gebhart/patrepeval huggingface dataset:
Restricted Presence of POU6F2 in Human Corneal Endothelial Cells Uncovered by Extension of the Promoter-level Expression Atlas (2017)

Corneal endothelial cells (CECs) are essential for maintaining the clarity of the cornea. Because CECs have limited proliferative ability, interest is growing in their potentially therapeutic regeneration from pluripotent stem cells. However, the molecular mechanisms of human CEC differentiation remain largely unknown. To determine the key regulators of CEC characteristics, here we generated a comprehensive promoter-level expression profile of human CECs, using cap analysis of gene expression (CAGE) with a single molecule sequencer. Integration with the FANTOM5 promoter-level expression atlas, which includes transcriptome profiles of various human tissues and cells, enabled us to identify 45 promoters at 28 gene loci that are specifically expressed in CECs. We further discovered that the expression of transcription factor POU class 6 homeobox 2 (POU6F2) is restricted to CECs, and upregulated during human CEC differentiation, suggesting that POU6F2 is pivotal to terminal differentiation of CECs. These CEC-specific promoters would be useful for the assessment of fully differentiated CECs derived from pluripotent stem cells. These findings promote the development of corneal regenerative medicine.
Cross-Reacting Allergens in Tree Pollen and Pollen-Related Food Allergy: Implications for Diagnosis of Specific IgE (1997)

rBet v 1a can be expected to represent an excellent tool for the diagnosis of patients allergic to birch pollen in Central, Northern, and Eastern Europe. Still, a much higher number of patients has to be tested. For their high degree of conservation, further protein families have to be identified to explain cross-reactivities of birch pollen allergens other than Bet v 1 and Bet v 2 with, e.g., allergens from vegetable food.
The Facility for 500 MeV Plasma Wake-Field Acceleration Experiments at Budker INP (2010)

The experimental PWFA facility currently under construction at the Budker INP is described. The objective is to use electron and positron beams extracted from the VEPP‐5 damping ring in PWFA experiments. Due to longitudinal beam compression many PWFA schemes including the efficient blowout regime as well as multibunch regime can be studied. The simulations of beam dynamics in the facility are presented. Also we propose a simple technique for longitudinal beam slicing using dipole kickers and collimator in the damping ring.
Effect of test environment on the surface breakdown characteristics of photoconducting silicon (1992)

The influence of test environments (vacuum and air) on the pre-breakdown and breakdown characteristics of photoconducting p-type silicon samples were investigated. The surface of all the samples were polished (mechanical and chemo-mechanical) to a fine finish (0.06 micrometers ) and cleaned by ultrasonic and RCA methods. The role of thermally grown thin amorphous SiO<SUB>2</SUB> layer and the insulating epoxy layer on the breakdown properties were also investigated. The breakdown characteristics of the samples were found to be modified by the surface condition while testing in vacuum. Contrarily, the influence of those surface parameters on the breakdown properties of the same samples were found to be insignificant when the test environment was air. In general, the samples exhibited higher breakdown strength in air compared to that in vacuum. Besides, the lock-on behavior of the samples was identified only in vacuum (not in air) environment.
Transcriptional Assessment of Striatal mRNAs as Valid Biomarkers of Disease Progression in Three Mouse Models of Huntington’s Disease (2020)

Our results show that transcripts linked to neurotransmission are significantly reduced and are consistent with disease progression in both zQ175KI and R6/2 transgenic mouse models.
Adherence characteristics of attaching and effacing strains of Escherichia coli from rabbits (1994)

Twelve strains of Escherichia coli previously reported to cause diarrhea in rabbits were examined for properties associated with virulence. Ten strains met the criteria for classification as enteropathogenic E. coli in that they were diarrheagenic strains that evoked attaching-effacing lesions in the small intestine and did not produce detectable enterotoxins or cytotoxins. These bacteria exhibited a variety of patterns when investigated for adherence to HEp-2 epithelial cells. Although several strains displayed localized and/or diffuse adherence to epithelial cells, they did not hybridize with DNA probes that recognize the genes responsible for these phenotypes in diarrheagenic E. coli from humans. The bacteria also varied in their ability to bind to erythrocytes and intestinal brush borders from various animal species. Six strains adhered to rabbit brush borders; two of these also adhered to brush borders from other animals. Two strains that did not adhere to rabbit brush borders adhered to those from guinea pigs or sheep. Only one of the strains investigated carried AF/R1 fimbriae, which are believed to govern the host specificity of this category of diarrheagenic E. coli. This strain was E. coli RDEC-1, which remains the only E. coli strain to date that is known to carry fimbriae of this type. The results indicate that although diarrheagenic E. coli strains from rabbits may have common properties associated with the ability to produce attaching-effacing lesions, they differ from each other and from enteropathogenic E. coli of humans in terms of some of the adhesins that mediate binding to eukaryotic cells.
Erectile Dysfunction Management for the Future (2009)

