gebhart/patrepeval huggingface dataset:
Frequent overexpression of the genes FXR1, CLAPM1 and EIF4G located on amplicon 3q26‐27 in squamous cell carcinoma of the lung (2007)

Previously, we reported gene amplification at chromosome 3q26-27 in more than one third of squamous cell carcinomas of the lung. Frequent amplification of eukaryotic translation initiation factor 4G on 3q27.1 indicated a possible role of this amplification in translation initiation. The analysis of 61 squamous cell lung carcinomas shows that the percentage of carcinomas with a 3q27.1 amplification increases in higher malignant tumors. Non-invasive (T1) and minimal-invasive (T2) tumor stages showed similar percentages of amplified and non-amplified tumors, whereas locally-invasive (T3) tumors revealed a statistically significant (p < 0.05) increased percentage of amplified tumors. Microarrays were used to analyze the expression pattern of genes mapping in the amplified domain and its flanking regions (3q25-28) as well as the expression of genes directly or indirectly associated with translation initiation in squamous cell carcinoma, large cell carcinoma, adenocarcinoma and small cell carcinoma. Three genes, namely FXR1, CLAPM1 and EIF4G, are most frequently overexpressed in the center of the amplified domain in squamous cell carcinomas. The eukaryotic translation initiation factors 4A1, 2B and 4B as well as the poly(A)-binding protein PABPC1 where found to be overexpressed in all lung cancer entities. We found, however, no overexpression of eIF4E. Our results contribute to the understanding of the frequent amplification processes in squamous cell carcinomas of the lung and to the understanding of the translation initiation that appears not to require eIF4E in lung carcinogenesis.
Aberrant Promoter Methylation Can be Useful as a Marker of Recurrent Disease in Patients with Cervical Intraepithelial Neoplasia Grade III (2007)

We suggest that aberrant promoter methylation may play a role and may serve as a useful biomarker in the recurrence of CIN.
Joint Localization of Events and Sources in Social Networks (2015)

Recent sensor network literature investigated the use of social networks as sensor networks, and formulated a physical event localization problem from social network data. This paper improves on the above results by formulating a joint localization problem of events and sources, leveraging the fact that sources on social networks often have a location affinity: They tend to comment more on events in their locations of interest. While social networks, such as Twitter, do not offer source location information for the majority of sources, we show that our algorithms for jointly inferring source and event location significantly improve localization quality by mutually enhancing location estimation of both events and sources. We evaluate the performance of our algorithm both in simulation and using Twitter data about current events. The results show that joint inference of source and event location allows us to localize many more of the events identified in real-world datasets.
High-Robust Force Control for Environmental Stiffness Variation Based on Duality of Two-Inertia System (2020)

The conventional force control has proposed load-side torque control based on the resonance ratio control (RRC) enhanced by an instantaneous state observer using the acceleration sensor; however, environmental stiffness variation (K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> variation) is not considered in such systems. This article evaluates the robust stability of the conventional method based on open-loop characteristics and the stability analysis results indicate that the conventional method becomes unstable during K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> variation. To realize superior high-robust stability, this article proposes a high-robust force control based on the duality of the two-inertia system. This article constructs an equivalent RRC (ERRC) combining the motor-side velocity control and the load-side velocity observer and demonstrates a torque-velocity duality. The results confirm that the load-side torque control based on ERRC is robust against K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> variation through the analysis of open-loop characteristics, and illustrate that the ERRC has the same as the conventional RRC proposed in position or velocity controls. The effectiveness of the proposed control method is validated through numerical simulations and experiments.
Translocation of Poly(ethylene glycol-co-hexadecyl)cyanoacrylate Nanoparticles into Rat Brain Endothelial Cells:  Role of Apolipoproteins in Receptor-Mediated Endocytosis (2007)

