gebhart/patrepeval huggingface dataset:
An innovative flexible and accurate packaging technique suited to fabricate low cost micro optoelectronic modules (2002)

Several groups are presently investigating the opportunity to fabricate miniaturized optical devices characterized by high attachment precision. An automated surface mounted technique based on standardized supports of 10/spl times/10/spl times/4 mm/sup 3/ size and on active in-situ alignment of the optical elements had been developed in our laboratories. This surface mounted device (SMD) technique is well suited for a flexible production of small optical devices and it allows a two dimensional layout. It is limited in precision to /spl plusmn/1 /spl mu/m and it is not adapted for further miniaturization. It is briefly described in this paper. Here, we mainly report on a new automated and low cost optical-SMD packaging technique, named "Three Dimensional Miniaturized Optical Surface Mounted Device (TRIMO-SMD)", based on a in-situ active alignment of standardized 2.5/spl times/3.5/spl times/1 mm/sup 3/ elements by a laser soldering reflow process. A sub micron alignment precision is achieved and a attachment strength of -20 N is guaranteed. The technique offers the potential of 3 dimensional layouts and integration on the same layout of electronic and optical elements.
Complete nucleotide sequence of an attenuated hepatitis A virus: comparison with wild-type virus. (1987)

The complete nucleotide sequence of an attenuated hepatitis A virus, HAV HM-175/7 MK-5, was determined from cloned cDNA. This virus was derived from wild-type HAV HM-175 after 32 passages in African green monkey kidney cells. The resultant cell culture-adapted virus is attenuated for chimpanzees. This virus was passaged an additional three times in monkey kidney cells to obtain sufficient virus for molecular cloning and was designated HM-175/7 MK-5. Three overlapping cDNA clones were obtained that together spanned the entire genome. Comparison of the nucleotide sequence of cDNA from wild-type virus (propagated in marmoset liver in vivo) with attenuated virus (grown in cell culture) showed 24 nucleotide changes distributed throughout the genome. Five base deletions occurred in the 5' noncoding region, and 12 of the 16 base substitutions in the coding region resulted in amino acid changes. Amino acid changes occurred in viral capsid proteins VP1 and VP2 and several of the nonstructural proteins. Thus, a small number of nucleotide changes are responsible for adaptation to cell culture and attenuation of HAV strain HM-175.
TTR Fibril Formation Inhibitors: Is there a SAR? (2012)

Transthyretin is a homotetrameric protein that carries thyroxine and retinol binding protein in plasma and is associated with a variety of amyloid diseases. One approach to the potential treatment of TTR amyloidosis is the stabilization of the native tetramer, over the dissociative transition state, through the binding of small molecules; this increases the kinetic barrier for tetramer dissociation and prevents protein misfolding. Several molecules discovered through focused screening, or created utilizing the structure-based design, were studied to identify the structural features that could make up for a good candidate drug. In this review, we examine several different chemical classes of TTR fibril formation inhibitors, highlighting the structural modifications that have led to an improvement or to a decrease of their potency and/or selectivity.
Micro-fluidic channels with integrated ultrasonic transducers (2002)

This paper describes the work done in an attempt to integrate ultrasonic sensors in micro-fluidic channels. We have developed a system with fluidic channels having embedded zinc oxide transducers. A zinc oxide film is deposited on a glass substrate and is sandwiched between two electrodes. The transducers made are found to resonate at 400 MHz in thickness mode. The channels are made both from PDMS using a silicon master and from glass. These channels are aligned on top of the transducer forming a narrow path for fluid flow. The fluid of interest is pumped in the microchannels by means of a syringe pump and pulse echo measurements are done with the necessary circuitry. This paper will also show the results of the first experiments on mixing induced by the transducer and the measurement of physical dimensions, temperature of fluid in the channel using broad band pulse echo techniques.
VEGF-A, VEGF-C, and VEGF-D in Colorectal Cancer Progression (2001)

