gebhart/patrepeval huggingface dataset:
T-cell growth factor: complete nucleotide sequence and organization of the gene in normal and malignant cells. (1984)

Using a cloned cDNA copy of T-cell growth factor (TCGF) mRNA from the Jurkat leukemic T-cell line, we have isolated three overlapping TCGF genomic clones from a human DNA library. The entire TCGF gene is contained within two adjacent EcoRI fragments spanning about 8 kilobases. The complete nucleic acid sequence was determined. The gene is divided into four exons. The 5' untranslated region and the first 49 amino acids of the protein, 20 of which constitute a signal polypeptide and are not present in the secreted protein, are encoded by the first exon. Exons 2 and 3, separated from each other by a long intervening sequence, contain coding information for the next 20 and 48 amino acids, respectively. The remaining 36 amino acids and the 3' untranslated region are contained in the fourth exon. A promoter sequence T-A-T-A-A-A is present 77 base pairs (bp) upstream from the translation initiation site, and a CAT homology region occurs 104 bp upstream from the initiation site. A putative site for initiation of mRNA transcription was identified 53 bp 5' of the translation initiation codon. The organization of the gene was shown by Southern blot analysis to be identical in normal peripheral blood lymphocytes and in a variety of malignant lymphoid cell types. Restriction analysis of these cellular DNAs produced results exactly as predicted by the map for the cloned genomic TCGF, indicating that there is only a single copy of the human TCGF gene.
TurboPixels: Fast Superpixels Using Geometric Flows (2009)

We describe a geometric-flow-based algorithm for computing a dense oversegmentation of an image, often referred to as superpixels. It produces segments that, on one hand, respect local image boundaries, while, on the other hand, limiting undersegmentation through a compactness constraint. It is very fast, with complexity that is approximately linear in image size, and can be applied to megapixel sized images with high superpixel densities in a matter of minutes. We show qualitative demonstrations of high-quality results on several complex images. The Berkeley database is used to quantitatively compare its performance to a number of oversegmentation algorithms, showing that it yields less undersegmentation than algorithms that lack a compactness constraint while offering a significant speedup over N-cuts, which does enforce compactness.
Multiple-stage microfabricated preconcentrator-focuser for micro gas chromatography system (2005)

The design, fabrication, and characterization of a multiple-stage Si microfabricated preconcentrator-focuser (/spl mu/PCF) for a micro gas chromatography (/spl mu/GC) system that can provide real-time quantification and identification of complex organic vapor mixtures are presented. The /spl mu/PCF consists of a Si microheater loaded with Carbopack B, Carbopack X, and Carboxen 1000 carbon adsorbent granules, and a Si micromachined cover plate. Deep reactive ion etching is utilized to produce mechanically robust fluidic interconnection adapters hermetically sealed to fused silica capillary tubing for connection to the other components in the /spl mu/GC. This three-stage device is designed to capture compounds spanning up to 4 orders of magnitude in volatility. The dead volume, thermal mass, heating efficiency, and pressure drop of the three-stage /spl mu/PCF are improved significantly over its single-stage /spl mu/PCF predecessor. We demonstrate the successful capture, desorption, and high-resolution chromatographic separation of a mixture of 30 common organic vapors using our three-stage /spl mu/PCF in a conventional GC system. The peak width at half height is <2.05 s for all compounds after elution from the GC column.
Elastic moduli of normal and pathological human breast tissues: an inversion-technique-based investigation of 169 samples (2007)

Understanding and quantifying the mechanical properties of breast tissues has been a subject of interest for the past two decades. This has been motivated in part by interest in modelling soft tissue response for surgery planning and virtual-reality-based surgical training. Interpreting elastography images for diagnostic purposes also requires a sound understanding of normal and pathological tissue mechanical properties. Reliable data on tissue elastic properties are very limited and those which are available tend to be inconsistent, in part as a result of measurement methodology. We have developed specialized techniques to measure tissue elasticity of breast normal tissues and tumour specimens and applied them to 169 fresh ex vivo breast tissue samples including fat and fibroglandular tissue as well as a range of benign and malignant breast tumour types. Results show that, under small deformation conditions, the elastic modulus of normal breast fat and fibroglandular tissues are similar while fibroadenomas were approximately twice the stiffness. Fibrocystic disease and malignant tumours exhibited a 3–6-fold increased stiffness with high-grade invasive ductal carcinoma exhibiting up to a 13-fold increase in stiffness compared to fibrogalndular tissue. A statistical analysis showed that differences between the elastic modulus of the majority of those tissues were statistically significant. Implications for the specificity advantages of elastography are reviewed.
Human telomerase RNA and telomerase activity in immortal cell lines and tumor tissues. (1996)

