gebhart/patrepeval huggingface dataset:
The histone methyltransferase EZH2, an oncogene common to benign and malignant parathyroid tumors (2013)

Primary hyperparathyroidism (pHPT) resulting from parathyroid tumors is a common endocrine disorder with incompletely understood etiology. In renal failure, secondary hyperparathyroidism (sHPT) occurs with multiple tumor development as a result of calcium and vitamin D regulatory disturbance. The aim of this study was to investigate a potential role of the histone 3 lysine 27 methyltransferase EZH2 in parathyroid tumorigenesis. Parathyroid tumors from patients with pHPT included adenomas and carcinomas. Hyperplastic parathyroid glands from patients with HPT secondary to uremia and normal parathyroid tissue specimens were included in this study. Quantitative RT-PCR, western blotting, bisulfite pyrosequencing, colony formation assay, and RNA interference were used. EZH2 was overexpressed in a subset of the benign and in all malignant parathyroid tumors as determined by quantitative RT-PCR and western blotting analyses. Overexpression was explained by EZH2 gene amplification in a large fraction of tumors. EZH2 depletion by RNA interference inhibited sHPT-1 parathyroid cell line proliferation as determined by tritium-thymidine incorporation and colony formation assays. EZH2 depletion also interfered with the Wnt/β-catenin signaling pathway by increased expression of growth-suppressive AXIN2, a negative regulator of β-catenin stability. Indeed, EZH2 contributed to the total level of aberrantly accumulated transcriptionally active (nonphosphoylated) β-catenin in the parathyroid tumor cells. To our knowledge EZH2 gene amplification presents the first genetic aberration common to parathyroid adenomas, secondary hyperplastic parathyroid glands, and parathyroid carcinomas. This supports the possibility of a common pathway in parathyroid tumor development.
MICROWAVE-ASSISTED EFFICIENT OXIDATIVE COUPLING OF 2-NAPHTHOLS IN THE SOLID STATE (2002)

ABSTRACT Microwave-assisted oxidative coupling of 2-naphthols at solid state gave the corresponding coupling products in high yields, which provides a simple, rapid and efficient approach to the preparation of binaphthols.
Benzene oxidation coupled to sulfate reduction (1995)

Highly reduced sediments from San Diego Bay, Calif., that were incubated under strictly anaerobic conditions metabolized benzene within 55 days when they were exposed initially to 1 (mu)M benzene. The rate of benzene metabolism increased as benzene was added back to the benzene-adapted sediments. When a [(sup14)C]benzene tracer was included with the benzene added to benzene-adapted sediments, 92% of the added radioactivity was recovered as (sup14)CO(inf2). Molybdate, an inhibitor of sulfate reduction, inhibited benzene uptake and production of (sup14)CO(inf2) from [(sup14)C]benzene. Benzene metabolism stopped when the sediments became sulfate depleted, and benzene uptake resumed when sulfate was added again. The stoichiometry of benzene uptake and sulfate reduction was consistent with the hypothesis that sulfate was the principal electron acceptor for benzene oxidation. Isotope trapping experiments performed with [(sup14)C]benzene revealed that there was no production of such potential extracellular intermediates of benzene oxidation as phenol, benzoate, p-hydroxybenzoate, cyclohexane, catechol, and acetate. The results demonstrate that benzene can be oxidized in the absence of O(inf2), with sulfate serving as the electron acceptor, and suggest that some sulfate reducers are capable of completely oxidizing benzene to carbon dioxide without the production of extracellular intermediates. Although anaerobic benzene oxidation coupled to chelated Fe(III) has been documented previously, the study reported here provides the first example of a natural sediment compound that can serve as an electron acceptor for anaerobic benzene oxidation.
Optogenetic activation of neocortical neurons in vivo with a sapphire-based micro-scale LED probe (2015)