The field of erectile dysfunction (ED) management over time has witnessed assorted interventions to enable men to perform sexual intercourse. In recent times, major progress in ED research has led to increasingly effective treatments based on a refined knowledge of the scientific basis for penile erection. Current concepts suggest that therapeutic prospects on the horizon include novel pharmacotherapies, growth factor therapy, gene therapy, and regenerative medicine. The purpose of this review is to present the foundations for future therapies in ED management.
A 0.032-mm2 43.3-fJ/Step 100–200-MHz IF 2-MHz Bandwidth Bandpass DSM Based on Passive N-Path Filters (2020)

In this article, we demonstrate a bandpass (BP) delta-sigma modulator (DSM) using passive N-path filters to implement resonators for high power efficiency, wide intermediate-frequency (IF) tuning range, and small area. The fourth-order modulator loop requires only one active element: an open-loop amplifier. The input magnitude of the amplifier is small due to the modulator's global negative feedback and the passive N-path filter preceding it. This lowers the power consumption of the amplifier and relaxes the design constraints of the switches in the N-path filter. A system model of the linear periodically time-variant structure of the proposed modulator is developed, and its nonidealities are analyzed. A BP DSM prototype realized in a 65-nm CMOS with an active area of 0.032 mm2 features an IF tunable from 100 to 200 MHz with a sampling frequency ranging from 400 to 800 MHz. Over a fixed 2-MHz bandwidth, the modulator achieves a signal to noise and distortion ratio (SNDR) greater than 55.5 dB over the entire IF range. A maximal SNDR of 60.5 dB is achieved at 175-MHz IF while consuming 150 μW, which corresponds to a Walden's and Schreier's figure of merits of 43.3 fJ/conv-step and 164.4 dB, respectively.
Search for pair production of vector-like quarks in the bWbW channel from proton–proton collisions at √s = 13TeV (2018)

A search is presented for the production of vector-like quark pairs, TT or YY, with electric charge of&#13;\n2/3 (T) or −4/3 (Y), in proton–proton collisions at √s = 13 TeV. The data were collected by the CMS&#13;\nexperiment at the LHC in 2016 and correspond to an integrated luminosity of 35.8 fb−1. The T and Y&#13;\nquarks are assumed to decay exclusively to a W boson and a b quark. The search is based on events with&#13;\na single isolated electron or muon, large missing transverse momentum, and at least four jets with large&#13;\ntransverse momenta. In the search, a kinematic reconstruction of the final state observables is performed,&#13;\nwhich would permit a signal to be detected as a narrow mass peak (≈7% resolution). The observed&#13;\nnumber of events is consistent with the standard model prediction. Assuming strong pair production of&#13;\nthe vector-like quarks and a 100% branching fraction to bW, a lower limit of 1295 GeV at 95% confidence&#13;\nlevel is set on the T and Y quark masses
Magnetic Resonance Imaging (MRI) as a Translational Tool for the Study of Neonatal Stroke (2011)

More than half of neonatal stroke survivors have long-term sequelae, including seizures and neurological deficits. Although the immature brain has tremendous potential for recovery, mechanisms governing repair are essentially unexplored. We investigated whether magnetic resonance imaging (MRI) early or late after transient middle cerebral arterial occlusion in postnatal day (P) 10 rats can serve as an intermediate endpoint for long-term studies. Injured animals selected by diffusion-weighted MRI during middle cerebral arterial occlusion were scanned using T2-weighted MRI at P18 and P25 (injury volumes on MRI and histology were compared) or were subjected to contrast-enhanced MRI at P13 to characterize cerebral microcirculatory disturbances and blood-brain barrier leakage. Injury volume during middle cerebral artery occlusion did not predict histological outcome at 2 weeks. Major reductions in injury volume occurred by P18, with no further changes by P25 and correlated with histological injury. Cerebral perfusion was significantly reduced in the injured caudate but blood-brain barrier leakage was small. Therefore, conventional T2-weighted MRI performed during a subchronic injury phase predicts a long-term histological outcome after experimental neonatal focal stroke.
Raf-1 is the predominant Raf isoform that mediates growth factor-stimulated growth in ovarian cancer cells (2005)

