gebhart/patrepeval huggingface dataset:
Results of the 2nd part Scientific Workshop of the ECCO (II): Measures and markers of prediction to achieve, detect, and monitor intestinal healing in Inflammatory Bowel Disease (2011)

The healing of the intestine is becoming an important objective in the management of inflammatory bowel diseases. It is associated with improved disease outcome. Therefore the assessment of this healing both in clinical studies and routine practice is a key issue. Endoscopy for the colon and terminal ileum and computerized tomography or magnetic resonance imaging for the small bowel are the most direct ways to evaluate intestinal healing. However, there are many unsolved questions about the definition and the precise assessment of intestinal healing using these endoscopic and imaging techniques. Furthermore, these are relatively invasive and expensive procedures that may be inadequate for regular patients' monitoring. Therefore, biomarkers such as C-reactive protein and fecal calprotectin have been proposed as surrogate markers for intestinal healing. Nevertheless, the sensitivity and specificity of these markers for the prediction of healing may be insufficient for routine practice. New stool, blood or intestinal biomarkers are currently studied and may improve our ability to monitor intestinal healing in the future.
Benefits and Challenges with Applying Unique Molecular Identifiers in Next Generation Sequencing to Detect Low Frequency Mutations (2016)

Indexing individual template molecules with a unique identifier (UID) before PCR and deep sequencing is promising for detecting low frequency mutations, as true mutations could be distinguished from PCR errors or sequencing errors based on consensus among reads sharing same index. In an effort to develop a robust assay to detect from urine low-abundant bladder cancer cells carrying well-documented mutations, we have tested the idea first on a set of mock templates, with wild type and known mutants mixed at defined ratios. We have measured the combined error rate for PCR and Illumina sequencing at each nucleotide position of three exons, and demonstrated the power of a UID in distinguishing and correcting errors. In addition, we have demonstrated that PCR sampling bias, rather than PCR errors, challenges the UID-deep sequencing method in faithfully detecting low frequency mutation.
Descent Methods for Tuning Parameter Refinement (2010)

This paper addresses multidimensional tuning parameter selection in the context of “train-validate-test ” and K-fold cross validation. A coarse grid search over tuning parameter space is used to initialize a descent method which then jointly optimizes over variables and tuning parameters. We study four regularized regression methods and develop the update equations for the corresponding descent algorithms. Experiments on both simulated and real-world datasets show that the method results in significant tuning parameter refinement. 1
Mammaglobin expression in primary, metastatic, and occult breast cancer. (1999)

The mammaglobin gene encodes a novel, breast cancer-associated glycoprotein. In this study, we have evaluated the frequency with which mammaglobin expression can be detected in primary and metastatic breast tumors and in breast tumor cells present in the peripheral circulation. Of 100 primary human breast tumors examined, 81 were strongly immunopositive for mammaglobin protein. Staining was independent of tumor grade and histological type. Ten of 11 lymph nodes from patients with metastatic breast cancer contained detectable mammaglobin mRNA, whereas mammaglobin expression in uninvolved lymph nodes was undetectable. Using a nested reverse transcription-PCR assay, mammaglobin mRNA was also detected in 9 of 15 products (60%) used for autologous stem cell transplant. These results suggest that larger clinical studies are warranted to investigate the full clinical utility of mammaglobin as a tool for breast cancer patient management.
Arm Movement‐related Neurons in the Visual Area V6A of the Macaque Superior Parietal Lobule (1997)

Area V6A is a cortical visual area located in the posterior face of the superior parietal lobule in the macaque monkey. It contains visual neurons as well as neurons not activated by any kind of visual stimulation. The aim of this study was to look for possible features able to activate these latter neurons. We tested 70 non-visual V6A neurons. Forty-three of them showed an arm movement-related neural discharge due to somatosensory stimulation and/or skeletomotor activity of the upper limbs of the animal. The arm movement-related neural discharge started before the onset of arm movement, often before the earliest electromyographic activity. Thus, although the discharge is probably supported by proprioceptive and tactile inputs it is not fully dependent on them. Arm movement-related neurons of area V6A seem to be well equipped for integrating motor signals related to arm movements with somatosensory signals evoked by those movements. Taking into account also the visual characteristics of V6A neurons, it seems likely that area V6A as a whole is involved in the visual guiding of reaching.
ICAM-1 and B7-1 provide similar but distinct costimulation for CD8+ T cells, while CD4+ T cells are poorly costimulated by ICAM-1 (1999)

