gebhart/patrepeval huggingface dataset:
On the relationships between local vortex identification schemes (2005)

We analyse the currently popular vortex identification criteria that are based on point-wise analysis of the velocity gradient tensor. A new measure of spiralling compactness of material orbits in vortices is introduced and using this measure a new local vortex identification criterion and requirements for a vortex core are proposed. The inter-relationships between the different criteria are explored analytically and in a few flow examples, using both zero and non-zero thresholds for the identification parameter. These inter-relationships provide a new interpretation of the various criteria in terms of the local flow kinematics. A canonical turbulent flow example is studied, and it is observed that all the criteria, given the proposed usage of threshold, result in remarkably similar looking vortical structures. A unified interpretation based on local flow kinematics is offered for when similarity or differences can be expected in the vortical structures educed using the different criteria.
The v-sea oncogene of avian erythroblastosis retrovirus S13: another member of the protein-tyrosine kinase gene family. (1989)

The cloning and sequencing of the oncogene of the avian erythroblastosis virus S13 is described. The oncogene, termed v-sea, was found to be another member of the protein-tyrosine kinase gene family. The oncogene was fused in frame with the retrovirus S13 envelope gene, thus generating a fusion protein with a structure resembling that of a growth factor receptor. Sequence comparisons revealed that the v-sea gene was most closely related to the insulin receptor family of protein-tyrosine kinases, the greatest similarity being with the human MET oncogene.
Tau protein concentrations in cerebrospinal fluid of patients with dementia of the Alzheimer type. (1995)

Tau protein concentrations were measured in the CSF of 23 patients with dementia of the Alzheimer type (DAT), 36 patients with multi-infarct dementia (MID), and 23 control subjects. Tau protein concentrations were significantly higher in patients with DAT than in controls (P < 0.001) and patients with MID (P < 0.001). A significantly positive correlation between CSF tau protein and glucose concentrations (r = 0.79, P < 0.001) and evolution of disease (r = 0.47, P < 0.05), and a negative correlation with Folstein's mental state examination test (r = -0.73, P < 0.001) were found in patients with DAT.
Insight into the mechanism of the peptide-based gene delivery system MPG: implications for delivery of siRNA into mammalian cells (2003)

The improvement of non-viral-based gene delivery systems is of prime importance for the future of gene and antisense therapies. We have previously described a peptide-based gene delivery system, MPG, derived from the fusion peptide domain of HIV-1 gp41 protein and the nuclear localisation sequence (NLS) of SV40 large T antigen. MPG forms stable non-covalent complexes with nucleic acids and improves their delivery. In the present work, we have investigated the mechanism through which MPG promotes gene delivery. We demonstrate that cell entry is independent of the endosomal pathway and that the NLS of MPG is involved in both electrostatic interactions with DNA and nuclear targeting. MPG/DNA particles interact with the nuclear import machinery, however, a mutation which affects the NLS of MPG disrupts these interactions and prevents nuclear delivery of DNA. Nevertheless, we show that this mutation yields a variant of MPG which is a powerful tool for delivery of siRNA into mammalian cells, enabling rapid release of the siRNA into the cytoplasm and promoting robust down-regulation of target mRNA. Taken together, these results support the potential of MPG-like peptides for therapeutic applications and suggest that specific variations in the sequence may yield carriers with distinct targeting features.
Surface point mutations that significantly alter the structure and stability of a protein's denatured state (1996)

