. An 18-80 V input, 5 V, 15 A output, 800 kHz, 0.93 in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> (1/16 brick equivalent) isolated dc-dc converter has been built and tested to verify the effectiveness of this architecture. By employing the MultiTrack architecture, utilizing GaN switches, and operating at higher frequencies, the prototype converter achieves a power density of 457.3 W/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> and a peak efficiency of 91.3%. Its power density is 3× higher than the state-of-the-art commercial converters with comparable efficiency across the wide operation range.
Analysis of safety implications for SJA-based robust UAS flight control technology (2015)

The cone of uncertainty of a small unmanned aerial vehicle's (UAV) flight trajectory induced by the aircraft's encounters with an upstream wake vortex or gust is addressed in the context of safety assessments for UAS operations. Such safety assessments will be a critical facet of the integration of unmanned aerial systems (UAS) into the National Airspace System (NAS), particularly in terminal airspace. This paper describes a predictive, robust feedback-loop flight control model that is applicable to various classes of UAVs and unsteady flight-path scenarios. The current test study investigates a new robust flight controller employing a `virtual' control surface, which is generated using arrays of synthetic-jet micro-actuators (SJA). For a given amplitude of the flow disturbance and UAS parameters, the model employed in this paper allows us to estimate UAS flight-path deviations and recovery time, as well as to identify the limits of the control authority. In addition, the computationally simplistic structure of the proposed robust flight control method can operate at a faster sample rate, which can enable a UAS to recover more quickly from external disturbances due to wind gusts, while effectively minimizing deviations from the desired flight trajectory.
Enhanced Macroblock Features for Dynamic Background Modeling in H.264/AVC Video Encoded at Low Bitrate (2016)

While H.264 is a well-established standard for video surveillance, its high-profile implementation, in particular, has the unique capabilities that pack more visual detail into a given bitrate. Several algorithms exist that detect moving objects from the H.264 bitstream, most of which end up incorrectly classifying the nonstationary or dynamic components (e.g., jitter camera, waving trees, ripples, etc.) of the background as foreground. Moreover, the coarse quantization schemes adopted at constrained bitrates pose new challenges for direct identification of moving objects/targets from the bitstream. This paper focuses on dynamic background modeling for the H.264 video encoded at very low bitrates. To this end, enhanced features of the fundamental coding unit, i.e., the macroblock (MB) are proposed. Based on the temporal statistics of the MB features gathered from initial frames, MBs that potentially contain parts of moving objects are selected in subsequent frames. The selected MBs constitute a coarse segmentation map of the foreground at the MB level. Finally, pixel-level segmentation of the foreground is obtained by comparing pixels constituting the selected MBs with the colocated counterparts of a background frame. Experimental results showing the comparison of bitstreams encoded at strikingly low bitrates are obtained over a diverse set of standardized surveillance sequences.
Biomechanical Comparison of Arthroscopic Repair Constructs for Meniscal Root Tears (2014)

Complex suture patterns can be placed via an all-inside arthroscopic technique delivering higher failure loads for meniscal root repair with little increase in surgical time.
Synthesis of bicyclic organo-peptide hybrids via oxime/intein-mediated macrocyclization followed by disulfide bond formation (2014)

A new strategy is described to generate bicyclic peptides that incorporate non-peptidic backbone elements starting from recombinant polypeptide precursors. These compounds are produced via a one-pot, two-step sequence, in which peptide macrocyclization by means of a bifunctional oxyamine/1,3-amino-thiol synthetic precursor is followed by intramolecular disulfide formation between the synthetic precursor-borne thiol and a cysteine embedded in the peptide sequence. This approach was found to be compatible with the cysteine residue occupying different positions within 8mer and 10mer target peptide sequences and across different synthetic precursor scaffolds, thereby enabling the formation of a variety of diverse bicyclic scaffolds.
Micro SIDs: A Solution for Efficient Representation of Segment IDs in SRv6 Networks (2022)

