gebhart/patrepeval huggingface dataset:
Experimental Characterization and Numerical Modeling of Tissue Electrical Conductivity during Pulsed Electric Fields for Irreversible Electroporation Treatment Planning (2012)

Irreversible electroporation is a new technique to kill cells in targeted tissue, such as tumors, through a nonthermal mechanism using electric pulses to irrecoverably disrupt the cell membrane. Treatment effects relate to the tissue electric field distribution, which can be predicted with numerical modeling for therapy planning. Pulse effects will change the cell and tissue properties through thermal and electroporation (EP)-based processes. This investigation characterizes these changes by measuring the electrical conductivity and temperature of ex vivo renal porcine tissue within a single pulse and for a 200 pulse protocol. These changes are incorporated into an equivalent circuit model for cells and tissue with a variable EP-based resistance, providing a potential method to estimate conductivity as a function of electric field and pulse length for other tissues. Finally, a numerical model using a human kidney volumetric mesh evaluated how treatment predictions vary when EP- and temperature-based electrical conductivity changes are incorporated. We conclude that significant changes in predicted outcomes will occur when the experimental results are applied to the numerical model, where the direction and degree of change varies with the electric field considered.
Performance, uniformity, and yield of 850-nm VCSELs deposited by MOVPE (1996)

Vertical-cavity surface-emitting lasers (VCSELs) emitting near 850 nm and fabricated with the metal-organic vapor phase epitaxy (MOVPE) epitaxial growth technique and a planar proton implant process have been demonstrated with excellent performance, uniformity, and yield across a 3-in wafer. Four thousand lasers were tested on a three-inch-diameter wafer, with a yield of 99.8%. This translates into a yield of 94% for fully functional 34/spl times/1 arrays. The average threshold current, threshold voltage, and dynamic resistance at 10 mA operating current were 3.07 mA, 1.59 V, and 34 ohms, respectively. Uniformity of better than /spl plusmn/9% in threshold current, /spl plusmn/1% in threshold voltage, and /spl plusmn/1.5% in maximum optical output power across a 34-element array was demonstrated.
Real-time reverse transcription PCR (qRT-PCR) and its potential use in clinical diagnosis (2005)

qRT-PCR (real-time reverse transcription-PCR) has become the benchmark for the detection and quantification of RNA targets and is being utilized increasingly in novel clinical diagnostic assays. Quantitative results obtained by this technology are not only more informative than qualitative data, but simplify assay standardization and quality management. qRT-PCR assays are most established for the detection of viral load and therapy monitoring, and the development of SARS (severe acute respiratory syndrome)-associated coronavirus qRT-PCR assays provide a textbook example of the value of this technology for clinical diagnostics. The widespread use of qRT-PCR assays for diagnosis and the detection of disease-specific prognostic markers in leukaemia patients provide further examples of their usefulness. Their value for the detection of disease-associated mRNA expressed by circulating tumour cells in patients with solid malignancies is far less apparent, and the clinical significance of results obtained from such tests remains unclear. This is because of conceptual reservations as well as technical limitations that can interfere with the diagnostic specificity of qRT-PCR assays. Therefore, although it is evident that qRT-PCR assay has become a useful and important technology in the clinical diagnostic laboratory, it must be used appropriately and it is essential to be aware of its limitations if it is to fulfil its potential.
[Endothelial cells and cardiac explants in three-dimensional culture system]. (2005)

To observe the morphological features of endothelial cells and cardiac explants cultured in two- or three-dimensional culture systems, several three-dimensional collagen type I culture systems, such as the in gel, on gel, sandwich model, and the microscope slide model, were used to examine the growth patterns of the cells and explants from heart by using immunofluorescence staining and microscopic observation in the presence or absence of vascular endothelial growth factor (VEGF). In two-dimensional cultures the primary cardiac endothelial cells arrayed into a cobblestone-like structure. When cultured in three-dimensional matrix, the cells were elongated and migrated into the gel, with a phenotype similar to that in the process of angiogenesis and vasculogenesis in vivo. VEGF promoted the process of the endothelial cells transforming into tube-like structure. Cardiac explants grew well in the collagen gel. Adjacent explants were connected to each other by the migrating cells with the occurrence of autorhythmic beating of the explants. Thin-layer collagen gel, microscope slide chamber and aorta-strip model were also tested and proved to be good tools for vasculogenesis or angiogenesis studies. Three-dimensional culture systems enable the endothelial cells to proliferate, migrate, and anchor to three-dimensional vascular structures, showing advantages for observing the feature of angiogenesis. Different three-dimensional culture models may be used for variable research purposes.
Epidemiologic Studies of the 1975 Avian Influenza Outbreak in Chickens in Alabama (1977)