Significantly different m values (1.9-2.7 kcal mol-1 M-1) were observed for point mutations at a single, solvent-exposed site (T53) in a variant of the B1 domain of streptococcal Protein G using guanidine hydrochloride (GuHCl) as a denaturant. This report focuses on elucidating the energetic and structural implications of these m-value differences in two Protein G mutants, containing Ala and Thr at position 53. These two proteins are representative of the high (m+) and low (m-) m-value mutants studied. Differential scanning calorimetry revealed no evidence of equilibrium intermediates. A comparison of GuHCl denaturation monitored by fluorescence and circular dichroism showed that secondary and tertiary structure denatured concomitantly. The rates of folding (286 S-1 for the m+ mutant and 952 S-1 for the m- mutant) and the rates of unfolding (11 S-1 for m+ mutant and 3 S-1 for the m- mutant) were significantly different, as determined by stopped-flow fluorescence. The relative solvation free energies of the transition states were identical for the two proteins (alpha ++ = 0.3). Small-angle X-ray scattering showed that the radius of gyration of the denatured state (Rgd) of the m+ mutant did not change with increasing denaturant concentrations (Rgd approximately 23 A); whereas, the Rgd of the m- mutant increased from approximately 17 A to 23 A with increasing denaturant concentration. The results indicate that the mutations exert significant effects in both the native and GuHCl-induced denatured state of these two proteins.
Crystal Structure and Magnetic Properties of A One-Dimensional Polymer [Mn(im2-py)(tp)(H2O)2]·1.25H2O (2003)

A new manganese(II) complex [Mn(im2-py)(tp)(H2O)2]·1.25H2O (im2-py=2-(2'-pyridyl)-4,4,5,5-tetramethylimidazoline-1-oxyl and tp=terephthalato dianion) has been synthesized and characterized structurally and magnetically. The crystal structure consists of neutral chains of manganese(II) ions linked by the terephthalate ligand. Variable temperature magnetic susceptibility data exhibit a weak antiferromagnetic coupling between the manganese(II) ion and the imino nitroxide radical.
A 25-year experience with 519 anterior colporrhaphy procedures. (1991)

A 25-year experience with 519 anterior colporrhaphies was reviewed to assess the results in treating genuine and mixed stress urinary incontinence, the incidence of new urinary incontinence following prolapse surgery, the incidence of new detrusor instability after incontinence and prolapse surgery, and the morbidity associated with anterior colporrhaphy. The cure rate in treating genuine stress incontinence in 194 patients was increased from 75 to 94% when a Kelly-Kennedy-type technique was modified to include a vaginal retropubic urethropexy. The surgical cure in treating mixed incontinence was unsatisfactory (64%) in unselected cases but good (84%) in selected cases. Previous incontinence surgery, especially more than one procedure, significantly reduced the cure rate for genuine stress incontinence. The incidence of new incontinence after prolapse surgery in one subgroup of patients was 11%, indicating the need for measures to minimize this possibility at prolapse surgery. The incidence of new detrusor instability after surgery was 6% (higher after incontinence surgery than after prolapse surgery). The incidence of significant morbidity, excluding incontinence, was minimal (1%) among the 519 anterior colporrhaphies.
The C'-terminal interaction domain of the thyroid hormone receptor confers the ability of the DNA site to dictate positive or negative transcriptional activity. (1990)

To investigate mechanisms responsible for positive and negative transcriptional control, we have utilized two types of promoters that are differentially regulated by thyroid hormone (T3) receptors. Promoters containing the palindromic T3 response element TCAGGTCA TGACCTGA are positively regulated by the T3 receptor after the administration of T3, whereas otherwise identical promoters containing the estrogen response element TCAGGTCA CTG TGACCTGA can be regulated negatively; converse effects are observed with the estrogen receptor. We describe evidence that the transcriptional inhibitory effects of the T3 or estrogen receptors on the estrogen or T3 response elements, respectively, are imposed by amino acid sequences in the C'-terminal region that colocalize with dimerization and hormone-binding domains and that these sequences can transfer inhibitory functions to other classes of transcription factors. Removal of the C'-terminal dimerization and hormone-binding domains of either the alpha T3 or estrogen receptors permits each receptor to act constitutively to enhance transcription on both T3 and estrogen response elements. It is, therefore, suggested that protein-protein interactions between receptor C' termini limit the subset of DNA binding sites on which transcriptional activation occurs.
Acute microelectrode array implantation into human neocortex: preliminary technique and histological considerations (2006)

