gebhart/patrepeval huggingface dataset:
Abstract 1145: Cytoplasmic p27 promotes epithelial-mesenchymal transition and tumor progression via Twist1 upregulation (2014)

Abstract p27 is a cell cycle regulator that acts largely to restrain normal cell growth. It is rarely mutated or deleted in human cancers, but is often degraded or mislocalized to the cytoplasm in aggressive tumors. Phosphorylation at T157 or T198 by different PI3K effector kinases leads to p27 cytoplasmic accumulation and enhanced cell motility and invasion in part via effects on the actin cytoskeleton, which are independent of its cell cycle role. However, the functional contributions of C-terminally phosphorylated, cytoplasmic p27 to cancer progression remain poorly understood. Targeted inhibition of PI3K/mTOR impaired tumor cell motility and metastasis via modulation of p27 in a bone metastatic model (Wander, S. et al. BCRT 2013). We observed that p27 knockdown in highly metastatic cancer lines with high levels of cytoplasmic p27pT157pT198 reverted EMT and impaired tumor cell invasion in vitro and metastasis in vivo. This led us to investigate whether PI3K-activated, phosphorylated p27 may function as a novel EMT regulator. A cell cycle defective (CK-) and double phosphomimetic p27 mutant (T157D/T198D or DD) was introduced into immortal human mammary epithelial cells with low PI3K activity. This revealed a novel, oncogenic function of p27 in regulating tumor progression, in that p27CK-DD induced epithelial-mesenchymal transition (EMT) and soft agar colony formation. p27CK-DD also increased motility, invasion and formation of metastasis in bladder and breast cancer models. A RT-PCR screen for potential p27-induced EMT mediators revealed a 20-fold increase in expression of the Twist1 transcription factor in p27CK-DD-transduced cells. Knockdown of Twist reversed the p27CK-DD-mediated increase in EMT marker expression. p27 knockdown rapidly attenuated Twist1-promoter activity and reduced Twist1 mRNA levels and also increased E-cadherin expression in metastatic cells, suggesting that Twist1 may play a critical role in p27CK-DD-induced EMT. These data extend our understanding of p27 function in human cancer and suggest that PI3K deregulated p27 may promote EMT and tumor metastasis through transcriptional activation of TWIST1. Citation Format: Dekuang Zhao, Alexandra H. Besser, Wen Zhou, Seth A. Wander, Jun Sun, Michael Durante, Feng Hong, Bin Wang, Tan Ince, Karoline Briegel, Joyce M. Slingerland. Cytoplasmic p27 promotes epithelial-mesenchymal transition and tumor progression via Twist1 upregulation. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1145. doi:10.1158/1538-7445.AM2014-1145
Two-phase flow (1986)

An experimental program to characterize the spray from candidate nozzles for icing-cloud simulation is discussed. One canidate nozzle, which is currently used for icing research, has been characterized for flow and drop size. The median-volume diameter (MVD) from this air-assist nozzle is compared with correlations in the literature. The new experimental spray facility is discussed, and the drop-size instruments are discussed in detail. Since there is no absolute standard for drop-size measurements and there are other limitations, such as drop -size range and velocity range, several instruments are used and results are compared. A two-phase model was developed at Pennsylvania State University. The model uses the k-epsilon model of turbulence in the continous phase. Three methods for treating the discrete phase are used: (1) a locally homogeneous flow (LHF) model, (2) a deterministic separated flow (DSF) model, and (3) a stochastic separated flow (SSF) model. In the LHF model both phases have the same velocity and temperature at each point. The DSF model provides interphase transport but ignores the effects of turbulent fluctuations. In the SSF model the drops interact with turbulent eddies whose properties are determined by the k-epsilon turbulence model. The two-phase flow model has been extended to include the effects of evaporation and combustion.
Phased Arrays for Radio Astronomy, Remote Sensing, and Satellite Communications (2018)

