gebhart/patrepeval huggingface dataset:
Functional significance of erythropoietin receptor on tumor cells (2006)

Erythropoietin (Epo) is the regulator of red blood cell formation. Its receptor (EpoR) is now found in many cells and tissues of the body. EpoR is also shown to occur in tumor cells and Epo enhances the proliferation of these cells through cell signaling. EpoR antagonist can reduce the growth of the tumor in vivo. In view of our current knowledge of Epo, its recombinant forms and receptor, use of Epo in cancer patients to enhance the recovery of hematocrit after chemotherapy treatment has to be carefully evaluated.
FTIR spectroscopy of biofluids revisited: an automated approach to spectral biomarker identification (2013)

The extraction of disease specific information from Fourier transform infrared (FTIR) spectra of human body fluids demands the highest standards of accuracy and reproducibility of measurements because the expected spectral differences between healthy and diseased subjects are very small in relation to a large background absorbance of the whole sample. Here, we demonstrate that with the increased sensitivity of modern FTIR spectrometers, automatisation of sample preparation and modern bioinformatics, it is possible to identify and validate spectral biomarker candidates for distinguishing between urinary bladder cancer (UBC) and inflammation in suspected bladder cancer patients. The current dataset contains spectra of blood serum and plasma samples of 135 patients. All patients underwent cytology and pathological biopsy characterization to distinguish between patients without UBC (46) and confirmed UBC cases (89). A minimally invasive blood test could spare control patients a repeated cystoscopy including a transurethral biopsy, and three-day stationary hospitalisation. Blood serum, EDTA and citrate plasma were collected from each patient and processed following predefined strict standard operating procedures. Highly reproducible dry films were obtained by spotting sub-nanoliter biofluid droplets in defined patterns, which were compared and optimized. Particular attention was paid to the automatisation of sample preparation and spectral preprocessing to exclude errors by manual handling. Spectral biomarker candidates were identified from absorbance spectra and their 1(st) and 2(nd) derivative spectra using an advanced Random Forest (RF) approach. It turned out that the 2(nd) derivative spectra were most useful for classification. Repeat validation on 21% of the dataset not included in predictor training with Linear Discriminant Analysis (LDA) classifiers and Random Forests (RFs) yielded a sensitivity of 93 ± 10% and a specificity of 46 ± 18% for bladder cancer. The low specificity can be most likely attributed to the unbalanced and small number of control samples. Using this approach, spectral biomarker candidates in blood-derived biofluids were identified, which allow us to distinguish between cancer and inflammation, but the observed differences were tiny. Obviously, a much larger sample number has to be investigated to reliably validate such candidates.
Models of Nociception: Hot‐Plate, Tail‐Flick, and Formalin Tests in Rodents (1999)

Abstract Experimental models of pain include tests of response thesholds to high intensity stimuli (acute pain tests) and changes in spontaneous or evoked behavioral responses in animals with peripheral injury or inflammation (persistent pain models). Acute thermal pain is modeled by the hot‐plate and tail‐flick test, while persistent pain can be modeled by the formalin test. This unit presents protocols for all three of these tests, including preparation of animals (rats or mice), administration of a compound being tested for its analgesic properties and data collection.
Separation of mitochondria by flow field-flow fractionation for proteomic analysis (2008)

Flow field-flow fractionation (FlFFF) has been utilized for size-based separation of rat liver mitochondria. Collected fractions of mitochondria of various sizes were examined by confocal microscopy, and mitochondria of each fraction were lysed and analyzed by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) for the comparison of protein patterns in differently sized mitochondria by densitometric measurements, and for protein characterization of some gel spots with nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS-MS). FlFFF fractions of the mitochondria were also tryptically digested for shotgun proteomic characterization of mitochondrial proteins/peptides by nLC-ESI-MS-MS. Peak area (integrated ion counts) of some peptides extracted from LC-MS chromatograms were examined at different fractions for the quantitative comparison. Among 130 proteins, 105 unique proteins were found to be mitochodrial from the off-line combination of FlFFF and nLC-ESI-MS-MS analysis. It also showed that 23 proteins were found in all fractions but some proteins were found exclusively in certain fractions. Among 25 proteins listed from other subcellular species, seven proteins were known to exist in mitochondria as well as in other subcellular locations, which may support the possible translocation or multiple localizations of proteins among organelles. This study demonstrated effective use of FlFFF for the isolation and/or enrichment of intact mitochondria isolated from cells, as well as its potential use for the fractionation of other subcellular components in the framework of subcellular functional proteomics.
Trading packet headers for packet processing (1995)