Previous in vivo observations in rats have shown that poly(ethylene glycol) polyhexadecylcyanoacrylate (PEG-PHDCA) nanoparticles could translocate into the brain after intravenous injection, which polyhexadecylcyanoacrylate (PHDCA) nanoparticles did not. Through the detailed analysis of the plasma protein adsorption onto the surface of PEG-PHDCA nanoparticles, the present study aimed at clarifying the mechanism by which nanoparticles could penetrate into rat brain endothelial cells (RBEC). Two-dimensional polyacrylamide gel electrophoresis and Western blotting revealed that, after incubation with rat serum, apolipoprotein E (ApoE) adsorbed more onto PEG-PHDCA than on PHDCA nanoparticles. Adsorption of apolipoprotein B-100 (ApoB-100) onto PEG-PHDCA nanoparticles was demonstrated by capillary electrophoresis experiments. Moreover, only when ApoE or ApoB-100 were preadsorbed onto PEG-PHDCA nanoparticles, nanoparticles were found to be more efficient than control nanoparticles for penetrating into RBEC, suggesting the involvement of a low density lipoprotein receptor in this process. Thus, these data clearly demonstrate the involvement of apolipoproteins in the brain transport of PEG-PHDCA nanoparticles, which may open interesting prospects for brain drug delivery.
Abstract 11653: The Dynamic Norwood Mortality Estimator: Characterizing Instantaneous, Personalized Risk Trajectories for Infants After the Norwood Operation (2017)

Background: Post-Norwood, mortality is high and unpredictable. Adverse events and re-interventions are also common. Current risk scores only incorporate baseline data. We sought to create a novel s...
System model for characterizing and reducing the mutual coupling in MIMO antennas (2010)

International audience
Pontine pathology mediates common symptoms of blast-induced chronic mild traumatic brain injury (2023)

Abstract Understanding how diffuse mild traumatic brain injuries can provoke common and persistent post-concussive symptoms (PCS), such as impaired sleep, is crucial to prevent and treat chronic disability and neurodegeneration. We mapped the spatially-resolved single cell landscape of diffuse mTBI pathology in a mouse model of blast exposure; identifying brainstem injuries predictive of later PCS. Repeated mTBI was necessary to establish chronic microglial activation and phagocytosis of myelin in the pontine reticular formation; where IL33 release by oligodendrocytes predicted microgliopathy. In postmortem brainstem tissues from patients with traumatic brain injury, chronic microglial activation and myelin phagocytosis was evident up to 20 years after diffuse mTBI caused by blast. In living patients with chronic blast mTBI, myelin injury in pontine projections mediated sleep disturbance and other PCS, with a dose dependent effect of mTBI number on sleep disturbance severity. These results support a mechanism for diffuse mTBIs to cause delayed persistent PCS.
Testosterone-induced suppression of autoimmune disease in lacrimal tissue of a mouse model (NZB/NZW F1) of Sjögren's syndrome. (1991)

The current investigation was designed to examine whether androgen administration might suppress autoimmune disease in lacrimal glands of a mouse model (NZB/NZW F1) of Sjögren's syndrome. Autoimmune, female mice were treated with vehicle or varying concentrations of testosterone for 0, 17, 34, or 51 days, and tears, lacrimal glands, as well as submandibular tissue, were collected from killed mice after androgen exposure. Glands were histologically processed and evaluated with a computer-assisted image analysis system. Results showed that testosterone administration induced a significant, time-dependent decrease in the extent of lymphocytic accumulation in the lacrimal gland. After 34-51 days of androgen therapy, the magnitude of lymphocyte infiltration had been suppressed 22- to 46-fold, compared with that in placebo-treated tissue. This hormone effect was associated with significant reductions in the number of focal infiltrates, the area of individual foci, and the total quantity of lymphocyte infiltration per lacrimal section. Testosterone exposure also stimulated an increase in lacrimal gland weight and a rise in tear volumes, relative to those measured in the same mice before treatment. In addition, androgens significantly diminished the extent of lymphocyte accumulation in submandibular tissue. In summary, our results demonstrate that androgen administration may inhibit the progression of autoimmune disease in lacrimal and submandibular glands of NZB/NZW F1 mice.
Estimating signal and structured noise in ultrasound data using prediction-error filters (2019)

