gebhart/patrepeval huggingface dataset:
Depth profiling of calcifications in breast tissue using picosecond Kerr-gated Raman spectroscopy (2006)

Breast calcifications are found in both benign and malignant lesions and their composition can indicate the disease state. Calcium oxalate (dihydrate) (COD) is associated with benign lesions, however calcium hydroxyapatite (HAP) is found mainly in proliferative lesions including carcinoma. The diagnostic practices of mammography and histopathology examine the morphology of the specimen. They can not reliably distinguish between the two types of calcification, which may indicate the presence of a cancerous lesion during mammography. We demonstrate for the first time that Kerr-gated Raman spectroscopy is capable of non-destructive probing of sufficient biochemical information from calcifications buried within tissue, and this information can potentially be used as a first step in identifying the type of lesion. The method uses a picosecond pulsed laser combined with fast temporal gating of Raman scattered light to enable spectra to be collected from a specific depth within scattering media by collecting signals emerging from the sample at a given time delay following the laser pulse. Spectra characteristic of both HAP and COD were obtained at depths of up to 0.96 mm, in both chicken breast and fatty tissue; and normal and cancerous human breast by utilising different time delays. This presents great potential for the use of Raman spectroscopy as an adjunct to mammography in the early diagnosis of breast cancer.
Cancer DNA Methylation: Molecular Mechanisms and Clinical Implications (2009)

DNA methylation plays a crucial role in the regulation of gene expression and chromatin organization within normal eukaryotic cells. In cancer, however, global patterns of DNA methylation are altered with global hypomethylation of repeat-rich intergenic regions and hypermethylation of a subset of CpG-dense gene-associated regions (CpG islands). Extensive research has revealed the cellular machinery that catalyzes DNA methylation, as well as several large protein complexes that mediate the transcriptional repression of hypermethylated genes. However, research is only just beginning to uncover the molecular mechanisms underlying the origins of cancer-specific DNA methylation. Herein, we present several recent advances regarding these mechanisms and discuss the relationship between histone modifications (i.e., H3K4me2/3, H4K16Ac, H3K9me2/3, H3K27me3, H4K20me3), chromatin-modifying enzymes (G9a, EZH2, hMOF, SUV4-20H), and aberrant DNA methylation. Additionally, the role played by inflammation, DNA damage, and miRNAs in the etiology of aberrant DNA methylation is considered. Finally, we discuss the clinical implications of aberrant DNA methylation and the utility of methylated biomarkers in cancer diagnosis and management.
Is there life after serials cancellation? (1996)

Describes how J. Murrey Atkins Library at the University of North Carolina, Charlotte, had to cut approximately $200,000 from its materials budget, necessitating the cancellation of 454 titles. The faculty was promised free document delivery in exchange for cancelled journal titles. Outlines the process of developing the document delivery proposal and the recommended policies and procedures.
A qualitative single case study of parallel processes (2007)

Abstract Parallel process in psychotherapy and supervision is a phenomenon manifest in relationships and interactions, that originates in one setting and is reflected in another. This article presents an explorative single case study of parallel processes based on qualitative analyses of two successive randomly chosen psychotherapy sessions with a schizophrenic patient and the supervision session given in between. The author's analysis is verified by an independent examiner's analysis. Parallel processes are identified and described. Reflections on the dynamics of parallel processes and supervisory interventions are reported and discussed.
Finite-state vector quantization over noisy channels and its application to LSP parameters (1992)

The authors describe a noisy channel finite-state vector quantizer (FSVQ) for quantizing speech line spectrum pair (LSP) parameters. First they show that under noiseless channel conditions, the ordinary FSVQ of J. Foster et al (1985), when used to encode the LSP parameters, achieves a 1-dB average spectral distortion at 24 b/frame; each LSP vector is split into three subvectors and an eight-state FSVQ is used for each subvector. However, when channel noise is present, the ordinary FSVQ performance degrades drastically. Therefore, the authors describe a modified FSVQ system that is designed taking into account the channel noise. It is shown by means of simulations that the new system is robust to channel noise and outperforms the channel-optimized VQ and the channel-matched multistage VQ of N. Phamdo et al, (1990) by saving 1.5-4 b/vector, depending on the level of noise in the channel.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Each Conserved Active Site Tyr in the Three Subunits of Human Isocitrate Dehydrogenase Has a Different Function (2010)