Discover a modern approach to the analysis, modeling and design of high sensitivity phased arrays. Network theory, numerical methods and computational electromagnetic simulation techniques are uniquely combined to enable full system analysis and design optimization. Beamforming and array signal processing theory are integrated into the treatment from the start. Digital signal processing methods such as polyphase filtering and RFI mitigation are described, along with technologies for real-time hardware implementation. Key concepts from interferometric imaging used in radio telescopes are also considered. A basic development of theory and modeling techniques is accompanied by problem sets that guide readers in developing modeling codes that retain the simplicity of the classical array factor method while incorporating mutual coupling effects and interactions between elements. Combining current research trends with pedagogical material suitable for a first-year graduate course, this is an invaluable resource for students, teachers, researchers, and practicing RF/microwave and antenna design engineers.
Using electroencephalography as a tool to understand auditory perception: Event-related and time-frequency analyses (2017)

Electroencephalography (EEG) largely reflects postsynaptic field potentials summed over many (hundreds of thousands of) neurons that are aligned in time and orientation. These electrical fields propagate in all directions such that determination of the sources of electrical fields measured at the surface of the head is much less accurate than localizations using fMRI. However, EEG can be measured with sub-millisecond timing resolution, offering a great advantage for studies of hearing. EEG can measure activity from various nuclei along the subcortical pathway, from primary and secondary auditory cortex and from cortical regions beyond. EEG can be particularly useful for understanding preconscious processing stages, and auditory processing in infants and others who can not make verbal responses. Traditional methods of analysis relate peaks (“components”) in the EEG time waveform to stages of processing. However, communication between brain circuits is reflected in neural oscillations, which can be measured through time-frequency analyses of EEG recordings. Such approaches reveal, for example, how frequency is encoded in the brainstem, and how predictive timing and predictive coding are accomplished in the cortex. I will illustrate these points with example applications largely from our lab and argue that EEG can greatly enhance our interpretation of psychophysical data.
Angiogenesis: A Possible Mechanism Underlying the Clinical Benefits of Transmyocardial Laser Revascularization (1997)

While clinical reports indicate that significant relief of angina is achieved with transmyocardial laser revascularization (TMLR), the mechanisms of benefit are still a matter of considerable controversy. Studies in our laboratory, as well as in the laboratories of other investigators, have challenged the classic hypothesis that benefits are derived from blood flow through chronically patent channels. While several alternatives have been proposed, our work has focused on investigating the possibility that TMLR stimulates vascular growth in the region around the TMLR channels. We have performed studies looking at histologic markers of vascular growth (including vessel counting and cellular proliferation assays) in order to test this hypothesis, the results of which are reviewed. In brief, we find that TMLR markedly enhances myocardial vascular growth above what is seen normally in ischemic myocardium. We hypothesize that the underlying mechanism relates to liberation of growth factors by inflammatory cells, which are recruited in response to the laser induced myocardial injury. Clarification of whether this mechanism contributes to observed clinical benefits is of fundamental importance, since such understanding may suggest means of enhancing the process.
Characterization of Stainless Steel and Refractory Metal Welds Made using a Diode-Pumped, Continuous Wave Nd: Yag Laser (2001)

A series of laser welds have been made on several materials using a Rofin-Sinar DY-033, 3.3 kW, Diode-Pumped Continuous Wave (CW) Nd:YAG laser system, located at Los Alamos National Laboratory. Materials welded in these experiments include 21-6-9 stainless steel, 304L stainless steel, vanadium, and tantalum. The effects of changes in the power input at a constant travel speed on the depth, width, aspect ratio, and total melted area of the welds have been analyzed. Increases in the measured weld pool dimensions as a function of power input are compared for each of the base metals investigated. These results provide a basis for further examining the characteristics of diode pumped CW Nd:YAG laser systems in welding applications.
Video assessment of finger tapping for Parkinson's disease and other movement disorders (2011)

