gebhart/patrepeval huggingface dataset:
A Novel Somatic Point Mutation of the <i>RET</i> Proto‐oncogene in Tumor Tissues of Small Cell Lung Cancer Patients (1995)

We examined whether the novel point mutation from GCC (Ala) to GAC (Asp) at codon 664 in exon 11 of RET proto-oncogene, which we had found in two small cell lung carcinoma (SCLC) cell lines, existed in genomic DNA of tumor tissues of the two SCLC patients from whom these SCLC cell lines were derived. Sequence analysis revealed that point mutation identical to that of the SCLC cell lines was present in amplified alleles of single-strand conformational variants in genomic DNA of the tumor tissues, whereas it was not detected in genomic DNA of non-tumor tissues of the patients. These results indicate that this mutation had initially occurred in the SCLC patients and was of somatic origin.
HPV16 and BPV1 Infection Can Be Blocked by the Dynamin Inhibitor Dynasore (2008)

The initial entry of papillomaviruses into their target cells has been shown to occur by clathrin-mediated endocytosis and caveolae-mediated endocytosis. These mechanisms entail the formation of nascent-coated vesicles at the plasma membrane. Such coated vesicles, clathrin or caveolin, form and pinch-off in a controlled mechanism that involves several proteins including dynamin. Dynamin is a GTPase that forms a dynamin ring at the stem connecting the nascent vesicle to the plasma membrane. In a still not fully characterized mechanism, dynamin's contraction and twisting results in the scission of the vesicle. In an effort to better characterize the role and molecular mechanisms of dynamin's function, researchers have identified dynasore, a dynamin GTPase inhibitor that prevents the scission of dynamin-dependent endocytic vesicles. Here, we have tested if infection by pseudovirus corresponding to the oncogenic human papillomavirus type 16 and bovine papillomavirus type 1 can be blocked by dynasore. We present data demonstrating that dynasore can block infection of human papillomavirus type 16 and bovine papillomavirus type 1 pseudovirions in a dose- and time-dependent manner with equal efficiency. Presently, there is no available therapy that can block infection by a wide range of papillomavirus regardless of species or genotypes. Targeting dynamin may lead to the rational design of drug able to prevent infection by papillomaviruses, and by other infectious agents dependent on this protein for initial internalization into target cells. Whether such an approach will prove successful needs further investigation.
Role of Cilia and Left-Right Patterning in Congenital Heart Disease (2016)

A central role for cilia in the pathogenesis of congenital heart disease was uncovered by our large-scale mouse mutagenesis screen for mutations causing congenital heart disease. This is supported by human clinical studies, which showed a high prevalence of ciliary dysfunction and respiratory symptoms and disease in patients with congenital heart disease. Our mouse studies indicate this involves essential roles for both primary and motile cilia in the pathogenesis of congenital heart disease. As laterality defects were also observed with high prevalence among the congenital heart disease mutants, this further suggested an important role for left-right patterning in the pathogenesis of congenital heart disease. This finding is reminiscent of the high prevalence of heterotaxy among human fetuses with congenital heart disease, indicating the fetal mouse screen may provide a window into the unborn human fetal population. Clinically, congenital heart disease patients with ciliary dysfunction were found to have more respiratory symptoms and disease, a finding with significant clinical implications, as congenital heart disease patients undergoing surgical palliation often have respiratory complications with high morbidity. While this is usually attributed to the heart disease, we propose this may involve intrinsic airway clearance deficits from ciliary dysfunction. Thus the presurgical screening of congenital heart disease patients for respiratory ciliary dysfunction may provide opportunities to provide perioperative pulmonary therapy to enhance airway clearance for at-risk patients. Such change in the standard of care may improve outcome, especially for those congenital heart disease patients who must endure multiple rounds of cardiac surgeries.
Dammarane-Type Glycosides from Steamed Notoginseng (2008)