The human NAD-dependent isocitrate dehydrogenase (IDH) is a heterotetrameric mitochondrial enzyme with 2alpha:1beta:1gamma subunit ratio. The three subunits share 40-52% identity in amino acid sequence and each includes a tyrosine in a comparable position: alphaY126, betaY137, and gammaY135. To study the role of the corresponding tyrosines of each of the subunits of human NAD-IDH, the tyrosines were mutated (one subunit at a time) to Ser, Phe, or Glu. Enzymes were expressed with one mutant and two wild-type subunits. The results of characterization of the mutant enzymes suggest that betaY137 is involved in NAD binding and allosteric activation by ADP. The alphaY126 is required for catalytic activity and likely acts as a general acid in the reaction. The gammaY135 is also required for catalytic activity and may be involved in proper folding of the enzyme. The corresponding tyrosines in the three dissimilar subunits of NAD-IDH thus have distinctive functions.
Aglycosylated antibodies and antibody fragments produced in a scalable in vitro transcription-translation system (2012)

We describe protein synthesis, folding and assembly of antibody fragments and full-length aglycosylated antibodies using an Escherichia coli-based open cell-free synthesis (OCFS) system. We use DNA template design and high throughput screening at microliter scale to rapidly optimize production of single-chain Fv (scFv) and Fab antibody fragments that bind to human IL-23 and IL-13α1R, respectively. In addition we demonstrate production of aglycosylated immunoglobulin G (IgG1) trastuzumab. These antibodies are produced rapidly over several hours in batch mode in standard bioreactors with linear scalable yields of hundreds of milligrams/L over a 1 million-fold change in scales up to pilot scale production. We demonstrate protein expression optimization of translation initiation region (TIR) libraries from gene synthesized linear DNA templates, optimization of the temporal assembly of a Fab from independent heavy chain and light chain plasmids and optimized expression of fully assembled trastuzumab that is equivalent to mammalian expressed material in biophysical and affinity based assays. These results illustrate how the open nature of the cell-free system can be used as a seamless antibody engineering platform from discovery to preclinical development of aglycosylated monoclonal antibodies and antibody fragments as potential therapeutics.
Immunological properties of apoB-containing lipoprotein particles in human atherosclerotic arteries (1993)

In this study, we have documented immunochemical properties of apolipoprotein (apo) B-containing particles (LpB) extracted from human atherosclerotic lesions obtained during vascular reconstructive surgery of patients. These properties were compared to those of particles purified from corresponding atherosclerotic plasma and healthy control plasma. LpB immunoreactivities were tested in solid phase competitive binding radioimmunoassays using five anti-apoB monoclonal antibodies (MAb) for which epitopes have been previously located on the protein. The regions encompassed amino acids 405 to 539 (MAb B1), 1854 to 1879 (MAb B4), 3506 (MAb BA11), and 4355 (MAb BL3). The fifth antibody (MAb BL5) recognizes a conformationally expressed epitope. LpB from lesions presented a significantly decreased immunoreactivity as compared to LpB from respective plasma except for the epitope recognized by MAb BA11 located precisely in the low density lipoprotein (LDL) receptor binding site. The accessibility of the four sequential epitopes was similar on LpB from atherosclerotic and healthy plasma while it was decreased for the conformational one in LpB from atherosclerotic samples. These altered immunoreactivities were not related to changes in chemical composition of LpB as this was quite comparable in all preparations. With regard to electronegativity, apoB fragmentation, immunological accessibility, and size distribution of the particles, changes seem to increase in the following order from healthy plasma, atherosclerotic plasma, and the corresponding lesions. The results confirm some structural characteristics of oxidatively modified particles from human atherosclerotic lesions and to a lesser degree from respective plasma, but more specifically demonstrate a global conformational change in LpB from lesions, this change being perhaps initiated in the plasma.
Diet-Induced Hypercholesterolemia in Mice: Prevention by Overexpression of LDL Receptors (1990)