The Segment Routing (SR) architecture is based on source routing. Within an SR enabled network, a list of instructions called segments can be added to the packet headers to influence the forwarding and the processing of the packets. In SRv6 (Segment Routing over IPv6 data plane) the segments are represented with IPv6 addresses, which are 16 bytes long. There are some SRv6 service scenarios that may require to carry a large number of segments in the IPv6 packet headers. Reducing the size of these overheads is useful to minimize the impact on MTU (Maximum Transfer Unit) and to enable SRv6 on legacy hardware devices with limited processing capabilities that could suffer from the long headers. In this paper we present the Micro SID solution for the efficient representation of segment identifiers. The proposed Micro SID solution has been implemented on three different architectures (VPP, Linux, P4) and interoperability tests have been performed. We also analyze the reduction of the header size that can be achieved with Micro SIDs and compare it with other proposals for segment list compression. Our results show that the header size can be reduced up to 75%. Finally, we mention that a fundamental asset of the proposed Micro SID solution is the full compatibility and seamless interoperability with existing SRv6 architecture.
Synthesis and Anti-HIV Activities of Suramin Conjugates of 3'-Fluoro- 2',3'-dideoxythymidine and 3'-Azido-2',3'-dideoxythymidine (2012)

Conjugates between suramin, a polyanionic naphthalene sulfonate derivative, and nucleoside reverse transcriptase inhibitors (NRTIs), 3'-azido-2',3'-dideoxythymidine (AZT) and 3'-fluoro-2',3'-dideoxythymidine (FLT), were designed to create an antiretroviral with multiple mechanisms of action that could be developed as an anti-HIV topical microbicide candidate. The anti-HIV activity of these conjugates was compared with that of suramin and the corresponding physical mixtures of suramin and nucleosides. The conjugates were synthesized as sulfonate esters by reaction of suramin with the nucleoside analogs in the presence of phosphorus pentoxide, and were tested against X4 and R5 labadapted strains of HIV-1. Suramin conjugates of AZT (EC50= 19.4 μg/ml) and FLT (EC50= 23.6 μg/ml) demonstrated improved anti-HIV activity against X4 strain of virus by 2.5 and 2 fold, respectively, when compared with suramin. The physical mixtures of suramin with nucleosides significantly improved anti-HIV activity of suramin against X4 strain by more than 55 fold.
Quantitative Trait Loci for Partial Resistance to <i>Phytophthora sojae</i> in Soybean (2003)

Partial resistance to Phytophthora sojae Kauffmann and Gerdemann in soybean [ Glycine max (L.) Merr.] is expressed as a reduced level of root rot and is effective against all populations of the pathogen. The objective of this study was to identify simple sequence repeat (SSR) markers associated with putative quantitative trait loci (QTLs) for partial resistance to P. sojae in the soybean ‘Conrad’. Three recombinant inbred soybean populations, Conrad × ‘Sloan’, Conrad × ‘Harosoy’, and Conrad × ‘Williams’, were evaluated for root lesion growth rate in growth chamber experiments following inoculation with P. sojae and with SSR markers to identify putative QTLs. The three populations segregated for root lesion growth rate after root inoculations. Two putative QTLs donated by Conrad were identified in all three populations and were positioned on soybean molecular linkage groups (MLGs) F and D1b+W. The QTL on MLG F explained 32.4, 35.0, and 21.4% of the genotypic variation for Conrad × Sloan, Conrad × Harosoy, and Conrad × Williams populations, respectively. The QTL on MLG D1b+W explained 10.6, 15.9, and 20.7% of the genotypic variation for the same three populations, respectively. The QTL on MLG F appears to be of more value based on the percentage of genotypic variation explained. Because the results indicate that QTLs for partial resistance to P. sojae map to different regions in soybean compared with the known Rps genes poses a challenge to soybean breeders. Marker‐assisted selection may expedite the process of combining both Rps genes with partial resistance into high‐yielding cultivars.
Stable P-wave modeling for reverse-time migration in tilted TI media (2011)

