gebhart/patrepeval huggingface dataset:
Novel Rac Inhibitors as Targeted Therapeutics for Metastatic Breast Cancer (2018)

Metastatic disease is the primary cause of breast cancer mortality, due to the lack of effective therapy. The Rho GTPase Rac is integral for the promotion of cancer cell migration/invasion, proliferation, and survival. Since metastatic breast cancers often overexpress or exhibit high Rac activity, inhibition of Rac is a viable strategy against metastatic cancer. Recently, we characterized EHop‐016, a small molecule that inhibits Rac activity of metastatic breast cancer cells with an IC 50 of 1 μM. EHop‐016, which is 10–100 times more active than previously available Rac inhibitors, inhibits the activity of the Rac downstream effector p21 activated kinase (PAK), lamellipodia extension, and cell migration of metastatic breast cancer cells. Moreover, EHop‐016 at ≥ 25 mg/kg Body Weight (BW) significantly reduced tumor growth, metastasis, and angiogenesis in a mouse model. However, our recent pharmacokinetic study of EHop‐016 in a mouse model demonstrated that its bioavailability should to be improved for further pharmacological development. Our hypothesis is that improvement of the EHop‐016 structure will provide probes with increased potency against Rac and improved bioavailability. Herein we have tested several Ehop‐016 derivatives for their effects on breast cancer cell viability, cell migration, and Rac activation. Using MTT assays we found that the Ehop‐016 derivatives, HV‐107 and HV‐118, significantly inhibit the viability of metastatic breast cancer cell lines MDAMB‐231 and MDA‐MB‐435; while presenting minimal toxicity towards non‐cancerous mammary epithelial cells. The effects of HV‐107 and HV‐118 on the inhibition of Rac activation were tested by ELISA‐based Rac activity assays and pulldown assays. Results show that at 250 nM, HV‐107 inhibits Rac activation by 55%, whereas HV‐118 has a similar effect at 100 nM in MDA‐MB‐231 and MDA‐MB‐435 cells. Moreover, using transwell assays we studied the effects of both Rac inhibitors in metastatic breast cancer cell migration and observed a significant reduction. Finally, we tested HV‐107 in a mouse model of metastatic breast cancer and found a 25% reduction in tumor growth in mice treated with 5 mg/kg BW HV‐107. Taken together, our findings suggest HV‐107 and HV‐118 as promising Ehop‐016 derivatives with potential as anti‐metastatic agents, that should be further characterized. Support or Funding Information This study was supported by awards from the Susan Komen for the Cure, NIH/NIMHHD U54MD008149, and the Puerto Rico Science and Technology Trust to SD; NIH/NCRR R25GM061838 to UPR MSC; NIH/NIMHHD RCMI 8G12MD007583RCMI, Title V PPOHA 031M10505 and Title V Cooperative P031S130068 from U.S. Department of Education to UCC; and PRINBRE (NIH/NIGMS P20GM103475‐13) Sub‐Award to LCP. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Distributed Extended Kalman Filtering Based Techniques for 3-D UAV Jamming Localization (2020)

Wireless networks are vulnerable to jamming attacks. Jamming in wireless communication becomes a major research problem due to ease in Unmanned Aerial Vehicle (UAV) launching and blocking of communication channels. Jamming is a subset of Denial of Service Attack (DoS) and an intentional interference where the malicious node disrupts the wireless communication by increasing the noise at the receiver node through transmission interference signal towards the target channel. In this work, the considered jammer is a UAV hovering around the target area to block the communication channel between two transceivers. We proposed a three-dimensional (3-D) UAV jamming localization scheme to track and detect the jammer position at each time step by employing a single boundary node observer. For this purpose, we developed two distributed Extended Kalman Filter (EKF) based schemes: (1) the Distributed EKF (DEKF) scheme using the information of the received power from the jammer at a single nearby boundary node only and (2) Distance Ratio aided Distributed EKF (DEKF-DR) based scheme utilizing an edge node in addition to a single boundary node. Extensive simulations are conducted in order to evaluate the performance of the proposed distributed algorithms for a 3-D trajectory and compared with that of the conventional Centralized EKF (EKF-Centr) based method (which is also modified for the 3-D scenario). The results show the clear supremacy of the proposed distributed algorithms with much lesser complexity in contrast to the conventional EKF-Centr technique.
Erlotinib sensitivity in NSCLC cell lines correlates with an epithelial to mesenchymal transition which induces a switch in receptor tyrosine kinase signaling. (2007)