Functional motor impairment due to Parkinson's disease and other movement disorders are currently assessed with visual rating scales such as the Unified Parkinson's Disease Rating Scale (UPDRS). These methods rely on the subjective judgment of a rater to assign scores representing the extent of impairment while subjects perform prescribed activities. We describe a new model-based framework that uses statistical video processing to automatically track movement during prescribed activities. This approach has many advantages over traditional clinical rating scales. It can completely characterize movement during prescribed tasks over time objectively and precisely using hardware that is inexpensive and readily available. We demonstrate the potential of this framework with a simple statistical model applied to a paced finger tapping test. This technology could be deployed in a natural home environment for frequent assessments. This technology could ultimately improve both clinical practice and clinical trials.
Correction of shallow-water electromagnetic data for noise induced by instrument motion (2005)

Abstract An unexpected noise source has been found in mag-netic- and sometimes electric-field data recorded on the bottom of lakes in the Archean Slave craton (northwestern Canada) during warm seasons. The noise is the result of instrument motion and in some instances direct induction by wind-driven surface gravity waves when the lakes are not ice covered. The noise can be reduced or eliminated by prefiltering the data with an adaptive correlation noise-canceling filter using instrument tilt records prior to estimation of magnetotelluric (MT) response functions. Similar effects are to be expected in other shallow-water environments, and the adaptive correlation canceler is a suitable method to preprocess MT data to reduce motion-related noise in the magnetic field. This underscores the importance of ancillary tilt measurements in shallow-water MT surveys. In coastal or lake-bottom surveys, special efforts to reduce hydrodynamic effects on the instrument should also be pursued.
GridDrones (2018)

We present GridDrones, a self-levitating programmable matter platform that can be used for representing 2.5D 15 voxel grid relief maps with capabilities of rendering overhangs and 3D spatial transformations. GridDrones consists of 15 cube-shaped nanocopters that can be placed in a volumetric 1xnxn mid-air grid. Grid deformations can be applied interactively to this voxel lattice by first selecting a set of voxels using a 3D wand, then assigning a continuous topological relationship between voxel sets that determines how voxels move in relation to each other, then drawing out selected voxels from the lattice structure. Using this simple technique, it is possible to create overhanging structures that can be translated and oriented freely in 3D. Shape transformations can also be recorded to allow for simple physical shape morphing animations. This work extends previous work on selection and editing techniques for 3D user interfaces.
Control of a chaotic polymerization reactor: A neural network based model predictive approach (1996)

Abstract Continuous polymerization processes may be very sensitive to small changes of the operation conditions. Continuous VA (vinyl acetate) solution homopolymerization reactors may present multiple steady‐states and oscillatory behavior. A predictive control scheme that uses an internal model of the process is employed to stabilize such reactors and make them less sensitive to disturbances while subject to “hard” control action constraints. An ANN (artificial neural network) is used as the internal model, leading to fairly good predictions of the reactor behavior, including its multiplicities. The performance of the resulting control algorithm is compared to that of a “well‐tuned” conventional proportional‐integral‐derivative (PID) controller.
Simplifying wireless social caching (2016)

Social groups give the opportunity for a new form of caching. In this paper, we investigate how a social group of users can jointly optimize bandwidth usage, by each caching parts of the data demand, and then opportunistically share these parts among them upon meeting. We formulate this problem as a Linear Program (LP) with exponential complexity. Based on the optimal solution, we propose a simple heuristic inspired by the bipartite set-cover problem that operates in polynomial time. Furthermore, we prove a worst case gap between the heuristic and the LP solutions. Finally, we assess the performance of our algorithm using real-world mobility traces from the MIT Reality Mining project dataset.
Automatic Embedding Technique for Histopathological Examination Increases R0 Resection Rates for Endoscopic Submucosal Dissection: A Major Impact in Decreasing Local Risk Status for Anorectal Cases (2021)

Aims Endoscopic submucosal dissection (ESD) allows « en-bloc » resection of superficial gastrointestinal neoplasia. Standardized macroscopic and microscopic approaches are required to adequately assess the curative status. Nevertheless, margin assessment is sometimes challenging especially if samples are not correctly orientated within paraffin blocks.The aim of the study was to compare margin status of ESD specimens embedded using one of two methods: a manual embedding technique (MET) or an automatic embedding technique (AET).
Temperature Dependence of Dipalmitoyi Phosphatidylcholine/Diheptanoyl Phosphatidylcholine Aqueous Mixtures (1991)

