gebhart/patrepeval huggingface dataset:
A shifted‐excitation Raman difference spectroscopy (SERDS) evaluation strategy for the efficient isolation of Raman spectra from extreme fluorescence interference (2015)

A biochemical characterization of pathologies in biological tissue can be provided by Raman spectroscopy. Often, the raw spectrum is severely affected by fluorescence interference. We report and compare various spectra‐processing approaches required for the purification of Raman spectra from heavily fluorescence‐interfered raw spectra according to the shifted‐excitation Raman difference spectroscopy method. These approaches cover the entire spectra‐processing chain from the raw spectra to the purified Raman spectra. In detail, we compared (1) area normalization versus z ‐score normalization, (2) direct reconstruction of the difference spectra versus reconstruction of zero‐centered difference spectra and (3) collective baseline correction of the reconstructed spectra versus piecewise baseline correction of the reconstructed spectra and, finally, (4) analyzed the influence of the shift of the excitation wavelength on the quality of the reconstructed spectra. Statistical analysis of the spectra showed that – in our experiments – the best results were obtained for the z ‐score normalization before subtraction of the normalized spectra, followed by zero‐centering of the difference spectra before reconstruction and a piecewise baseline correction of the pure Raman spectra. With our equipment, a wavelength shift from 784 to 785 nm provided reconstructed spectra of best quality. The analyzed specimens were different tissue types of pigs, tissue from the oral cavity of humans and a model solution of dye dissolved in ethanol. © 2015 The Authors. Journal of Raman Spectroscopy published by John Wiley &amp; Sons Ltd.
Changes in influenza A (H5N1) epidemiology discussed at World Health Organization intercountry consultation in Manila (2005)

In May 2005 the World Health Organization (WHO) organised an intercountry consultation in Manila to discuss the implications of an apparent change in the epidemiology of Influenza A (H5N1) infection in Asia
Select Paramyxoviral V Proteins Inhibit IRF3 Activation by Acting as Alternative Substrates for Inhibitor of κB Kinase ϵ (IKKe)/TBK1 (2008)

V accessory proteins from Paramyxoviruses are important in viral evasion of the innate immune response. Here, using a cell survival assay that identifies both inhibitors and activators of interferon regulatory factor 3 (IRF3)-mediated gene induction, we identified select paramyxoviral V proteins that inhibited double-stranded RNA-mediated signaling; these are encoded by mumps virus (MuV), human parainfluenza virus 2 (hPIV2), and parainfluenza virus 5 (PIV5), all members of the genus Rubulavirus. We showed that interaction between V and the IRF3/7 kinases, TRAF family member-associated NFkappaB activator (TANK)-binding kinase 1 (TBK1)/inhibitor of kappaB kinase epsilon (IKKe), was essential for this inhibition. Indeed, V proteins were phosphorylated directly by TBK1/IKKe, and this, intriguingly, resulted in lowering of the cellular level of V. Thus, it appears that V mimics IRF3 in both its phosphorylation by TBK1/IKKe and its subsequent degradation. Finally, a PIV5 mutant encoding a V protein that could not inhibit IKKe was much more susceptible to the antiviral effects of double-stranded RNA than the wild-type virus. Because many innate immune response signaling pathways, including those initiated by TLR3, TLR4, RIG-I, MDA5, and DNA-dependent activator of IRFs (DAI), use TBK1/IKKe as the terminal kinases to activate IRFs, rubulaviral V proteins have the potential to inhibit all of them.
Condensing enzymes from Cuphea wrightii associated with medium chain fatty acid biosynthesis (1998)

