gebhart/patrepeval huggingface dataset:
Treatment of Invasive Retinoblastoma in a Murine Model Using an Oncolytic Picornavirus (2007)

Retinoblastoma, the most common intraocular malignancy of childhood, metastasizes by initial invasion of the choroid and the optic nerve. There is no effective treatment for metastatic retinoblastoma, especially when the central nervous system (CNS) is involved, and prevention of this complication is a treatment priority. Seneca Valley Virus (SVV-001) is a conditionally replication-competent picornavirus that is not pathogenic to normal human cells but can kill human retinoblastoma cells in vitro with an IC(50) of <1 viral particle (vp) per cell. A xenograft murine model of metastatic retinoblastoma was used to examine the therapeutic potential of SVV-001. Histopathologic analysis of ocular and brain tissues after a single tail vein injection of SVV-001 (1 x 10(13) vp/kg) showed effective treatment of choroid and ocular nerve tumor invasion (1 of 20 animals with invasive disease in the treated group versus 7 of 20 animals with invasive disease in the control group; P = 0.017) and prevention of CNS metastasis (0 of 20 animals with CNS metastatic disease in the treated group versus 4 of 20 animals with CNS disease in the control group; P = 0.036). There were no observed adverse events due to the virus in any of the treated animals. SVV-001 may be effective as a treatment of locally invasive and metastatic retinoblastoma.
Nutation Spectroscopy of a Nanomagnet Driven into Deeply Nonlinear Ferromagnetic Resonance (2019)

Strongly out-of-equilibrium regimes in magnetic nanostructures exhibit novel properties, linked to the nonlinear nature of magnetization dynamics, which are of great fundamental and practical interest. Here, we demonstrate that ferromagnetic resonance driven by microwave magnetic fields can occur with substantial spatial coherency at an unprecedented large angle of magnetization precessions, which is normally prevented by the onset of spin-wave instabilities and magnetization turbulent dynamics. Our results show that this limitation can be overcome in nanomagnets, where the geometric confinement drastically reduces the density of spin-wave modes. When the obtained deeply nonlinear ferromagnetic resonance regime is perturbed, the magnetization undergoes eigenoscillations around the steady state due to torques tending to restore the stable large-angle periodic trajectory. These eigenoscillations are substantially different from the usual spin-wave modes around the ground state because their existence is connected to the presence of a large coherent precession. They are experimentally investigated by a new spectroscopic technique based on the application of a second microwave excitation field that is tuned to resonantly drive them. This two-tone spectroscopy enables us to show that they consist in slow coherent magnetization nutations around the large-angle steady precession, whose frequencies are set by the balance of restoring torques. Our experimental findings are well accounted for by an analytical model derived for systems with uniaxial symmetry. They also provide a new means for controlling highly nonlinear magnetization dynamics in nanostructures, opening interesting applicative opportunities in the context of magnetic nanotechnologies.
Impact of pre-imputation SNP-filtering on genotype imputation results (2014)

Even a moderate filtering has a detrimental effect on the imputation quality. Therefore little or no SNP filtering prior to imputation appears to be the best strategy for imputing small to moderately sized datasets. Our results also showed that for these datasets, MaCH performs slightly better than IMPUTE2 in most scenarios at the cost of increased computing time.
ChemInform Abstract: Structure—Activity Relationships of a Series of Benzothiophene‐Derived NPY Y1 Antagonists: Optimization of the C‐2 Side Chain. (1999)

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.
<i>Helicobacter</i> species are potent drivers of colonic T cell responses in homeostasis and inflammation (2017)