Optogenetics has proven to be a revolutionary technology in neuroscience and has advanced continuously over the past decade. However, optical stimulation technologies for in vivo need to be developed to match the advances in genetics and biochemistry that have driven this field. In particular, conventional approaches for in vivo optical illumination have a limitation on the achievable spatio-temporal resolution. Here we utilize a sapphire-based microscale gallium nitride light-emitting diode (μLED) probe to activate neocortical neurons in vivo. The probes were designed to contain independently controllable multiple μLEDs, emitting at 450 nm wavelength with an irradiance of up to 2 W/mm(2). Monte-Carlo stimulations predicted that optical stimulation using a μLED can modulate neural activity within a localized region. To validate this prediction, we tested this probe in the mouse neocortex that expressed channelrhodopsin-2 (ChR2) and compared the results with optical stimulation through a fiber at the cortical surface. We confirmed that both approaches reliably induced action potentials in cortical neurons and that the μLED probe evoked strong responses in deep neurons. Due to the possibility to integrate many optical stimulation sites onto a single shank, the μLED probe is thus a promising approach to control neurons locally in vivo.
Development of Directional MEMS Microphone Single Module for High Directivity and SNR (2021)

A unidirectional microelectromechanical system (MEMS) microphone single module for handsfree and voice recognition systems in automobiles is presented. Because in-cabin noise and temperature variation affect the reduction in the handsfree and voice recognition system performance, noise suppression and increasing the signal-to-noise ratio (SNR) of the microphone are required. In this study, a capacitive MEMS microphone module with a high SNR and a unidirectional characteristic is achieved by designing the structure, package, and module of the MEMS microphone. To improve the SNR, the microphone is developed using a slit-edged membrane. The slit structure is designed to release the residual stress of the membrane to achieve improved sensitivity and SNR. The unidirectional characteristic of the microphone enables suppression of noise signals from undesired directions. The directional characteristic of the microphone is realized by attaching a porous SU-8 filter to delay the time to one of the two acoustic ports on the package. Tests on the proposed unidirectional MEMS microphone package and module show that an SNR of 62.4 dB and a front-back ratio of 27.1 dB are achieved.
An Open Source Environment for Cell Broadband Engine System Software (2007)

The cell broadband engine provides the first implementation of a chip multiprocessor with a significant number of general-purpose programmable cores targeting a broad set of workloads. Open source software played a critical role in the development of the cell software stack. The system includes a power architecture processor and eight attached processor element. The cell team turned to open source software to accelerate the development of an ecosystem for the cell architecture. Using a quadword-based memory interface simplifies the data alignment logic and reduces operation latency.
Multiple Microalterations Detected at High Frequency in Oral Cancer (2005)

The development of array comparative genomic hybridization (array CGH) at tiling-path resolution has enabled the detection of gene-sized segmental DNA copy number gains and losses. Here, we present the first application of whole genome tiling-path array CGH to archival clinical specimens for the detailed analysis of oral squamous cell carcinomas (OSCC). We describe the genomes of 20 OSCCs as well as a selection of matched normal DNA in unprecedented detail. Examination of their whole genome profiles enabled the identification of alterations ranging in size from whole-arm, segmental, to gene size alterations. Tiling-path resolution enabled the detection of many more alterations within each tumor than previously reported, many of which include narrow alterations found to be frequent events among the 20 OSCCs. We report the presence of several novel frequent submegabase alterations, such as the 0.58 Mb gain at 5p15.2 containing triple functional domain (TRIO), detected in 45% of cases. We also report the first coamplification of two gene clusters, by fine-mapping the precise base pair boundaries of the high-level amplification at 11q22.2-22.3 containing both matrix metalloproteinase and baculoviral IAP repeat-containing protein 2 (BIRC) gene clusters. These results show the large improvement in detection sensitivity and resolution compared with genome interval marker arrays and the utility of tiling resolution array CGH for the detection of both submegabase and single copy gains and losses in cancer gene discovery.
Analytical fan-beam and cone-beam reconstruction algorithms with uniform attenuation correction for SPECT (2005)