When using ultrasound to image heterogeneous media, echoes from multiple and off-axis scattering can overwrite the recorded ballistic wavefronts of interest. This reduces the coherence of signals across the aperture and causes clutter in the final image. Therefore, separating those unwanted events from the signal of interest is necessary to improve the visibility of structures in a B-mode image, and also to enable other processing methods that require coherent channel signals, such as various phase-aberration-correction techniques and sound-speed estimators. We used prediction-error filters (PEFs) to model the signal and the assumed additive noise in the data acquired through a 10 mm thick layer of beef tissue placed above a speckle region of a phantom. The PEF coefficients used to model the signal were first computed from the phantom data collected without tissue and subsequently employed to deconvolve the tissue data and find the PEF associated with the noise. These two filters were then used in a joint-inversion framework to separate the signal and noise components recorded within the original tissue data. In order to be able to apply our method in scenarios where direct measurements of the signal proxy are not available, we also evaluated the signal-PEF coefficients from the theoretical model of the signal from diffuse targets as provided by the van-Cittert Zernike (VCZ) theorem. To evaluate the quality of the separation of signal from the noise, we compared the original channel data acquired through the tissue with its estimated ballistic-wave component, as well as their corresponding spectra. We also compared performance of the proposed technique to F-X filter, which is a popular linear-predictionbased filter used to suppress noise in channel data. After the removal of acoustic noise from the channel data, coherence across the aperture increases. The average nearest-neighbor cross-correlation computed on the original data is 0.47, while the nearest-neighbor cross-correlation of the estimated ballistic-wave component is 0.81 or 0.97, depending whether the experimental or theoretical signal-PEFs are used in the estimation process.
Abstract B04: NRF2 regulates serine biosynthesis in pancreatic ductal adenocarcinoma (2016)

Abstract Tumors have high energetic and anabolic needs for rapid growth and proliferation, and the serine biosynthetic pathway has recently been identified as an important source of metabolic intermediates for these processes. We recently demonstrated that a substantial fraction of NSCLC cell lines displayed significant serine/glycine biosynthetic activity due to KEAP1 and NRF2 mutations (DeNicola et al. Nature Genetics 2015). We demonstrated that NRF2 regulates glucose flux to serine by controlling transcription of serine biosynthetic genes through the transcription factor ATF4. Importantly, elevated expression of these genes conferred poor prognosis in human NSCLC. Thus, a substantial fraction of human NSCLC activates an NRF2-dependent transcriptional network that regulates serine and glycine metabolism and is linked to clinical aggressiveness. Pancreatic ductal adenocarcinoma (PDAC) also demonstrates high NRF2 activity due to mutations in KRAS and high MAPK signaling (DeNicola et al. Nature 2011). We demonstrate that serine biosynthesis enzyme expression is elevated in a mouse model of PDAC and that NRF2 regulates PHGDH expression in human PDAC cell lines. Furthermore, PDAC cell lines are resistant to serine starvation. PHGDH knockdown impairs the growth of tumor organoid orthotopic transplants, and the role of PHGDH in tumor maintenance is currently being investigated. These results suggest that the serine biosynthesis pathway is regulated by NRF2 in multiple cancers and may be an important therapeutic target. Citation Format: Gina M. DeNicola, Pei-Hsuan Chen, Edouard Mullarky, Christine Chio, John M. Asara, John D. Minna, David A. Tuveson, Ralph J. DeBerardinis, Lewis C. Cantley.{Authors}. NRF2 regulates serine biosynthesis in pancreatic ductal adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr B04.
Terahertz Meta-Device for Airy Beam Manipulation (2022)

The existing meta-lens designs and methods usually have limitations of single focus steering direction or few specified achievable areas. We demonstrate a design of the terahertz Airy beam meta-device. It could control the focal spots of the Airy beam in a full two-dimensional (2D) plane, and the position of the focal spots can be tuned continuously. We developed a 3D-printing method enabling large-scale and low-cost fabrication of the terahertz metasurfaces with high precision. The manipulation capability for the focal spots and the advanced fabrication method enables practical applications.
Supplementary Figures S1 - S8 from Biallelic Alteration and Dysregulation of the Hippo Pathway in Mucinous Tubular and Spindle Cell Carcinoma of the Kidney (2023)