Daryl C. Johnson, Burton G. Maxfield, James I. Moulthrop, Epidemiologic Studies of the 1975 Avian Influenza Outbreak in Chickens in Alabama, Avian Diseases, Vol. 21, No. 2 (Apr. - Jun., 1977), pp. 167-177
Myeloid Cells in the Tumor Microenvironment: Modulation of Tumor Angiogenesis and Tumor Inflammation (2010)

Myeloid cells are a heterogeneous population of bone marrow-derived cells that play a critical role during growth and metastasis of malignant tumors. Tumors exhibit significant myeloid cell infiltrates, which are actively recruited to the tumor microenvironment. Myeloid cells promote tumor growth by stimulating tumor angiogenesis, suppressing tumor immunity, and promoting metastasis to distinct sites. In this review, we discuss the role of myeloid cells in promoting tumor angiogenesis. Furthermore, we describe a subset of myeloid cells with immunosuppressive activity (known as myeloid-derived suppressor cells). Finally, we will comment on the mechanisms regulating myeloid cell recruitment to the tumor microenvironment and on the potential of myeloid cells as new targets for cancer therapy.
Longitudinal movements and resulting shear strain of the arterial wall (2006)

There has been little interest in the longitudinal movement of the arterial wall. It has been assumed that this movement is negligible compared with the diameter change. Using a new high-resolution noninvasive ultrasonic method, we measured longitudinal movements and diameter change of the common carotid artery of 10 healthy humans. During the cardiac cycle, a distinct bidirectional longitudinal movement of the intima-media complex could be observed in all the subjects. An antegrade longitudinal movement, i.e., in the direction of blood flow, in early systole [0.39 mm (SD 0.26)] was followed by a retrograde longitudinal movement, i.e., in the direction opposite blood flow [−0.52 mm (SD 0.27)], later in systole and a second antegrade longitudinal movement [0.41 mm (SD 0.33)] in diastole. The corresponding diameter change was 0.65 mm (SD 0.19). The adventitial region showed the same basic pattern of longitudinal movement; however, the magnitude of the movements was smaller than that of the intima-media complex, thereby introducing shear strain and, thus, shear stress within the wall [maximum shear strain between the intima-media complex and the adventitial region was 0.36 rad (SD 0.26). These phenomena have not previously been described. Measurements were also performed on the abdominal aorta ( n = 3) and brachial ( n = 3) and popliteal ( n = 3) arteries. Our new information seems to be of fundamental importance for further study and evaluation of vascular biology and hemodynamics and, thus, for study of atherosclerosis and vascular diseases.
Expander flows, geometric embeddings and graph partitioning (2004)

We give a O(√log n)-approximation algorithm for sparsest cut, balanced separator, and graph conductance problems. This improves the O(log n)-approximation of Leighton and Rao (1988). We use a well-known semidefinite relaxation with triangle inequality constraints. Central to our analysis is a geometric theorem about projections of point sets in Rd, whose proof makes essential use of a phenomenon called measure concentration. We also describe an interesting and natural "certificate" for a graph's expansion, by embedding an n-node expander in it with appropriate dilation and congestion. We call this an expander flow.
Interferon-Beta Prevents Cytokine-Induced Neutrophil Infiltration and Attenuates Blood–Brain Barrier Disruption (2003)