In this paper, we developed an analytical fan-beam reconstruction algorithm that compensates for uniform attenuation in SPECT. The new fan-beam algorithm is in the form of backprojection first, then filtering, and is mathematically exact. The algorithm is based on three components. The first one is the established generalized central-slice theorem, which relates the 1D Fourier transform of a set of arbitrary data and the 2D Fourier transform of the backprojected image. The second one is the fact that the backprojection of the fan-beam measurements is identical to the backprojection of the parallel measurements of the same object with the same attenuator. The third one is the stable analytical reconstruction algorithm for uniformly attenuated Radon data, developed by Metz and Pan. The fan-beam algorithm is then extended into a cone-beam reconstruction algorithm, where the orbit of the focal point of the cone-beam imaging geometry is a circle. This orbit geometry does not satisfy Tuy's condition and the obtained cone-beam algorithm is an approximation. In the cone-beam algorithm, the cone-beam data are first backprojected into the 3D image volume; then a slice-by-slice filtering is performed. This slice-by-slice filtering procedure is identical to that of the fan-beam algorithm. Both the fan-beam and cone-beam algorithms are efficient, and computer simulations are presented. The new cone-beam algorithm is compared with Bronnikov's cone-beam algorithm, and it is shown to have better performance with noisy projections.
The effects of anesthetics on tumor progression. (2013)

More and more cancer patients receive surgery and chronic pain control. Cell-mediated immunosuppression from surgical stress renders perioperative period a vulnerable period for tumor metastasis. Retrospective studies suggest that regional anesthesia reduces the risk of tumor metastasis and recurrence. This benefit may be due to the attenuation of immunosuppression by regional anesthesia. On the other hand, accumulating evidence points to a direct role of anesthetics in tumor progression. A variety of malignancies exhibit increased activity of voltage-gated sodium channels. Blockade of these channels by local anesthetics may help inhibit tumor progression. Opioids promote angiogenesis, cancer cell proliferation and metastasis. It will be interesting to examine the therapeutic potential of peripheral opioid antagonists against malignancy. Volatile anesthetics are organ-protective against hypoxia, however; this very protective mechanism may lead to tumor growth and poor prognosis. In this review, we examine the direct effects of anesthetics in tumor progression in hope that a thorough understanding will help to select the optimal anesthetic regimens for better outcomes in cancer patients.
Surface Microscopy and Microanalysis in the Medical Device Industry (2008)

Extended abstract of a paper presented at Microscopy and Microanalysis 2008 in Albuquerque, New Mexico, USA, August 3 – August 7, 2008
Bax is Crucial for IFN-γ-Induced Resolution of Allergen- Induced Mucus Cell Metaplasia (2002)

Allergic airway responses cause proliferation of epithelial cells and mucus cell metaplasia (MCM), and the resolution of MCM involves reduction of cell numbers. The role of inflammation and apoptosis on this process was investigated in P-selectin +/+ and -/- mice sensitized and challenged with OVA by analyzing the expression and the role of regulators of apoptosis in metaplastic mucus cells. No differences were observed in MCM at 5 days of allergen exposure between +/+ and -/- mice, despite reduced IL-13 levels in -/- mice. Although IL-4 levels were similar in both -/- and +/+ mice, IL-13 and IL-5 levels had decreased and IFN-gamma levels were increased earlier in -/- compared with +/+ mice. MCM levels were decreased 4-fold at 7 days of allergen exposure in -/- mice and at 15 days in +/+ mice. The percentage of Bax-expressing mucus cells increased significantly at 7 days in -/- mice and at 10 days in +/+ mice. The Bax-positive mucus cells exhibited caspase-specific cleavage of cytokeratin 18. IFN-gamma caused Bax expression in IL-13-induced MCM in microdissected airway cultures. MCM remained significantly elevated in Bax -/- mice following 15 days of allergen exposure compared with +/+ mice, while the number of eosinophils was reduced in both Bax +/+ and -/- mice at 15 days. Together, these data demonstrate that reduced IL-13 levels were sufficient to elicit maximum MCM, that IFN-gamma induces Bax in metaplastic mucus cells, and that Bax plays a critical role in the resolution of MCM, but not in the resolution of eosinophils.
Haemopoietic CD34+ progenitor cells are not infected by HIV‐1 <i>in vivo</i> but show impaired clonogenesis (1993)