Telomerase activity has been detected in many human immortal cells lines and in tumor tissues, whereas it is generally absent from primary cell strains and from many tumor adjacent tissue samples. With the recently cloned human telomerase RNA (hTR), we used Northern analysis to follow the levels of hTR in primary, precrisis, and immortalized cells. It was surprising that the amount of hTR was high in cell strains that lacked telomerase activity, and the levels did not parallel the increases in telomerase activity, which accompanies immortalization. In addition, although the hTR levels were somewhat higher in tumor samples compared to nontumor tissues, the level of hTR in a variety of different human tumors did not predict the level of telomerase activity in the tumor. Thus, whereas hTR was detected in all samples that have telomerase activity, the presence of the RNA was not a good predictor of the presence or amount of telomerase activity.
Bioinspired Carbon Nanotube Fuzzy Fiber Hair Sensor for Air‐Flow Detection (2014)

Artificial hair sensors consisting of a piezoresistive carbon-nanotube-coated glass fiber embedded in a microcapillary are assembled and characterized. Individual sensors resemble a hair plug that may be integrated in a wide range of host materials. The sensors demonstrate an air-flow detection threshold of less than 1 m/s with a piezoresistive sensitivity of 1.3% per m/s air-flow change.
Aptamers Selected by Cell-SELEX for Application in Cancer Studies (2010)

Rapid development of anticancer therapies has occurred, but many challenges remain, including difficulties in early detection and the side effects from chemotherapy. To address these problems, aptamers, which are single-stranded DNA or RNA oligonucleotides with high selectivity, affinity and stability, have attracted considerable attention for biomedical applications. These oligonucleotides, which are selected by an in vitro process known as cell systematic evolution of ligands by exponential enrichment (cell-SELEX), have demonstrated the merits required to recognize disease cells. As such, they show great potential for applications in both clinical and laboratory settings. This review focuses on recently developed techniques utilizing aptamers in cancer research, including cancer cell detection, sorting and enrichment, as well as targeted drug delivery for cancer therapy.
Theoretical Aspects of Microwave Dielectric Heating (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Apoptosis and Heart Failure (1999)

Programmed cell death (apoptosis) was unknown to William Osler and Paul Dudley White, but physicians today must grapple with the uneasy knowledge that all of our cells actively maintain the machinery of self-destruction and must continuously hold it in check to avoid that fate.Apoptosis was first observed as a driving force that shapes the structure of tissues during embryonic development. A familiar example is the separation of the digits of our hands and feet from the blunt ends of the fetal limbs. Today, we also recognize apoptosis as a mechanism whereby damaged cells are removed from the body during . . .
Activation of Endothelium byBorrelia burgdorferiIn Vitro Enhances Transmigration of Specific Subsets of T Lymphocytes (2001)

Lyme disease, caused by Borrelia burgdorferi, is characterized by the accumulation of lymphocytes and monocytes in the affected tissue. Endothelial cells line the blood vessel walls and control the trafficking of inflammatory leukocytes from the blood into the surrounding tissues. A model of the blood vessel wall, consisting of human umbilical vein endothelial cells (HUVEC) grown on amniotic connective tissue, was utilized to examine the effects of B. burgdorferi on the transendothelial migration of T lymphocytes. Maximal migration occurred when the HUVEC-amnion cultures were preincubated with B. burgdorferi for 24 h and T lymphocytes were added for an additional 4 h, yielding a two- to fourfold increase compared to migration across unstimulated cultures. The number of T lymphocytes that migrated was proportional to the number added. The anti-inflammatory cytokine interleukin 10 (IL-10), added during activation of the HUVEC, significantly diminished (by an average of 70% +/- 21%) the migration of T lymphocytes across endothelium stimulated for 8 or 24 h with B. burgdorferi, but not IL-1. Compared to the initially added population of T lymphocytes, the population that migrated across untreated endothelium or HUVEC activated with B. burgdorferi or IL-1 contained a significantly smaller percentage of CD45RA+RO- (naïve) cells and a greater proportion of CD45RA+RO+ cells. The migratory population was also enriched for CD8+ T lymphocytes when the endothelium was incubated with either control medium or B. burgdorferi, but not IL-1. B. burgdorferi thus activates endothelium in a manner that promotes the transmigration of T lymphocytes, and IL-10 inhibits this activation. These data further suggest that endothelium plays an active role in promoting the recruitment of specific subpopulations of T lymphocytes.
Cortactin potentiates bone metastasis of breast cancer cells. (2001)