Notoginseng, the root of Panax notoginseng (Burk.) F. H. Chen (Araliaceae), is a Chinese traditional medicine, which is used in both raw and processed forms due to their different pharmacological activities. Detailed chemical investigation on steamed notoginseng led to the isolation of 27 dammarane-type triterpenoids (1-27), including 4 new glycosides, namely, notoginsenosides ST-1-ST-3 and ST-5 (1-4), in addition to 3 other known compounds. Of the new compounds, 1-3 possess new aglycones. Their structures were elucidated on the basis of detailed analyses of their 1D and 2D NMR spectra and chemical reactions. The known compounds, koryoginsenoside-R1 (19), yesanchinoside D (20), 6''-O-acetylginsenoside Rg3 (24), and 3beta,6alpha,12beta-trihydroxydammar-20(21),24-diene ( 25), were isolated from notoginseng for the first time.
Optimized Slater‐type basis sets for the elements 1–118 (2003)

Seven different types of Slater type basis sets for the elements H (Z = 1) up to E118 (Z = 118), ranging from a double zeta valence quality up to a quadruple zeta valence quality, are tested in their performance in neutral atomic and diatomic oxide calculations. The exponents of the Slater type functions are optimized for the use in (scalar relativistic) zeroth-order regular approximated (ZORA) equations. Atomic tests reveal that, on average, the absolute basis set error of 0.03 kcal/mol in the density functional calculation of the valence spinor energies of the neutral atoms with the largest all electron basis set of quadruple zeta quality is lower than the average absolute difference of 0.16 kcal/mol in these valence spinor energies if one compares the results of ZORA equation with those of the fully relativistic Dirac equation. This average absolute basis set error increases to about 1 kcal/mol for the all electron basis sets of triple zeta valence quality, and to approximately 4 kcal/mol for the all electron basis sets of double zeta quality. The molecular tests reveal that, on average, the calculated atomization energies of 118 neutral diatomic oxides MO, where the nuclear charge Z of M ranges from Z = 1-118, with the all electron basis sets of triple zeta quality with two polarization functions added are within 1-2 kcal/mol of the benchmark results with the much larger all electron basis sets, which are of quadruple zeta valence quality with four polarization functions added. The accuracy is reduced to about 4-5 kcal/mol if only one polarization function is used in the triple zeta basis sets, and further reduced to approximately 20 kcal/mol if the all electron basis sets of double zeta quality are used. The inclusion of g-type STOs to the large benchmark basis sets had an effect of less than 1 kcal/mol in the calculation of the atomization energies of the group 2 and group 14 diatomic oxides. The basis sets that are optimized for calculations using the frozen core approximation (frozen core basis sets) have a restricted basis set in the core region compared to the all electron basis sets. On average, the use of these frozen core basis sets give atomic basis set errors that are approximately twice as large as the corresponding all electron basis set errors and molecular atomization energies that are close to the corresponding all electron results. Only if spin-orbit coupling is included in the frozen core calculations larger errors are found, especially for the heavier elements, due to the additional approximation that is made that the basis functions are orthogonalized on scalar relativistic core orbitals.
Device specific characterization of yield limiting pattern geometries by combining layout profiling with high sensitivity wafer inspection (2015)

This paper reports on a new approach to capture the impact of marginal pattern geometries on occurrence of systematic yield-limiting defects. Layout profiling and Hot-Spot checking techniques were used to mark new incoming device layout for regions that approached the known marginal pattern geometries at a varying degree of match quality. Further these regions were translated into inputs for advanced high-sensitivity wafer inspection tools of the Broadband Plasma family with Context Based Inspection capability. Finally specially prepared wafers for this device were exercised through high sensitivity targeted inspections to assess the defect occurrence at each of the regions picked based on layout profiling. Finally all the data was assimilated into an easy-to-interpret visual which shows where the printing margins are smallest on this device.
β‐Lactamase Recovery from <i>E. coli</i> Cell Lysate via Two‐Phase Electrophoresis (1996)

beta-Lactamase was recovered from Escherichia coli cell lysate by a novel cell debris removal method using two-phase electrophoresis. The cells were harvested by centrifugation after fermentation, resuspended in a low ionic strength electrophoresis buffer, lysed, and combined with a poly(ethylene glycol)/dextran aqueous two-phase system in the same buffer. The cell lysate was subjected to a 40 V/cm electric field oriented perpendicular to the phase interface for 90 min. Experiments were conducted both with and without a nucleic acid precipitation step using poly(ethylene imine) (PEI). For PEI-treated lysate at pH 5, the positively charged beta-lactamase was directed to the upper phase, while negatively charged contaminants (including cell debris, nucleic acid/PEI precipitates, and negatively charged proteins) were directed to the lower phase with the applied field. beta-Lactamase yield in the upper phase was 81%, while cell debris and nucleic acids partitioned almost exclusively to the lower phase. For untreated lysate, beta-lactamase did not move in the electric field due to strong interaction with nucleic acids in solution.
Wnt/β-Catenin and MAPK Signaling: Allies and Enemies in Different Battlefields (2012)