We evaluated the role of CD34+ bone marrow progenitor cells in vivo, in the pathogenesis of AIDS-related haematological abnormalities. The clonogenic activity of CD34+ cells from seven patients with HIV-1 infection, without bone marrow involving opportunistic infections or neoplasms, was assessed in semisolid cultures. The number of CFU-GM was significantly reduced as compared to the controls (P = 0.017), independently from myelotoxic therapy, while the number of BFU-E was not. The presence of retroviral sequences in CFU-GM colonies from four patients and in the total population of CD34+ cells from six patients with advanced stage HIV infection was investigated using the polymerase chain reaction. The presence of HIV-1 sequences was also searched for in a purified suspension of CD34+ cells after 3 weeks liquid culture. All these cells were always HIV-1 negative, while viral sequences were always detected in bone marrow mononuclear cells from these and other patients. The number of HIV-1 DNA copies decreased with increasing enrichment. At most 1:10,000 CD34+ cells are infected in vivo. Other mechanisms than direct viral infection of progenitor cells must account for the defective haemopoiesis in HIV-1 infected patients.
Adhesive curing through low-voltage activation (2015)

Instant curing adhesives typically fall within three categories, being activated by either light (photocuring), heat (thermocuring) or chemical means. These curing strategies limit applications to specific substrates and can only be activated under certain conditions. Here we present the development of an instant curing adhesive through low-voltage activation. The electrocuring adhesive is synthesized by grafting carbene precursors on polyamidoamine dendrimers and dissolving in aqueous solvents to form viscous gels. The electrocuring adhesives are activated at -2 V versus Ag/AgCl, allowing tunable crosslinking within the dendrimer matrix and on both electrode surfaces. As the applied voltage discontinued, crosslinking immediately terminated. Thus, crosslinking initiation and propagation are observed to be voltage and time dependent, enabling tuning of both material properties and adhesive strength. The electrocuring adhesive has immediate implications in manufacturing and development of implantable bioadhesives.
Nucleosome, the Main Autoantigen in Systemic Lupus Erythematosus, Induces Direct Dendritic Cell Activation via a MyD88-Independent Pathway: Consequences on Inflammation (2005)

Nucleosome is the major autoantigen in systemic lupus erythematosus. It is found as a circulating complex in the sera of patients and seems to play a key role in disease development. In this study, we show for the first time that physiologic concentrations of purified nucleosomes directly induce in vitro dendritic cell (DC) maturation of mouse bone marrow-derived DC, human monocyte-derived DC (MDDC), and purified human myeloid DC as observed by stimulation of allogenic cells in MLR, cytokine secretion, and CD86 up-regulation. Importantly, nucleosomes act as free complexes without the need for immune complex formation or for the presence of unmethylated CpG DNA motifs, and we thus identified a new mechanism of DC activation by nucleosomes. We have clearly demonstrated that this activation is nucleosome-specific and endotoxin-independent. Particularly, nucleosomes induce MDDC to secrete cytokines known to be detected in high concentrations in the sera of patients. Moreover, activated MDDC secrete IL-8, a neutrophil chemoattractant also detected in patient sera, and thus might favor the inflammation observed in patients. Both normal and lupus MDDC are sensitive to nucleosome-induced activation. Finally, injection of purified nucleosomes to normal mice induces in vivo DC maturation. Altogether, these results strengthen the key role of nucleosomes in systemic lupus erythematosus and might explain how peripheral tolerance is broken in patients.
Microstrip-Fed Circularly Polarized Square-Ring Patch Antenna for GPS Applications (2009)

A novel coupling technique for circularly polarized square-ring patch antenna is developed and discussed. The circular polarization (CP) radiation of the square-ring patch antenna is achieved by a simple microstrip feed line through the coupling of a square patch on the same plane of the antenna. Proper positioning of the coupling square patch excites two orthogonal resonant modes with 90deg phase difference, and a pure circular polarization is obtained. The dielectric material is a square block of ceramic with a permittivity of 58 and that reduces the size of the antenna. The prototype has been designed, fabricated and found to have an impedance bandwidth of 1.1% and a 3-dB axial-ratio bandwidth of about 0.03% at GPS frequency of 1573 MHz. The characteristics of the proposed antenna have been studied by simulation software HFSS and experiments. The measured and simulated results are in good agreement.
Integrating virtual and biochemical screening for protein tyrosine phosphatase inhibitor discovery (2013)