A high-density microelectrode array designed to function as a direct cortical interface device can be implanted into human cortical tissue without acute clinical complications. Further modifications to the insertion device and array design are ongoing and future work will assess the functional significance of the tissue reactions observed.
In vitro evaluation of c7E3-Fab (ReoPro™) eluting polymer-coated coronary stents (2000)

c7E3-Fab can be passively adsorbed onto polymer-coated stents. It elutes slowly and in a predictable manner, significantly inhibiting platelet deposition in vitro. These studies pave the way to developing stent-based delivery of a potent anti-platelet agent that may additionally affect smooth muscle cell activity.
Colony-Stimulating Factor-1 Receptor in the Polarization of Macrophages: A Target for Turning Bad to Good Ones? (2015)

Macrophages, which are found in all tissues, are an essential component of the innate immune system, and they play important roles in host defense, inflammation, autoimmune diseases as well as cancer. Functionally, macrophages are classified into two types: classically-activated M1 macrophages and alternatively-activated M2 macrophages. The M1 macrophages typically produce high levels of proinflammatory cytokines and chemokines, whereas M2 macrophages show an efficient phagocytic and scavenging activity. Because the phenotypes of polarized M1 and M2 macrophages can be induced, and reversed to some extent, by various signals, different phases of many diseases are associated with dynamic changes in the balance between M1 and M2 macrophages. The colony-stimulating factor 1 receptor (CSF-1R), a class III receptor tyrosine kinase, sustains the survival, proliferation and differentiation of monocytes and macrophages. Drugging CSF-1R may be the only way to target macrophages within a pathological context. However, CSF-1R-dependent signals may be either positive or detrimental depending on the disease and even on the phase of disease. The role of CSF-1R and its ligands, the colony-stimulating factor-1 and interleukin-34, in macrophages with respect to the pathogenesis of several inflammatory or neoplastic diseases has been reviewed previously. This review will focus specifically on evidences obtained about the role of CSF-1R in macrophage polarization in the context of physiological as well as pathological conditions including inflammation and cancer. The possibility to target CSF-1R, using the several inhibitors already available, for the treatment of inflammatory diseases as well as cancer will be also discussed.
Disruption of PPARγ/β-catenin–mediated regulation of apelin impairs BMP-induced mouse and human pulmonary arterial EC survival (2011)

Reduced bone morphogenetic protein receptor 2 (BMPR2) expression in patients with pulmonary arterial hypertension (PAH) can impair pulmonary arterial EC (PAEC) function. This can adversely affect EC survival and promote SMC proliferation. We hypothesized that interventions to normalize expression of genes that are targets of BMPR2 signaling could restore PAEC function and prevent or reverse PAH. Here we have characterized, in human PAECs, a BMPR2-mediated transcriptional complex between PPARγ and β-catenin and shown that disruption of this complex impaired BMP-mediated PAEC survival. Using whole genome-wide ChIP-Chip promoter analysis and gene expression microarrays, we delineated PPARγ/β-catenin-dependent transcription of target genes including APLN, which encodes apelin. We documented reduced PAEC expression of apelin in PAH patients versus controls. In cell culture experiments, we showed that apelin-deficient PAECs were prone to apoptosis and promoted pulmonary arterial SMC (PASMC) proliferation. Conversely, we established that apelin, like BMPR2 ligands, suppressed proliferation and induced apoptosis of PASMCs. Consistent with these functions, administration of apelin reversed PAH in mice with reduced production of apelin resulting from deletion of PPARγ in ECs. Taken together, our findings suggest that apelin could be effective in treating PAH by rescuing BMPR2 and PAEC dysfunction.
Limited value of positron emission tomography in treatment of pancreatic cancer: Surgeon’s view (2001)