We aimed to assess the relationship of the angiogenic cytokines VEGF-A, VEGF-C, and VEGF-D and their receptors VEGFR-2 and VEGFR-3 in the adenoma-carcinoma sequence and in metastatic spread of colorectal cancer (CRC). mRNA expression levels were measured using semi-quantitative reverse transcription polymerase chain reaction in 70 CRC (35 with paired mucosae) and 20 adenomatous polyps. Immunohistochemistry and ELISA assessed protein expression. VEGF-D mRNA expression was significantly lower in both polyps and CRCs compared with normal mucosa (P=.0002 and.002, respectively), whereas VEGF-A and VEGF-C were significantly raised in CRCs (P=.006 and.004, respectively), but not polyps (P=.22 and P=.5, respectively). Receptor expression was similar in tumor tissue and normal mucosae. Tumors with lymph node metastases had significantly higher levels of VEGF-A compared with non-metastatic tumors (P=.043). There was no association between VEGF-C or VEGF-D and lymphatic spread. The decrease in VEGF-D occurring in polyps and carcinomas may allow the higher levels of VEGF-A and VEGF-C to bind more readily to the VEGF receptors, and produce the angiogenic switch required for tumor growth. Increased expression of VEGF-A within CRCs was associated with lymphatic metastases, and therefore, this member of the VEGF family may be the most important in determining metastatic spread.
Eotaxin and Impaired Lung Function in Asthma (1999)

We performed an association study of plasma eotaxin levels, eosinophil counts, total IgE levels, asthma diagnosis, and lung function in an ethnically diverse and geographically dispersed population. We studied 515 asthmatic and 519 normal subjects, none of whom was taking inhaled or oral corticosteroids. Logistic regression analysis demonstrated a direct relationship between asthma diagnosis and eotaxin levels (p < 0.0001). The odds of an asthma diagnosis increased with eotaxin quartile, with the highest quartile having an odds ratio of 5.4 (95% CI 3.2 to 9.2, p < 0.001) compared with the lowest eotaxin quartile. Eotaxin levels were inversely related to lung function (p < 0.001), with the mean percent predicted FEV(1) in the highest eotaxin quartile being 13.5 percentage points (SEM 2.1, p < 0.001) less than that in the lowest quartile. Plasma eotaxin levels were associated with asthma and inversely related to lung function independent of age, race, sex, or smoking status. When combined with eosinophil counts and IgE levels, eotaxin levels contributed to the odds of an asthma diagnosis and of impaired lung function. Our results are the first to associate eotaxin levels with asthma diagnosis and compromised lung function in a large geographically and ethnically diverse population.
Anellated Hemicyanine Dyes in a Neuron Membrane:  Molecular Stark Effect and Optical Voltage Recording (2003)

The voltage sensitivity of hemicyanine dyes ANNINE-6 and ANNINE-5 with anellated benzene rings and without free CC single and double bonds is studied in Retzius neurons from Hirudo medicinalis. For comparison, biaryl hemicyanine BNBIQ and styryl hemicyanines di-4-ANEPBS and RH-421 are investigated. Fluorescence spectra are recorded by an independent variation of the wavelengths of excitation and emission at two defined membrane voltages. With extracellular staining, a positive change in the intracellular voltage shifts all excitation spectra to the blue. That modulation is assigned to a molecular Stark effect that increases in the series RH-421, di-4-ANEPBS, BNBIQ, ANNINE-5, and ANNINE-6 with displacements of elementary charge by 0.24, 0.43, 0.51, 0.65, and 0.81 nm across the membrane. For BNBIQ, ANNINE-5, and ANNINE-6, an almost identical blue shift is observed for the emission that is also assigned to a Stark effect. The ANNINE dyes are the most efficient fluorescent probes of neuronal activity on the basis of a well-defined physical mechanism. The implications with respect to the optical recording of voltage transients are considered.
NMR of Proteins (1993)

The last years have witnessed great advances in the application of nuclear magnetic resonance techniques in molecular biology. Significant strides have been made both with respect to studying structural and dynamical properties of proteins. Within NMR of Proteins are presented details of some of the advances, drawn from NMR laboratories around the world. The contributions reflect some of the huge variety and different emphasis found amongst researchers engaged in biological NMR and give the reader an insight into the wealth of possible applications of NMR in their own area of research
The frequency of a novel KANK1 and NTRK3 translocation and BRAFV600E mutation in patients diagnosed with metanephric adenoma utilizing molecular mechanisms. (2017)