A200 The elucidation of mechanisms of sensitivity and resistance to EGFR kinase inhibitors is of great importance in optimizing the clinical benefit which can be achieved with this class of drugs. We have previously shown that protein markers which correlate with an epithelial to mesenchymal transition (EMT) in NSCLC cell lines can predict the sensitivity of these cell ljnes to the anti-proliferative effects of erlotinib. Cell lines expressing markers of an epithelial nature, such as E-cadherin and χ-catenin, are sensitive to erlotinb in vitro and in vivo, whereas those cells expressing markers of a mesenchymal-like nature, such as vimentin and ZEB1, are less sensitive to the effects of this drug.  Here we expand on this work and describe an in vitro model of EMT which accurately replicates the hallmarks of EMT in NSCLC cell lines. Treatment of H358 cells with TGFβ3 induces a dramatic change in cell phenotype, with the cells changing from non-migratory epithelial cells to highly motile mesenchymal-like cells. This coincides with a decrease in epithelial markers and an increase in the expression of mesenchymal markers and in addition correlates with a decreased sensitivity to erlotinib-mediated growth inhibition, potentially explained by decreased sensitivity to inhibition of the ERK MAP kinase pathway. Profiling of this model indicates that upon induction of EMT the cell become less dependent upon EGFR signaling and begin to express alternate receptor tyrosine kinases, such as PDGFR and FGFR, suggesting a switch in the signaling axes the mesenchymal cell utilize for proliferation and survival. The gene expression changes that are observed in this model are also observed in a panel of mesenchymal-like NSCLC cell lines.  These data indicate that one mechanism for insensitivity to EGFR TKIs in NSCLC may be an epithelial to mesenchymal transition which initiates a change in the predominant receptor tyrosine kinase pathways which are utilized by the tumor cells for proliferation and survival. These insights provide a rational for the combination of inhibitors targeted to different RTKs as a means of improving therapeutic responses.
A strategy for quantitative spectral imaging of tissue absorption and scattering using light emitting diodes and photodiodes (2009)

A diffuse reflectance spectroscopy system was modified as a step towards miniaturization and spectral imaging of tissue absorption and scattering. The modified system uses a tunable source and an optical fiber for illumination and a photodiode in contact with tissue for detection. Compared to the previous system, it is smaller, less costly, and has comparable performance in extracting optical properties in tissue phantoms. Wavelength reduction simulations show the feasibility of replacing the source with LEDs to further decrease system size and cost. Simulated crosstalk analysis indicates that this evolving system can be multiplexed for spectral imaging in the future.
Rapid Process for Manufacturing Aluminum Nitride Powder (1994)

A rapid, direct nitridation process for the manufacture of sinterable aluminum nitride (A1N) powder was developed at the pilot scale. Atomized aluminum metal and nitrogen gas were heated and reacted rapidly to synthesize A1N while they passed through the reaction zone of a transport flow reactor. The heated walls of the reactor simultaneously initiated the reaction and removed the generated heat to control the exotherm. Several variations of the process were required to achieve high conversion and reduce wall deposition of the product. The fine A1N powder produced did not require a postreaction grinding step to reduce particle size. However, a secondary heat treatment, following a mild milling step to expose fresh surface, was necessary to ensure complete conversion of the aluminum. In some instances, a final air classification step to remove large particles was necessary to promote densification by pressureless sintering. The A1N powder produced was pressureless sintered with 3 wt% yttria to fabricate fully dense parts which exhibited high thermal conductivity. The powder was shown to be less sinterable than commercially available car‐bothermally produced powders.
Population Genetics of Lactobacillus sakei Reveals Three Lineages with Distinct Evolutionary Histories (2013)