We aimed to assess, from a surgical point of view, the value of positron emission tomography (PET) in the routine preoperative diagnostic evaluation of a pancreatic mass. In particular, we were interested in PET's ability to distinguish a malignancy from a nonmalignant process and its impact on surgical decision making. We documented prospectively the results of preoperative ultrasonography, computed tomography (CT), endoscopic retrograde cholangiopancreatography (ERCP), and PET in terms of a correct diagnosis of malignancy in 103 patients. All patients underwent surgery at our department and had a complete histologic workup. We then related the preoperative findings to the intraoperative and histologic findings and analyzed the advantages and limitations of PET in comparison with conventional diagnostic techniques. Both CT and PET showed high sensitivities (82% and 84%, respectively) but rather low specificities (61%). ERCP showed good specificity at 83% but weak sensitivity at 46%. The positive predictive value was higher than 80% for all methods, whereas the negative predictive value was around 60% at best. Both the CT and the PET diagnoses were wrong in 15% of the cases. In all cases with a false CT diagnosis, the results of the other conventional examinations provided sufficient evidence to indicate the need for surgical intervention. In all cases where PET gave misleading results, CT findings indicated the need for surgery. PET overlooked pT1 cancers in three of the patients. PET does not reliably prove or exclude malignancy in situations where conventional diagnostic procedures leave doubt as to the nature of a pancreatic mass. PET does introduce a new procedure-related spectrum of misinterpretations to the diagnostic process.
The Cellular Basis of Site-Specific Tumor Metastasis (1990)

THE year 1989 marked the 100th anniversary of the publication of a seminal paper in the study of the biology of human tumors. Stephen Paget, having collected the autopsy records of 735 patients who died of breast cancer, noted that the majority of the metastatic lesions were found in the liver and brain, whereas other organs, such as the kidney and spleen, were much less frequently involved. Paget inferred from this observation that certain tumors were predisposed to spread to particular tissues, on the basis of the tissue's ability to support the growth of these tumors.1 He likened this process . . .
Study of IL-2, IL-6, TNF alpha, IFN gamma and beta in the serum and synovial fluid of patients with juvenile chronic arthritis. (1995)

In the last few years the important role played by various cytokines in the pathogenesis of chronic inflammatory diseases has emerged. In the present study, serum and synovial fluid levels of IL-2, IL-6, TNF alpha, IFN beta and IFN gamma were evaluated in a group of 66 patients with juvenile chronic arthritis (JCA). At the same time the ESR, CRP, hemoglobin, immunoglobulins, platelet count and Ritchie index were measured. In the serum of pauciarticular patients, IL-6 and TNF alpha levels were only slightly elevated compared with controls, but there was no correlation between these cytokines and clinical and other laboratory parameters. Serum IL-2 and IFN gamma were undetectable. In contrast, in the synovial fluid IL-6 levels were very high in all of the patients examined and there was a significant correlation between synovial fluid IL-6 levels and Ritchie's articular index. TNF alpha tended to be elevated but to a lesser extent, while synovial fluid IL-2 and IFN gamma were undetectable or very low, as in the serum. In polyarticular and systemic patients, on the other hand, serum IL-6 was elevated and statistically correlated with the majority of the laboratory parameters and with the Ritchie articular index. TNF alpha levels were only slightly elevated; on the other hand, IL-2 and IFN gamma were undetectable. There was an inverse correlation between IFN beta levels and the Ritchie articular index and a significant correlation with hemoglobin levels. In conclusion, our study demonstrates that not only IL-1 (as shown in other studies), but also IL-6 and to a lesser extent TNF alpha play a central role in the pathogenesis of JCA. IFN beta on the other hand, would seem to play an anti-inflammatory role.
Solid-Phase Synthesis of 2-[18F]Fluoropropionyl Peptides (2006)