1537 Background: Renal metanephric adenoma (MA) is a very rare benign renal tumor, which is frequently misclassified when microscopic features alone are applied. Despite the classification of adenoma as a benign tumor, it is difficult to differentiate from other renal carcinomas such as malignant papillary renal cell carcinomas and in children it can be mistaken with Wilms tumor. The correct classification of a renal tumor is critical for diagnostic, prognostic, and therapeutic purposes. Despite the advancements in cancer genomics, there is limited data available regarding the genetic alterations critical to the metanephric adenoma development. Recent data suggest that 90% of MA have BRAF V600E mutations; the genetics of the remaining 10 % are unclear. Methods: This study was conducted on 13 FFPE specimens from patients who were diagnosed with renal metanephric adenoma. H&amp;E stained slides from all cases were reviewed by study pathologist, and representative tissue blocks were further selected for BRAF V600E sequencing and fluorescent in situ hybridization was adapted to detect chromosomal rearrangement between KANK1 on chromosome 9 (9p24.3) and NTRK3 on chromosome 15 (15q25.3). Results: In this study, we identified a novel chromosomal translocation t(9;15)(p24;q24) between KANK1 and NTRK3, and provided new insights into molecular mechanisms which might identify a subset of metanephric adenomas. Such findings imply that recurrent cytogenetic aberrations may be of prognostic significance as well. Interestingly, our data suggested mutual exclusivity of BRAF V600E and t(9;15) aberrations. Conclusions: Molecular and cytogenetic analyses have allowed us to elucidate a genetic aberration, which may be specific to metanephric adenoma. Aberrant expression of the KANK1-NTRK3 gene fusion may be one mechanism by which functionally relevant genes are altered in the development of metanephric adenoma, and thus mark a subgroup of metanephric adenomas with particular clinicopathological features. Also, our study adds KANK1 and NTRK3 to the list of candidate genes that may play a role in the 10% of renal metanephric adenomas that lack a BRAF V600E mutation.
MOS gated Si:SiGe quantum wells formed by anodic oxidation (1998)

We have used electrochemical anodic oxidation to form gate oxides on strained n-channel Si:SiGe quantum wells. The oxides are characterized by current-voltage and capacitance-voltage measurements. Comparison of measured and calculated electron sheet densities in the quantum well, indicates that the oxide growth does not cause degradation of the Si:SiGe material. This is confirmed by low-temperature measurements of the electron mobility and sheet density in the quantum well.
Migration of electrons and holes in crystalline d(CGATCG)-anthracycline complexes X-irradiated at 4 K. (1998)

Electrons and holes generated in irradiated DNA migrate to stable trapping sites. Protonation and deprotonation reactions at these sites promote the trapping of electrons and holes, thereby inhibiting further migration. The extent of migration determines the final distribution of damage in irradiated DNA. In this study, electron and hole migration is investigated in a crystalline DNA hexamer intercalated with an anthracycline drug. The intercalator is no further than 2 base pairs away from any DNA base. From EPR measurements, there is no evidence of DNA-centered radicals in the irradiated DNA hexamer. The aromatic region of the anthracycline intercalator evidently sequesters most or all of the electrons and most of the holes. Further hole trapping and radical stabilization appear to occur on the anthracycline's amino sugar group, which is nestled in the minor groove of the hexamer. The relatively large yield of this proposed amino sugar radical suggests that holes generated in the DNA solvation shell migrate to the amino sugar, where they become trapped. This would be the first observation of a radical formed by the direct effect of low-dose, low-LET radiation that is trapped within the DNA helix, yet lies outside of the stacked bases. With respect to holes generated in the DNA bases at 4 K, we conclude that most, if not all, are capable of migrating to an intercalator < or = 2 base pairs away. With respect to dry electrons, we conclude that anthracycline competes effectively for electron trapping over a region of at least 2 base pairs; our experiments cannot distinguish between electron attachment to the bases followed by transfer to the intercalator and direct attachment to the intercalator.
<title>MAPP2200: a second-generation smart optical sensor</title> (1992)