The function of purified ICAM-1 in costimulating CD4+ and CD8+ T cell responses has been directly compared to that of B7-1 in a model system that minimizes contributions of other receptor-ligand interactions. While B7-1 costimulates both subsets of T cells, ICAM-1 is much more effective in the costimulation of CD8+ cells. ICAM-1 also synergizes with B7-1 for the induction of IL-2 production in CD8+ but not CD4+ T cells. These differences are not explained by differences in LFA-1 receptor expression on the two subsets of T cells. The CD8+ T cell response to ICAM-1 costimulation is associated with increased proliferation and IL-2 production at levels similar to those seen with B7-1 costimulation, but clonal expansion in response to ICAM-1 is not as great due to decreased cell survival. ICAM-1-mediated costimulation is effective for both naive and memory CT8+ T cells, is independent of CD28 engagement, and does not appear to be due solely to effects on adhesion. These results suggest that ICAM-1-dependent, B7-independent costimulation may be important in initiating a CTL response to class I antigen presented by cells that are not professional APC.
Preparation of Ti-Al alloy sheet by electron beam physical vapor deposition (2007)

Ti-Al thin sheet with dimension of 450 mm×450 mm×0.2 mm was prepared by electron beam physical vapor deposition(EB-PVD) technology. The surface and cross-section pattern of as-deposited sample were studied by SEM and AFM,and then the composition and phase were analysed by XRD and EPMA. Finally,the effect on deposit by re-evaporation of Al was explored by calculating the ratio of re-evaporating capacity with depositing capacity of Al on the substrate. The results indicate that the evaporation process with Nb addition into the molten pool makes it earlier to reach the steady-state. The existing equiaxed crystal and columnar crystal along the cross-sectional may be caused by the transformation latent heat released during the transition course of atoms from gaseous state to solid state. The effect on deposit by re-evaporation of Al can be neglected because the re-evaporating capacity of Al is far below that of the depositing capacity.
Inactivation of the integrin beta 6 subunit gene reveals a role of epithelial integrins in regulating inflammation in the lung and skin. (1996)

The integrin alpha v beta 6 is only expressed in epithelial cells. In healthy adult epithelia, this receptor is barely detectable, but expression is rapidly induced following epithelial injury. Mice homozygous for a null mutation in the gene encoding the beta 6 subunit had juvenile baldness associated with infiltration of macrophages into the skin, and accumulated activated lymphocytes around conducting airways in the lungs. Beta 6-/- mice also demonstrated airway hyperresponsiveness to acetylcholine, a hallmark feature of asthma. These results suggest that the epithelial integrin alpha v beta 6 participates in the modulation of epithelial inflammation. Genetic or acquired alterations in this integrin could thus contribute to the development of inflammatory diseases of epithelial organs, such as the lungs and skin.
Monoclonal Antibodies for Diagnosis of Infectious Diseases in Humans (1983)

Monoclonal antibody techniques are now widely practiced. and antibodies of diagnostic potential have been prepared in research laboratories against a battery of viruses, bacteria, fungi, and parasites. In this article the diagnostic utility of monoclonal antibodies for gonococcal, chlamydial, and herpesvirus infections is described. With immunofluorescence being used as an assay system, the antibodies demonstrated sensitivities of 94 to 99 percent for culture confirmation and 85 to 90 percent for direct diagnosis of specimens smeared on microscope slides. Since the direct diagnostic tests only required 15 to 20 minutes to perform, they represented a major advance in the diagnosis of infections which previously required 3 to 6 days to accomplish. It is anticipated that in the next decade an entirely new spectrum of antibody-based diagnostics will be developed, allowing the rapid, precise, and semiautomated diagnosis of many infectious diseases.
Identification and Characterization of a Pro-tumor Necrosis Factor-α-processing Enzyme from the ADAM Family of Zinc Metalloproteases (1997)