The current studies were designed to determine whether chronic overexpression of low density lipoprotein (LDL) receptors in the liver would protect mice from the increase in plasma LDL-cholesterol that is induced by high-fat diets. A line of transgenic mice was studied that express the human LDL receptor gene in the liver under control of the transferrin promoter. When fed a diet containing cholesterol, saturated fat, and bile acids for 3 weeks, the transgenic mice, in contrast to normal mice, did not develop a detectable increase in plasma LDL. The current data indicate that unregulated overexpression of LDL receptors can protect against diet-induced hypercholesterolemia in mice.
Identification of the Residues in the Extracellular Region of KDR Important for Interaction with Vascular Endothelial Growth Factor and Neutralizing Anti-KDR Antibodies (2000)

The kinase domain receptor (KDR) of vascular endothelial growth factor (VEGF) is the main human receptor responsible for the angiogenic activity of VEGF. The extracellular region of KDR is comprised of seven immunoglobulin-like domains, of which the first three have been shown to be required for ligand binding. We have previously described antibodies directed against the extracellular region of KDR, including MAB383 and MAB664, which were shown to block the binding of VEGF to the receptor and to inhibit both VEGF-induced mitogenesis of human endothelial cells in vitro and tumor growth in vivo. Here we generated a series of KDR deletion mutants consisting of truncated extracellular regions and mapped out the domain(s) responsible for binding to VEGF and the neutralizing anti-KDR antibodies. All neutralizing antibodies were found to require domain 3 for efficient binding. Alanine-scanning mutagenesis of domain 3 identified two different sets of five residues, Ile(256), Asp(257), Glu(261), Leu(313), and Thr(315) and Tyr(262), Pro(263), Ser(264), Ser(265), and Lys(266), that were critical for binding to MAB383 and MAB664, respectively. Combination of alanine mutations affecting both MAB383 and MAB664 binding resulted in a variant that also lost binding to VEGF. These results suggest that the residues within this region of domain 3 are critical for VEGF binding. Our studies provide a basis for the mechanism of action of our anti-KDR antibodies and establish a functional foundation for the development of other classes of antagonists to the receptor.
A transposon insertion in the Arabidopsis SSR16 gene causes an embryo‐defective lethal mutation (1996)

The SSR16 gene of Arabidopsis has been identified as a gene encoding a ribosomal protein S16 homolog through analysis of a transposon insertion mutation. The insertion mutation is lethal, arresting embryonic development at approximately the transition from the globular to the heart stage of embryonic development. Co-segregation of the mutant phenotype with the transposon-borne drug-resistance marker and loss of the inserted transposon concomitant with phenotypic reversion provided evidence that the transposon had caused the mutation. Sequences flanking the insertion site were amplified from DNA of viable heterozygotes by thermal asymmetric interlaced (TAIL) PCR. The amplified fragment flanking the 3' end of the inserted element was sequenced and found to be identical to an Arabidopsis expressed sequence tag (EST). The EST, in turn, contained a coding sequence homologous to the ribosomal protein S16 (RPS16) of bacteria such as Escherichia coli, Bacillus subtilis and Salmonella typhimurium, as well as Neurospora crassa mitochondria and higher plant plastids. Thus the gene identified by the embryo-defective lethal insertion mutation encodes an RPS16 homolog and has been designated the SSR16 gene.
Quartz Binding Peptides as Molecular Linkers towards Fabricating Multifunctional Micropatterned Substrates (2009)

Quartz-binding peptides (QBPs) are used as both ink and linker for microcontact printing and self-assembly, for the co-immobilization of streptavidin-coated quantum dots and fluorescein. Directed assembly of the quantum dots is carried out following microcontact printing of biotinylated QBP1 on a quartz surface. The remaining untouched regions are occupied by the mediated-assembly of fluorescein linked with QBP1. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Anti-HMGB1 Neutralizing Antibody Ameliorates Gut Barrier Dysfunction and Improves Survival after Hemorrhagic Shock (2006)