A new smart optical sensor, the MAPP2200 is presented. It is based on four years of practical experiences with an earlier line sensor device, the LAPP1100. Using a 256*256 array of photo diodes, the new device is capable of capturing a full image. The chip includes circuitry for A/D-conversion and digital image processing. The processor, being a line-parallel SIMD machine, handles line data at a rate of 4 MHz. The device performs common early vision tasks such as filtering, edge detection, histogramming, and correlation at rates of 10 - 100 frames per second. Simpler tasks such as binary template matching can be performed at more than 1000 frames per second. The paper covers both hardware and software aspects of the new device.
Retroviral-mediated gene transfer of human phenylalanine hydroxylase into NIH 3T3 and hepatoma cells. (1986)

Phenylketonuria (PKU) is caused by deficiency of the hepatic enzyme phenylalanine hydroxylase (PAH). A full-length human PAH cDNA sequence has been inserted into pzip-neoSV(X), which is a retroviral vector containing the bacterial neo gene. The recombinant has been transfected into psi 2 cells, which provide synthesis of the retroviral capsid. Recombinant virus was detected in the culture medium of the transfected psi 2 cells, which is capable of transmitting the human PAH gene into mouse NIH 3T3 cells by infection leading to stable incorporation of the recombinant provirus. Infected cells express PAH mRNA, immunoreactive PAH protein, and exhibit pterin-dependent phenylalanine hydroxylase activity. The recombinant virus is also capable of infecting a mouse hepatoma cell line that does not normally synthesize PAH. PAH activity is present in the cellular extracts and the entire hydroxylation system is reconstituted in the hepatoma cells infected with the recombinant viruses. Thus, recombinant viruses containing human PAH cDNA provide a means for introducing functional PAH into mammalian cells of hepatic origin and can potentially be introduced into whole animals as a model for somatic gene therapy for PKU.
Identification of Proteins of the Yeast Protein Map using Genetically Manipulated Strains and Peptide‐Mass Fingerprinting (1996)

In this study we used genetically manipulated strains in order to identify polypeptide spots of the protein map of Saccharomyces cerevisiae. Thirty-two novel polypeptide spots were identified using this strategy. They corresponded to the product of 23 different genes. We also explored the possibilities of using peptide-mass fingerprinting for the identification of proteins separated on our gels. According to this strategy, proteins contained in spots are digested with trypsin and the masses of generated peptides are determined by matrix-assisted laser desorption-ionization mass spectrometry (MALDI-MS). The peptide masses are then used to search a yeast protein database for proteins that match the experimental data. Application of this strategy to previously identified polypeptide spots gave evidence of the feasibility of this approach. We also report predictions on the identities of nine unknown spots using MALDI-MS.
Clinical appraisal of chronic traumatic encephalopathy (2011)

On the basis of recent research in the fields of dementia and traumatic brain injury, several in-vivo procedures (including neurological examination, neuropsychological assessment, neuroimaging techniques, and blood and cerebrospinal fluid biomarkers) each have the potential to contribute unique information about the manifestations of CTE, including clinical and preclinical stages. More research is needed to develop a set of consensus diagnostic criteria that provide a reliable and valid indicator of neuropathologically verified CTE. Until such criteria are developed, the clinical assessment of CTE should be informed by modern research that is of relevance to traumatic brain injury and neurodegenerative diseases.
Electrospray interface for liquid chromatographs and mass spectrometers (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrospray interface for liquid chromatographs and mass spectrometersCraig M. Whitehouse, Robert N. Dreyer, Masamichi. Yamashita, and John B. FennCite this: Anal. Chem. 1985, 57, 3, 675–679Publication Date (Print):March 1, 1985Publication History Published online1 May 2002Published inissue 1 March 1985https://pubs.acs.org/doi/10.1021/ac00280a023https://doi.org/10.1021/ac00280a023research-articleACS PublicationsRequest reuse permissionsArticle Views3745Altmetric-Citations1219LEARN 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 Get e-Alerts
Dephosphorylation and activation of the T cell tyrosine kinase pp56lck by the leukocyte common antigen (CD45). (1990)