Gene amplification of the chromosome 11q13 in breast cancer and squamous carcinomas in the head and neck results in frequent overexpression of cortactin, a prominent substrate of Src-related tyrosine kinases in the cell cortical areas. To investigate the role of cortactin in tumor progression, we analyzed MDA-MB-231 breast cancer cells overexpressing green fluorescent protein-tagged murine cortactin (GFP-cortactin) and a cortactin mutant deficient in tyrosine phosphorylation under the control of a retroviral vector. Injection of MDA-MB-231 cells overexpressing GFP-cortactin into nude mice through cardiac ventricles caused bone osteolysis at a frequency approximately 85% higher than that of cells expressing the vector alone, whereas injection of cells overexpressing the mutant deficient in tyrosine phosphorylation induced 74% fewer osteolytic metastases as compared with the control group. Interestingly, the cells expressing either GFP-cortactin or the mutant did not show significant differences in growth in vitro or when injected m.f.p. in vivo. On the other hand, the cells overexpressing GFP-cortactin but not the mutant acquired a >60% enhanced capability for transendothelial invasion and endothelial cell adhesion. These data suggest that cortactin contributes to tumor metastasis by enhancing the interaction of tumor cells with endothelial cells and the invasion of tumor cells into bone tissues.
Identification of minimal sequences of the Rhopalosiphum padi virus 5′ untranslated region required for internal initiation of protein synthesis in mammalian, plant and insect translation systems (2007)

Rhopalosiphum padi virus (RhPV) is a member of the family Dicistroviridae. The genomes of viruses in this family contain two open reading frames, each preceded by distinct internal ribosome entry site (IRES) elements. The RhPV 5' IRES is functional in mammalian, insect and plant translation systems and can form 48S initiation complexes in vitro with just the mammalian initiation factors eIF2, eIF3 and eIF1. Large regions of the 5' untranslated region (UTR) can be deleted without affecting initiation-complex formation. The minimal sequences required for directing internal initiation in mammalian (rabbit reticulocyte lysate), plant (wheatgerm extract) and insect (Sf21 cells) translation systems have now been defined. A fragment (nt 426-579) from the 3' portion of the 5' UTR can direct translation in each of these translation systems. In addition, a distinct region (nt 300-429) is also active. Thus, unstructured regions within the 5' UTR seem to be critical for IRES function.
Cell multiplexing in ATM networks (1996)

Formulates, analyzes, and compares several connection multiplexing algorithms for a multiplexer residing in the equivalent terminal of the asynchronous transfer mode (ATM) layer at the user premise. The primary goal is to find an algorithm that efficiently combats the cell delay variation (CDV) introduced by the multiplexer. Several performance criteria are examined, one of which is unique to ATM networks. This one is the proportion of arriving cells that do not conform to the traffic contract of the connection. The conformance is being tracked by a generic cell rate algorithm (GCRA) recommended (but not mandatory) by CCITT. Other criteria are the classical buffer requirements and the cell delay. Service fairness among connections is also evaluated with respect to each performance criterion. The impact of the following five multiplexing policies on the performance criteria are evaluated for constant bit rate (CBR) traffic sources. The policies are first in, first out (FIFO), round robin (RR), least time to reach bound (LTRB), most behind expected arrival (MBEA), and golden ratio (GR). Extensive numerical examples reveal that there is no single policy that is best across all criteria. With respect to cell conformance, most behind expected arrival (MBEA) emerges as the preferred one. FIFO is best with respect to cell delay, except for high utilizations where RR dominates. The LTRB is marginally better than all other policies with respect to buffer requirements.
Osteoarthritis of the knee: comparison of radiography, CT, and MR imaging to assess extent and severity. (1991)