Seed oils of most Cuphea species contain > 90% medium chain (C8-C14) fatty acids. Thioesterases with specificity for these substrates are important determinants of the medium chain phenotype. The role of condensing enzymes, however, has not been investigated. cDNA clones encoding beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS) were isolated from C. wrightii, a C10/C12-producing species. Deduced amino acid sequences of four unique clones were approximately 60% identical to plant KAS I sequences and approximately 75% identical to a distinct class of KAS sequences recently identified in castor and barley. A 46 kDa protein that was observed only in developing and mature seed was detected using antiserum directed against recombinant Cuphea KAS protein. The 46 kDa protein was abundant in developing seeds of six medium chain-producing Cuphea species but barely detected in one long chain-producing species. A 48 kDa protein identified immunologically as KAS I was expressed in both medium and long chain-producing Cuphea species and was detected in all tissues tested. In in vitro assays, extracts from C. wrightii and C. viscosissima developing embryos were unable to extend fatty acid chains beyond C10 following treatment with 10 microns cerulenin, a potent inhibitor of KAS I. However, a C. viscosissima mutant, cpr-1, whose seed oils are deficient in caprate relative to wild type, was impaired in extension of C8 to C10 in this assay and Western analysis revealed a specific deficiency in 46 kDa KAS in cpr-1 embryos. These results implicate cerulenin-resistant condensing activity in production of medium chain fatty acids in Cuphea.
Determinants of Tumor Response and Survival With Erlotinib in Patients With Non—Small-Cell Lung Cancer (2004)

Erlotinib was active and well tolerated in this patient population, and further clinical development is clearly warranted. Cutaneous rash seems to be a surrogate marker of clinical benefit, but this finding should be confirmed in ongoing and future studies.
Microsatellite instability in primary and metastatic colorectal cancers (1995)

Microsatellite instability characterizes a sub-set of sporadic colorectal cancers (CRCs) as well as CRCs from patients with hereditary non-polyposis colorectal cancer (HNPCC). In order to clarify when the cells acquire a replication-error phenotype (RER) during colorectal-tumor progression, we examined the incidence of RER in 80 primary tumors and 36 liver metastases at 8 microsatellite loci; 1 mono-, 5 di-, 1 tetra- and 1 pentanucleotide. RER were detected in 20.1% (17/80) of primary tumors, including 5 tumors showing RER at 2 or more loci (RER2), while the incidence of RER in liver metastases (22.2%, 8/36) was almost the same as that in primary tumors, and there was only one RER2 case in metastases. There were 3 cases in which both primary tumors and liver metastases had the same type of RER at the same locus, and there were 2 cases that showed RER in primary tumors but not in liver metastases. In contrast, there was no case in which RER was detected in a metastasis but not in the corresponding primary tumor. The RER phenotype did not show correlation with any clinicopathological parameters of cancer-cell aggressiveness, such as clinical staging, histological grade and survival. These results indicate that a sub-set of CRCs acquire the RER phenotype in the relatively early stages of colorectal carcinogenesis, and that the RER phenotype is not associated with aggressiveness of CRCs.
Swine flu sequelae (1980)

THE SEQUELA of an inflammatory neuritis, the Guillain-Barré syndrome (GBS), following administration of the swine flu vaccine, presents a unique opportunity to view the usually submerged world of Poisson statistics. Out of more than 40 million Americans who received swine flu immunization, only about 500 showed development of the neuritis, approximately five times the normal incidence of this disease. In a less massive immunization program (which, following the swine flu debacle, all future programs will probably be), the chances of detecting such a rare complication would have been remote. In fact, even with the large numbers of people immunized with the vaccine, it was almost miraculous that the association was first entertained and then established, particularly since GBS is not a reportable disease. Although the association of the syndrome with influenza immunization is instructive to physicians, the cost to society for this instruction is sobering. Claims approaching $1 billion have
Some Illumination on the Mechanism of SiO2 Etching in  HF  Solutions (1983)

The etching of in aqueous buffered solutions can be impeded or stopped through the application of an electric field. In CMOS fabrication, very low levels of light can cause the effect. Parallel reaction paths are proposed for the dissolution process, coupled with the electric field's ability to stop or redirect the reaction at an intermediate step.
Extracellular Conversion of Epidermal Growth Factor (EGF) to des-Arg53-EGF by Carboxypeptidase M (1995)