Specific gut commensal bacteria improve host health by eliciting mutualistic regulatory T (T<sub>reg</sub>) cell responses. However, the bacteria that induce effector T (T<sub>eff</sub>) cells during inflammation are unclear. We addressed this by analyzing bacterial-reactive T cell receptor (TCR) transgenic cells and TCR repertoires in a murine colitis model. Unexpectedly, we found that mucosal-associated <i>Helicobacter</i> species triggered both T<sub>reg</sub> cell responses during homeostasis and T<sub>eff</sub> cell responses during colitis, as suggested by an increased overlap between the T<sub>eff</sub>/T<sub>reg</sub> TCR repertoires with colitis. Four of six T<sub>reg</sub> TCRs tested recognized mucosal-associated <i>Helicobacter</i> species in vitro and in vivo. By contrast, the marked expansion of luminal <i>Bacteroides</i> species seen during colitis did not trigger a commensurate T<sub>eff</sub> cell response. Unlike other T<sub>reg</sub> cell-inducing bacteria, <i>Helicobacter</i> species are known pathobionts and cause disease in immunodeficient mice. Thus, our study suggests a model in which mucosal bacteria elicit context-dependent T<sub>reg</sub> or T<sub>eff</sub> cell responses to facilitate intestinal tolerance or inflammation.
The effect of bifonazole on the structure of Trichophyton. (1983)

The effect of a new azole antimycotic, 1-[(4-biphenylyl)-phenylmethyl]-1H-imidazole (bifonazole, Bay h 4502, Mycospor) on the morphology of hyphae of Trichophyton mentagrophytes grown in a liquid medium was studied by high-resolution scanning electron microscopy. With bifonazole at concentrations ranging from 1 to 10 ng/ml that were much lower than the MIC value of the drug for this test strain (630 ng/ml), the hyphal growth was significantly inhibited and several morphological changes of the hyphae were produced. They were characterized by: (1) development of wavy or curled hyphae, (2) occasional formation of swollen cells often arranging in chain; (3) partial exfoliation of hyphal walls; and (4) excretion of fibrillar materials. These morphological changes of the hyphae became more prominent with increasing drug concentrations up to 200 ng/ml, and many hyphae were collapsed and distorted. These results strongly suggest that subinhibitory concentrations of bifonazole profoundly affected the normal growth and induced degenerative changes of the hyphae of T. mentagrophytes probably by damaging the cell membrane.
Spiral-Shaped Piezoelectric MEMS Cantilever Array for Fully Implantable Hearing Systems (2017)

Fully implantable, self-powered hearing aids with no external unit could significantly increase the life quality of patients suffering severe hearing loss. This highly demanding concept, however, requires a strongly miniaturized device which is fully implantable in the middle/inner ear and includes the following components: frequency selective microphone or accelerometer, energy harvesting device, speech processor, and cochlear multielectrode. Here we demonstrate a low volume, piezoelectric micro-electromechanical system (MEMS) cantilever array which is sensitive, even in the lower part of the voice frequency range (300⁻700 Hz). The test array consisting of 16 cantilevers has been fabricated by standard bulk micromachining using a Si-on-Insulator (SOI) wafer and aluminum nitride (AlN) as a complementary metal-oxide-semiconductor (CMOS) and biocompatible piezoelectric material. The low frequency and low device footprint are ensured by Archimedean spiral geometry and Si seismic mass. Experimentally detected resonance frequencies were validated by an analytical model. The generated open circuit voltage (3⁻10 mV) is sufficient for the direct analog conversion of the signals for cochlear multielectrode implants.
An overview of angiogenesis and renal cell carcinoma (2012)

Renal cell carcinoma (RCC) is the most common malignant tumor of the kidney, and the incidence is increasing very rapidly across all population groups. Accumulation of hypoxia-induced factors and the over-expression of vascular endothelial growth factor (VEGF) are the most important predisposing factors for the progression of the disease. Angiogenesis facilitates tumor growth progression by supplying adequate oxygen and nutrition to the tumor cells through a series of interrelated steps. VEGF, Placental Growth Factor (PIGF), and Basic Fibroblast Growth Factor (bFGF) work together to increase angiogenesis in RCC. This review focuses on the possible targets in the treatment of the disease. Our literature review covers the last 15 years of reaseach related to this topic. We conclude that targeted therapies for RCC should be directed against specific molecules and signaling pathways and the therapy should be more selective for better tolerance.
Real‐time soft tissue motion estimation for lung tumors during radiotherapy delivery (2013)

