gebhart/patrepeval huggingface dataset:
Myeloperoxidase-rich Ly-6C+ myeloid cells infiltrate allografts and contribute to an imaging signature of organ rejection in mice (2010)

Rates of graft rejection are high among recipients of heart transplants. The onset and progression of clinically significant heart transplant rejection are currently monitored by serial biopsy, but this approach is highly invasive and lacks sensitivity. Here, we have developed what we believe to be a new technique to measure organ rejection noninvasively that involves the exploration of tissue-infiltrating leukocytes as biomarker sources for diagnostic imaging. Specifically, we profiled the myeloid response in a murine model of heart transplantation with the aim of defining and validating an imaging signature of graft rejection. Ly-6Chi monocytes, which promote inflammation, accumulated progressively in allografts but only transiently in isografts. Ly-6Clo monocytes, which help resolve inflammation, did not accumulate, although they composed the majority of the few remaining monocytes in isografts. The persistence of Ly-6Chi monocytes in allografts prompted us to screen for a Ly-6Chi monocyte-associated imaging marker. Low-density array data revealed that Ly-6Chi monocytes express 10-fold higher levels of myeloperoxidase (MPO) than Ly-6Clo monocytes. Noninvasive magnetic resonance imaging of MPO with an MPO-activatable Gd-chelate revealed a spatially defined T1-weighted signal in rejected allografts but not in isografts or MPO-deficient allograft recipients. Flow cytometry, enzymography, and histology validated the approach by mapping MPO activity to Ly-6Chi monocytes and neutrophils. Thus, MPO imaging represents a potential alternative to the current invasive clinical standard by which transplants are monitored.
The correlation ofin vivoandex vivotissue dielectric properties to validate electromagnetic breast imaging: initial clinical experience (2009)

Electromagnetic (EM) breast imaging provides low-cost, safe and potentially a more specific modality for cancer detection than conventional imaging systems. A primary difficulty in validating these EM imaging modalities is that the true dielectric property values of the particular breast being imaged are not readily available on an individual subject basis. Here, we describe our initial experience in seeking to correlate tomographic EM imaging studies with discrete point spectroscopy measurements of the dielectric properties of breast tissue. The protocol we have developed involves measurement of in vivo tissue properties during partial and full mastectomy procedures in the operating room (OR) followed by ex vivo tissue property recordings in the same locations in the excised tissue specimens in the pathology laboratory immediately after resection. We have successfully applied all of the elements of this validation protocol in a series of six women with cancer diagnoses. Conductivity and permittivity gauged from ex vivo samples over the frequency range 100 Hz-8.5 GHz are found to be similar to those reported in the literature. A decrease in both conductivity and permittivity is observed when these properties are gauged from ex vivo samples instead of in vivo. We present these results in addition to a case study demonstrating how discrete point spectroscopy measurements of the tissue can be correlated and used to validate EM imaging studies.
Enhanced mucosal and systemic immune responses to Helicobacter pylori antigens through mucosal priming followed by systemic boosting immunizations (2003)

It is estimated that Helicobacter pylori infects the stomachs of over 50% of the world's population and if not treated may cause chronic gastritis, peptic ulcer disease, gastric adenocarcinoma and gastric B-cell lymphoma. The aim of this study was to enhance the mucosal and systemic immune responses against the H. pylori antigens cytotoxin-associated gene A (CagA) and neutrophil-activating protein (NAP), through combinations of mucosal and systemic immunizations in female BALB/c mice. We found that oral or intranasal (i.n.) followed by i.m. immunizations induced significantly higher serum titres against NAP and CagA compared to i.n. alone, oral alone, i.m. alone, i.m. followed by i.n. or i.m. followed by oral immunizations. However, only oral followed by i.m. immunizations induced anti-NAP antibody-secreting cells in the stomach. Moreover, mucosal immunizations alone or in combination with i.m., but not i.m. immunizations alone, induced mucosal immunoglobulin A (IgA) responses in faeces. Any single route or combination of immunization routes with NAP and CagA preferentially induced antigen-specific splenic interleukin-4-secreting cells and far fewer interferon-gamma-secreting cells in the spleen. Moreover, i.n. immunizations alone or in combination with i.m. immunizations induced predominantly serum IgG1 and far less serum IgG2a. Importantly, we found that while both i.n. and i.m. recall immunizations induced similar levels of serum antibody responses, mucosal IgA responses in faeces were only achieved through i.n. recall immunization. Collectively, our data show that mucosal followed by systemic immunization significantly enhanced local and systemic immune responses and that i.n. recall immunization is required to induce both mucosal and systemic memory type responses.
Genetics and lung disease. (1991)

We agree with Dr Gregg that comparison with normal values may be misleading. Clearly, pre- dicted values must be established for individual patients by their doctor.
Biofilm exopolysaccharides: a strong and sticky framework (2001)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
On combining classifiers (1998)

We develop a common theoretical framework for combining classifiers which use distinct pattern representations and show that many existing schemes can be considered as special cases of compound classification where all the pattern representations are used jointly to make a decision. An experimental comparison of various classifier combination schemes demonstrates that the combination rule developed under the most restrictive assumptions-the sum rule-outperforms other classifier combinations schemes. A sensitivity analysis of the various schemes to estimation errors is carried out to show that this finding can be justified theoretically.
Quantitative Epigenetics Through Epigenomic Perturbation of Isogenic Lines (2011)