&lt;p&gt;Supplementary Figures S1 - S8. Supplementary Figure S1. Intra-tumor mutational heterogeneity in MTSCC. Supplementary Figure S2. Copy number variation and Hippo pathway mutation in the MTSCC validation cohort and the TCGA KIRP outlier samples. Supplementary Figure S3. MTSCC Gene Expression Analyses. Supplementary Figure S4. PTPN14 function and Hippo pathway signature in kidney. Supplementary Figure S5. Gene set enrichment analysis. Supplementary Figure S6. HNF genes expression in normal human tissues, MTSCC and TCGA kidney cancer RNA-seq data. Supplementary Figure S7. Summary of YAP1 immunohistochemistry. Supplementary Figure S8. Gene expression correlation between MTSCC and nephron sections.&lt;/p&gt;
Safety of carotid endarterectomy while on clopidogrel (Plavix) (2010)

Findings in this study support the safety of preoperative clopidogrel in patients undergoing CEA.
Experimental Demonstration of Tunable Optical Channel Slicing and Stitching to Enable Dynamic Bandwidth Allocation (2017)

A tunable optical channel slicing and stitching scheme is experimentally demonstrated in QPSK/16QAM systems. Its application to dynamic bandwidth allocation in WDM channels brings &gt;6dB OSNR improvement at 1e-3 BER comparing to direct channel insertion.
Charge Analysis in SAR ADC with Discrete-Time Reference Driver (2020)

This paper provides detailed mathematical analysis that investigate the effect of charge-sharing between an analog-to-digital converter (ADC) reference decoupling capacitor and a charge-redistribution based differential split-monotonic capacitive digital-to-analog converter (CDAC). A discrete-time reference driver is used to charge the decoupling capacitor in the sampling phase, forming a closed-system in the hold phase which allows us to apply a charge-based analysis to determine the voltages at several nodes within the system such as the reference capacitors and comparator inputs. The generalized mathematical model can be used to accurately determine the voltage shift on the comparator inputs and hence quantify the effect on the SAR comparator decision level with a varying reference decoupling capacitor which can ultimately be used to optimize the size of the capacitor while maintaining high SNDR/SFDR. In this design, we utilize a differential decoupling capacitor which provides a 4x capacitor area decrease compared to its single ended counterparts.
Field-based Simulations of Directed Self-Assembly in a Mixed Brush System. (2016)

Abstract not provided.
Meloidogyne duytsi n. sp. ( Nematoda : Heteroderidae ), a root-knot nematode from Dutch coastal foredunes (1998)

A root-knot nematode, Meloidogyne duytsi n. sp., is described and illustrated from Elymus farctus (Viv.) Melderis from Dutch coastal foredunes. This new species is characterized by the following characters: female with styler slightly curved dorsally, 13.3 mu m long, with large transversely ovoid knobs set off from the shaft, asymetrical perineal pattern with a relatively low dorsal arch and coarse striae, lateral lines indistinct, and lateral wing present in most patterns, male with styler 19.8 mu m long, with large transversely ovoid knobs set off from the shaft, head region high and set off, labial disc slightly raised, lateral lips small, and tail conical with rounded tip, and second-stage juvenile 424 mu m long, with hemizonid anterior to excretory pore, tail 70.4 mu m long, tapering and slightly curved ventrally, and hyaline tail terminus distinct, 11.3 mu m long. A previously unknown malate dehydrogenase pattern and a slow esterase isozyme band were detected. M. duytsi n. sp. was also found in mixture with M. maritima Jepson, 1987 on Ammophila arenaria (L.) Link. [KEYWORDS: foredunes; Elymus farctus; Meloidogyne duytsi; morphology; root-knot nematode Arenaria l link; identification]
Association Between Decline in Slow Vital Capacity and Respiratory Insufficiency, Use of Assisted Ventilation, Tracheostomy, or Death in Patients With Amyotrophic Lateral Sclerosis (2017)

The rate of decline in SVC is associated with meaningful clinical events in ALS, including respiratory failure, tracheostomy, or death, suggesting that it is an important indicator of clinical progression.
Signcryption from NTRU Lattices Without Random Oracles (2019)

