gebhart/patrepeval huggingface dataset:
Phylogenetic analysis of the three polymerase genes (PB1, PB2 and PA) of influenza B virus (2000)

Phylogenetic patterns of the three polymerase (PB2, PB1 and PA) genes of a total of 20 influenza B viruses isolated during a 58 year period, 1940-1998, were analysed in detail in a parallel manner. All three polymerase genes consistently showed evolutionary divergence into two major distinct lineages and their amino acid profiles demonstrated conserved lineage-specific substitutions. Dendrogram topologies of the PB2 and PB1 genes were very similar and contrasted with that of the PA gene. It was of particular interest to reveal that even though the PA gene evolved into two major lineages, that of three recent Asian Victoria/1/87-like strains formed a branch cluster located in the same lineage as that of recent Yamagata/16/88-like isolates. Differences in the phylogenetic pathways of three polymerase genes were not only a reflection of genetic reassortment between co-circulating influenza B viruses, but also an indication that the polymerase genes were not co-evolving as a unit. As a result, comparison of the phylogenetic patterns of the three polymerase genes with previously determined patterns of the HA, NP, M and NS genes of 18 viruses defined the existence of eight distinct genome constellations. Also, similar phylogenetic profiles among the PA, NP and M genes, as well as between the PB2 and PB1 genes, were observed, suggesting possible functional interactions among these proteins. Completion of evolutionary analysis of the six internal genes and the HA gene of influenza B viruses revealed frequent genetic reassortment among co-circulating variable strains and suggested co-dependent evolution of genes.
The mouse skin carcinogenesis model. (1996)

Skin carcinogenesis can be divided into at least three major stages: initiation, promotion, and progression. In the mouse skin model, the first stage is thought to involve the interaction of a tumor initiator with the genetic material of stem cells, leading to an irreversible alteration in growth control or differentiation, probably by activation of the Ha-ras oncogene. The major effect of all skin-tumor promoters seems to be the specific expansion of the initiated stem cells. The correlation between the abilities of tumor promoters to induce sustained hyperplasia and their tumor-promoting activities is very good. We found that the appearance of alpha-glutamyl transpeptidase (GGT) and keratin 13 and the lack of expression of keratins 1 and 10 are good markers for skin tumor progression. These alterations occur when papillomas change from a diploid to an aneuploid state, mainly as a result of developing trisomies 6 and 7. To evaluate the role of GGT in skin-tumor progression, we transfected a functional GGT cDNA into two cell lines that normally produce papillomas when grafted into the skin of nude mice. When injected subcutaneously, all of the GGT-transfected clones formed malignant tumors, whereas only 24% of vector-transfected cells did. When GGT-transfected clones were placed into grafts, the grafts had an average mass almost three times that of grafts of vector-transfected cells. Our recent studies also suggest that the ribonucleoprotein telomerase and the gap-junctional proteins connexins (Cxs) are also important in skin-tumor progression. A progressive increase in telomerase activity was associated with the increased level of genomic instability during tumor progression. In addition, the level and expression of Cx26, Cx43, and Cx31.1 were significantly altered during skin tumor promotion and progression. The differences of various mouse stocks and strains in susceptibility to multistage skin carcinogenesis seem to be related more to alterations in tumor promotion than to tumor initiation; however, the critical events have not been determined. Results with an inbred strain of SENCAR mice, which are very sensitive to papilloma formation by the two-stage protocol, also suggest that susceptibility is related to promotion. Despite the high incidence of papillomas in these inbred SENCAR mice, the number of malignant tumors was extremely low, suggesting that sensitivity to promotion and progression are independent in these mice.
Differential Expression of TGF-β1, 2 and 3 Isotypes in Alzheimerʼs Disease: A Comparative Immunohistochemical Study with Cerebral Infarction, Aged Human and Mouse Control Brains (1995)