In high speed networks, packet processing is relatively expensive while bandwidth is cheap. Thus it pays to add information to packet headers to make packet processing easier. While this is an old idea, we describe several specific new mechanisms based on this principle. We describe a new technique, source hashing, which can provide O(1) lookup costs at the Data Link, Routing, and Transport layers. Source hashing is especially powerful when combined with the old idea of a flow ID; the flow identifier allows packet processing information to be cached, and source hashing allows efficient cache lookups. Unlike Virtual Circuit Identifiers (VCIs), source hashing does not require a round trip delay for set up. In an experiment with the BSD Packet Filter implementation, we found that adding a flow ID and a source hash improved packet processing costs by a factor of 7. We also found a 45% improvement when we conducted a similar experiment with IP packet forwarding. We also describe two other new techniques: threaded indices, which allows fast VCI-like lookups for datagram protocols like IP; and a Data Manipulation Layer, which compiles out all the information needed for Integrated Layer Processing into an easily accessible portion of each packet.
Pertussis resurgence in Toronto, Canada: a population-based study including test-incidence feedback modeling (2011)

Toronto's recent surge in pertussis reflects a true increase in local disease activity; the apparent size of the outbreak has likely been magnified by increasing use of pertussis testing by clinicians, and by improved test sensitivity since 2005. These findings may be applicable to changes in pertussis epidemiology that have been noted elsewhere in North America.
THE EFFECTS OF INBREEDING AT LOCI WITH HETEROZYGOTE ADVANTAGE (1968)

INCE the early studies of FISHER and WRIGHT the theory of selection within populations of finite size has received much attention. KIMURA (1964) has reviewed the part of the theory that is based on continuous models in which it is usually assumed that individuals mate at random within small closed sub-populations or lines. In such a situation we are concerned with the distribution of the frequency of individual genes over many replicate lines, or, equivalently, the distribution of the frequency of identical genes within the same line. In this report we study selection favouring heterozygous individuals with random mating within lines and no selection or crossing occurring between lines. The model for inbreeding which we discuss must be distinguished from an alternative situation, perhaps more common in plants, in which inbreeding occurs within an infinitely large population as a result of non-random mating, for example by selfing or mixed selfing and outcrossing. In the latter type of model, selection also may occur between sublines and recurrent mutation is not required for equilibria of gene frequency to occur without fixation, whereas it is in our model. These equilibrium situations have been analysed recently in some detail by ALLARD and co-workers. Many of their results for single loci are reviewed by JAIN and
Protein Sizing on a Microchip (2001)

We have developed a microfabricated analytical device on a glass chip that performs a protein sizing assay, by integrating the required separation, staining, virtual destaining, and detection steps. To obtain a universal noncovalent fluorescent labeling method, we have combined on-chip dye staining with a novel electrophoretic dilution step. Denatured protein-sodium dodecyl sulfate (SDS) complexes are loaded on a chip and bind a fluorescent dye as the separation begins. At the end of the separation channel, an intersection is used to dilute the SDS below its critical micelle concentration before the detection point. This strongly reduces the background due to dye molecules bound to SDS micelles and also increases the peak amplitude by 1 order of magnitude. Both the on-chip staining and SDS dilution steps occur in the 100-ms time scale and are approximately 10(4) times faster than their conventional counterparts in SDS-PAGE. This represents a much greater speed increase due to microfabrication than has been obtained in other assay steps such as electrophoretic separations. We have designed and tested a microchip capable of sequentially analyzing 11 different samples, with sizing accuracy better than 5% and high sensitivity (30 nM for carbonic anhydrase).
Multiple and Persistent Viral Infections in a Patient With Bare Lymphocyte Syndrome (1987)