There is currently much interest in the role of the Raf family in cancer, particularly since mutated B-Raf has been shown to be oncogenic in certain disease types. In this study we have explored the expression, signaling and function of the three known Raf isoforms (Raf-1, A-Raf and B-Raf) in patients with ovarian cancer. While increased expression of Raf-1 was associated with poor survival, increased expression of B-Raf was associated with improved survival. Using a panel of ovarian cancer cell lines, all three isoforms were shown to be involved in growth factor initiated signaling. Antisense inhibition of function in ovarian cancer cell lines indicated that both Raf-1 and A-Raf, but not B-Raf, were linked to cell proliferation. Raf-1 (but not A-Raf or B-Raf) was also associated with reduced apoptosis. While individual Raf reduction by isoform-targeted antisense oligonucleotides (ODNs) produced growth inhibition in some cell lines, similar use of the MEK inhibitor UO126 produced growth inhibition in all cell lines tested. These data suggest that Raf-1 is the predominant Raf isoform responsible for regulating cellular growth in ovarian cancer cells and may be particularly important in high grade serous ovarian cancers.
Immune Responses of Breast Cancer Patients to Mutated Epidermal Growth Factor Receptor (EGF-RvIII, ΔEGF-R, and de2–7 EGF-R) (2004)

Mutated epidermal growth factor receptor (EGF-RvIII, DeltaEGF-R, and de2-7 EGF-R) is the result of an 801-bp deletion within the extracellular domain of wild-type EGF-R and is expressed by breast carcinomas, but not by normal breast tissues. EGF-RvIII is expressed both on the surface and in the cytoplasm of tumor cells. Thus, EGF-RvIII is a potential tumor-specific target for both Abs and T cells. However, it is not known whether breast cancer patients can raise immune responses to EGF-RvIII expressed by their tumors. The demonstration of EGF-RvIII-specific immune responses in patients would suggest that immunization of patients with EGF-RvIII vaccines is feasible, because these vaccines may boost a pre-existing immune response. We have evaluated humoral and cellular immune responses to EGF-RvIII in 16 breast cancer patients and three healthy donors. Seven of 16 patients developed EGF-RvIII-specific Abs that bound to isolated EGF-RvIII protein or the protein expressed by EGF-RvIII-transfected mouse fibroblasts. The Abs that bound to EGF-RvIII did not bind to wild-type EGF-R, and anti-EGF-RvIII Abs were not found in the sera of healthy donors. Three patients had EGF-RvIII peptide-specific lymphoproliferative responses, and two of these patients also had humoral immune responses. Humoral and cellular immune responses correlated with EGF-RvIII expression by patients' tumors in most cases. These studies demonstrate that breast cancer patients specifically recognize EGF-RvIII with an overall immune response rate of 50%, suggesting that patients may benefit from vaccination against EGF-RvIII, boosting pre-existing immune responses.
CFD simulations of electric motor end ring cooling for improved thermal management (2022)

Proper thermal management of an electric motor for vehicle applications extends its operating range. One cooling approach is to impinge Automatic Transmission Fluid (ATF) onto the rotor end ring. Increased ATF coverage correlates to enhanced heat transfer. Computational Fluid Dynamics (CFD) analytical tools provide a mechanism to assess motor thermal management prior to hardware fabrication. The complexity of the fluid flow ( e.g. , jet atomization, interface tracking, wall impingement) and heat transfer makes these simulations challenging. Computational costs are high when solving these flows on high-speed rotating meshes. Typically, a Volume-of Fluid (VOF) technique ( i.e. , two-fluid system) is used to resolve ATF dynamics within this rotating framework. Suitable numerical resolution of the relevant physics for thin films under strong inertial forces at high rotor speeds is computationally expensive, further increasing the run times. In this work, a numerical study of rotor-ring cooling by ATF is presented using a patent automated Cartesian cut-cell based method coupled with Automatic Mesh Refinement (AMR). This approach automatically creates the Cartesian mesh on-the-fly and can effectively handle complex rotating geometries by adaptively refining the mesh based on local gradients in the flow field which results in better resolution of the air-ATF interface. A Single non-inertial Reference Frame (SRF) approach is used to account for the rotating geometry and to further improve the overall computational efficiency. Quasi-steady state conditions are targeted in the analysis of the results. Important physics such as ATF jet structure, velocity detail near the air-jet interface, ATF coverage/accumulation on the ring surface, and cooling capacity are presented for a low-resolution Reynolds averaged Navier-Stokes (RANS), high-resolution RANS, and high-resolution Large-Eddy Simulation (LES) models. Computations are scaled over hundreds of cores on a supercomputer to maximize turnaround time. Each numerical approach is shown to capture the general trajectory of the oil jet prior to surface impingement. The high-resolution LES simulation, however, is superior in capturing small scale details and heat transfer between the free jet and surrounding air.
TH‐CD‐206‐10: Clinical Application of the MIND Demons Algorithm for Symmetric Diffeomorphic Deformable MR‐To‐CT Image Registration in Spinal Interventions (2016)

