gebhart/patrepeval huggingface dataset:
Rigorous and thorough bioinformatic analyses of olfactory receptor promoters confirm enrichment of O/E and homeodomain binding sites but reveal no new common motifs (2011)

Our rigorous approach provides a template for the analysis of the regulation of large gene families and demonstrates some of the difficulties and pitfalls of such analyses. Although currently available bioinformatics methods cannot detect all transcriptional regulatory elements, our thorough analysis of OR promoters shows that in the case of this gene family, experimental approaches have probably already identified all the binding factors common to large fractions of OR promoters.
Supplemental Figures (revised) from MACC1 Induces Tumor Progression in Transgenic Mice and Colorectal Cancer Patients via Increased Pluripotency Markers Nanog and Oct4 (2023)

&lt;p&gt;Supplementary Figure 1. Generation of transgenic mice with IEC-specific overexpression of MACC1. Supplementary Figure 2. Characterization of the vil-MACC1 transgenic mice Supplementary Figure 3. MACC1 transgene expression in the vil-MACC1/ApcMin mice. Supplementary Figure 4. Characterization of the vil-MACC1/ApcMin mice. Supplementary Figure 5. Pathway analysis of the Affymetrix microarray.&lt;/p&gt;
Design and Implementation of Self-Consolidating Concrete for Connecting Precast Concrete Deck Panels to Bridge Girders (2016)

An experimental program was undertaken to develop and evaluate the performance of self-consolidating concrete (SCC) designed for connecting precast concrete deck panels to supporting bridge girders. The effect of curing conditions on early-age expansion and shrinkage of SCC made with expansive materials was evaluated. The effect of batching sequence, concrete temperature, and superplasticizer/water demand on SCC performance was investigated. Field mockup testing was conducted to evaluate the flowability and pumpability of the proposed SCC. Test results showed that the proposed SCC can maintain high filling and passing ability for 2 h and can exhibit adequate stability. The slump flow of the recommended SCC is 730±50 mm (29±2 in.), the L-box blocking ratio is greater than 0.80, the difference between slump flow and J-ring is less than 50 mm (2 in.), and the V-funnel flow time is less than 6 s. The developed SCC mixture was implemented in the construction of the Kearney East Bypass Bridge Project in Kearney, Nebraska, in August 2015. A total of 92 m3 (120 yd3) of the developed SCC was successfully placed through 100-mm (4-in.) diameter grouting/inspection holes located at 1.2-m (4-ft) spacing on the deck surface. The SCC was found to completely fill the shear pockets and haunches between the deck and the girders.
Spin Gunn Effect (2006)

We predict that the flow of unpolarized current in electron-doped GaAs and InP at room temperature is unstable at high electric fields to the dynamic formation of spin-polarized current pulses. Spin-polarized current is spontaneously generated because the conductivity of a spin-polarized electron gas differs from that of an unpolarized electron gas, even in the absence of spin-orbit interaction. Magnetic fields are not required for the generation of these spin-polarized current pulses, although they can help align the polarization of sequential pulses along the same axis.
Net carbon exchange in grapevine canopies responds rapidly to timing and extent of regulated deficit irrigation (2011)

Whole-canopy net CO2 exchange (NCEC) was measured near key stages of fruit development in grapevines (Vitis vinifera L. cv. Cabernet Sauvignon) that were managed under three approaches to regulated deficit irrigation (RDI): (1) standard practice (RDIS), or weekly replacement of 60-70% of estimated evapotranspiration for well watered grapevines; (2) early additional deficit (RDIE), or one-half of RDIS applied between fruit set and the onset of ripening (veraison), followed by RDIS; and (3) RDIS followed by late additional deficit (RDIL), or one-half of RDIS applied between veraison and harvest. Summed between fruit set and harvest, nearly 40% less irrigation was applied to RDIE vines and ~20% less to RDIL vines than to those continuously under RDIS. After ~5 weeks of additional deficit, NCEC in RDIE vines was 43-46% less per day than in RDIS vines. After RDIL vines had been under additional water deficit for ~3 weeks, NCEC was ~33% less per day than in RDIS vines. Instantaneous rates of NCEC responded rapidly to irrigation delivery and elapsed time between irrigation sets. Concurrent single-leaf measurements (NCEL) reflected the relative differences in NCEC between irrigation treatments, and were linearly associated with NCEC (r2=0.61). Despite halving the water applied under commercial RDI, mid-day stomatal conductance values in RDIE and RDIL of ~50-125mmolm-2s-1 indicated that the additional deficit imposed only moderate water stress. There was no effect of additional deficit on yield or berry maturity.
Amélioration du circuit visuel des contrôleurs aériens pour relier les données entre visualisations en utilisant des transitions animées (2011)