Journal Article Multiple and Persistent Viral Infections in a Patient With Bare Lymphocyte Syndrome Get access Max Q. Arens, Max Q. Arens Please address requests for reprints to Dr. Max Arens, St. Louis University Medical Center, 1465 South Grand, St. Louis. Missouri 63104. Search for other works by this author on: Oxford Academic PubMed Google Scholar Alan P. Knutsen, Alan P. Knutsen Search for other works by this author on: Oxford Academic PubMed Google Scholar Kathleen B. Schwarz, Kathleen B. Schwarz Search for other works by this author on: Oxford Academic PubMed Google Scholar Stanford T. Roodman, Stanford T. Roodman Search for other works by this author on: Oxford Academic PubMed Google Scholar Ella M. Swierkosz Ella M. Swierkosz Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 156, Issue 5, November 1987, Pages 837–840, https://doi.org/10.1093/infdis/156.5.837 Published: 01 November 1987 Article history Received: 16 March 1987 Revision received: 05 June 1987 Published: 01 November 1987
Non-replicating expression vectors: applications in vaccine development and gene therapy (1996)

SUMMARY This review presents experimental, preclinical and clinical data illustrating the multiple uses of recombinant non-replicating virus vectors in the fields of immunoprophylaxis and gene therapy.
A top-down low power design technique using clustered voltage scaling with variable supply-voltage scheme (2002)

A novel design technique which combines a variable supply-voltage scheme and a clustered voltage scaling is presented (VS-CVS scheme). A theory to choose the optimum supply voltages in the VS-CVS scheme is discussed which enables us to perform chip design in a top-down fashion. Level-shifting flip-flops are developed which reduce power, delay and area penalties significantly. Application of this technique to an MPEG4 video codec saves 55% of the power dissipation without degrading circuit performance compared to a conventional CMOS design.
Short form 36 questionnaire. (1995)

In a recent article by Ziebland,' the author attempted to assess the usefulness of the short form 36 (SF 36) health status ques- tionnaire in measuring health gain in popu-
Antisense oligodeoxynucleotide-mediated disruption of hippocampal cAMP response element binding protein levels impairs consolidation of memory for water maze training (1997)

Extensive evidence suggests that long term memory (LTM) formation is dependent on the activation of neuronal second messenger systems and requires protein synthesis. The cAMP response element binding protein (CREB) is a constitutively expressed regulatory transcription factor that couples changes in second messenger levels to changes in cellular transcription. Several recent studies suggest that CREB and related transcription factors regulate gene expression necessary for neuronal plasticity and LTM. However, the role of CREB, within defined mammalian brain structures, in mediating the cellular events underlying LTM formation has not been investigated. We examined whether CREB-mediated transcription within the dorsal hippocampus is critical to LTM consolidation of water maze spatial training, which is known to depend on dorsal hippocampal function. Pretraining infusions of antisense oligodeoxynucleotides (ODN) directed against CREB mRNA were used to disrupt hippocampal CREB protein levels in adult rats. Control groups received pretraining infusions of ODN of the same base composition but in a randomized order (scrambled ODN) or buffer. Task acquisition and memory up to 4 h (i.e., short term memory) were similar in CREB antisense ODN and control groups. In contrast, CREB antisense ODN-infused rats exhibited significantly impaired memory 48 h later (i.e., LTM). Moreover, administration of antisense ODN 1 day after training did not affect subsequent retention performance. These findings provide the first evidence that CREB-mediated transcription is integral to hippocampal-dependent memory consolidation processes.
DNA methylation and cancer (1994)