We present an approach for P-wave modeling in inhomogeneous transversely isotropic media with tilted symmetry axis (TTI media), suitable for anisotropic reverse-time migration. The proposed approach is based on wave equations derived from first principles — the equations of motion and Hooke’s law — under the acoustic TI approximation. Consequently, no assumptions are made about the spatial variation of medium parameters. A rotation of the stress and strain tensors to a local coordinate system, aligned with the TI-symmetry axis, makes it possible to benefit from the simple and sparse form of the TI-elastic tensor in that system. The resulting wave equations can be formulated either as a set of five first-order or as a set of two second-order partial differential equations. For the constant-density case, the second-order TTI wave equations involve mixed and nonmixed second-order spatial derivatives with respect to global, nonrotated coordinates. We propose a numerical implementation of these equations using high-order centered finite differences. To minimize modeling artifacts related to the use of centered first-derivative operators, we use discrete second-derivative operators for the nonmixed second-order spatial derivatives and repeated discrete first-derivative operators for the mixed derivatives. Such a combination of finite-difference operators leads to a stable wave propagator, provided that the operators are designed properly. In practice, stability is achieved by slightly weighting down terms that contain mixed derivatives. This has a minor, practically negligible, effect on the kinematics of wave propagation. The stability of the presented scheme in inhomogeneous TTI models with rapidly varying anisotropic symmetry axis direction is demonstrated with numerical examples.
Phenotypic Effect of Isogenic<i>uspA1</i>and<i>uspA2</i>Mutations on<i>Moraxella catarrhalis</i>035E (1998)

The UspA surface antigen of Moraxella catarrhalis was recently shown to be comprised of two different proteins (UspA1 and UspA2) which share an internal region containing 140 amino acids with 93% identity (C. Aebi, I. Maciver, J. L. Latimer, L. D. Cope, M. K. Stevens, S. E. Thomas, G. H. McCracken, Jr., and E. J. Hansen, Infect. Immun. 65:4367-4377, 1997). Isogenic uspA1, uspA2, and uspA1 uspA2 mutants were tested in a number of in vitro systems to determine what effect these mutations, either individually or together, might exert on the phenotype of M. catarrhalis 035E. Monoclonal antibodies specific for UspA1 or UspA2 were used in an indirect antibody accessibility assay to prove that both of these proteins were expressed on the surface of M. catarrhalis. All three mutants grew in vitro at the same rate and did not exhibit autoagglutination or hemagglutination properties that were detectably different from those of the wild-type parent strain. When tested for the ability to adhere to human epithelial cells, the wild-type parent strain and the uspA2 mutant readily attached to Chang conjunctival cells. In contrast, the uspA1 mutant and the uspA1 uspA2 double mutant both attached to these epithelial cells at a level nearly 2 orders of magnitude lower than that obtained with the wild-type parent strain, a result which suggested that expression of UspA1 by M. catarrhalis is essential for attachment to these epithelial cells. Both the wild-type parent strain and the uspA1 mutant were resistant to the bactericidal activity of normal human serum, whereas the uspA2 mutant and the uspA1 uspA2 double mutant were readily killed by this serum. This latter result indicated that the presence of UspA2 is essential for expression of serum resistance by M. catarrhalis.
Two-way adaptation for robust input interpretation in practical multimodal conversation systems (2005)

Multimodal conversation systems allow users to interact with computers effectively using multiple modalities, such as natural language and gesture. However, these systems have not been widely used in practical applications mainly due to their limited input understanding capability. As a result, conversation systems often fail to understand user requests and leave users frustrated. To address this issue, most existing approaches focus on improving a system's interpretation capability. Nonetheless, such improvements may still be limited, since they would never cover the entire range of input expressions. Alternatively, we present a two-way adaptation framework that allows both users and systems to dynamically adapt to each other's capability and needs during the course of interaction. Compared to existing methods, our approach offers two unique contributions. First, it improves the usability and robustness of a conversation system by helping users to dynamically learn the system's capabilities in context. Second, our approach enhances the overall interpretation capability of a conversation system by learning new user expressions on the fly. Our preliminary evaluation shows the promise of this approach.
A glycoprotein E deletion mutant of bovine herpesvirus 1 is avirulent in calves (1994)