International audience
Abstract 1582: Identification of BCAR genes relevant for breast cancer progression and endocrine therapy resistance (2008)

Abstract Endocrine therapy of breast cancer is effective and widely applied. In advanced disease, about half of the patients will experience a clinical benefit from tamoxifen treatment, but ultimately the disease will progress into a resistant phenotype. The molecular basis of this general failure of endocrine therapy is not understood yet. Although gene expression profiling experiments provide gene lists to identify patients who may benefit from specific treatments, these genes mostly do not define the underlying molecular mechanisms. We have executed a functional screen for the identification of BCAR genes causing anti-estrogen resistance in a human breast cancer model and evaluated their role in a large breast cancer cohort. Estrogen-dependent ZR-75-1 human breast cancer cells were subjected to insertion mutagenesis with replication-defective retroviruses and selected for proliferation in the presence of 4-hydroxy tamoxifen. In our panel of 79 tamoxifen-resistant cell lines, the target genes of the retroviruses have been identified and were functionally tested following transfection into ZR-75-1 cells. Seven BCAR genes (AKT1, AKT2, BCAR1, BCAR3, EGFR, GRB7 and TRERF1) causing the tamoxifen-resistant phenotype were identified. Furthermore, additional putative BCAR genes and loci have been pinpointed. To determine the relevance of the identified genes in clinical breast cancer, we have studied 561 estrogen receptor-positive primary breast cancers for tumor aggressiveness and tamoxifen therapy resistance. Quantitative RT-PCR of ten genes was performed to measure the tumor mRNA levels. The endpoint for tumor aggressiveness was metastasis-free survival (MFS) of a cohort of lymph node-negative patients. Therapy resistance was evaluated in a group of patients treated with tamoxifen as first-line therapy for recurrent disease and the endpoint of this analysis was progression-free survival (PFS). Statistically significant associations with MFS were found for AKT2, EGFR, TLE3 and TRERF1 mRNA levels. In multivariate analyses including the traditional prognostic factors, AKT2, EGFR and TRERF1 were independent prognostic factors for MFS and thus are associated with tumor aggressiveness. In the analyses of PFS, mRNA levels of BCAR3, ERBB2, GRB7, TLE3 and TRERF1 were associated with the duration of clinical benefit of tamoxifen therapy, independently of the classical predictive factors. Our functional screen identified a set of clinically relevant BCAR genes offering insight in the molecular and cellular pathways of breast tumor aggressiveness and tamoxifen resistance, and thereby provides novel targets for personalized treatment and prevention strategies. Supported by the Dutch Cancer Society, the Susan G Komen Breast Cancer Foundation and the Association for International Cancer Research.
Flow-Pattern Transition and Hydrodynamic Modeling of Churn Flow (1999)

Summary A thorough review of the existing models for slug-churn transition in vertical and upward inclined two-phase flow is presented. A new transition model based on the drift flux approach and experimental data has been proposed. The new transition model performed the best when it was compared with the existing models and agreed very well with the published experimental data. Two separate hydrodynamic models are presented to predict pressure drop and liquid holdup in churn flow. One is a modified slug model, and the other is a model based on drift flux approach. The performances of the hydrodynamic models are evaluated against a well databank that contains 46 churn flow cases including laboratory and field data.
3D capillary force assembly: fabrication of white light emitters (2012)

International audience
Microscopic Assessment of Healing and Effectiveness of a Foam-Based Peripheral Occlusion Device (2019)

The IMPEDE Embolization Plug is a catheter-delivered vascular occlusion device that utilizes a porous shape memory polymer foam as a scaffold for thrombus formation and distal coils to anchor the device within the vessel. In this study, we investigated the biological response of porcine arteries to the IMPEDE device by assessing the extent of healing and overall effectiveness in occluding the vessel at 30, 60, and 90 days. Compared to control devices (Amplatzer Vascular Plug and Nester Embolization Coils), the host response to IMPEDE showed increased cellular infiltration (accommodated by the foam scaffold), which led to advanced healing of the initial thrombus to mature collagenous connective tissue (confirmed by transmission electron microscopy (TEM)). Over time, the host response to the IMPEDE device included degradation of the foam by multinucleated giant cells, which promoted fibrin and polymer degradation and advanced the healing response. Device effectiveness, in terms of vessel occlusion, was evaluated histologically by assessing the degree of recanalization. Although instances of recanalization were often observed at all time points for both control and test articles, the mature connective tissue within the foam scaffold of the IMPEDE devices improved percent vessel occlusion; when recanalization was observed in IMPEDE-treated vessels, channels were exclusively peri-device rather than intradevice, as often observed in the controls, and the vessels mostly remained >75% occluded. Although total vessel occlusion provides the optimal ischemic effect, in cardiovascular pathology, there is a progressive ischemic effect on the downstream vasculature as a vessel narrows. As such, we expect a sustained ischemic therapeutic effect to be observed in vessels greater than 75% occluded. Overall, the current study suggests the IMPEDE device presents advantages over controls by promoting an enhanced degree of healing within the foam scaffold, which decreases the likelihood of intradevice recanalization and ultimately may lead to a sustained ischemic therapeutic effect.
High performance, waveguide integrated Ge photodetectors (2007)