Tumor necrosis factor-alpha (TNF) is initially expressed as a 26-kDa membrane-bound precusor protein (pro-TNF) that is shed proteolytically from the cell surface, releasing soluble 17-kDa TNF. We have identified human ADAM 10 (HuAD10) from THP-1 membrane extracts as a metalloprotease that specifically clips a peptide substrate spanning the authentic cleavage site between Ala76 and Val77 in pro-TNF. To confirm that HuAD10 has TNF processing activity, we cloned, expressed, and purified an active, truncated form of HuAD10. Characterization of recombinant HuAD10 (rHuAD10) suggests that this enzyme has many of the properties (i.e. substrate specificity, metalloprotease activity, cellular location) expected for a physiologically relevant TNF-processing enzyme.
Characterization of a New Solvent-Sensitive Two-Photon-Induced Fluorescent (Aminostyryl)pyridinium Salt Dye (1996)

A newly synthesized hemicyanine dye, trans-4-[p-[N-ethyl-N-(hydroxyethyl)amino]styryl]-N-methylpyridinium tetraphenylborate (ASPT), has recently been shown to be an excellent dye for both one- and two-photon-pumped lasing and for applications in optical power limiting. We report on the absorption, one- and two-photon-induced emission, quantum yield, and the excited-state lifetime of ASPT in different solvents of varying polarity. We also present the spectral characteristics of ASPT within a reverse-micelle and β-cyclodextrin cavity. Our results demonstrate that ASPT is one of the few dyes which exhibits highly solvent-polarity-dependent fluorescence in the useful orange-red region of the spectrum (560−620 nm). Therefore, it offers many applications in the biomedical field as a fluorescent probe molecule. In addition, ASPT is fluorescent upon excitation with an infrared (IR) source (two-photon-induced emission) making it even more attractive, since the background fluorescence from biological fluids upon IR excitation is highly reduced compared to ultraviolet or visible excitation. The solvatochromic effect of ASPT is proposed to be due to a change in the dipole moment and reduced hydrogen bonding effects of the dye upon excitation. On the basis of our results, we propose that ASPT exists in two mesomeric forms. One is predominant in the ground-state and the other in the excited-state. We observe a low quantum yield of the dye (<10%) in all the investigated solvents. The excited-state lifetime of ASPT is also observed to be solvent-dependent (30−400 ps). The calculated radiative decay rate is observed to remain constant but the nonradiative decay rate increases in solvents of increasing polarity. Finally, we report on the spectral feature of ASPT within a reverse-micelle cavity with varying water loadings and upon binding to a β-CD cavity.
Mature dendritic cells can enhance CD8+ cell noncytotoxic anti-HIV responses: the role of IL-15 (2003)

The CD8+ cell noncytotoxic anti-HIV response (CNAR) is associated with a long-term healthy clinical state in HIV-infected individuals. Over time CNAR is reduced concomitant with progression to disease. In studies to evaluate whether the interaction between CD8+ cells and dendritic cells (DCs) could increase CNAR, CD8+ cells from individuals who showed a decrease in this antiviral activity were cocultured with monocyte-derived dendritic cells matured with CD40 ligand. After coculture with these mature DCs, the CD8+ cells showed an increase in CNAR greater than that observed with CD8+ cells costimulated with CD3/CD28 antibodies. This antiviral response appeared to be mediated primarily by production of interleukin-15 (IL-15) by the mature DCs. Purified IL-15 also enhanced CNAR, whereas IL-12 showed no substantial effect. These studies provide another potential approach by which the immune system in HIV infection could be restored by cytokine therapy, particularly IL-15 administration.
Cloning of the NCX2 isoform of the plasma membrane Na(+)-Ca2+ exchanger (1994)