Lactobacillus sakei plays a major role in meat fermentation and in the preservation of fresh meat. The large diversity of L. sakei strains represents a valuable and exploitable asset in the development of a variety of industrial applications; however, an efficient method to identify and classify these strains has yet to be developed. In this study, we used multilocus sequence typing (MLST) to analyze the polymorphism and allelic distribution of eight loci within an L. sakei population of 232 strains collected worldwide. Within this population, we identified 116 unique sequence types with an average pairwise nucleotide diversity per site (π) of 0.13%. Results from Structure, goeBurst, and ClonalFrame software analyses demonstrated that the L. sakei population analyzed here is derived from three ancestral lineages, each of which shows evidence of a unique evolutionary history influenced by independent selection scenarios. However, the signature of selective events in the contemporary population of isolates was somewhat masked by the pervasive phenomenon of homologous recombination. Our results demonstrate that lineage 1 is a completely panmictic subpopulation in which alleles have been continually redistributed through the process of intra-lineage recombination. In contrast, lineage 2 was characterized by a high degree of clonality. Lineage 3, the earliest-diverging branch in the genealogy, showed evidence of both clonality and recombination. These evolutionary histories strongly indicate that the three lineages may correspond to distinct ecotypes, likely linked or specialized to different environmental reservoirs. The MLST scheme developed in this study represents an easy and straightforward tool that can be used to further analyze the population dynamics of L. sakei strains in food products.
Polymorphic Type Inference for Machine Code (2016)

For many compiled languages, source-level types are erased very early in the compilation process. As a result, further compiler passes may convert type-safe source into type-unsafe machine code. Type-unsafe idioms in the original source and type-unsafe optimizations mean that type information in a stripped binary is essentially nonexistent. The problem of recovering high-level types by performing type inference over stripped machine code is called type reconstruction, and offers a useful capability in support of reverse engineering and decompilation. In this paper, we motivate and develop a novel type system and algorithm for machine-code type inference. The features of this type system were developed by surveying a wide collection of common source- and machine-code idioms, building a catalog of challenging cases for type reconstruction. We found that these idioms place a sophisticated set of requirements on the type system, inducing features such as recursively-constrained polymorphic types. Many of the features we identify are often seen only in expressive and powerful type systems used by high-level functional languages. Using these type-system features as a guideline, we have developed Retypd: a novel static type-inference algorithm for machine code that supports recursive types, polymorphism, and subtyping. Retypd yields more accurate inferred types than existing algorithms, while also enabling new capabilities such as reconstruction of pointer const annotations with 98% recall. Retypd can operate on weaker program representations than the current state of the art, removing the need for high-quality points-to information that may be impractical to compute.
Recent Advances in Oligonucleotide Synthesis and Their Applications (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
A Novel Patterning Method of Low-resistivity Metals (2004)

Abstract Photocatalytic layers of amorphous TiO2 and polyvinyl alcohol were used for the patterning of low-resistivity metals such as copper and silver without using high cost materials and equipment.
Quasi-remote laser pulse compression and applications (2010)

Summary form only given. Chirped pulse amplification (CPA) is a widely used technique for producing extremely short laser pulses. In particular, Ti: sapphire laser pulses are routinely compressed to pulse lengths below 50 femtoseconds (fsec) and in vacuum can be focused to intensities as high as 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">21</sup> W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . These intense pulses can be used for a variety of potential applications, mostly involving the conversion of the laser pulse energy to electromagnetic radiation at a different wavelength or to energetic particles which can then be used to probe a target. Nonlinear effects and plasma generation place severe restrictions on the intensity of the pulse that can be propagated to a distant target or device in air. However, if the pulse compression apparatus, focusing system, and radiation or particle beam converter are placed close to the target or sample, it may be possible to propagate a radially-expanded, chirped/stretched pulse through the air at a sufficiently low intensity to avoid plasma generation and nonlinear effects. This pulse can be compressed and focused onto the converter while keeping the largest and most expensive components of the CPA system far from the target. The dominant source of pulse degradation in most cases will come from atmospheric turbulence. This paper describes analytical and simulation calculations that estimate how much the stretched pulse degrades as it propagates through a turbulent atmosphere, and the effect of this degradation on axial compression and focused spot size as the standoff distance to the compressor/focusing/converter assembly is increased. The implications of these results for various potential applications will be discussed.
Full chip impact study of power delivery network designs in monolithic 3D ICs (2014)