Photonic systems based on complementary metal oxide semiconductor (CMOS) technology require the integration of passive and active photonic devices. The integration of waveguides and photodetector is one of the most important technologies. We report a Ge p-i-n photodetector that is monolithically integrated with silicon oxynitride and silicon nitride waveguides. All processes and materials are CMOS compatible and can be implemented in the current integrated circuit process technology. The small size of the devices results in low absolute dark current. The waveguidecoupled Ge devices show high efficiency (~90%) over a wide range of wavelengths well beyond the direct band gap of Ge, resulting in a responsivity of 1.08 A/W for 1550 nm light. The device speed of 7.2 GHz at 1V reverse bias is strongly affected by the capacitance of the probe pads. The high-performance of the devices at low voltage ( </= 1V) facilitates the integration with CMOS circuits.
SU‐C‐BRB‐01: Spatially Fractionated Radiation Therapy (GRID) Using a TomoTherapy Unit (2011)

Purpose: To present a new technique to plan and deliver spatially‐fractionated radiotherapy (GRID) utilizing helical TomoTherapy IGRT system. Methods: In a single large dose (20 Gy), GRID offers an effective radiation therapy for bulky malignant tumors. The conventional GRID irradiation is delivered through a dedicated grid block or field intensity modulation using a multileaf collimator (MLC). However, the dose to nearby organs‐at‐risk (OAR) becomes a concern when treating deep seated bulky lesions in GRID technique. So With its capability of delivering highly conformal and multifocal dose distributions, TomoTherapy emerges as a promising radiotherapy modality for GRID therapy that delivers high single dose to deep seated tumors with excellent normal tissue sparing. It is called TOMO GRID. Planning CT images and contours are exported from a Pinnacle3 planning workstation via DICOM connection to the in‐house developed software system, DICOMan, where Boolean operations are applied to GTV contours to create multiple parallel GRID targets. An avoidance (GTV ‐ GRID targets) structure is also created to help the inverse planning process to achieve the desired peak‐valley ratio. Those CT images and contours will be repackaged in DICOMan and sent to TomoTherapy planning workstation.Results: TOMO GRID delivers highly non‐uniform dose distributions that resemble more or less those of breachytherapy. The TOMO GRID targets (virtual implants) can be configured in various patterns (templates), sectional shapes and sizes. At each “insert” position, the implant can be in either “needle” or “seed‐spacer” train. Tested in both phantom and real patient datasets, our results show that it is feasible to deliver GRID therapy on TomoTherapy unit for deep seated lesions Conclusions: TomoTherapy has a great potential to deliver GRID therapy with a superior quality than conventional GRID therapy. More studies need to be conducted to justify the applicability of this technology in clinics.
Synthesis of Titanium Dioxide (TiO&lt;SUB&gt;2&lt;/SUB&gt;) Nanomaterials (2006)

Titanium dioxide (TiO2) is a promising material for many emerging applications. Even more promising are the benefits offered by the material when its length scale is reduced to the nanometer range. Nanomaterials usually exhibit unique properties resulting from either the extremely large surface area-to-volume ratio or the quantum confinement effect of energy carriers. In this article we present an overview of recent progress in the synthesis of TiO2 nanomaterials. The topics include synthesis of TiO2 nanoparticles, nanorods, nanowires, nanotubes, and mesoporous/nanoporous materials using different preparation approaches such as sol-gel, sol, hydrothermal, solvothermal, and vapor deposition. The applications of TiO2 nanomaterials are also briefly summarized.
Magnetics Design for Active Transient Voltage Compensator (2006)

This paper is mainly focused on how to design the transformer to meet the requirements of active transient voltage compensator (ATVC) circuit. The FEM transformer design method is discussed in detail. ATVC is a solution to the challenging transient requirement of VRM under high slew rate load current. It only works in transient periods and the main VR operates in low frequency which results in high efficiency. In the steady state, the transformer is just a paralleled large filter inductor. In transient periods, ATVC acts as a transformer, injecting or absorbing high slew rate current that is determined by the transformer leakage inductance. The numerical FEM method is used to design the transformer according to the transformer's actual working conditions. The accurate and frequency dependable transformer magnetizing inductance value and the leakage inductance value of each winding can be decided from the FEM results directly. The simulation and experiment results verify this transformer design. The circuit slew rate can reach the 0.11A//spl mu/s.
Monensin enhances the cytotoxic effect of antitransferrin receptor immunotoxin on cultured RPE cells (1993)