pp56lck, encoded by the lck proto-oncogene, is a non-receptor tyrosine protein kinase (TPK) found in all T lymphocytes. A significant fraction of pp56lck is tightly associated with the cytoplasmic domains of CD4 and CD8 glycoproteins, suggesting an important role for it in thymic development and T cell activation. We have studied the regulation of the tyrosine kinase activity of pp56lck and found recently that it becomes rapidly activated in isolated T cell membranes by an endogenous mechanism apparently involving a phosphotyrosine phosphatase (PTPase). Moreover pp56lck was activated upon addition of isolated CD45 (leukocyte common antigen), a major membrane PTPase, and activation was absent in T cell mutants lacking CD45. Here, we address in more detail the mechanisms of pp56lck activation by the CD45 PTPase and show that this event is time-dependent, sensitive to Na3VO4 (which blocks the PTPase activity of CD45), and is accompanied by dephosphorylation of a regulatory tyrosine residue (Tyr-505) near the C-terminus of pp56lck. This provides a molecular mechanism for regulation of the catalytic activity of pp56lck by CD45, which thus is likely to be the physiological activator of pp56lck. Activation of pp56lck by the CD45 PTPase may underlie many of the reported immunomodulatory effects of antibodies to CD45, and provides further support for the notion that CD45-mediated tyrosine dephosphorylation plays a critical role in T cell activation and growth.
Oral manifestations in patients with Sjögren's syndrome. (1998)

The oral health of this group of patients with SS was deficient. Adequate management of dry mouth was not achieved, mainly for the modifiable components such as dental decay and oral candidiasis. Therefore. treatment and prevention plans are mandatory. These measures might help to reduce the discomfort associated with oral dryness and to reduce dental loss.
Origin, Microbiology, Nutrition, and Pharmacology of D‐Amino Acids (2010)

Exposure of food proteins to certain processing conditions induces two major chemical changes: racemization of all L-amino acids (LAAs) to D-amino acids (DAAs) and concurrent formation of cross-linked amino acids such as lysinoalanine (LAL). The diet contains both processing-induced and naturally-formed DAA. The latter include those found in microorganisms, plants, and marine invertebrates. Racemization impairs digestibility and nutritional quality. Racemization of LAA residues to their D-isomers in food and other proteins is pH-, time-, and temperature-dependent. Although racemization rates of LAA residues in a protein vary, relative rates in different proteins are similar. The nutritional utilization of different DAAs varies widely in animals and humans. Some DAAs may exert both adverse and beneficial biological effects. Thus, although D-Phe is utilized as a nutritional source of L-Phe, high concentrations of D-Tyr in such diets inhibit the growth of mice. Both D-Ser and LAL induce histological changes in the rat kidney. The wide variation in the utilization of DAAs is illustrated by the fact that, whereas D-Meth is largely utilized as a nutritional source of the L-isomer, D-Lys is not. Similarly, although L-CysSH has a sparing effect on L-Meth when fed to mice, D-CysSH does not. Since DAAs are consumed as part of their normal diet, a need exists to develop a better understanding of their roles in foods, microbiology, nutrition, and medicine. To contribute to this effort, this overview surveys our present knowledge of the chemistry, nutrition, safety, microbiology, and pharmacology of DAAs. Also covered are the origin and distribution of DAAs in food and possible roles of DAAs in human physiology, aging, and the etiology and therapy of human diseases.
Solenoidal microcoil design. Part I: Optimizing RF homogeneity and coil dimensions (2001)

In Part I of this two part series, the spatial uniformity of the NMR response inside a solenoid-shaped transceiver coil is related to its dimensions, the size of the sample, and the type of radio frequency (RF) pulse sequence employed. The results establish practical guidelines for maximizing NMR sensitivity by defining minimum coil dimensions necessary for sufficient RF field homogeneity in common NMR experiments. In Part II, strategies for optimizing other coil parameters are developed by considering how the signal-to-noise ratio (SNR) is influenced by a solenoid's size, number of turns, wire diameter, and operating frequency, particularly when its minimum dimensions are fixed by RF homogeneity constraints. © 2001 John Wiley & Sons, Inc. Concepts Magn Reson 13: 128–142, 2001