Epidermal growth factor (EGF) is a 53-amino-acid mitogenic polypeptide present in a variety of tissues and fluids including kidney, urine, and amniotic fluid. An EGF isoform, des-Arg53-EGF, has been identified in urine and is the earliest metabolite generated in target cells upon EGF binding. In this study, purified carboxypeptidase M efficiently released the COOH-terminal arginine residue from EGF with a Km = 56 microM, kcat = 388 min-1, and kcat/Km = 6.9 microM-1 min-1. When EGF was incubated with urine or amniotic fluid, des-Arg53-EGF was the only metabolite detected. This conversion was blocked by immunoprecipitation with specific antiserum to carboxypeptidase M or by 10 microM DL-2-mercaptomethyl-3-guanidinoethylthiopropanoic acid (a carboxypeptidase M inhibitor), indicating that the major EGF metabolizing enzyme in these fluids is carboxypeptidase M. When incubated on a confluent monolayer of Madin-Darby canine kidney (MDCK) cells, EGF was readily converted to a single metabolite, des-Arg53-EGF, by carboxypeptidase M. To investigate one possible functional consequence of this conversion, mitogenic activities of EGF and des-Arg53-EGF were tested. Both peptides were equipotent in stimulating [3H]thymidine incorporation in MDCK cells at all doses tested. In addition, inhibition of the conversion of EGF to des-Arg53-EGF by the carboxypeptidase M inhibitor did not affect the mitogenic potency of EGF. These data indicate that carboxypeptidase M, present in a variety of cells and biological fluids, can convert EGF to des-Arg53-EGF. However, in contrast to many other peptide hormones whose activity depends on a final carboxypeptidase processing step, removal of Arg53 of EGF is not required for its mitogenic activity.
Autism Spectrum Disorders: A Research Review for Practitioners (2003)

Part I: Introduction. From Kanner to the millennium: scientific advances that have shaped clinical practice. Part II: Interdisciplinary Approaches to Assessment. Contributions of the psychiatrist. Contributions of psychology. Contributions of pediatrics. Contributions of neurology. Part III: Treatment. Nonmedical interventions for autism spectrum disorders. Pharmacotherapy. Alternative theories: assessment and therapy options. Cultural issues in autism. Professional-parent collaboration: the M.I.N.D. Institute model. Afterword: some thoughts on the M.I.N.D. Institute model. Appendix: resources. Index.
A new complement function: solubilization of antigen-antibody aggregates. (1975)

Antigen-antibody aggregates are solubilized when incubated with fresh serum at 37 degrees, yielding immune-complexes of relatively small molecular weight which contain antigen, antibody, and complement (C3)determinants. Solubilization is complement-dependent,requires free Mg++ but not Ca++, and proceeds in sera from C4- or C5-deficient animals. It is accelerated in the presence of Ca++ in normal or C4-deficient guinea pig serum, suggesting involvement of the Cl-bypass activation of the properdin system. Immune precipitates can also be solubilized by monovalent fragments (Fab) of antibodies directed against determinants of the antibody molecules included in the antigen-antibody lattice. Similarly, it is suggested that complement-mediated solubilization might be induced by the combination of a complement fragment with the antibody in the immune-aggregate.
Systematic Review of Intestinal Microbiota Transplantation (Fecal Bacteriotherapy) for Recurrent Clostridium difficile Infection (2011)

Clostridium difficile infection (CDI) is a gastrointestinal disease believed to be causally related to perturbations to the intestinal microbiota. When standard treatment has failed, intestinal microbiota transplantation (IMT) is an alternative therapy for patients with CDI. IMT involves infusing intestinal microorganisms (in a suspension of healthy donor stool) into the intestine of a sick patient to restore the microbiota. However, protocols and reported efficacy for IMT vary. We conducted a systematic literature review of IMT treatment for recurrent CDI and pseudomembranous colitis. In 317 patients treated across 27 case series and reports, IMT was highly effective, showing disease resolution in 92% of cases. Effectiveness varied by route of instillation, relationship to stool donor, volume of IMT given, and treatment before infusion. Death and adverse events were uncommon. These findings can guide physicians interested in implementing the procedure until better designed studies are conducted to confirm best practices.
Vancomycin (2005)

Dr. McNamara is Instructor of Medicine, Mayo Clinic College of Medicine, Rochester, MN. Dr. Steckelberg is Professor of Medicine, Mayo Clinic College of Medicine. None of the following authors or the departments with which they are affiliated has received anything of value from or owns stock in a commercial company or institution related directly or indirectly to the subject of this article: Dr. McNamara and Dr. Steckelberg. Reprint requests: Dr. Steckelberg, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905.
Follow-up Study of Fecal Microbiota Transplantation (FMT) for the Treatment of Refractory Irritable Bowel Syndrome (IBS) (2013)