The 2-[(18)F]fluoropropionic (2-[(18)F]FPA) acid is used as a prosthetic group for radiolabeling proteins and peptides for targeted imaging using positron emission tomography (PET). Radiolabeling of compounds with more than one acylable functional group can lead to complex mixtures of products; however, peptides can be labeled regioselectively on the solid phase. We investigated the use of a solid-phase approach for the preparation of 2-[(18)F]fluoropropionyl peptides. [(18)F]FPA was prepared and conjugated to the peptides attached to the solid phase support. The (18)F-labeled peptides were obtained in 175 min with decay corrected yields of 10% (related to [(18)F]fluoride) and with a purity of 76-99% prior HPLC purification. The suitability of various coupling reagents and solid supports were tested for radiolabeling of several peptides of various lengths.
Photochemistry of intercalated methylene blue: photoinduced hydrogen atom abstraction from guanine and adenine (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemistry of intercalated methylene blue: photoinduced hydrogen atom abstraction from guanine and adenineStephen J. Atherton and Anthony HarrimanCite this: J. Am. Chem. Soc. 1993, 115, 5, 1816–1822Publication Date (Print):March 1, 1993Publication History Published online1 May 2002Published inissue 1 March 1993https://doi.org/10.1021/ja00058a028RIGHTS & PERMISSIONSArticle Views1003Altmetric-Citations116LEARN 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 InReddit PDF (930 KB) Get e-Alerts Get e-Alerts
Case-Based Reasoning: Foundational Issues, Methodological Variations, and System Approaches (1994)

Case-based reasoning is a recent approach to problem solving and learning that has got a lot of attention over the last few years. Originating in the US, the basic idea and underlying theories have spread to other continents, and we are now within a
Generating mouse models of degenerative diseases using Cre/lox-mediated in vivo mosaic cell ablation (2011)

Most degenerative diseases begin with a gradual loss of specific cell types before reaching a threshold for symptomatic onset. However, the endogenous regenerative capacities of different tissues are difficult to study, because of the limitations of models for early stages of cell loss. Therefore, we generated a transgenic mouse line (Mos-iCsp3) in which a lox-mismatched Cre/lox cassette can be activated to produce a drug-regulated dimerizable caspase-3. Tissue-restricted Cre expression yielded stochastic Casp3 expression, randomly ablating a subset of specific cell types in a defined domain. The limited and mosaic cell loss led to distinct responses in 3 different tissues targeted using respective Cre mice: reversible, impaired glucose tolerance with normoglycemia in pancreatic β cells; wound healing and irreversible hair loss in the skin; and permanent moderate deafness due to the loss of auditory hair cells in the inner ear. These mice will be important for assessing the repair capacities of tissues and the potential effectiveness of new regenerative therapies.
The C-S lysis of L-cysteine conjugates by aspartate and alanine aminotransferase enzymes (1995)

One biotransformation pathway which is responsible for the generation of mutagenic and cytotoxic metabolites is that of the C-S lysis (CSL) of L-cysteine conjugates. Thirteen cysteine S-conjugates, synthesised in our laboratories, were incubated with porcine heart aspartate aminotransferase (ASAT) and alanine aminotransferase (ALAT), and the C-S lyase activity for each enzyme-substrate combination was determined. ASAT and ALAT were shown to exhibit CSL activity. It was also demonstrated that this activity was inhibited in the presence of the pyridoxal phosphate (PLP)-dependent enzyme inhibitor amino(oxyacetic acid) (AOAA) confirming the pyridoxal phosphate dependent mechanism by which C-S lysis is known to take place. Since the activities of these enzymes are used as biomarkers for the assessment of organ damage, the potential interaction of L-cysteine conjugates with them may suppress their activity through direct inhibition.
Generating ∼90 nanometer features using near-field contact-mode photolithography with an elastomeric phase mask (1998)

This article describes a near-field photolithographic method that uses an elastomeric phase mask in conformal contact with photoresist. The method is capable of generating ∼90 nm lines in commercially available photoresist, using broadband, incoherent light with wavelengths between 330 and 460 nm. Transfer of these patterns into silicon dioxide and gold demonstrates the integrity of the patterned resist.