The effect of monensin on the cytotoxic effect of antitransferrin receptor immunotoxin (IT) was determined on cultured, human retinal pigment epithelial (hRPE) cells. Human RPE cells were treated with 0.1-10,000 ng/ml IT with and without 0.01-0.1 microM monensin, a lysosomotropic reagent that can influence IT activity. Monensin (0.01 microM) shortened the onset of cell kill with IT (10,000 ng/ml) from 48 to 24 hours (p = 0.0016). Although 0.01 microM monensin alone was not cytotoxic to hRPE cells, a single 7-day treatment with monensin caused up to a 4.1-fold increase in antiproliferative potency of IT on proliferating hRPE cells (p < or = 0.0001). Enhancement was obtained with only a 1-hour exposure to 0.1 microM monensin (p = 0.0001). In contrast, IT (0.1-10,000 ng/ml) combined with monensin (0.01 microM) had minimal effect on density-arrested cells. IT with or without monensin did not inhibit proliferation of Rhesus monkey RPE cells. Our results indicate that monensin enhances the selective cytotoxic effect of IT on proliferating hRPE cells in culture.
&lt;title&gt;Resonantly enhanced nonlinearaties in rare-earth-doped fibers and waveguides&lt;/title&gt; (1996)

The use of rare-earth dopants for all-optical switching is of interest because of the very low pump powers required to achieve full switching. In addition, the ease with which rare-earth ions can be incorporated into silica based fibers and waveguides makes them ideally suited for the fabrication of fiber compatible components. The principal disadvantages of this type of nonlinearity are that the relaxation times are characteristically slow, and relatively long interaction lengths are required to achieve phase changes of the order of (pi) . In this presentation, an overview of the work being carried out in Australia will be given, concentrating on the techniques developed to minimize the relaxation times and power length products of these nonlinearities.
ChemInform Abstract: A Facile One‐Pot Synthesis of Polyfunctionalized 2‐Unsubstituted Benzo( b)furans. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Accuracy of Carotid Ultrasonography in the Treatment of Carotid Stenosis: A Comparison to Digital Substraction Angiography in 631 Consecutive Cases (2006)

s of Oral Proceedings: 2006 Joint Annual Meeting of the AANS/CNS Cerebrovascular Section and the American Society of Interventional & Therapeutic Neuroradiology Caribe Royale Orlando—Orlando, Florida February 17–20, 2006: Anatomy: Cerebrovascular
Revisiting the Sample Complexity of Sparse Spectrum Approximation of Gaussian Processes (2020)

We introduce a new scalable approximation for Gaussian processes with provable guarantees which hold simultaneously over its entire parameter space. Our approximation is obtained from an improved sample complexity analysis for sparse spectrum Gaussian processes (SSGPs). In particular, our analysis shows that under a certain data disentangling condition, an SSGP's prediction and model evidence (for training) can well-approximate those of a full GP with low sample complexity. We also develop a new auto-encoding algorithm that finds a latent space to disentangle latent input coordinates into well-separated clusters, which is amenable to our sample complexity analysis. We validate our proposed method on several benchmarks with promising results supporting our theoretical analysis.
Recognition of highly restricted regions in the β-propeller domain of αIIb by platelet-associated anti-αIIbβ3 autoantibodies in primary immune thrombocytopenia (2012)

Platelet-associated (PA) IgG autoantibodies play an essential role in primary immune thrombocytopenia (ITP). However, little is known about the epitopes of these Abs. This study aimed to identify critical binding regions for PA anti-αIIbβ3 Abs. Because PA anti-αIIbβ3 Abs bound poorly to mouse αIIbβ3, we created human-mouse chimera constructs. We first examined 76 platelet eluates obtained from patients with primary ITP. Of these, 26 harbored PA anti-αIIbβ3 Abs (34%). Further analysis of 15 patients who provided sufficient materials showed that the epitopes of these Abs were mainly localized in the N-terminal half of the β-propeller domain in αIIb (L1-W235). We could identify 3 main recognition sites in the region; 2 eluates recognized a conformation formed by the W1:1-2 and W2:3-4 loops, 5 recognized W1:2-3, and 4 recognized W3:4-1. The remaining 4 eluates could not be defined by the binding sites. Within these regions, we identified residues critical for binding, including S29 and R32 in W1:1-2; G44 and P45 in W1:2-3; and P135, E136, and R139 in W2:3-4. Of 11 eluates whose recognition sites were identified, 5 clearly showed restricted κ/λ-chain usage. These results suggested that PA anti-αIIbβ3 Abs in primary ITP tended to recognize highly restricted regions of αIIb with clonality.