There is great interest in the process of lipid self-assembly, especially the microstructure formed from lipid mixtures. Spontaneous unilamellar vesicles have been reported by Roberts from mixtures of long-chain lecithins and short-chain lecithins. Alone, dipalmitoyi phophatidylcholine (DPPC) forms normal multilamellar phases, a solid Lβ phase up to about 37°C, a Pβ or ripple phase from 37 to 43°C, and a fluid or Lα phase above 43°C. Diheptanoyl phosphatidylcholine (DHPC) by itself generally aggregates as spherical micelles over this temperature range. At temperatures below 40°C the two lipids, DPPC and DHPC, phase separate, leading to the possibility of physical segregation of the two lipid species. As a result of this separation, the DHPC might migrate to the boundaries of the DPPC-rich bilayers where it could stabilize the bilayer edge to allow the formation of bilayer discs, as first described by Fromherz and Rüppel.
Variable-period permanent-magnet helical undulator (2014)

We realized a variable-period permanent-magnet helical undulator with high ($\ensuremath{\sim}1\text{ }\text{ }\mathrm{T}$) field amplitude, which is almost constant over undulator periods of 23--26 mm. Each undulator period has four modular sections of iron poles and permanent magnets embedded in nonmagnetic disks with holes along the undulator axis. Modular plates undergo a longitudinal repulsive force from the magnetic field pressure and the spring coils between modular plates. The undulator period can thus be controlled by mechanically changing the end plate longitudinal position. This compact design is suitable for tabletop terahertz free electron lasers.
New severity grading system for Fuchs endothelial corneal dystrophy using anterior segment optical coherence tomography (2020)

We devised a new severity grading using only objective evaluation and quantitatively demonstrated corneal thickening, predominant flattening of the posterior corneal surface compared with the anterior surface, and displacement of the thinnest point away from the central cornea with FECD progression.
A newly emerged fiber technology for DWDM and ULH network applications and future deployment (2005)

This paper illustrates detailed numerical analysis, lab tests, and field trials of MCI's next generation fiber development process from the years 2000 to 2004. The new Medium Dispersion Fiber (MDF) has dispersion of around 7~8 ps/nm/km, which will satisfy MCI and worldwide next generation transmission fiber technical specifications and requirements at 20 Pb/s*km for "short fat" (20 Tb/s x 1000 km) and "long thin" (6.67 Tb/s x 3000 km) future DWDM and ULH network application and deployment.
Specialty Fibers and Components for Fiber-Optic Sensing Technology (2017)

An optical fiber is used not only as a transmission medium but also as a sensor in fiber-optic sensing technology. Novel specialty fibers and relevant technologies have been developed for various application fields, such as avionics, infrastructures, atomic plants and oil&gas industries. In this paper, recent progress in the fiber-optic sensing is reviewed with a focus on the specialty fibers and fiber-optic components.
Immunogenicity and Protective Efficacy in Mice and Hamsters of a β-Propiolactone Inactivated Whole Virus SARS-CoV Vaccine (2010)