The Na(+)-Ca2+ exchanger is an important regulator of cellular Ca2+ levels, and one isoform of this transporter, NCX1, has been cloned previously (Nicoll, D.A., Longoni, S., and Philipson, K.D. (1990) Science 250, 562-565). We now report the cloning of a second isoform (NCX2) of the Na(+)-Ca2+ exchanger which was present in a rat brain cDNA library. NCX2 is predicted to code for a protein of 921 amino acids. NCX1 and NCX2 are 61 and 65% identical at the nucleotide and amino acid levels, respectively, and are the products of different genes. The genes for NCX1 and NCX2 are located on human chromosomes 2 and 14, respectively. Hydropathy profiles of the two exchangers are very similar. Transcripts of NCX2 are detected in brain and skeletal muscle. NCX2 was expressed in Xenopus oocytes and Na(+)-Ca2+ exchange activity was analyzed electrophysiologically by the giant inside-out, excised patch technique. Outward currents were evoked by the application of Na+ with the exchanger operating in the reversed mode (extracellular Ca2+ exchanging for intracellular Na+). The affinity for Na+ (30 mM) and the current-voltage relationship of NCX2 are similar to those for NCX1. Like NCX1, NCX2 is secondarily regulated by intracellular Ca2+, but the affinity of NCX2 for regulatory Ca2+ (1.5 microM) upon initial application of Na+ is lower than that of NCX1 (0.3 microM). The existence of multiple Na(+)-Ca2+ exchanger isoforms may provide flexibility for regulation and expression.
Contemporary Nutrition Support Practice: A Clinical Guide (1998)

Part I: Introduction. The Nutrition Support Team. Part II: Assessment of Nutritional General Systemic Disorders. History and Physical Exam. Anthropometry and Body Composition Analysis. Laboratory Monitoring of Nutritional Status. Evaluating Immunocompetence. Part III: Nutrients for Nutrition Physiologic Stress. Energy Dynamics. Protein. Carbohydrate. Lipids. Fluids and Electrolytes. Vitamins. Minerals and Trace Elements. Fiber. Part IV: Principles of Nutrition. Determining the Nutrition Support Regimen. Enteral Nutrition: A Comprehensive Overview. Enteral Equipment. Management of Complications of Enteral Nutrition. Principles of Parenteral Nutrition. Management of Complications of Parenteral Nutrition. Critical Evaluation of Enteral and Parenteral Nutrition Formulas. Preoperative, Intraoperative and Early Nutrition Support. Dual and Transitional Feedings. General Pharmacologic Issues. Part V: Nutrition Support Throughout the Life Cycle. Pregnancy. Neonatology. Pediatrics. Geriatrics. Part VI: Nutrition Support in Specific System Disorders. Neurologic Impairment. Cardiac Failure. Pulmonary Failure Status. Gastrointestinal and Pancreatic Disease. Hepatic Failure. Renal Failure. Part VII: Nutrition Support in Status. Cancer. Immune Dysfunction/Sepsis. Human Immunodeficiency Virus Infection. Diabetes Mellitus. Obesity. Part VIII: Nutrition Support in Stress. Metabolic Stress. Solid Organ Transplant. Bone Marrow Transplant. Wound Healing. Burns. Part IX: Management and Professional Issues. Home/Long-Term Nutrition Support. Quality Assessment and Improvement. Ethical Considerations in Nutrition Support. Economics of Nutrition Support. Research. Epilogue.
Epstein-Barr Virus (EBV) Induced Polyclonal and Monoclonal B-Cell Lymphoproliferative Diseases Occurring after Renal Transplantation (1983)

Nineteen renal allograft recipients developed B-cell lymphoproliferative diseases. Clinically there were two groups: a) young patients (mean age, 23 years) who presented soon (mean, 9 months) after transplantation or antirejection therapy with fever, pharyngitis, and lymphadenopathy resembling infectious mononucleosis, and b) older patients (mean age, 48 years) who presented later (mean, 6 years) after transplantation with localized tumor masses. Histologically, the diseases were classified as polymorphic diffuse B-cell hyperplasia (PDBH) or polymorphic B-cell lymphoma (PBL). Immunologic cell typing revealed either polyclonal or monoclonal B-cell proliferations. Malignant transformation of polyclonal proliferations in two patients was suggested by the finding of clonal cytogenetic abnormalities. Epstein-Barr virus (EBV) specific serology, staining of biopsy specimens for the Epstein-Barr nuclear antigen, and EBV DNA molecular hybridization studies implicated EBV as the cause of both PDBH and PBL. Acyclovir, an antiviral agent that blocks EBV replication in vitro, inhibited oropharyngeal shedding of EBV and caused complete remission in four patients with polyclonal B-cell proliferations. The monoclonal tumors were acyclovir resistant. We suggest that surgical treatment, radiotherapy, or chemotherapy may be more appropriate therapy in selected patients with acyclovir resistant tumors. Therapeutic decisions require not only documentation of the viral etiology of these tumors, but also immunologic and cytogenetic analysis to determine the stage of tumor evolution in individual patients.
UV-assisted capillary force lithography for engineering biomimetic multiscale hierarchical structures: From lotus leaf to gecko foot hairs (2009)