Intestinal barrier dysfunction occurs following hemorrhagic shock and resuscitation (HS/R). High-mobility group B1 (HMGB1) has been shown to increase the permeability of Caco-2 human enterocyte-like epithelial monolayers in vitro. In this study, we found that serum concentrations of HMGB1 were higher in blood samples obtained from 25 trauma victims with hemorrhagic shock than in 9 normal volunteers. We also studied whether treatment with anti-HMGB1 antibody can ameliorate HS/R-induced gut barrier dysfunction in mice. Animals were shocked by withdrawal of blood to maintain mean arterial pressure at 25 to 30 mmHg for 2 h. After resuscitation with shed blood plus Ringer's lactate solution, the mice were treated with either anti-HMGB1 antibody or nonimmune rabbit IgG. Serum HMGB1 concentrations were significantly higher in trauma victims than control mice. Treatment with anti-HMGB1 antibody improved survival at 24 h and ameliorated the development of ileal mucosal hyperpermeability to FITC-labeled dextran. At 24 h after HS/R, treatment with anti-HMGB1 antibody decreased bacterial translocation to mesenteric lymph nodes and was associated with lower circulating concentrations of IL-6 and IL-10. These data support the notion that HMGB1 is a mediator of HS/R-induced gut barrier dysfunction and suggest that anti-HMGB1 antibodies warrant further evaluation as a therapeutic to ameliorate the morbidity of HS/R in trauma patients.
Use the Force (or something) - Pressure and Pressure- Like Input for Mobile Music Performance (2010)

force is an important dimension for percussive musical instruments such as the piano. We explore three possible mechanisms how to get impact forces on mobile multi-touch devices: using built-in accelerometers, the pressure sensing capability of Android phones, and external force sensing resistors. We find that accelerometers are difficult to control for this purpose. Android's pressure sensing shows some promise, especially when combined with augmented playing technique. Force sensing resistors can offer good dynamic resolution but this technology is not currently offered in commodity devices and proper coupling of the sensor with the applied impact is difficult. Keywordsimpact, pressure, multi-touch, mobile phone, mobile music making.
Identification and Characterization of Specific DNA-binding Complexes Containing Members of the Myc/Max/Mad Network of Transcriptional Regulators (1998)

In the past, eukaryotic cell-derived complexes of the Myc/Max/Mad network of transcriptional regulators have largely been refractory to DNA binding studies. We have developed electrophoretic mobility shift assay conditions to measure specific DNA binding of Myc/Max/Mad network complexes using a COS7 cell-based overexpression system. With the established protocol, we have measured on- and off-rates of c-Myc/Max, Max/Max, and Mad1/Max complexes and determined relative affinities. All three complexes appeared to bind with comparable affinity to a Myc E-box sequence. Furthermore, our data derived from competition experiments suggested that the Mad3/Max and Mad4/Max complexes also possess comparable DNA binding affinities. The conditions established for COS7 cell-overexpressed proteins were then used to identify c-Myc/Max, Max/Max, and Mnt/Max complexes in HL-60 cells. However, no Mad1/Max could be detected, despite the induction of Mad1 expression during differentiation. Whereas the DNA binding activity of c-Myc/Max complexes was down-regulated, Max/Max binding increased, and Mnt/Max binding remained unchanged. In addition, we have also tested for upstream stimulatory factor (USF) binding and observed that, in agreement with published data, USF comprises a major Myc E-box-binding factor that is more abundant than any of the Myc/Max/Mad network complexes. Similar to the Mnt/Max complex, the binding activity of USF remained constant during HL-60 differentiation. Our findings establish conditions for the analysis of DNA binding of Myc/Max/Mad complexes and indicate posttranslational regulation of the Max/Max complex.
Adoption of the Q transcriptional regulatory system for zebrafish transgenesis (2013)