Inflammation can contribute to brain injury, such as that resulting from ischemia or trauma. The authors have previously shown that the cytokine interferon-beta (IFN-beta) affords protection against ischemic brain injury, which was associated with a diminished infiltration of neutrophils and a reduction in blood-brain barrier (BBB) disruption. The goal of the current study was to directly assess the effects of IFN-beta on neutrophil infiltration, with the use of an in vivo assay of neutrophil infiltration with relevance to ischemic brain injury. Intrastriatal injection of recombinant rat cytokine-induced neutrophil chemoattractant-1, a member of the interleukin-8 family (1 microg in 1 microl), triggered massive infiltration of neutrophils and extensive BBB disruption 6 hours later, as measured using immunofluorescence microscopy and magnetic resonance imaging in the rat, respectively. Depleting the animals of neutrophils before interleukin-8 injection prevented BBB disruption. Treatment with IFN-beta (5 x 106 U/kg) almost completely prevented neutrophil infiltration and attenuated BBB damage. Gelatinase zymography showed matrix metalloproteinase-9 expression in the ipsilateral striatum after interleukin-8 injection. Both neutrophil depletion and IFN-beta treatment downregulated matrix metalloproteinase-9. IFN-beta has already been approved for human use as a treatment for the chronic inflammatory disorder multiple sclerosis. The potential value of IFN-beta as a treatment that can attenuate acute brain inflammation is considered.
Full-Wave Three-Dimensional Microwave Imaging With a Regularized Gauss–Newton Method— Theory and Experiment (2007)

A reconstruction algorithm is detailed for three-dimensional full-vectorial microwave imaging based on Newton-type optimization. The goal is to reconstruct the three-dimensional complex permittivity of a scatterer in a homogeneous background from a number of time-harmonic scattered field measurements. The algorithm combines a modified Gauss-Newton optimization method with a computationally efficient forward solver, based on the fast Fourier transform method and the marching-on-in-source-position extrapolation procedure. A regularized cost function is proposed by applying a multiplicative-additive regularization to the least squares datafit. This approach mitigates the effect of measurement noise on the reconstruction and effectively deals with the non-linearity of the optimization problem. It is furthermore shown that the modified Gauss-Newton method converges much faster than the Broyden-Fletcher-Goldfarb-Shanno quasi-Newton method. Promising quantitative reconstructions from both simulated and experimental data are presented. The latter data are bi-static polarimetric free-space measurements provided by Institut Fresnel, Marseille, France.
100K Q-factor toroidal ring gyroscope implemented in wafer-level epitaxial silicon encapsulation process (2014)

This paper reports a new type of degenerate mode gyroscope with measured Q-factor of > 100,000 on both modes at a compact size of 1760 μm diameter. The toroidal ring gyroscope consists of an outer anchor ring, concentric rings nested inside the anchor ring and an electrode assembly at the inner core. Current implementation uses n = 3 wineglass mode, which is inherently robust to fabrication asymmetries. Devices were fabricated using high-temperature, ultra-clean epitaxial silicon encapsulation (EpiSeal) process. Over the 4 devices tested, lowest as fabricated frequency split was found to be 8.5 Hz (122 ppm) with a mean of 21 Hz (Δf/f = 300 ppm). Further electrostatic tuning brought the frequency split below 100 mHz (<; 2 ppm). Whole angle mechanization and pattern angle was demonstrated using a high speed DSP control system. Characterization of the gyro performance using force-rebalance mechanization revealed ARW of 0.047°/√hr and an in-run bias stability of 0.65 deg/hr. Due to the high Q-factor and robust support structure, the device can potentially be instrumented in whole angle mechanization for applications which require high rate sensitivity and robustness to g-forces.
Exploring Visual and Motion Saliency for Automatic Video Object Extraction (2013)

This paper presents a saliency-based video object extraction (VOE) framework. The proposed framework aims to automatically extract foreground objects of interest without any user interaction or the use of any training data (i.e., not limited to any particular type of object). To separate foreground and background regions within and across video frames, the proposed method utilizes visual and motion saliency information extracted from the input video. A conditional random field is applied to effectively combine the saliency induced features, which allows us to deal with unknown pose and scale variations of the foreground object (and its articulated parts). Based on the ability to preserve both spatial continuity and temporal consistency in the proposed VOE framework, experiments on a variety of videos verify that our method is able to produce quantitatively and qualitatively satisfactory VOE results.
An in vivo function for the transforming Myc protein: elicitation of the angiogenic phenotype. (2000)