Based upon the hypothesis that growth regulatory and inflammatory mechanisms participate in the pathogenesis of Alzheimer's disease, we studied cases of Alzheimer's disease for immunoreactivity to each of the three mammalian transforming growth factor beta (TGF-beta) isotypes: TGF-beta 1, TGF-beta 2, TGF-beta 3. Results were compared with those seen in control brains and in a destructive pathological process, subacute infarction. In the cases of Alzheimer's disease, TGF-beta 1 immunoreactivity was limited to neuritic profiles within senile plaques. Neuronal neurofibrillary tangles, plaque neurites, microglia, astrocytes and macrophages expressed TGF-beta 2 immunoreactivity. TGF-beta 3 produced strikingly selective staining of Hirano bodies. In contrast, in cases with infarction, reactive astrocytes and macrophages were positive with all three antibodies. Ramified microglia labeled selectively, as in the Alzheimer brains, with the TGF-beta 2 antibody. Subtle generalized astrocyte and microglial immunoreactivity for TGF-beta 2 was seen in pathological and control brains. The localization of TGF-beta isotypes to the lesions of Alzheimer's disease supports the hypothesis that these cytokines may influence lesion expression. Their presence in reactive cells associated with cerebral infarction suggest that they may play a broader role in the pathogenesis of CNS disease.
Specific c-kit mutations in sinonasal natural killer/T-cell lymphoma in China and Japan. (2000)

Sinonasal lymphoma is one of the constituents of lethal midline granuloma, which is a clinical term for progressive, destructive lesions affecting the midline of the face. The majority of sinonasal lymphomas, especially those showing polymorphous patterns of proliferation and thus termed polymorphic reticulosis, recently were categorized as sinonasal natural killer/T-cell lymphomas. They are more prevalent in Asia than Europe or North America and are associated with EBV infection. Twenty-three cases with sinonasal natural killer/T-cell lymphomas were collected from two high-incidence regions: Beijing, China (14 cases) and Osaka, Japan (9 cases). c-kit mutations were analyzed on paraffin-embedded specimens by PCR-single-strand conformation polymorphism followed by direct sequencing; the c-kit proto-oncogene encodes a receptor of tyrosine kinase, which plays an important role in the regulation of normal and neoplastic hematopoiesis by the interaction with its specific ligand, termed stem cell factor. Twelve single nucleotide substitution mutations were seen in 23 cases. Ten of 14 Chinese cases (71.4%) had mutations at exon 11 or exon 17, whereas only two of nine Japanese cases (22.2%) had mutations, showing a significant difference in frequency between Chinese and Japanese cases. Furthermore, seven of eight mutations (92%) in exon 17 occurred at codon 825 and three of four mutations (75%) in exon 11 occurred at codon 561. Such a specificity has not been reported before, and these results, taken together, suggest that location-specific differences in etiological factors cause specific mutations in c-kit gene.
Perplexity minimization for translation model domain adaptation in statistical machine translation (2012)

We investigate the problem of domain adaptation for parallel data in Statistical Machine Translation (SMT). While techniques for domain adaptation of monolingual data can be borrowed for parallel data, we explore conceptual differences between translation model and language model domain adaptation and their effect on performance, such as the fact that translation models typically consist of several features that have different characteristics and can be optimized separately. We also explore adapting multiple (4–10) data sets with no a priori distinction between in-domain and out-of-domain data except for an in-domain development set.
Role of PDGF-B and PDGFR-β in recruitment of vascular smooth muscle cells and pericytes during embryonic blood vessel formation in the mouse (1999)