Changes in the pattern of DNA methylation have been a consistent finding in cancer cells. The mostly descriptive nature of these studies and the fact that both hypo- and hypermethylation have been observed at various loci have made it difficult to assess whether these changes are causally involved in the transformation process or whether they reflect the altered physiology of rapidly dividing cancer cells. It is clear, however, that DNA methylation plays an important role in the generation of mutations in human tumors. The high incidence of C-to-T transitions found in the p53 tumor-suppressor gene is attributed to the spontaneous deamination of 5-methylcytosine residues. The multiple observations linking DNA methylation to cancer can be resolved in a model proposing that the high rate of mutation at CpG dinucleotides is due in part to methyltransferase-facilitated deamination. Support for a role of DNA methyltransferase as a mutator enzyme is provided by work with a prokaryotic DNA methyltransferase under S-adenosyl-methionine methyl-donor limiting conditions. Methyl-donor limiting conditions might arise in early stages of tumor development, leading to high rates of methyltransferase-mediated CpG mutagenesis, as seen in human tumors. Such a mechanism is consistent with the frequently reported methionine auxotrophy of cancer cells and with the tumorigenic effects of methyl-deficient diets. Methyl deficiency in tumor cells is also consistent with the commonly observed global hypomethylation of tumor cell DNA, despite normal or even high levels of DNA methyltransferase expression.
Explaining Outliers by Subspace Separability (2013)

Outliers are extraordinary objects in a data collection. Depending on the domain, they may represent errors, fraudulent activities or rare events that are subject of our interest. Existing approaches focus on detection of outliers or degrees of outlierness (ranking), but do not provide a possible explanation of how these objects deviate from the rest of the data. Such explanations would help user to interpret or validate the detected outliers. The problem addressed in this paper is as follows: given an outlier detected by an existing algorithm, we propose a method that determines possible explanations for the outlier. These explanations are expressed in the form of subspaces in which the given outlier shows separability from the inliers. In this manner, our proposed method complements existing outlier detection algorithms by providing additional information about the outliers. Our method is designed to work with any existing outlier detection algorithm and it also includes a heuristic that gives a substantial speedup over the baseline strategy.
High-dose melphalan +/- total body irradiation and autologous hematopoietic stem cell rescue for adult patients with Ewing's sarcoma or peripheral neuroectodermal tumor. (1996)

The role of high-dose therapy and autologous stem cell transplantation (ASCT) in the treatment of patients with Ewing's sarcoma (EWS) remains uncertain. From November 1985 to September 1994, 13 patients aged 16-30 years (median 20.5) received high-dose melphalan (HDM) 140-200 mg/m2 +/- 500 cGy TBI followed by ASCT for relapsed/refractory (n = 4), metastatic (n = 2), or non-metastatic (n = 6) EWS, or for peripheral neuroectodermal tumor (PNET) (n = 1). This regimen was well tolerated with no transplant-related mortality and no toxicity requiring life sustaining measures. Three of the four patients treated for relapsed/refractory EWS had progression-free survivals (PFS) less than 5 months. The only long-term survivor of these four patients received HDM while in complete remission following pulmonary irradiation. Both patients with pulmonary metastases at presentation died just 5 and 6 months post-ASCT. All four patients with non-metastatic, bulky (> 8 cm) osseous EWS progressed at a median of 11 months (range 7-22 months) while the two patients with non-bulky EWS remain progression-free 25+ and 28+ months post-HDM/TBI + ASCT. The 19-year-old patient with a PNET of the thoracoabdominal wall relapsed 4 months post-ASCT. Overall, only three of these 13 patients remain progression-free at 25+, 28+, and 108+ months following HDM +/- TBI and ASCT. In conclusion, HDM +/- TBI did not obviously improve the outcome of these 13 patients relative to that expected following conventional dose therapy alone.
Proliferation of Functional Hair Cells in Vivo in the Absence of the Retinoblastoma Protein (2005)