The immunogenicity and efficacy of β-propiolactone (BPL) inactivated whole virion SARS-CoV (WI-SARS) vaccine was evaluated in BALB/c mice and golden Syrian hamsters. The vaccine preparation was tested with or without adjuvants. Adjuvant Systems AS01(B) and AS03(A) were selected and tested for their capacity to elicit high humoral and cellular immune responses to WI-SARS vaccine. We evaluated the effect of vaccine dose and each adjuvant on immunogenicity and efficacy in mice, and the effect of vaccine dose with or without the AS01(B) adjuvant on the immunogenicity and efficacy in hamsters. Efficacy was evaluated by challenge with wild-type virus at early and late time points (4 and 18 wk post-vaccination). A single dose of vaccine with or without adjuvant was poorly immunogenic in mice; a second dose resulted in a significant boost in antibody levels, even in the absence of adjuvant. The use of adjuvants resulted in higher antibody titers, with the AS01(B)-adjuvanted vaccine being slightly more immunogenic than the AS03(A)-adjuvanted vaccine. Two doses of WI-SARS with and without Adjuvant Systems were highly efficacious in mice. In hamsters, two doses of WI-SARS with and without AS01(B) were immunogenic, and two doses of 2 μg of WI-SARS with and without the adjuvant provided complete protection from early challenge. Although antibody titers had declined in all groups of vaccinated hamsters 18 wk after the second dose, the vaccinated hamsters were still partially protected from wild-type virus challenge. Vaccine with adjuvant provided better protection than non-adjuvanted WI-SARS vaccine at this later time point. Enhanced disease was not observed in the lungs or liver of hamsters following SARS-CoV challenge, regardless of the level of serum neutralizing antibodies.
A New Algorithm for the Evaluation of Shotgun Peptide Sequencing in Proteomics:  Support Vector Machine Classification of Peptide MS/MS Spectra and SEQUEST Scores (2002)

Shotgun tandem mass spectrometry-based peptide sequencing using programs such as SEQUEST allows high-throughput identification of peptides, which in turn allows the identification of corresponding proteins. We have applied a machine learning algorithm, called the support vector machine, to discriminate between correctly and incorrectly identified peptides using SEQUEST output. Each peptide was characterized by SEQUEST-calculated features such as delta Cn and Xcorr, measurements such as precursor ion current and mass, and additional calculated parameters such as the fraction of matched MS/MS peaks. The trained SVM classifier performed significantly better than previous cutoff-based methods at separating positive from negative peptides. Positive and negative peptides were more readily distinguished in training set data acquired on a QTOF, compared to an ion trap mass spectrometer. The use of 13 features, including four new parameters, significantly improved the separation between positive and negative peptides. Use of the support vector machine and these additional parameters resulted in a more accurate interpretation of peptide MS/MS spectra and is an important step toward automated interpretation of peptide tandem mass spectrometry data in proteomics.
Jun N-terminal Kinase: a potential target for the treatment of head and neck squamous cell carcinoma (HNSCC) (2005)

2564 Jun N-terminal Kinase (JNK) is a stress-activated protein kinase responsible for the phosphorylation of c-Jun, a component of the activator protein-1 (AP-1) transcription factor complex. Changes in JNK or AP-1 activity can potentially affect a range of processes that are important for tumor growth including cell proliferation and angiogenesis. This preclinical study was carried out to investigate whether JNK is a potential target for treating HNSCC. Initially, JNK activity was evaluated in twenty paired samples (tumor vs. adjacent normal) of human HNSCC. Increased JNK activity was observed in >90% of the tumor samples. Subsequently, a HNSCC (1483 cell line) xenograft model was used to evaluate the anti-tumor activity of SP600125, a selective inhibitor of JNK. Treatment of mice bearing HNSCC xenografts with SP600125 (50 mg/kg/day) resulted in >60% inhibition of tumor growth relative to vehicle-treated animals [p in vitro studies to characterize the growth inhibitory and anti-angiogenic effects of SP600125. Treatment with SP600125 led to both dose- and time-dependent growth inhibition of 1483 cells. Growth inhibition was a consequence of reduced DNA synthesis and slowing of cell cycle progression through the S and G2 phases. To define the anti-angiogenic effects of SP600125, both 1483 tumor cells and human endothelial cells were employed. Treatment of 1483 cells with SP600125 caused a dose-dependent reduction in the production of VEGF. Inhibition of JNK activity also inhibited human microvascular endothelial cell proliferation and impaired endothelial cell capillary tube formation. Thus, SP600125-mediated inhibition of JNK activity appears to suppress angiogenesis via effects on both tumor cells and endothelial cells. Taken together, the results of this study provide a strong rationale for evaluating whether selective inhibitors of JNK activity will have a role in the treatment of HNSCC.