Development of a vascular system involves the assembly of two principal cell types - endothelial cells and vascular smooth muscle cells/pericytes (vSMC/PC) - into many different types of blood vessels. Most, if not all, vessels begin as endothelial tubes that subsequently acquire a vSMC/PC coating. We have previously shown that PDGF-B is critically involved in the recruitment of pericytes to brain capillaries and to the kidney glomerular capillary tuft. Here, we used desmin and alpha-smooth muscle actin (ASMA) as markers to analyze vSMC/PC development in PDGF-B-/- and PDGFR-beta-/- embryos. Both mutants showed a site-specific reduction of desmin-positive pericytes and ASMA-positive vSMC. We found that endothelial expression of PDGF-B was restricted to immature capillary endothelial cells and to the endothelium of growing arteries. BrdU labeling showed that PDGFR-beta-positive vSMC/PC progenitors normally proliferate at sites of endothelial PDGF-B expression. In PDGF-B-/- embryos, limb arterial vSMC showed a reduced BrdU-labeling index. This suggests a role of PDGF-B in vSMC/PC cell proliferation during vascular growth. Two modes of vSMC recruitment to newly formed vessels have previously been suggested: (1) de novo formation of vSMC by induction of undifferentiated perivascular mesenchymal cells, and (2) co-migration of vSMC from a preexisting pool of vSMC. Our data support both modes of vSMC/PC development and lead to a model in which PDGFR-beta-positive vSMC/PC progenitors initially form around certain vessels by PDGF-B-independent induction. Subsequent angiogenic sprouting and vessel enlargement involves PDGF-B-dependent vSMC/PC progenitor co-migration and proliferation, and/or PDGF-B-independent new induction of vSMC/PC, depending on tissue context.
PD-1–PD-1 ligand interaction contributes to immunosuppressive microenvironment of Hodgkin lymphoma (2008)

Programmed death-1 (PD-1)-PD-1 ligand (PD-L) signaling system is involved in the functional impairment of T cells such as in chronic viral infection or tumor immune evasion. We examined PD-L expression in lymphoid cell lines and found that they were up-regulated on Hodgkin lymphoma (HL) and several T-cell lymphomas but not on B-cell lymphomas. PD-L expression was also demonstrated in primary Hodgkin/Reed-Sternberg (H/RS) cells. On the other hand, PD-1 was elevated markedly in tumor-infiltrating T cells of HL, and was high in the peripheral T cells of HL patients as well. Blockade of the PD-1 signaling pathway inhibited SHP-2 phosphorylation and restored the IFN-gamma-producing function of HL-infiltrating T cells. According to these results, deficient cellular immunity observed in HL patients can be explained by "T-cell exhaustion," which is led by the activation of PD-1-PD-L signaling pathway. Our finding provides a potentially effective immunologic strategy for the treatment of HL.
Impaired signaling via the high-affinity IgE receptor in Wiskott-Aldrich syndrome protein-deficient mast cells (2003)

Wiskott-Aldrich syndrome protein (WASP) is the product of the gene deficient in boys with X-linked Wiskott-Aldrich syndrome. We assessed the role of WASP in signaling through the high-affinity IgE receptor (FcepsilonRI) using WASP-deficient mice. IgE-dependent degranulation and cytokine secretion were markedly diminished in bone marrow-derived mast cells from WASP-deficient mice. Upstream signaling events that include FcepsilonRI-triggered total protein tyrosine phosphorylation, and protein tyrosine phosphorylation of FcepsilonRIbeta and Syk were not affected by WASP deficiency. However, tyrosine phosphorylation of phospholipase Cgamma and Ca(2+) mobilization were diminished. IgE-dependent activation of c-Jun N-terminal kinase, cell spreading and redistribution of cellular F-actin in mast cells were reduced in the absence of WASP. We conclude that WASP regulates FcepsilonRI-mediated granule exocytosis, cytokine production and cytoskeletal changes in mast cells.
The effect of baseband impedance termination on the linearity of GaN HEMTs (2010)

This paper demonstrates the significant effect of baseband impedance termination on the linearity performance of a 10W GaN HEMT device driven to deliver a peak envelope power of approximately 40dBm. The paper also proposes a further refinement to a state-of-art active IF load-pull measurement system to allow the precise independent control of all significant baseband components generated as a result of the multi-tone excitation used. The presentation of specific baseband impedances has delivered a 20dBc and 17dBc improvement in IM<inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> and IM<inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> inter-modulation products respectively, relative to the case of a classical, ideal short circuit. As expected for this device, this was achieved by emulating appropriate negative impedances lying outside of the Smith chart, and when this observation is considered alongside the Envelope Tracking PA architecture, this raises the interesting possibility of significantly improving PA linearity using the very mechanisms that are employed to improve PA efficiency.
Silicon Evanescent Racetrack Laser (2007)