Protein tyrosine phosphatases (PTPs) represent an important class of enzymes that mediate signal transduction and control diverse aspects of cell behavior. The importance of their activity is exemplified by their significant contribution to disease etiology with over half of all human PTP genes implicated in at least one disease. Small molecule inhibitors targeting individual PTPs are important biological tools, and are needed to fully characterize the function of these enzymes. Moreover, potent and selective PTP inhibitors hold the promise to transform the treatment of many diseases. While numerous methods exist to develop PTP-directed small molecules, we have found that complimentary use of both virtual (in silico) and biochemical (in vitro) screening approaches expedite compound identification and drug development. Here, we summarize methods pertinent to our work and others. Focusing on specific challenges and successes we have experienced, we discuss the considerable caution that must be taken to avoid enrichment of inhibitors that function by non-selective oxidation. We also discuss the utility of using "open" PTP structures to identify active-site directed compounds, a rather unconventional choice for virtual screening. When integrated closely, virtual and biochemical screening can be used in a productive workflow to identify small molecules targeting PTPs.
Changes in the serum proteome associated with the development of hepatocellular carcinoma in hepatitis C-related cirrhosis (2006)

Early diagnosis of hepatocellular carcinoma (HCC) is the key to the delivery of effective therapies. The conventional serological diagnostic test, estimation of serum alpha-fetoprotein (AFP) lacks both sensitivity and specificity as a screening tool and improved tests are needed to complement ultrasound scanning, the major modality for surveillance of groups at high risk of HCC. We have analysed the serum proteome of 182 patients with hepatitis C-induced liver cirrhosis (77 with HCC) by surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI). The patients were split into a training set (84 non-HCC, 60 HCC) and a 'blind' test set (21 non-HCC, 17 HCC). Neural networks developed on the training set were able to classify the blind test set with 94% sensitivity (95% CI 73-99%) and 86% specificity (95% CI 65-95%). Two of the SELDI peaks (23/23.5 kDa) were elevated by an average of 50% in the serum of HCC patients (P<0.001) and were identified as kappa and lambda immunoglobulin light chains. This approach may permit identification of several individual proteins, which, in combination, may offer a novel way to diagnose HCC.
HC Measurements by Means of Flame Ionization: Background and Limits of Low Emission Measurement (2003)

<div class="htmlview paragraph">Flame Ionization Detectors (FID) can be used to detect organic hydrocarbons that occur in plastics, lacquers, adhesives, solvents and gasoline. These substances are ionized in the hydrogen flame of the FID. The ionization current that is produced depends on the amount of hydrocarbon in the sample.</div> <div class="htmlview paragraph">With the lowering of emissions limits, measuring instruments, including the FID, have to be able to detect very low values. For SULEV (Super-Ultra Low Emissions Vehicle) measurements the accuracy and also the general applicability of the CVS (Constant Volume Sampling) measuring technique are now questioned. Basic understanding is necessary to ask the right questions.</div> <div class="htmlview paragraph">One important issue is the science behind the measurement principle of the FID. And in this case especially the influence of contamination of the operating gases, cross sensitivity and data processing on the Limit of Detection (LOD).</div> <div class="htmlview paragraph">The studies show that an optimized FID within a modern CVS system is able to detect the emissions of SULEV level with high precision and repeatability.</div>
Effect of Thermal Convection on Liquid Phase Epitaxy of GaN by Na Flux Method (2007)

In the liquid phase epitaxy (LPE) growth of GaN single crystals using the Na flux method, we achieved an increase in the growth rate and a change in the growth thickness distribution by generating thermal convection in the Ga–Na melt. The effect of thermal convection on the growth rate and growth thickness distribution became stronger with the strength of the convection, which indicates that thermal convection can produce a high dissolution rate of nitrogen gas into the melt as well as homogenize the nitrogen concentration.