The Gal4-UAS regulatory system of yeast is widely used to modulate gene expression in Drosophila; however, there are limitations to its usefulness in transgenic zebrafish, owing to progressive methylation and silencing of the CpG-rich multicopy upstream activation sequence. Although a modified, less repetitive UAS construct may overcome this problem, it is highly desirable to have additional transcriptional regulatory systems that can be applied independently or in combination with the Gal4/UAS system for intersectional gene expression. The Q transcriptional regulatory system of Neurospora crassa functions similarly to Gal4/UAS. QF is a transcriptional activator that binds to the QUAS upstream regulatory sequence to drive reporter gene expression. Unlike Gal4, the QF binding site does not contain essential CpG dinucleotide sequences that are subject to DNA methylation. The QS protein is a repressor of QF mediated transcriptional activation akin to Gal80. The functionality of the Q system has been demonstrated in Drosophila and Caenorhabditis elegans and we now report its successful application to a vertebrate model, the zebrafish, Danio rerio. Several tissue-specific promoters were used to drive QF expression in stable transgenic lines, as assessed by activation of a QUAS:GFP transgene. The QS repressor was found to dramatically reduce QF activity in injected zebrafish embryos; however, a similar repression has not yet been achieved in transgenic animals expressing QS under the control of ubiquitous promoters. A dual reporter construct containing both QUAS and UAS, each upstream of different fluorescent proteins was also generated and tested in transient assays, demonstrating that the two systems can work in parallel within the same cell. The adoption of the Q system should greatly increase the versatility and power of transgenic approaches for regulating gene expression in zebrafish.
Hyperstable U1snRNA complementary to the K-ras transcripts induces cell death in pancreatic cancer cells (2002)

One of the critical steps that governs the inhibitory effect of antisense RNA on target gene expression is the association of the antisense RNA with the target RNA molecules. However, until now, no systematic method has been available to select the suitable parts of a gene as antisense targets. In this study, we utilised U1 small nuclear RNA (snRNA) that binds physiologically to the 5' splice site (5'ss) of pre-mRNA, to develop a novel vector system that permits imposed binding of antisense RNA to its target. The 5' free end of U1snRNA was replaced with the antisense sequence against the K-ras gene to generate a hyperstable U1snRNA, whose binding stability to 5'ss of the K-ras transcript is ten-fold higher than that of wild-type U1snRNA. The efficacy of such hyperstable U1snRNA was examined by transducing the expression plasmids into human pancreatic cancer cell lines. This revealed that two of the hyperstable U1snRNAs induced cell death after gene transduction, and significantly reduced the number of G418-resistant colonies to less than 10% of the controls. Furthermore, hyperstable U1snRNA suppressed intraperitoneal dissemination of pancreatic cancer cells in vivo. Hyperstable U1snRNA might be a novel approach to express effective antisense RNA in target cells.
Early detection of critical material degradation by means of electromagnetic multi-parametric NDE (2014)

With an increasing number of power plants operated in excess of their original design service life an early recognition of critical material degradation in components will gain importance. Many years of reactor safety research allowed for the identification and development of electromagnetic NDE methods which detect precursors of imminent damage with high sensitivity, at elevated temperatures and in a radiation environment. Regarding low-alloy heat-resistant steel grade WB 36 (1.6368, 15NiCuMoNb5), effects of thermal and thermo-mechanical aging on mechanical-technological properties and several micromagnetic parameters have been thoroughly studied. In particular knowledge regarding the process of copper precipitation and its acceleration under thermo-mechanical load has been enhanced. Whilst the Cu-rich WB 36 steel is an excellent model material to study and understand aging effects related to neutron radiation without the challenge of handling radioactive specimens in a hot cell, actually neutron-irradiated reactor pressure vessel materials were investigated as well. The neutron fluence experienced and the resulting shift of the ductile-brittle transition temperature were determined electromagnetically, and it was shown that weld and base material can be distinguished from the cladded side of the RPV wall. Low-cycle fatigue of the austenitic stainless steel AISI 347 (1.4550, X6CrNiNb18-10) has been characterized with electromagnetic acoustic transducers (EMATs) at temperatures of up to 300 °C. Time-of-flight and amplitude of the transmitted ultrasound signal were evaluated against the number of load cycles applied and observed as an indication of the imminent material failure significantly earlier than monitoring stresses or strains.