We describe the utilization of hybrid silicon evanescent waveguides, consisting of III-V quantum wells bonded to silicon rib-waveguides for evanescently coupled gain, to achieve an on-chip racetrack laser integrated with photodetectors on a silicon platform.
Magnetic field and tissue dependencies of human brain longitudinal 1H2O relaxation in vivo (2007)

Brain water proton (1H2O) longitudinal relaxation time constants (T1) were obtained from three healthy individuals at magnetic field strengths (B0) of 0.2 Tesla (T), 1.0T, 1.5T, 4.0T, and 7.0T. A 5-mm midventricular axial slice was sampled using a modified Look-Locker technique with 1.5 mm in-plane resolution, and 32 time points post-adiabatic inversion. The results confirmed that for most brain tissues, T1 values increased by more than a factor of 3 between 0.2T and 7T, and over this range were well fitted by T1 (s)=0.583(B0)0.382, T1(s)=0.857(B0)0.376, and T1(s)=1.35(B0)0.340 for white matter (WM), internal GM, and blood 1H2O, respectively. The ventricular cerebrospinal fluid (CSF) 1H2O T1 value did not change with B0, and its average value (standard deviation (SD)) across subjects and magnetic fields was 4.3 (+/-0.2) s. The tissue 1/T1 values at each field were well correlated with the macromolecular mass fraction, and to a lesser extent tissue iron content. The field-dependent increases in 1H2O T1 values more than offset the well-known decrease in typical MRI contrast reagent (CR) relaxivity, and simulations predict that this leads to lower CR concentration detection thresholds with increased magnetic field.
Planar Geometric Projections and Viewing Transformations (1978)

article Free Access Share on Planar Geometric Projections and Viewing Transformations Authors: Ingrid Carlbom Program in Computer Science, Brown University, Providence, Rhode Island Program in Computer Science, Brown University, Providence, Rhode IslandView Profile , Joseph Paciorek Computervision Corporation, Bedford, Massachusetts Computervision Corporation, Bedford, MassachusettsView Profile Authors Info & Claims ACM Computing SurveysVolume 10Issue 4Dec. 1978 pp 465–502https://doi.org/10.1145/356744.356750Published:01 December 1978Publication History 113citation3,664DownloadsMetricsTotal Citations113Total Downloads3,664Last 12 Months199Last 6 weeks39 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Design of symmetric‐sweep spectral‐spatial RF pulses for spectral editing (2004)

Spectral-spatial RF (SSRF) pulses allow simultaneous selection in both frequency and spatial domains. These pulses are particularly important for clinical and research MR spectroscopy (MRS) applications for suppression of large water and lipid resonances. Also, the high bandwidth of the subpulses (5-10 kHz) greatly reduces the spatial-shift errors associated with different chemical shifts. However, the use of high-bandwidth subpulses along with enough spectral bandwidth to measure a typical range of metabolite frequencies (e.g., 300 Hz at 3 T) can require RF amplitudes beyond the limits of the RF amplifier of a typical scanner. In this article, a new method is described for designing nonlinear-phase 180 degrees SSRF pulses that can be used for spectral editing. The novel feature of the pulses is that the spectral profile develops as a symmetric sweep, from the outside edges of the spectral window towards the middle, so that coupled components are tipped simultaneously and over a short interval. Pulses were designed for lactate editing at 1.5 T and 3 T. The spectral and spatial spin-echo profiles of the new pulses were measured experimentally. Spectra acquired in phantom experiments showed a well-resolved, edited lactate doublet, with 91% to 93% editing efficiency.
Loss of EphB6 expression in metastatic melanoma (2003)