The authors demonstrate for the first time real-time markerless lung tumor motion estimation from BEV images alone. The described system can operate at a frame rate of 12.8 Hz and does not require prior knowledge to establish traceable landmarks for tracking on the fly. The authors show that the geometric accuracy is similar to (or better than) previously published markerless algorithms not operating in real-time.
Use of Radiolabeled Somatostatin Analogs in the Identification and Treatment of Somatostatin Receptor-Bearing Tumors (1993)

Radiolabeled somatostatin analogs are potentially of considerable value in both the localization and treatment of somatostatin receptor-bearing tumors. Whole body 123I-labeled Tyr3-octreotide scintigraphy is capable of detecting and localizing primary tumors and metastatic disease that may not be detectable by other methods. Although it is possible that this technique may be applicable to a wide variety of neoplasms, 123I-Tyr3-octreotide scans appear particularly useful for imaging various gut neuroendocrine tumors, meningiomas, and paragangliomas. This primarily reflects the level of expression of somatostatin receptors by these lesions. In addition to whole body scintigraphy, intraoperative localization by receptor identification utilizing a hand-held gamma detector probe may prove to be an effective means of identifying spread and micrometastasis of somatostatin receptor-bearing tumors. Aside from identification and topographic localization of disease, the detection of an 123I-Tyr3-octreotide labeled tumor may be utilized as in vivo assay for the presence of somatostatin receptors. Such observations may prove useful in predicting the susceptibility of an individual tumor to octreotide therapy. Additionally, it may prove possible to deliver a therapeutic dose of radiation to receptor-bearing tumors by the administration of specific radiolabeled somatostatin analogs.
Unimanual Pen+Touch Input Using Variations of Precision Grip Postures (2018)

We introduce a new pen input space by forming postures with the same hand that also grips the pen while writing, drawing, or selecting. The postures contact the multitouch surface around the pen to enable detection without special sensors. A formative study investigates the effectiveness, accuracy, and comfort of 33 candidate postures in controlled tasks. The results indicate a useful subset of postures. Using raw capacitive sensor data captured in the study, a convolutional neural network is trained to recognize 10 postures in real time. This recognizer is used to create application demonstrations for pen-based document annotation and vector drawing. A small usability study shows the approach is feasible.
EMI Reduction via Spread Spectrum in DC/DC Converters: State of the Art, Optimization, and Tradeoffs (2015)

Spread spectrum is a technique introduced for mitigating electromagnetic interference (EMI) problems in many class of circuits. In this paper, with particular emphasis on switching DC/DC converters, we consider the most common and most efficient known spreading techniques, looking for spreading parameters that ensure the highest EMI reduction and the lowest performance reduction in the circuit where the spreading is applied. The result is an interesting tradeoff not only between EMI reduction and performance drop, but also on the EMI reduction itself when considering different EMI victim models. The proposed analysis is supported by measurements on two switching DC/DC converters: 1) based on pulse-width modulation and 2) based on the resonant converter class.
α5β1 Integrin Ligand PHSRN Induces Invasion and α5 mRNA in Endothelial Cells to Stimulate Angiogenesis (2009)