Two papers published in Science Signaling reveal extensive crosstalk between Wnt/β-catenin and mitogen-activated protein kinase (MAPK) signaling in cancer. Although both studies describe previously unknown links between these two signaling pathways, the relationship between Wnt/β-catenin and MAPK signaling depends on the specific cellular context. Indeed, in melanoma, hyperactivated MAPK signaling down-regulates the Wnt/β-catenin signal transduction cascade, thereby establishing a negative crosstalk between the two signaling pathways. In contrast, in colorectal cancer, stimulation of the Wnt/β-catenin pathway leads to activation of the MAPK pathway through Ras stabilization, representing an example of positive crosstalk. Moreover, activation of Wnt/β-catenin signaling has context-dependent functions that trigger opposing effects on tumor growth. In melanoma, aberrant activation of Wnt/β-catenin signaling may have anti-oncogenic functions by promoting programmed cell death; by contrast, in the intestine, Wnt/β-catenin signaling drives malignant transformation. Thus, there is no single correct way to target the Wnt/β-catenin pathway for all cancers.
Depth and image recovery using a MRF model (1994)

This paper deals with the problem of depth recovery and image restoration from sparse and noisy image data. The image is modeled as a Markov random field and a new energy function is developed to effectively detect discontinuities in highly sparse and noisy images. The model provides an alternative to the use of a line process. Interpolation over missing data sites is first done using local characteristics to obtain initial estimates and then simulated annealing is used to compute the maximum a posteriori (MAP) estimate. A threshold on energy reduction per iteration is used to speed up simulated annealing by avoiding computation that contributes little to the energy minimization. Moreover, a minor modification of the posterior energy function gives improved results for random as well as structured sparsing problems. Results of simulations carried out on real range and intensity images along with details of the simulations are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Special Skills and Techniques (1999)

Part 1 Advanced Tests and Techniques: Diagnostic Testing Psychophysical Testing Microbiology. Part 2 Biometry and Echography: Axial Eye Length A-Scans and Intraocular Lens Calculations Diagnostic A- and B-Scan Ultrasonography. Part 3 Electrophysiology Testing: Electroretinography Electro-Oculography Visual Evoked Response. Appendices: Disability Determination- Who Qualifies and Who Doesn't Universal Precautions.
Study of an external passive shock-absorbing mechanism for walking robots (2008)

This paper proposes a compliant sole as an external shock-absorbing mechanism and investigates its effect comparatively to an ankle-located joint-flexible mechanism. The proposed mechanism is mounted under the HRP-2 humanoid feet only using simulation. The comparative evaluation has been conducted for contact resulting from walking using the HRP-2 embedded pattern-generator. The characteristics of the sole material, Young and Poisson coefficients, are set following an ad-hoc minimization of their influence on the vertical acceleration and lateral inclination. Preliminary results suggest that the solution proposed is worth to be considered further and to be developed for real application use.
Human Ghrelin Ameliorates Organ Injury and Improves Survival after Radiation Injury Combined with Severe Sepsis (2009)