In this paper, we present a comprehensive study on the impact of power delivery network (PDN) on full-chip wirelength, routability, power, and thermal effects in monolithic 3D ICs. Our studies first show that the full PDN worsens routing congestion more severely in monolithic 3D ICs than in 2D designs due to the significant reduction in resources for 3D connections. The increase in signal wirelength translates into additional net switching power dissipation, which significantly contributes to total power. This in turn aggravates thermal issues in 3D ICs. In addition, we observe that PDN tradeoffs among wirelength, power, and thermal are more pronounced in monolithic 3D ICs than TSV-based 3D and 2D designs. This is because of the higher integration density and the severe competition between signal and power connections. Lastly, we develop various PDN design optimization techniques for monolithic 3D ICs and obtain up to 8% signal wirelength and 5% maximum temperature reduction under the given IR drop budget.
A Secure Receipt Issuing Scheme for e-Voting with Improved Usability (2007)

Current electronic voting systems are not sufficient to satisfy trustworthy elections as they do not provide any proof or confirming evidence of their honesty. This lack of trustworthiness is the main reason why e-voting is not widespread even though e-voting is expected to be more efficient than the current plain paper voting. Many experts believe that the only way to assure voters that their intended votes are casted is to use paper receipts. In this paper, we propose an efficient scheme for issuing receipts to voters in an e-voting environment using the well-known cut-and-choose method. Our scheme does not require any special printers or scanners, nor frequent observations of voting machines. In addition, our scheme is more secure than the previous schemes.
Resource Modeling and Scheduling for Extensible Embedded Platforms (2006)

Modern embedded processors have the flexibility of dynamic switching between power operation modes, such as using voltage and frequency scaling. Platforms with heterogeneous processors and reconfigurable buses further extend the energy/timing trade-off flexibility and provide the opportunity to fine tune resource usage for particular applications. This paper gives a resource model for heterogeneous multi-processor embedded platforms and formulates power-aware real-time resource scheduling problems as integer linear programming problems. In particular, we take the time and energy costs of mode switching into account, which considerably improves the accuracy of the model. We apply the resource model to a stackable multiprocessor embedded platform, called mPlatform , and present a case study of scheduling a sound source localization application in a stack of four MSP430-based sensing boards and one ARM7based processing board.
Fermentation, isolation, characterization and structure of antibiotic U-58,431. (1980)

A new antibiotic U-58,431 has been isolated from the fermentation broth of Streptomyces helicus DIETZ and LI, sp. n. (UC-5837) and the structure of this antibiotic, namely, 6-amino-3,4,5,8-tetrahydro-4,9-dihydroxy-3-methyl-5,8-dioxo-1,4-ethano-1H-2-benzopyron-7-carboxamide has been determined by X-ray crystallography. The antibiotic inhibits a variety of Gram-positive and Gram-negative bacteria in vitro. However, it is toxic to mice and does not protect experimentally infected animals when administered at the maximum tolerated dose.
Tissue-Engineered Total Meniscus Replacement With a Fiber-Reinforced Scaffold in a 2-Year Ovine Model (2018)

An off-the-shelf meniscus device that can be remodeled into functional tissue and thus prevent or delay the onset of osteoarthritis could address a widespread clinical need after meniscus injury.
Terminal Sliding Modes In Nonlinear Control Systems (1993)

Control systems of proposed type called controllers offers increased precision and stability of robotic operations in presence of unknown and/or changing parameters. Systems include special computer hardware and software implementing novel control laws involving terminal sliding modes of motion: closed-loop combination of robot and terminal controller converge, in finite time, to point of stable equilibrium in abstract space of velocity and/or position coordinates applicable to particular control problem.
An analysis of the clinical and biologic significance of TP53 loss and the identification of potential novel transcriptional targets of TP53 in multiple myeloma (2008)