This feature article provides an overview of the recently developed two-step UV-assisted capillary force lithography and its application to fabricating well-defined micro/nanoscale hierarchical structures. This method utilizes an oxygen inhibition effect in the course of UV irradiation curing and a two-step moulding process, to form multiscale hierarchical or suspended nanobridge structures in a rapid and reproducible manner. After a brief description of the fabrication principles, several examples of the two-step UV-assisted moulding technique are presented. In addition, emerging applications of the multiscale hierarchical structures are briefly described.
Surface‐ and tip‐enhanced Raman scattering of DNA components (2006)

Abstract While surface‐enhanced Raman scattering (SERS) is an established technique to significantly enhance the Raman signal from samples bound to metal surfaces, a quantitative interpretation is very difficult because of the rough and arbitrary nature of the substrate. A distinction between concentration and enhancement effects is virtually impossible. Tip‐enhanced Raman scattering (TERS), a scattering type of near‐field optical microscopy technique, circumvents the problem of random enhancement by concentrating the roughness to only a small region directly at the apex of a scanning probe tip. In this paper, TERS spectra of DNA pyrimidine bases have been collected and compared with standard SERS and Raman measurements of the nucleotides and the pure bases. The results are discussed in terms of electromagnetic and chemical effects of the SERS enhancement of the TERS probes. Copyright © 2006 John Wiley &amp; Sons, Ltd.
An immunotoxin cytotoxic for breast cancer cells in vitro. (1987)

A potent immunotoxin was formed by conjugating the murine monoclonal antibody 323/A3 to the A chain of ricin. The 323/A3 antibody recognizes an antigen expressed by most human breast cancers. When binding of 323/A3 is examined by enzyme-linked immunosorption assay, three human breast cell lines displayed strong binding, whereas two human breast cell lines and three non-breast cell lines displayed little or no binding. When the cell lines were tested at a concentration of 0.1 microgram/ml, those cell lines which displayed an abundance of antigen by enzyme-linked immunosorption assay were most sensitive to the effects of the 323/A3 immunotoxin. On the other hand, cell lines which displayed little or no antigen by enzyme-linked immunosorption assay were not inhibited by the immunotoxin at this concentration. Further examination of the effects of immunotoxin concentration on protein synthesis confirmed the sensitivity of those cell lines rich in the 323/A3 antigen over a broad dose range. Similarly, three cell lines which displayed little of the 323/A3 antigen demonstrated little inhibition of protein synthesis with various concentrations of 323/A3 immunotoxin. However, two cell lines which displayed little antigen were intermediate in their sensitivity to the 323/A3 immunotoxin. Preclinical evaluation of immunotoxins as potential therapeutic agents will require accurate and sensitive screening of a wide variety of cell types. The 323/A3 remains of interest in studying the effects of immunotoxin in a defined in vivo model system.
The CF mouse: an important tool for studying cystic fibrosis (2001)

Cystic fibrosis (CF) is a common and fatal recessive disease, which is caused by dysfunction of a chloride ion channel, termed the CF transmembrane conductance regulator (CFTR). The CF gene was cloned in 1989; subsequently, several mouse models have been created using gene targeting within embryonic stem cells. This report describes how such animal models provide the opportunity to elucidate disease pathogenesis, correlate genotype with phenotype and develop novel therapies. The current models encompass mice with a complete knockout of CFTR function, with residual CFTR function, and with precise mutations corresponding to those in humans that precipitate CF. All the CF mice demonstrate the characteristic CF ion-transport defect and show some evidence of intestinal disease, but they have a variable level of survival. Genetic background has also been shown to affect the intestinal phenotype of CF mice and this has allowed identification of a genetic modifier locus of CF in humans. Lung disease in human CF is the major cause of death in early adulthood. This is not entirely reproduced in CF mice, but repeat exposure of the lung to clinical pathogens does reveal a significantly abnormal pathogen-related response in the residual-function mice. CF mice have been successfully used to investigate the safety and efficacy of various pharmacological and gene-therapy protocols. As new cloning techniques become available, the models can be refined to ensure that in vivo models continue to be an essential tool for studying CF.