Overexpression of various members of the Eph receptor tyrosine kinases and their ephrin ligands has been frequently reported in cancer. In contrast, a loss of EphB6 gene expression has been correlated with a poor prognosis in human neuroblastoma, suggesting a distinct role for this receptor compared to other family members. More recently, an important role of EphB6 signalling in T-cells has been described, suggesting possibly deleterious immunologic effects of a loss of EphB6 in cancer progression. We investigated the expression of EphB6 in melanocytic tumors. EphB6 mRNA of 22 microdissected tissues (7 benign nevi, 7 melanomas, 8 metastases) and 10 different cell lines (normal melanocytes, non-metastatic/metastatic melanoma cell lines) were measured by quantitative real-time RT-PCR. For visualization of EphB6 protein expression, immunohistochemistry of 32 melanocytic lesions were performed. On the mRNA level, the benign nevi revealed the highest EphB6 expression (mean = 1.43), while melanomas (mean = 0.63) and metastases (mean = 0.08; p=0.001) displayed a progressive and significant reduction of EphB6 expression. Accordingly, established melanoma cell lines with metastatic potential showed low EphB6 expression in comparison to normal melanocytes and to most of the melanoma cell lines. Immunohistochemistry revealed homogeneous staining in common nevi, whereas in malignant melanomas and metastases a heterogeneously positive to completely negative EphB6 staining was observed. Remarkably, Spitz nevi stained similarly to ordinary melanocytic nevi. Taken together, we show that melanoma progression to metastatic disease is associated with a significant reduction of EphB6 gene expression which may have considerable consequences for the prognosis of malignant melanoma patients and possible gene-therapeutic approaches.
Utility of WT‐1, p63, MOC31, mesothelin, and cytokeratin (K903 and CK5/6) immunostains in differentiating adenocarcinoma, squamous cell carcinoma, and malignant mesothelioma in effusions (2007)

To distinguish carcinoma, either adenocarcinoma (ADC) or squamous cell carcinoma (SCC), and malignant mesothelioma (MM) in effusion can be a diagnostic challenge based on morphology alone. This study evaluates the utility of WT-1, p63, MOC31, mesothelin, and cytokeratin (K903 and CK5/6) immunostains in effusions when ADC and SCC of the lung are in the differential diagnosis with MM. A cohort of 43 effusions consisting of lung ADC (N = 10), SCC (N = 15), and MM (N = 18, mostly (16) pleural based), was subjected to immunostains using the above mentioned antibodies. WT-1 was positive in 100% MM, 0% ADC, and 0% SCC cases while p63 was positive in 0% MM, 30% ADC, and 80% SCC cases. Stain for MOC31 was positive in 100% ADC, 67% SCC, and 35% MM cases. Similarly, mesothelin antibody stained 100% ADC, 60% SCC, and 47% MM cases. Antibodies for K903 and CK5/6 stained 100% SCC cases but fewer ADC cases (40 and 10%, respectively). In conclusion, in this cohort of mostly pleural malignant effusion, MM can be identified with positive staining for WT-1 and negative staining for p63. Conversely, negative staining with WT-1 and positive staining for p63 exclude MM. Used as part of an immunostain panel, cytokeratin markers (CK5/6 and K903) are useful in differentiating SCC from ADC when MM is already excluded, and MOC31 might have limited value in differentiating ADC from MM. A negative stain with MOC31 can exclude lung ADC. Mesothelin, on the other hand, is not useful in the differential diagnosis of ADC, SCC, and MM.
Fiber optic chemical sensors (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFiber optic chemical sensorsMark A. ArnoldCite this: Anal. Chem. 1992, 64, 21, 1015A–1025APublication Date (Print):November 1, 1992Publication History Published online22 September 2008Published inissue 1 November 1992https://pubs.acs.org/doi/10.1021/ac00045a001https://doi.org/10.1021/ac00045a001research-articleACS PublicationsRequest reuse permissionsArticle Views752Altmetric-Citations41LEARN 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
Acceleration of Integra Incorporation in Complex Tissue Defects with Subatmospheric Pressure (2004)

In an effort to accelerate vascularization and simplify the care of Integra (Ethicon, Inc., Somerville, N.J.), topical subatmospheric pressure was used for eight patients (age range, 2 to 60 years) with complex wounds. Bone was exposed in 62.5 percent of cases, joint in 50 percent, tendon in 37.5 percent, and bowel in 25 percent. The estimated Integra take rate was 96 percent. Split-thickness skin grafting was performed at 4 to 11 days (mean, 7.25 days), with a 93 percent take rate. No adverse side effects were observed with this technique. Application of subatmospheric pressure improved the take rate and time to vascularization of Integra, compared with previous published results, even with complicated wounds. This technique may be a practical alternative to flap closure.