Purpose: The etiology of IBS is multifactorial, with intestinal microbiota being increasingly implicated in its pathogenesis. FMT restores fecal microbiome diversity in patients with refractory C. difficile infection, and has impressive cure rates. We postulated FMT treatment of refractory IBS might result in similar benefit. Methods: A follow-up study was conducted of all patients who had FMT for refractory IBS after interventions of dietary modification, probiotics, antibiotics, and/or anti-depressants had failed. A 41-point questionnaire assessed demographic and pre- and post-FMT data, quantifying severity of abdominal pain, bloating, flatus, and dyspepsia (severe=3, moderate=2, mild=1, none=0); diarrhea (nl=0, 1-2 BM/day>nl= 1, 3-4 BM/day>nl=2, >4 BM/day>nl= 3), constipation (nl=0, >4 BM/wk=1, 2-3 BM/wk=2, <2 BM/wk=3), and global well-being (poor=3, acceptable=2, good=1). Results: Thirteen of 15 eligible patients (54% women) completed the study. Average age was 45 years (range: 23-75 years). Patients had IBS for an average of 73 months before FMT (range: 12-180 months). Average time from FMT to data collection was 11 months (range: 6-18 months). Nine patients (64%) had IBS-D, three (21%) had IBS-C and one had IBS-M. Eleven patients (79%) had FMT once, one patient twice, and one patient three times. Eleven patients (79%) had abdominal pain before FMT (mean score: 2.55); after FMT, resolution, improvement, or no change was reported in three (27%), five (46%), and three (27%) patients, respectively (mean score: 1.45). Twelve patients (80%) complained of bloating before FMT (mean score: 2.25), which resolved, improved, or did not change in two (17%), four (33%), and six (50%) patients, respectively (mean score: 1.42). Before FMT, 12 patients (92%) had flatus (mean score: 2.4), and after FMT, resolution, improvement, no change, or worsening of flatus was reported in one (8%), four (33%), six (50%), and one (8%) patient, respectively (mean score: 1.75). Six patients (43%) had dyspepsia before FMT (mean score: 1.83) and two patients (33.3%) reported resolution, two (33.3%) noted improvement, and two (33.3%) had no change after FMT (mean score: 1.17). In nine IBS-D patients, pre-FMT score was 1.89 and post-FMT mean score was 0.78. Of the three patients with IBS-C, mean pre-FMT score was 1.33 and post-FMT mean score was 0.33. One patient had IBS-M and had improved diarrhea and constipation after FMT. Three patients (23%) reported no improvement. Before FMT, global well-being was reported as “good” in zero patients, “acceptable” in four patients (30%), and “poor” in nine patients (69%) (mean score: 2.69). After FMT, global well-being was “good” in three patients (23%), “acceptable” in six (46%) and “poor” in four (30%) (mean score: 1.92). Conclusion: FMT resolved or improved symptoms in 70% of our patients with refractory IBS, including abdominal pain (72%), bowel habit (69%), dyspepsia (67%), bloating (50%), and flatus (42%). FMT also resulted in improved quality of life (46%).
A new, fast and reliable radioimmunoassay of brain natriuretic peptide in human plasma. Reference values in healthy subjects and in patients with different diseases (1997)

A new, fast and reliable radioimmunoassay for measurement of brain natriuretic peptide (BNP) in human plasma has been developed and its application is reported in healthy subjects and in patients with congestive heart failure, chronic renal failure, liver cirrhosis and essential hypertension. The antibody was raised in rabbits, the tracer was made by the iodogen method and polyethylene glycol was used for separation of free and bound tracer. BNP was extracted from plasma using Sep-Pak C18 cartridges. The recovery of unlabelled BNP added to plasma was 77.5 +/- 6.2% (mean +/- SD). The detection limit in plasma was 0.55 pmol l-1. No cross-reactivity existed with the natriuretic peptides ANP, CNP or urodilatin. In 124 healthy subjects the mean BNP was 1.8 +/- 1.0 pmol l-1 (SD), range 0.6-5.5. BNP increased slightly with age, was higher in women than men and had no circadian rhythm. In eight patients with congestive heart failure the median BNP level was 30.5 pmol l-1, range 3.9-65.3. In 14 patients with chronic renal failure the median BNP level was 50.5 pmol l-1, range 10.9-219.8 before dialysis, and 38.0 pmol l-1, range 9.4-180.0 immediately following dialysis. In 25 patients with liver cirrhosis the median BNP value was 7.8 pmol l-1, range 1.2-43.1. There was no difference between patients with or without ascites. In 18 medically treated patients with essential hypertension the median BNP level was 5.0 pmol l-1, range 1.2-45.5 pmol l-1.
REGULATION OF HUMAN IMMUNODEFICIENCY VIRUS REPLICATION (1991)

Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years, we have witnessed the emergence of two zoonotic, highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and ...Read More
Stream warehousing with DataDepot (2009)

We describe DataDepot, a tool for generating warehouses from streaming data feeds, such as network-traffic traces, router alerts, financial tickers, transaction logs, and so on. DataDepot is a streaming data warehouse designed to automate the ingestion of streaming data from a wide variety of sources and to maintain complex materialized views over these sources. As a streaming warehouse, DataDepot is similar to Data Stream Management Systems (DSMSs) with its emphasis on temporal data, best-effort consistency, and real-time response. However, as a data warehouse, DataDepot is designed to store tens to hundreds of terabytes of historical data, allow time windows measured in years or decades, and allow both real-time queries on recent data and deep analyses on historical data. In this paper we discuss the DataDepot architecture, with an emphasis on several of its novel and critical features. DataDepot is currently being used for five very large warehousing projects within AT&T; one of these warehouses ingests 500 Mbytes per minute (and is growing). We use these installations to illustrate streaming warehouse use and behavior, and design choices made in developing DataDepot. We conclude with a discussion of DataDepot applications and the efficacy of some optimizations.
Golimumab, a human antibody to tumour necrosis factor α given by monthly subcutaneous injections, in active rheumatoid arthritis despite methotrexate therapy: the GO-FORWARD Study (2008)

The addition of golimumab to methotrexate in patients with active RA despite methotrexate therapy significantly reduced the signs and symptoms of RA and improved physical function.
STATs and Gene Regulation (1997)

STATs (signal transducers and activators of transcription) are a family of latent cytoplasmic proteins that are activated to participate in gene control when cells encounter various extracellular polypeptides. Biochemical and molecular genetic explorations have defined a single tyrosine phosphorylation site and, in a dimeric partner molecule, an Src homology 2 (SH2) phosphotyrosine-binding domain, a DNA interaction domain, and a number of protein-protein interaction domains (with receptors, other transcription factors, the transcription machinery, and perhaps a tyrosine phosphatase). Mouse genetics experiments have defined crucial roles for each known mammalian STAT. The discovery of a STAT in Drosophila, and most recently in Dictyostelium discoideum, implies an ancient evolutionary origin for this dual-function set of proteins.
Design and Use of Fluorescent Fusion Proteins in Cell Biology (2005)

This unit describes strategies for designing functional fluorescent fusion protein constructs. Such constructs can be exploited as probes of cellular environments, protein dynamics, protein life histories, protein binding partners, and markers in living cells. The properties and uses of many currently available fluorescent proteins are discussed. In addition, alternative approaches and troubleshooting guidelines are provided.
Anti-interleukin 5 But Not Anti-IgE Prevents Airway Inflammation and Airway Hyperresponsiveness (1999)

The role of IL-5 and allergen-specific IgE in the development of eosinophilic airway inflammation and airway hyperresponsiveness (AHR) was investigated in a murine model. BALB/c mice were sensitized to ovalbumin (OVA) by intraperitoneal injection on Days 1 and 14, followed by airway challenge with OVA on Days 28 and 29. Anti-IL-5 (TRFK-5) or anti-IgE (antibody 1-5) was administered before each airway challenge. Sensitized and challenged mice developed increased OVA-specific IgE serum levels, Th2 cytokine production by peribronchial lymph node (PBLN) cells, increased numbers of eosinophils (predominantly located in the peribronchial regions of the lungs), and increased airway responsiveness to methacholine (MCh). Anti-IgE treatment significantly decreased serum anti-OVA IgE levels and prevented the development of anaphylaxis but failed to affect T cell function, eosinophil airway infiltration, and AHR in sensitized and challenged mice. In contrast, treatment with anti-IL-5 antibody did not affect B cell (Ig serum levels), T cell (cytokine production), or mast cell function (immediate cutaneous reactivity) but completely inhibited development of eosinophilic lung inflammation and AHR. These data identify IL-5-mediated eosinophilia as a major target for development of AHR in this model, with little effect resulting from neutralization of IgE.