The ability of neoplastic cells to recruit blood vasculature is crucial to their survival in the host organism. However, the evidence linking dominant oncogenes to the angiogenic switch remains incomplete. We demonstrate here that Myc, an oncoprotein implicated in many human malignancies, stimulates neovascularization. As an experimental model, we used Rat-1A fibroblasts that form vascular tumors upon transformation by Myc in immunocompromised mice. Our previous work and the use of neutralizing antibodies reveal that in these cells, the angiogenic switch is achieved via down-modulation of thrombospondin-1, a secreted inhibitor of angiogenesis, whereas the levels of vascular endothelial growth factor, a major activator of angiogenesis, remain high and unaffected by Myc. Consistent with this finding, overexpression of Myc confers upon the conditioned media the ability to promote migration of adjacent endothelial cells in vitro and corneal neovascularization in vivo. Furthermore, mobilization of estrogen-dependent Myc in vivo with the appropriate steroid provokes neovascularization of cell implants embedded in Matrigel. These data suggest that Myc is fully competent to trigger the angiogenic switch in vivo and that secondary events may not be required for neovascularization of Myc-induced tumors.
Structural reorganization of the interleukin-7 signaling complex (2012)

We report here an unliganded receptor structure in the common gamma-chain (γ(c)) family of receptors and cytokines. The crystal structure of the unliganded form of the interleukin-7 alpha receptor (IL-7Rα) extracellular domain (ECD) at 2.15 Å resolution reveals a homodimer forming an "X" geometry looking down onto the cell surface with the C termini of the two chains separated by 110 Å and the dimer interface comprising residues critical for IL-7 binding. Further biophysical studies indicate a weak association of the IL-7Rα ECDs but a stronger association between the γ(c)/IL-7Rα ECDs, similar to previous studies of the full-length receptors on CD4(+) T cells. Based on these and previous results, we propose a molecular mechanism detailing the progression from the inactive IL-7Rα homodimer and IL-7Rα-γ(c) heterodimer to the active IL-7-IL-7Rα-γ(c) ternary complex whereby the two receptors undergo at least a 90° rotation away from the cell surface, moving the C termini of IL-7Rα and γ(c) from a distance of 110 Å to less than 30 Å at the cell surface. This molecular mechanism can be used to explain recently discovered IL-7- and γ(c)-independent gain-of-function mutations in IL-7Rα from B- and T-cell acute lymphoblastic leukemia patients. The mechanism may also be applicable to other γ(c) receptors that form inactive homodimers and heterodimers independent of their cytokines.
Detection of Nucleic Acids by Cycling Probe Technology on Magnetic Particles: High Sensitivity and Ease of Separation (1999)

Cycling Probe Technology (CPT) is a signal amplification system that allows detection of nucleic acid target sequences without target amplification. CPT employs a sequence specific chimeric probe, typically DNA-RNA-DNA, which hybridizes to a complementary target DNA sequence and becomes a substrate for RNase H. Cleavage occurs at the RNA internucleotide linkages and results in dissociation of the probe from the target, thereby making it available for the next probe molecule. This communication describes the use of oligonucleotides attached to solid supports for target capture and release followed by solution and solid phase cycling. Through the attachment of chimeric probes to Sera-Mag magnetic particles (SMP) a simple and effective method of separating the cleaved probe from non-cycled probe has been developed. By capturing the target DNA on particles and separating it from the extraneous non-specific DNA we are able to dramatically reduce background and thus discriminate between samples of Methicillin Resistant (MRSA) and Methicillin Sensitive (MSSA) Staphylococcus Aureus. We conjugated oligonucleotide probes to SMPs (approximately 1 um) and Nylon beads (NB) which were coated with ID Biomedical's proprietary coating materials (R, patent pending). The general structure of the constructs is shown below: [table: see text]
High Distribution of CD40 and TRAF2 in Th40 T Cell Rafts Leads to Preferential Survival of this Auto-Aggressive Population in Autoimmunity (2008)