Angiogenesis requires endothelial cell invasion and is crucial for wound healing and for tumor growth and metastasis. Invasion of native collagen is mediated by the alpha(5)beta(1) integrin fibronectin receptor. Thus, alpha(5)beta(1) up-regulation on the surfaces of endothelial cells may induce endothelial cell invasion to stimulate angiogenesis. We report that the interaction of alpha(5)beta(1) with its PHSRN peptide ligand induces human microvascular endothelial cell invasion and that PHSRN-induced endothelial cell invasion is regulated by alpha(4)beta(1) integrin and requires matrix metalloproteinase 1 (MMP-1). Moreover, our results show that exposure to PHSRN causes rapid, specific up-regulation of surface levels of alpha(5)beta(1) integrin and significantly increases alpha(5) integrin mRNA in microvascular endothelial cells. Consistent with these results, alpha(5) small interfering RNA abrogates PHSRN-induced surface alpha(5) and MMP-1 up-regulation, as well as blocking invasion induction. We also observed dose-dependent, PHSRN-induced alpha(5)beta(1) integrin up-regulation on endothelial cells in vivo in Matrigel plugs. We further report that the PHSCN peptide, an alpha(5)beta(1)-targeted invasion inhibitor, blocks PHSRN-induced invasion, alpha(5)beta(1) up-regulation, alpha(5) mRNA induction, and MMP-1 secretion in microvascular endothelial cells and that systemic PHSCN administration prevents PHSRN-induced alpha(5)beta(1) up-regulation and angiogenesis in Matrigel plugs. These results demonstrate a critical role for alpha(5)beta(1) integrin and MMP-1 in mediating the endothelial cell invasion and angiogenesis and suggest that PHSRN-induced alpha(5) transcription and alpha(5)beta(1) up-regulation may form an important feed-forward mechanism for stimulating angiogenesis.
Novel zero-voltage switching techniques for pulse-width-modulated converters (1991)

Two new classes of soft switching pulse-width-modulated (PWM) converters, named zero-voltage-switched (ZVS) PWM converters and zero-voltage-transition (ZVT) PWM converters, are proposed. The proposed ZVS-PWM converters combine the merits of conventional PWM and ZVS-QRC techniques. They are capable of regulating the output for a wide load and input voltage range while maintaining constant-frequency operation. By employing a saturable inductor, the load range under which ZVS is maintained can be significantly extended without increasing the voltage stress of the power switch. The parasitic oscillations between the diode junction capacitance and the resonant inductor are also significantly reduced. In the new class of ZVT-PWM converters, both the power switch and the rectifier diode are operated with zero-voltage switching, and are subjected to low voltage and current stresses associated with those in their PWM counterparts. Thus switching losses are significantly reduced at a slight increase in conduction losses. In addition, the circuit optimization is simplified because of constant-frequency operation. The operation principles of the proposed converters are described by using several examples. Several breadboarded converters are implemented to verify the theoretical analysis and to demonstrate the feasibility of the proposed technologies.
Regional Mapping of Genes Encoding Human Steroidogenic Enzymes: P450scc to 15q23–q24, Adrenodoxin to 11q22; Adrenodoxin Reductase to 17q24–q25; and P450c17 to 10q24–q25 (1991)

Steroid hormones are synthesized by a complex array of 10 enzymes. The genes for each of these have now been cloned, and previous work has determined the regional chromosomal assignments of six of these. We used in situ hybridization to determine the regional chromosomal assignments of the four remaining enzymes. The CYP11A1 gene encodes mitochondrial P450scc, which converts cholesterol to pregnenolone, and is located on 15q23-q24. The gene for adrenodoxin, which receives electrons from adrenodoxin reductase and transfers them to P450scc, is on 11q22 while its pseudogenes are on 20q11-q12. The gene for adrenodoxin reductase is on 17q24-q25. The CYP17 gene encodes P450c17, which has both 17 alpha-hydroxylase and 17,20-lyase activities, and is located on 10q24-q25. None of the 10 genes involved in human steroidogenesis is closely linked to another gene for a steroidogenic enzyme.
Treatment for Advanced and Recurrent Endometrial Carcinoma: Combined Modalities (2010)

Women with recurrent or advanced endometrial cancer constitute a heterogeneous group of patients. Depending on previous treatment, women with recurrent endometrial cancer may be appropriate candidates for surgery, radiation therapy, hormonal therapy, or chemotherapy. Women with advanced stage disease at presentation may also be appropriate candidates for systemic and local therapies. We review the treatment options available to treat recurrent and locally advanced endometrial cancer. Treatment choice depends largely on the localization of disease, the patient's performance status and previous treatment history, as well the tumor's hormonal receptor status. Radiation therapy is appropriate for isolated vaginal recurrences in patients with no previous history of radiation therapy. Patients with recurrent low-grade tumors overexpressing estrogen and progesterone receptors may be treated with progestin therapy. Systemic therapy is appropriate for patients with disseminate recurrences or advanced stage disease at presentation, or for those with receptor-negative tumors. We review all these different treatment strategies available to patients with advanced or recurrent endometrial cancer.
Design of an ASIC for straight line detection in an image (2002)