Purpose. Accurate intraoperative localization of target anatomy (e.g., tumors and vertebral levels) and critical structures (e.g., nerves and vessels) is essential to safe, effective surgery. Preoperative CT/MR images can be used to identify such vital anatomy in intraoperative images through multimodality deformable registration. We proposed a deformable registration method to align preoperative MR to intraoperative CT using modality‐independent neighborhood descriptors (MIND) and a Huber metric for robust registration. Methods. The method, called MIND Demons, estimates time‐dependent diffeomorphisms between two images by optimizing a constrained symmetric energy functional incorporating priors on smoothness, conservation of momentum, geodesic length, invertibility, and closure under composition. Alternating optimization is performed using a regularized Gauss‐Newton (GN) method in a multiresolution scheme. Performance was measured in phantom experiments emulating image‐guided spine‐surgery and in a retrospective clinical study (N=15 patients) evaluated in terms of target registration error (TRE) and diffeomorphic properties of the resulting deformations. Results. The MIND Demons method outperformed free‐form deformation (FFD) methods and conventional Demons in phantom experiments (median TRE = 1.5 mm, compared to 10.2 mm for mutual information (MI) based FFD, 2.6 mm for local‐MI FFD, and 5.1 mm for normalized‐MI Demons). The resulting deformations resolved realistic deformation in clinical data with sub‐voxel TRE (&lt;2 mm) in cases of cervical, thoracic, and lumbar spine and preserved topology with sub‐voxel invertibility (0.004 mm) and positive‐determinant nonsingular spatial‐Jacobians. Conclusion. A modality‐independent deformable registration method has been developed, incorporating the constrained symmetric energy functional and the Huber metric to yield stable and accurate registration, with computational efficiency improved using the GN optimization. The approach yielded registration accuracy suitable to application in image‐guided spine‐surgery across each region of the spine under realistic modes of deformation. S. Vogt and G. Kleinszig is with Siemens Healthcare XP.
On overannealing of GaIn(N)As/Ga(N)As multiple quantum wells grown by molecular beam epitaxy (2007)

Evolution of photoluminescence (PL) and strain is investigated in GaIn(N)As/Ga(N)As multiple quantum wells (MQWs) over a wide range of annealing temperatures from 700 to 900 °C. We observe two optimal annealing temperatures (Topt) that result in reduced PL linewidth and increased PL intensity irrespective of the thermal-induced strain relaxation. The decrease of PL intensity accompanied by peak splitting after the first Topt is mainly associated with the deterioration of the GaAs cap layer and the optical quenching after the second Topt is due to the overannealing-induced degradation of the bottom QWs. The strain relaxation in GaInAs/GaAs MQWs at elevated temperatures, which gives rise to extrinsic defects at the bottom of the MQWs stack, only plays a minor role in PL evolution, while no strain relaxation is observed in GaInNAs/GaNAs MQWs.
Supplementary Video S2 from Nonlinear Optics with Near-Infrared Excitation Enable Real-Time Quantitative Diagnosis of Human Cervical Cancers (2023)

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Development of Methods for Quantitative Comparison of Pooled shRNAs by Mass Sequencing (2011)