A marker vaccine elicits an antibody response in the host that can be distinguished from the antibody response induced by a wild-type strain. To obtain a bovine herpesvirus 1 (BHV-1) marker vaccine, we constructed a glycoprotein E (gE) deletion mutant. This was obtained by removing the complete gE coding region from the BHV-1 genome. To attenuate the gE deletion mutant further, we also introduced a small deletion in the thymidine kinase (TK) gene. We selected three mutants: the gE deletion mutant, a TK deletion mutant and a gE/TK double deletion mutant, and examined their virulence and immunogenicity in calves. After intranasal inoculation, the TK deletion mutant showed some residual virulence, whereas the gE and gE/TK deletion mutants were avirulent. The calves inoculated with the deletion mutants were protected against disease after challenge exposure and shed significantly less virus than control calves. Deleting the gE gene, therefore, has little effect on the immunogenicity of BHV-1, but is sufficient to reduce the virulence of BHV-1 in calves. These findings led us to conclude that the gE deletion mutant is a good candidate for a modified live BHV-1 marker vaccine.
Targeting Bacterial Nitric Oxide Synthase with Aminoquinoline-Based Inhibitors (2016)

Nitric oxide is produced in Gram-positive pathogens Bacillus anthracis and Staphylococcus aureus by the bacterial isoform of nitric oxide synthase (NOS). Inhibition of bacterial nitric oxide synthase (bNOS) has been identified as a promising antibacterial strategy for targeting methicillin-resistant S. aureus [Holden, J. K., et al. (2015) Chem. Biol. 22, 785-779]. One class of NOS inhibitors that demonstrates antimicrobial efficacy utilizes an aminoquinoline scaffold. Here we report on a variety of aminoquinolines that target the bacterial NOS active site, in part, by binding to a hydrophobic patch that is unique to bNOS. Through mutagenesis and crystallographic studies, our findings demonstrate that aminoquinolines are an excellent scaffold for further aiding in the development of bNOS specific inhibitors.
Registration of central paths and colonic polyps between supine and prone scans in computed tomography colonography: Pilot study (2004)

Computed tomography colonography (CTC) is a minimally invasive method that allows the evaluation of the colon wall from CT sections of the abdomen/pelvis. The primary goal of CTC is to detect colonic polyps, precursors to colorectal cancer. Because imperfect cleansing and distension can cause portions of the colon wall to be collapsed, covered with water, and/or covered with retained stool, patients are scanned in both prone and supine positions. We believe that both reading efficiency and computer aided detection (CAD) of CTC images can be improved by accurate registration of data from the supine and prone positions. We developed a two-stage approach that first registers the colonic central paths using a heuristic and automated algorithm and then matches polyps or polyp candidates (CAD hits) by a statistical approach. We evaluated the registration algorithm on 24 patient cases. After path registration, the mean misalignment distance between prone and supine identical anatomic landmarks was reduced from 47.08 to 12.66 mm, a 73% improvement. The polyp registration algorithm was specifically evaluated using eight patient cases for which radiologists identified polyps separately for both supine and prone data sets, and then manually registered corresponding pairs. The algorithm correctly matched 78% of these pairs without user input. The algorithm was also applied to the 30 highest-scoring CAD hits in the prone and supine scans and showed a success rate of 50% in automatically registering corresponding polyp pairs. Finally, we computed the average number of CAD hits that need to be manually compared in order to find the correct matches among the top 30 CAD hits. With polyp registration, the average number of comparisons was 1.78 per polyp, as opposed to 4.28 comparisons without polyp registration.