In the terrorist radiation exposure scenario, radiation victims are likely to suffer from additional injuries such as sepsis. Our previous studies have shown that ghrelin is protective in sepsis. However, it remains unknown whether ghrelin ameliorates sepsis-induced organ injury and mortality after radiation exposure. The purpose of this study is to determine whether human ghrelin attenuates organ injury and improves survival in a rat model of radiation combined injury (RCI) and, if so, the potential mechanism responsible for the benefit. To study this, adult male rats were exposed to 5-Gy whole body irradiation followed by cecal ligation and puncture (CLP, a model of sepsis) 48 h thereafter. Human ghrelin (30 nmol/rat) or vehicle (saline) was infused intravenously via an osmotic minipump immediately after radiation exposure. Blood and tissue samples were collected at 20 h after RCI (68 h after irradiation or 20 h after CLP) for various measurements. To determine the longterm effect of human ghrelin after RCI, the gangrenous cecum was removed at 5 h after CLP and 10-d survival was recorded. In addition, vagotomy or sham vagotomy was performed in sham and RCI animals immediately prior to ghrelin administration, and various measurements were performed at 20 h after RCI. Our results showed that serum levels of ghrelin and its gene expression in the stomach were decreased markedly at 20 h after RCI. Administration of human ghrelin attenuated tissue injury markedly, reduced proinflammatory cytokine levels, decreased tissue myeloperoxidase activity, and improved survival after RCI. Furthermore, elevated plasma levels of norepinephrine (NE) after RCI were reduced significantly by ghrelin. However, vagotomy prevented ghrelin’s beneficial effects after RCI. In conclusion, human ghrelin is beneficial in a rat model of RCI. The protective effect of human ghrelin appears to be attributed to rebalancing the dysregulated sympathetic/parasympathetic nervous systems.
Cyclooxygenase-2 Is Widely Expressed in Atherosclerotic Lesions Affecting Native and Transplanted Human Coronary Arteries and Colocalizes With Inducible Nitric Oxide Synthase and Nitrotyrosine Particularly in Macrophages (1999)

Inflammation appears to have a major role in the development of atherosclerotic lesions affecting native and transplanted coronary arteries. The subsequent risk of plaque rupture and acute ischemic events correlates with the degree of inflammation and may be modified by aspirin, an anti-inflammatory cyclooxygenase inhibitor. Cyclooxygenase-2 (Cox-2) and inducible nitric oxide synthase (iNOS) are involved in the inflammatory response via the rapid and exaggerated production of prostanoids and nitric oxide, both of which may have proatherosclerotic effects. These effects may be mediated by the formation of peroxynitrite in the case of nitric oxide and involve "cross talk" between the two enzyme systems. This study aimed to investigate native and transplant atherosclerosis for the presence and distribution of Cox-2 and iNOS. Immunocytochemical studies were performed on atherosclerotic lesions from patients with native (n=12) and transplant (n=5) coronary disease by using antibodies to Cox-2, iNOS, and nitrotyrosine (an indicator of peroxynitrite production). Control tissue was obtained from unused donor hearts and at the time of autopsy. Cox-2 and iNOS colocalized predominantly in macrophages/foam cells in both types of atherosclerosis. Cox-2 expression was also detected in medial smooth muscle cells and endothelial cells, including those of the vasa vasorum. Nitrotyrosine was found in the same distribution as that of iNOS and was colocalized with Cox-2 in macrophages. Cox-2 and iNOS are coexpressed in native and transplant atherosclerosis, possibly allowing for interaction between the enzymes and suggesting an alternative mechanism for the benefits of aspirin via inhibition of Cox-2 activity.
Operational amplifier based test structure for transistor threshold voltage variation (2008)

A new test structure has been developed, which is comprised of MOSFET arrrays and an on-chip operational amplifier feedback loop for measuring threshold voltage variation. The test structure also includes an on-chip clock generator and address decoders to scan through the arrays. It can be used in an inline test environment to provide rapid assessment of Vt variation for technology development and chip manufacturing. Hardware results in a 65nm technology are presented.
An Innovative Ultrasound Technique for Evaluation of Tumor Vascularity in Breast Cancers: Superb Micro-Vascular Imaging (2016)

Tumor vascularity is an important indicator for differential diagnosis, tumor growth, and prognosis. Superb micro-vascular imaging (SMI) is an innovative ultrasound technique for vascular examination that uses a multidimensional filter to eliminate clutter and preserve extremely low-velocity flows. Theoretically, SMI could depict more vessels and more detailed vascular morphology, due to the increased sensitivity of slow blood flow. Here, we report the early experience of using SMI in 21 breast cancer patients. We evaluated tumor vascular features in breast cancer and compared SMI and conventional color or power Doppler imaging. SMI was superior to color or power Doppler imaging in detecting tumor vessels, the details of vessel morphology, and both peripheral and central vascular distribution. In conclusion, SMI is a promising ultrasound technique for evaluating microvascular information of breast cancers.
In Utero Intraventricular Injection and Electroporation of E15 Mouse Embryos (2007)