Pooled short-hairpin RNA (shRNA) library screening is a powerful tool for identifying a set of genes in biological pathways that require stable expression to produce a desired phenotype. Massive parallel sequencing of half-hairpins has proven highly variable and has not given satisfactory results concerning the relative abundance of different shRNAs before and after selection. Here, the authors describe a method for quantitative comparison of half-hairpins from pooled shRNAs in the mir30-based pGIPZ vector that is analyzed by massive parallel sequencing. Introducing a multiplexing code and refining the sample preparation scheme resulted in the predicted ability to detect twofold enrichments. These improvements should permit half-hairpin sequencing to analyze either dropout screens or selective pooled shRNA screens of limited stringency to analyze phenotypes not accessible in transient experiments.
A method for fast 3D tracking using tuned fiducial markers and a limited projection reconstruction FISP (LPR‐FISP) sequence (2001)

This work demonstrates the feasibility of using wireless, tuned fiducial markers with a limited projection reconstruction-fast imaging with steady-state free precession sequence (LPR-FISP) to accurately obtain tracking information necessary for interactive scan plane selection in magnetic resonance imaging (MRI). The position and orientation of a rigid interventional device can be uniquely determined from the 3D coordinates of three fiducial markers mounted in a known configuration on the device. Three fiducial markers were tuned to the proton resonant frequency in a 0.2T open MR scanner and mounted to the surface of a cylindrical water phantom. An LPR-FISP sequence was developed to suppress the water phantom signal while preserving that of the fiducial markers through a nonselective low-tip-angle excitation and a dephaser gradient applied prior to data acquisition. A localization algorithm was developed to accurately calculate the 3D coordinates of the fiducial markers using four LPR-FISP projections in two orthogonal scan planes. The sequence repetition time (TR = 21 msec) and the limited projection set resulted in fast LPR-FISP coordinate acquisition times of approximately 170 msec with an accuracy (max error) of 3 mm on a 0.2T MR system. This fast, accurate tracking method provides the fundamental technology for interactive MRI scan plane definition for rigid interventional devices without the need for stereotactic cameras or reference frames.
Plasma Polymerized Films of Vinylferrocene on Thermally Oxidized Titanium and Single‐Crystal Titanium Dioxide (1984)

Titanium, thermally oxidized titanium, and single‐crystal have been coated with polyvinylferrocene by an argon‐vinylferrocene radio frequency plasma discharge. Voltammetry is observed consistent with the oxidation of ferrocene sites in the polymeric coating at potentials 1.5V positive of the flatband potential for in . As the thickness of the oxide phase is increased, the ease with which ferrocene sites are oxidized decreases. Comparisons are made to substrates coated with polyvinylferrocene by evaporative deposition; these electrodes give a more classical blocking response. The plasma discharge physically alters the semiconductor surface, most likely by generating surface states. In addition, the voltammetric response for plasma‐coated electrodes is improved if conducting materials (e.g., Pt or glassy carbon) are also present in the plasma reactor during plasma deposition. We show that very small minority carrier oxidation currents can be measured by trapping the oxidative charge as ferricenium in the polymer film via potentiostatic experiments at quite positive potentials.
Genomic Alterations in PIK3CA -Mutated Breast Cancer Result in mTORC1 Activation and Limit the Sensitivity to PI3Kα Inhibitors (2021)

PI3Kα inhibitors have shown clinical activity in PIK3CA-mutated estrogen receptor-positive (ER<sup>+</sup>) patients with breast cancer. Using whole genome CRISPR/Cas9 sgRNA knockout screens, we identified and validated several negative regulators of mTORC1 whose loss confers resistance to PI3Kα inhibition. Among the top candidates were TSC1, TSC2, TBC1D7, AKT1S1, STK11, MARK2, PDE7A, DEPDC5, NPRL2, NPRL3, C12orf66, SZT2, and ITFG2. Loss of these genes invariably results in sustained mTOR signaling under pharmacologic inhibition of the PI3K-AKT pathway. Moreover, resistance could be prevented or overcome by mTOR inhibition, confirming the causative role of sustained mTOR activity in limiting the sensitivity to PI3Kα inhibition. Cumulatively, genomic alterations affecting these genes are identified in about 15% of <i>PIK3CA</i>-mutated breast tumors and appear to be mutually exclusive. This study improves our understanding of the role of mTOR signaling restoration in leading to resistance to PI3Kα inhibition and proposes therapeutic strategies to prevent or revert this resistance. SIGNIFICANCE: These findings show that genetic lesions of multiple negative regulators of mTORC1 could limit the efficacy of PI3Kα inhibitors in breast cancer, which may guide patient selection strategies for future clinical trials.