In mammals, hair cell loss causes irreversible hearing and balance impairment because hair cells are terminally differentiated and do not regenerate spontaneously. By profiling gene expression in developing mouse vestibular organs, we identified the retinoblastoma protein (pRb) as a candidate regulator of cell cycle exit in hair cells. Differentiated and functional mouse hair cells with a targeted deletion of Rb1 undergo mitosis, divide, and cycle, yet continue to become highly differentiated and functional. Moreover, acute loss of Rb1 in postnatal hair cells caused cell cycle reentry. Manipulation of the pRb pathway may ultimately lead to mammalian hair cell regeneration.
Detection of Recent Cannabis Use by Saliva 9-THC Radioimmunoassay (1985)

A non-invasive saliva sample delta 9-THC radioimmunoassay has been applied to 352 samples from 25 male and 10 female marijuana users after administration of one-half to two standard cigarettes (27 mg delta 9-THC/cigarette) and 72 control negative subjects who ingested a large variety of foods, condiments, or medications in an attempt to demonstrate interferences. The shortest duration of a positive was 2 hrs and the longest was 5 hrs after administration of the cannabis. No positives occurred in control subjects.
High level IL-12 production by murine dendritic cells: upregulation via MHC class II and CD40 molecules and downregulation by IL-4 and IL-10. (1996)

We have shown previously that dendritic cells (DC) produce IL-12 upon interaction with CD4+ T cells. Here we ask how this IL-12 production is induced and regulated. Quantitative PCR and in situ hybridization for IL-12 p40 and an ELISA specific for the p70 heterodimer were used to determine IL-12 production. We demonstrate that ligation of either CD40 or MHC class II molecules independently trigger IL-12 production in DC, and that IL-12 production is downregulated by IL-4 and IL-10. The levels of bioactive IL-12 that can be released by triggering with an anti-CD40 mAb or with a T cell hybridoma are high (range 260-4700 pg/ml from 1 X 10(6) DC in 72 h). The CD40-mediated pathway indicates that IL-12 production is induced in DC upon interaction with activated, CD40 ligand-expressing helper T cells, even in the absence of cognate antigen recognition. Side-by-side comparison of IL-12 production, and blocking experiments employing an anti-CD40 ligand mAb, suggest that the CD40-mediated pathway is quantitatively more significant than induction via the MHC class II molecule. The importance of the CD40/CD40 ligand interaction for IL-12 induction in DC likely contributes to the recent finding that mice lacking the CD40 ligand are impaired in mounting Th1 type cell-mediated immune responses.
Generality of the NUX Rule: Kinetic Analysis of the Results of Systematic Mutations in the Trinucleotide at the Cleavage Site of Hammerhead Ribozymes (1995)

In order to study in detail the generality of the NUX (N = A, U, G, or C; X = A, U, or C) rule for the GUC triplet adjacent to the cleavage site in hammerhead ribozymes, two kinetic parameters, namely, kcat and Km, were determined for substrates with mutations in this triplet, which included double mutants with mutations of both N and X. All substrates with mutated cleavage sites were cleaved with reduced efficiency compared to the wild type. However, some mutations mainly affected kcat and others mainly affected Km, a phenomenon that could not have been predicted from previous results. A as the first or third base increased Km by 35- or 30-fold, respectively, while the effect on kcat was small. U as the first or third base decreased kcat by 8- or 15-fold, respectively, while the effect on Km was small. The effect of C as the first base on kinetic parameters was relatively small. The kinetic parameters of double mutants generally were determined by the effects of both individual point mutations. The AUA triplet gave a very much higher kcat than the other double mutants tested. In general, all of the mutants except for the mutant substrate with the CUC triplet had very low cleavage efficiencies, which ranged from 0.6% to 8% of the wild-type value, as a result of the deleterious effects of the mutations on kcat, Km, or both.(ABSTRACT TRUNCATED AT 250 WORDS)