A signcryption scheme provides both the function of digital signature and encryption scheme at the same time. Additionally, it has lower cost than traditional sign-then-encrypt or encrypt-then-sign approaches. Many useful applications have been found where confidentiality and non-repudiation are both required. On the other hand, with the current development of rapid quantum computing, currently schemes based on traditional numerical assumptions (e.g., decisional Diffie-Hellman assumption) are more likely to be attacked by quantum computers. Therefore, lattice-based signcryption schemes have been extensively studied in recent years. However, most of them are either inefficient or secure-proved under the assumptions of random oracles. Although some of them are proved in the standard model, they are not practical in low-cost devices. Since the security is based on "Learning with Errors" (LWE) or "Short Integer Solution" problems, it will result in extremely large size of keys. In this paper, we propose an efficient NTRU-based signcryption scheme, which is inspired from Pion et al.'s key encapsulation mechanism. We provide rigorous security proofs for the confidentiality and unforgeability under NTRU-based assumptions in the standard model. Compared with other schemes, we conclude that our scheme is more efficient and secure.
Enhancement of elastohydrodynamic friction by elastic hysteresis in a periodic structure (2020)

Lubricated contacts are present in many engineering and biological systems involving soft solids. Typical mechanisms considered for controlling the sliding friction in such lubricated conditions involve bulk material compliance, fluid viscosity, viscoelastic response of the material (hysteretic friction), and breaking of the fluid film where dry contact occurs (adhesive friction). In this work we show that a two-phase periodic structure (TPPS), with a varying modulus across the sliding surface, provides significant enhancement of lubricated sliding friction when the system is in the elastohydrodynamic lubrication (EHL) regime. We propose that the enhanced friction is due to extra energy loss during periodic transitions of the sliding indenter between the compliant and stiff regions during which excess energy is dissipated through the fluid layer. This is a form of elastic hysteresis that provides a novel mechanism for friction enhancement in soft solids under lubricated conditions.
Phomopsidone, a Novel Depsidone from an Endophyte of the Medicinal Plant Eupatorium arnottianum (2007)

The medicinal plant Eupatorium arnottianum can be found in the Northeast and center of Argentina and the South of Bolivia. From plant material collected in Argentina an endophytic Phomopsis was isolated. The fungus was identified by microscopic features and analysis of its ITS sequence. Cultures yielded, besides mellein and nectriapyrone, a novel depsidone derivative for which we propose the name phomopsidone (1). The structure of 1 was determined from its spectroscopic data.
Fluorine separation and generation device (2023)

A process and apparatus for the electrolytic separation of fluorine from a mixture of gases is disclosed. Also described is the process and apparatus for the generation of fluorine from fluorine/fluoride containing solids, liquids or gases.
Preorganized Homochiral Pyrrole‐Based Receptors that Display Enantioselective Anion Binding (2022)

Herein, a new scaffold for anion recognition based on a tripodal tris(pyrrolamide) motif is presented. The receptors were able to bind to a variety of anions with high affinity. Using density functional theory methods, the three-dimensional geometry of the receptor-anion complex was calculated. These calculations show that the receptors bind anions via a preorganized cavity of amide and pyrrole hydrogen bond donor groups. Based on these findings, homochiral tris(pyrrolamide) receptors were prepared, which produced as much as a 1.6-fold greater affinity for (<i>S</i>)-(+)-mandelate over (<i>R</i>)-(-)-mandelate, demonstrating the ability to differentiate between these enantiomeric anions. The interaction of (<i>S</i>)-(+)-mandelate and (<i>R</i>)-(-)-mandelate within the homochiral receptor was examined by solution NMR spectroscopy and density functional theory calculations. These findings indicate that the preorganized positioning of the pyrrole groups and subsequent sterics allows to differentiate between the stereoisomeric anions.
Three-dimensional Polarization Ray Tracing and Diattenuation Calculation (2010)

A three-by-three polarization ray tracing matrix P for calculating polarization transformations associated with ray paths through optical systems is presented. Diattenuation of the optical system is calculated via singular value decomposition of the P matrix.
EDITORIAL FOR 100TH VOLUME OF INTEGRATED FERROELECTRICS (2008)

With the publication of this 100th the Volume of Integrated Ferroelectrics, it is appropriate to reflect on the progress that has been made in this field of science and technology since Volume 1 wa...