Although conventional radiography is the method most frequently used for monitoring progression of osteoarthritis, it may not show osteoarthritic changes of the knee until late in the disease, and it may show involvement of only one or two compartments in patients who have tricompartmental disease. We compared radiography, CT, and MR imaging for assessing the extent and severity of osteoarthritis of the knee in 20 patients. Radiography included posteroanterior weight-bearing, true lateral, and sunrise patellar projections. Axial CT scans were reformatted in sagittal and coronal planes. MR imaging consisted of spin-echo (600-800/20; 2000/60, 120 [TR/TE]), and gradient-echo (600/30, theta = 30 degrees) sequences. The severity of osteoarthritic changes was graded from 0 to 3. MR frequently showed tricompartmental cartilage loss when radiography and CT showed only bicompartmental involvement in the medial and patellofemoral compartments. In the lateral compartment, MR showed a higher prevalence of cartilage loss (60%) than radiography (35%) and CT (25%) did. In the medial compartment, CT and MR showed osteophytes in 100% of the knees, whereas radiography showed osteophytes in only 60%. Notably, radiography often failed to show osteophytes in the posterior medial femoral condyle. On MR images, meniscal degeneration or tears were found in all 20 knees studied. Partial and complete tears of the anterior cruciate ligament were found in three and seven patients, respectively. MR is more sensitive than radiography and CT for assessing the extent and severity of osteoarthritic changes and frequently shows tricompartmental disease in patients in whom radiography and CT show only bicompartmental involvement. MR imaging is unique for evaluating meniscal and ligamentous disease related to osteoarthritis.
Feed-Forward Compensation for High-Speed Atomic Force Microscopy Imaging of Biomolecules (2006)

High-speed imaging by atomic force microscopy (AFM) requires the implementation of a fast control of tip–surface distance to maintain a constant interaction force. In particular, a well-controlled low load force is essential for observing soft biological molecules without causing damage to the sample. The accurate control of tip–surface distance where only feedback control is used is intrinsically difficult particularly for fast scanning. Here, we demonstrate that the combination of feedback and feed-forward control is useful for a more accurate distance control. We evaluate the bandwidth performance of the closed loop with and without feed-forward compensation using a model AFM system.We show that the combination of feedback and feed-forward control yields a greater than two fold improvement in bandwidth. We have applied this technique to the observation of myosin V and actin filaments at a high scanning rate.
Human CD27+IgM+IgD+ B cells: T-cell or TLR-dependent? (2012)

In this issue of Blood,Weller et al studied patients with rare immunodeficiencies to demonstrate a role for Toll-like receptors (TLRs) in homeostasis of human CD27+IgM+IgD+B cells.
Human Tumor Antigens Tn and Sialyl Tn Arise from Mutations in Cosmc (2008)

Neoplastic lesions typically express specific carbohydrate antigens on glycolipids, mucins, and other glycoproteins. Such antigens are often under epigenetic control and are subject to reversion and loss upon therapeutic selective pressure. We report here that two of the most common tumor-associated carbohydrate antigens, Tn and sialyl Tn (STn), result from somatic mutations in the gene Cosmc that encodes a molecular chaperone required for formation of the active T-synthase. Diverse neoplastic lesions, including colon cancer and melanoma-derived cells lines, expressed both Tn and STn antigen due to loss-of-function mutations in Cosmc. In addition, two human cervical cancer specimens that showed expression of the Tn/STn antigens were also found to have mutations in Cosmc and loss of heterozygosity for the cross-linked Cosmc locus. This is the first example of somatic mutations in multiple types of cancers that cause global alterations in cell surface carbohydrate antigen expression.
Deposition of the terminal C5b-9 complement complex in infarcted areas of human myocardium. (1986)