CD40 may act as a switch between life and death promoting signals and NOD Th40 cells are poised for survival via this switch. This may explain how they expand in autoimmunity to thwart T cell homeostasis.
Quantitative viscoelastic parameters measured by harmonic motion imaging (2009)

Quantifying the mechanical properties of soft tissues remains a challenging objective in the field of elasticity imaging. In this work, we propose an ultrasound-based method for quantitatively estimating viscoelastic properties, using the amplitude-modulated harmonic motion imaging (HMI) technique. In HMI, an oscillating acoustic radiation force is generated inside the medium by using focused ultrasound and the resulting displacements are measured using an imaging transducer. The proposed approach is a two-step method that uses both the properties of the propagating shear wave and the phase shift between the applied stress and the measured strain in order to infer to the shear storage (G') and shear loss modulus (G''), which refer to the underlying tissue elasticity and viscosity, respectively. The proposed method was first evaluated on numerical phantoms generated by finite-element simulations, where a very good agreement was found between the input and the measured values of G' and G''. Experiments were then performed on three soft tissue-mimicking gel phantoms. HMI measurements were compared to rotational rheometry (dynamic mechanical analysis), and very good agreement was found at the only overlapping frequency (10 Hz) in the estimate of the shear storage modulus G' (14% relative error, averaged p-value of 0.34), whereas poorer agreement was found in G'' (55% relative error, averaged p-value of 0.0007), most likely due to the significantly lower values of G'' of the gel phantoms, posing thus a greater challenge in the sensitivity of the method. Nevertheless, this work proposes an original model-independent ultrasound-based elasticity imaging method that allows for direct, quantitative estimation of tissue viscoelastic properties, together with a validation against mechanical testing.
Comparative Effects of Two Ventilatory Modes on Speech in Tracheostomized Patients with Neuromuscular Disease (2003)

Many patients with respiratory failure related to neuromuscular disease receive chronic invasive ventilation through a tracheostomy. Improving quality of life, of which speech is an important component, is a major goal in these patients. We compared the effects on breathing and speech production of assist-control ventilation (ACV) and bilevel positive-pressure ventilation (BPPV) in nine patients with neuromuscular disease. Ventilator-delivered flow was measured using a pneumotachograph, and respiratory rate, inspiratory time, and ventilator-delivered volume were measured on this flow signal. Gas exchange was assessed using oxygen saturation and end-tidal carbon dioxide measurement. Microphone speech recordings were subjected to quantitative analysis. At rest, ventilatory parameters were similar with both modes. Speech induced an increase in inspiratory time during BPPV, with a greater increase in the volume released by the ventilator during speech as compared with ACV (172 +/- 194 versus 26 +/- 31 ml). Consequently, speech duration was longer during inspiration with BPPV. Moreover, BPPV allowed speech production to extend into expiration, and three patients could speak continuously during several respiratory cycles while receiving BPPV. Blood gas exchange was not modified by speech with BPPV or ACV. This study shows that BPPV provides better speech duration than ACV with no detectable short-term deleterious effects.
Surface Plasmon Resonance Sensors for Detection of Chemical and Biological Species (2008)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSurface Plasmon Resonance Sensors for Detection of Chemical and Biological SpeciesJiří HomolaView Author Information Institute of Photonics and Electronics ASCR, Chaberská 57, 182 51 Prague 8, Czech Republic Cite this: Chem. Rev. 2008, 108, 2, 462–493Publication Date (Web):January 30, 2008Publication History Received31 May 2007Published online30 January 2008Published inissue 1 February 2008https://pubs.acs.org/doi/10.1021/cr068107dhttps://doi.org/10.1021/cr068107dresearch-articleACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views32405Altmetric-Citations3416LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Biopolymers,Immunology,Peptides and proteins,Sensors,Surface plasmon resonance Get e-Alerts