The detection of straight lines in an image is an important problem in image processing. The detection of features such as straight lines in an image involves high computational overhead. In order to achieve high throughput, an appropriate application specific circuit (ASIC) appears to be only effective alternative. This paper describes an architecture for computing Hough transform for detection of line segments. The trigonometric functions required in the computation of Hough Transform are realized using a CORDIC based scheme. The proposed VLSI implementation uses a pipelined architecture for calculation of Hough transform and detection of straight lines from the parameter space. The architecture has been simulated and verified using Verilog for functional correctness with Cadence design tools.
Role of Advanced Diagnostics for Eosinophilic Esophagitis (2014)

In eosinophilic esophagitis (EoE), diagnostic tests aid in the identification of pathophysiologic consequences and accurate detection of the disease. The EoE Endoscopic Reference Score (EREFS) classifies and grades the severity of the five major endoscopically identified esophageal features of EoE (edema, rings, exudates, furrows and strictures). The EREFS may be useful in the evaluation of disease severity and as an objective outcome of response to therapy. pH monitoring identifies the presence of abnormal degrees of acid exposure in the esophagus that characterizes gastroesophageal reflux disease. The presence of acid reflux, however, does not indicate that the reflux is responsible for esophageal eosinophilia. Esophageal manometry has not demonstrated a characteristic abnormality with sufficient sensitivity to make the test of diagnostic value in clinical practice. On the other hand, manometric characteristics of esophageal pressurization and longitudinal muscle dysfunction may help identify important pathophysiologic consequences of EoE. Esophageal impedance testing has demonstrated increased baseline mucosal impedance that correlates with increased epithelial permeability in EoE. Reduced mucosal integrity may provide intraluminal allergens access to antigen-presenting cells, serving as an early event in the pathogenesis of EoE. The functional luminal impedance probe (FLIP) provides quantitative assessment of esophageal mural compliance, a physiologic correlate of remodeling in EoE. Studies using FLIP have associated reductions in esophageal distensibility in EoE with the important outcome of food impaction risk. Finally, confocal endomicroscopy, multiphoton fluorescence microscopy and novel eosinophil-enhancing contrast agents are emerging methods that may allow for in vivo visualization of esophageal eosinophilic inflammation, thereby improving the detection and understanding of this emerging disease.
Probing β‐lactamase structure and function using random replacement mutagenesis (1992)

A new analytical mutagenesis technique is described that involves randomizing the DNA sequence of a short stretch of a gene (3-6 codons) and determining the percentage of all possible random sequences that produce a functional protein. A low percentage of functional random sequences in a complete library of random substitutions indicates that the region mutagenized is important for the structure and/or function of the protein. Repeating the mutagenesis over many regions throughout a protein gives a global perspective of which amino acid sequences in a protein are critical. We applied this method to 66 codons of the gene encoding TEM-1 beta-lactamase in 19 separate experiments. We found that TEM-1 beta-lactamase is extremely tolerant of amino acid substitutions: on average, 44% of all mutants with random substitutions function and 20% of the substitutions are expressed, secreted, and fold well enough to function at levels similar to those for the wild-type enzyme. We also found a few exceptional regions where only a few random sequences function. Examination of the X-ray structures of homologous beta-lactamases indicates that the regions most sensitive to substitution are in the vicinity of the active site pocket or buried in the hydrophobic core of the protein. DNA sequence analysis of functional random sequences has been used to obtain more detailed information about the amino acid sequence requirements for several regions and this information has been compared to sequence conservation among several related beta-lactamases.