Poly- and monoclonal antibodies to neoantigens of the human C5b-9 complement complex, as well as polyclonal antibodies to C5, C8, and C9, were used to detect and identify C5b-9 deposits in human myocardial tissue. Immunocytochemical studies were performed on fresh-frozen autopsy material derived from patients with myocardial infarctions; in addition, in 17 of these patients, paraffin sections of formalin-fixed tissue were investigated. Sixteen autopsies from patients with noncardiac diseases were analyzed as controls. Without exception, C5b-9 positivity was registered selectively and exclusively on and in myocardial cells located within the zones of infarction. The selectivity of staining was confirmed by control reactions for succinic dehydrogenase activity performed in adjacent, respective double-stained sections. Most intensive staining with anti-neoantigen antibodies was observed in the peripheral areas of the infarctions. Weak staining for C3d, rather strong staining for C5 and C9, and intermediate staining with anti-C8 antibodies were observed in the same localizations. Stainings for C4 and IgA were negative, whereas immunocytochemical reactions for IgG and IgM revealed an irregular and very weak staining. Only very weak staining was also observed with a monoclonal antibody to complement S-protein, indicating that the terminal complement components were deposited mainly in the form of membrane-damaging C5b-9 complexes. Immunocytochemical staining for C5b-9 was found to represent a most sensitive tool for detection of ischemic myocardial lesions, permitting easy detection even of single cell necroses. As a working hypothesis, we suggest that initial ischemia may cause loss of the ability of the heart muscle cells to regulate complement turnover at the membrane level. The resulting deposition of C5b-9 on the cell membranes may contribute to functional disturbance and irreversible damage of myocardial cells during the infarction process.
Analysis of Chimeric Proteins Identifies the Regions in the Carbohydrate Recognition Domains of Rat Lung Collectins That Are Essential for Interactions with Phospholipids, Glycolipids, and Alveolar Type II Cells (1998)

Pulmonary surfactant proteins A (SP-A) and D (SP-D) are collectins in the C-type lectin superfamily. SP-A binds to dipalmitoylphosphatidylcholine and galactosylceramide, and it regulates the uptake and secretion of surfactant lipids by alveolar type II cells. In contrast, SP-D binds to phosphatidylinositol (PI) and glucosylceramide (GlcCer). We investigated the functional region in the carbohydrate recognition domain of rat SP-A and SP-D that is involved in binding lipids and interacting with alveolar type II cells by using chimeric proteins. Chimeras ad3, ad4, and ad5 were constructed with SP-A/SP-D splice junctions at Gly194/Glu321, Gln173/Thr300, and Met134/Cys261, respectively. All three chimeras lost SP-A-specific functions. Chimeras ad3, ad4, and ad5 bound to PI with increasing activity. In contrast, chimeras ad3 and ad4 did not bind to GlcCer, whereas ad5 avidly bound this lipid. From these results, we conclude that 1) the SP-A region of Glu195-Phe228 is required for lipid and type II cell interactions, 2) the SP-D region of Cys261-Phe355 is required for optimal lipid interactions, and 3) the structural requirement for the binding of SP-D to PI is different from that for GlcCer.
Cyclic 3',5'-Adenosine Monophosphate Modulates Retinal Pigment Epithelial Cell Migration In Vitro (1986)

Retinal pigment epithelial (RPE) cell migration has been implicated in the pathogenesis of proliferative vitreoretinopathy (PVR). Using a modified Boyden chamber assay, we have examined the effect of cyclic nucleotides on human RPE cell migration in vitro. Dibutyryl cyclic 3',5'-adenosine monophosphate (cAMP) (10(-3) mmol/L) inhibits RPE cell random migration by 83%, fibronectin-induced chemotaxis by 61%, and platelet-derived growth factor-induced chemotaxis by 68%. Random and directed migration of RPE cells is not significantly affected by 8-bromo cyclic 3',5'-guanosine monophosphate. Agents that significantly increase intracellular levels of cAMP are also inhibitors of RPE cell migration. Though there is a fairly good correlation for most drugs for their ability to stimulate cAMP production and their ability to inhibit cell migration, it is not perfect, suggesting that some drugs may modulate migration by more than one mechanism. Timolol blocked both the isoproterenol-induced stimulation of RPE adenylate cyclase and attenuated the ability of isoproterenol to inhibit RPE migration. These data suggest that cAMP may modulate RPE cell migration in an inhibitory fashion. Elucidation of the biochemical events involved in RPE cell migration could provide information that might be useful in planning a strategy to attempt pharmacologic control of proliferative vitreoretinopathy.