TP53 is a tumor suppressor gene that functions as transcriptional regulator influencing cellular responses to DNA damage. Here we explored the clinical and transcriptional effects of TP53 expression in multiple myeloma (MM). We found that low expression of TP53, seen in approximately 10% of newly diagnosed patients, is highly correlated with TP53 deletion, an inferior clinical outcome, and represents an independent risk factor. Analysis of the expression of 122 known TP53 target genes in TP53-high vs -low MM cells from 351 newly diagnosed cases, revealed that only a few were highly correlated with TP53 expression. To elucidate TP53 regulatory networks in MM, we overexpressed TP53 in 4 MM cell lines. Gene expression profiling of these cell lines detected 85 significantly differentially expressed genes, with 50 up-regulated and 35 down-regulated. Unsupervised hierarchical clustering of myeloma samples from 351 newly diagnosed and 90 relapsed patients using the 85 putative TP53 target genes revealed 2 major subgroups showing a strong correlation with TP53 expression and survival. These data suggest that loss of TP53 expression in MM confers high risk and probably results in the deregulation of a novel set of MM-specific TP53-target genes. TP53 target gene specificity may be unique to different cell lineages.
Optimal Dispatch of Photovoltaic Inverters in Residential Distribution Systems (2014)

Low-voltage distribution feeders were designed to sustain unidirectional power flows to residential neighborhoods. The increased penetration of roof-top photovoltaic (PV) systems has highlighted pressing needs to address power quality and reliability concerns, especially when PV generation exceeds the household demand. A systematic method for determining the active- and reactive-power set points for PV inverters in residential systems is proposed in this paper, with the objective of optimizing the operation of the distribution feeder and ensuring voltage regulation. Binary PV-inverter selection variables and nonlinear power-flow relations render the optimal inverter dispatch problem nonconvex and NP-hard. Nevertheless, sparsity-promoting regularization approaches and semidefinite relaxation techniques are leveraged to obtain a computationally feasible convex reformulation. The merits of the proposed approach are demonstrated using real-world PV-generation and load-profile data for an illustrative low-voltage residential distribution system.
Investigation of surface enhanced Raman spectroscopy for hemozoin detection in malaria diagnosis (2016)

We report two methods of surface enhanced Raman spectroscopy (SERS) for hemozoin detection in malaria infected human blood. In the first method, silver nanoparticles were synthesized separately and then mixed with lysed blood; while in the second method, silver nanoparticles were synthesized directly inside the parasites of <i>Plasmodium falciparum</i>.
Site-directed polyclonal antibodies inhibit binding of activated estrogen receptor to DNA (1990)

We have generated three polyclonal antisera to the DNA-binding domain of the human estrogen receptor (hER). Antiserum AT2A was generated against a peptide spanning amino acids 231-245 of hER, while antisera AT3A and AT3B were generated against a peptide spanning amino acids 247-261 of hER. The interaction of these three antisera with ER has been characterized by sucrose density gradient analysis. The antisera bound to the unactivated (8S), salt-activated (4S), and heat transformed (5S) ER complex. All the antisera appeared to be site-specific since binding of salt-activated ER to the antisera was blocked by the presence of excess free synthetic peptides. Antisera AT3A and AT3B inhibited the binding to DNA of the KCl-activated 4S ER and the heat-transformed 5S ER. Although antiserum AT2A bound to ER, it did not inhibit DNA binding of activated ER complexes. The ability of antisera AT3A and AT3B to inhibit ER binding to DNA was concentration dependent. Once bound to the DNA, ER complexes were not significantly affected by incubation with the antisera, suggesting that binding of DNA to ER inhibits antibody ER interaction and renders that domain inaccessible to the antibodies. These results demonstrate that site-directed antibodies to ER inhibit binding of activated ER complexes to DNA in vitro.