In-utero in-vivo injection and electroporation of the embryonic mouse neocortex provides a powerful tool for the manipulation of individual progenitors lining the walls of the lateral ventricle. This technique is now widely used to study the processes involved in corticogenesis by over-expressing or knocking down genes and observing the effects on cellular proliferation, migration, and differentiation. In comparison to traditional knockout strategies, in-utero electroporation provides a rapid means to manipulate a population of cells during a specific temporal window. In this video protocol we outline the experimental methodology for preparing mice for surgery, exposing the uterine horns through laporatomy, injecting DNA into the lateral ventricles of the developing embryo, electroporating DNA into the progenitors lining the lateral wall, and caring for animals post-surgery. Our laboratory uses this protocol for surgeries on E13-E16 mice, however it is most commonly performed at E15 as shown in this video.
Energy-Efficient Air Conditioning Systems Utilizing Pneumatic Variable Compressors (2009)

<div class="htmlview paragraph">Air Conditioning systems with reheat reduction based for energy efficiency have generally been implemented with either electronic variable compressors through active stroke control or with fixed displacement compressors through modifying the cycling set point. The present work demonstrates a unique concept of achieving energy efficiency via cycling a pneumatic variable compressor at elevated set points. The energy efficiency of such a system approaches that of an electronic variable but significantly higher than that of a fixed displacement compressor system. The cost of the system, on the other hand, is substantially lower than that of an electronic compressor. Secondary benefits include a softer start than with a fixed compressor and a considerably simpler control scheme than that required by an electronic variable compressor.</div>
Low loss, 3.7GHz wideband BAW filters, using high power single crystal AlN-on-SiC resonators (2017)

Bulk acoustic wave (BAW) filters operating at center frequency of 3.7GHz, comprising of BAW resonators utilizing single crystal aluminum nitride (AlN) piezoelectric films epitaxially grown on silicon carbide (SiC) substrates, are reported. Metal-organic chemical vapor deposition (MOCVD) growth was used to obtain single crystal AlN films on 150-mm diameter c-plane semi-insulating SiC substrates with (0004) X-ray diffraction (XRD) rocking curve full-width half-maximum (FWHM) of 0.025°. The fabricated filters (1.25×0.9 sq.mm) had a center frequency of 3.71GHz and a 3dB bandwidth of 100MHz, an insertion loss of 2.0dB and narrow band rejection of 40dB and out-of-band rejection in excess of 37dB to 8GHz. Individual resonators on the same wafer show an electro-mechanical coupling as high as 7.63% and maximum quality-factors up to 1572. Insertion loss of 5ohm resonators configured as individual 2-port devices changed by 0.15dB after high power survival test at 10W. This is the first demonstration of single crystal AlN-on-SiC based BAW resonator and filter technology at 3.7GHz and illustrates the potential of a single crystal AlN-on-SiC based BAW technology platform enabling compact, high power and high performance filter solutions for high frequency mobile, Wi-Fi and infrastructure applications.
Designing Class Participation Experiences for the Introverted Student (1995)

Class participation for students is such a common expectation of nurse educators that it is easy to overlook the need to tailor class participation activities to individual student needs. An understanding of the various temperaments of individuals, especially preferences related to extroversion and introversion, can help nurse educators to plan class participation experiences that foster skills in critical thinking and enhance personal growth.
Quantified Tree Risk Assessment Used in the Management of Amenity Trees (2005)

Abstract A system of tree risk assessment is proposed that expands concepts developed by others and enables a probability of significant harm to be applied to tree failure risk. By evaluating the components of a tree failure hazard and assigning to them estimates of probability, the proposed system enables the skilled tree inspector to calculate the product of those probabilities to produce a numerical estimate of risk. The use of quantification in the assessment of tree hazards enables property owners and managers to operate, as far as is reasonably practicable, to a predetermined limit of reasonable or acceptable risk.