Interindividual differences in chromatin states at a locus (epialleles) can result in gene expression changes that are sometimes transmitted across generations. In this way, they can contribute to heritable phenotypic variation in natural and experimental populations independent of DNA sequence. Recent molecular evidence shows that epialleles often display high levels of transgenerational instability. This property gives rise to a dynamic dimension in phenotypic inheritance. To be able to incorporate these non-Mendelian features into quantitative genetic models, it is necessary to study the induction and the transgenerational behavior of epialleles in controlled settings. Here we outline a general experimental approach for achieving this using crosses of epigenomically perturbed isogenic lines in mammalian and plant species. We develop a theoretical description of such crosses and model the relationship between epiallelic instability, recombination, parent-of-origin effects, as well as transgressive segregation and their joint impact on phenotypic variation across generations. In the limiting case of fully stable epialleles our approach reduces to the classical theory of experimental line crosses and thus illustrates a fundamental continuity between genetic and epigenetic inheritance. We consider data from a panel of Arabidopsis epigenetic recombinant inbred lines and explore estimates of the number of quantitative trait loci for plant height that resulted from a manipulation of DNA methylation levels in one of the two isogenic founder strains.
Thy1‐hAPPLond/Swe+ mouse model of Alzheimer's disease displays broad behavioral deficits in sensorimotor, cognitive and social function (2012)

Alzheimer's disease (AD), the most common form of dementia, is an age-dependent progressive neurodegenerative disorder. β-amyloid, a metabolic product of the amyloid precursor protein (APP), plays an important role in the pathogenesis of AD. The Thy1-hAPP(Lond/Swe+) (line 41) transgenic mouse overexpresses human APP751 and contains the London (V717I) and Swedish (K670M/N671L) mutations. Here, we used a battery of behavioral tests to evaluate general activity, cognition, and social behavior in six-month-old male Thy1-hAPP(Lond/Swe+) mice. We found hyperactivity in a novel environment as well as significant deficits in spontaneous alternation behavior. In fear conditioning (FC), Thy1-hAPP(Lond/Swe+) mice did not display deficits in acquisition or in memory retrieval in novel context of tone-cued FC, but they showed significant memory retrieval impairment during contextual testing in an identical environment. Surprisingly, in a standard hidden platform water maze, no significant deficit was detected in mutant mice. However, a delayed-matching-to-place paradigm revealed a significant deficit in Thy1-hAPP(Lond/Swe+) mice. Lastly, in the social novelty session of a three-chamber test, Thy1-hAPP(Lond/Swe+) mice exhibited a significantly decreased interest in a novel versus a familiar stranger compared to control mice. This could possibly be explained by decreased social memory or discrimination and may parallel disturbances in social functioning in human AD patients. In conclusion, the Thy1-hAPP(Lond/Swe+) mouse model of AD displayed a behavioral phenotype that resembles, in part, the cognitive and psychiatric symptoms experienced in AD patients.
Molecular Cloning and Characterization of a Mitogen-activated Protein Kinase-associated Intracellular Chloride Channel (1999)

ERK7, a member of the mitogen-activated protein kinase family, has a carboxyl-terminal tail that is required for ERK7 activation, cellular localization, and its ability to inhibit DNA synthesis. To identify proteins that interact with ERK7, we utilized a yeast two-hybrid screen with the COOH-terminal tail of ERK7 as bait and isolated the cDNA for a novel protein termed CLIC3. The interaction between CLIC3 and ERK7 in mammalian cells was confirmed by co-immunoprecipitation. CLIC3 has significant homology to human intracellular chloride channels 1 (NCC27/CLIC1) and 2 and bovine kidney chloride channel p64. Like NCC27/CLIC1, CLIC3 is predominantly localized in the nucleus and stimulates chloride conductance when expressed in cells. Taken together, these results suggest that CLIC3 is a new member of the human CLIC family. The observed interaction between CLIC3 and ERK7 is the first demonstration of a stable complex between a protein that activates chloride ion transport and a member of the mitogen-activated protein kinase family of signal transducers. The specific association of CLIC3 with the COOH-terminal tail of ERK7 suggests that CLIC3 may play a role in the regulation of cell growth.
Amino Acid and Peptide Absorption in Man (1977)

An intestinal perfusion technique has been used in man to study absorption of glycine and L-alanine from the dipeptide glycyl-L-alanine and the tripeptide L-alanylglycylglycine. Glycine was absorbed faster from both peptides than from their equivalent free amino acid mixtures, and in the dipeptide experiments the differential in absorption rate of glycine and L-alanine observed when the equivalent mixtures of free amino acids were perfused was not observed during the perfusions with glycyl-L-alanine. These findings suggest that peptide-bound and free amino acids are absorbed from the normal human intestine by separate transport processes. Absorption of individual amino acids from two partial enzymic hydrolysates of casein which consisted predominantly of small peptides was then studied. Absorption of α-amino nitrogen was greater from the casein hydrolysates than from their two equivalent mixtures of amino acids. There was considerable variation in absorption of individual amino acids during perfusion of the two free amino acid mixtures, but this was much reduced when the enzymic hy-drolysate solutions were perfused. This was so because a number of individual amino acid residues that were poorly absorbed from the free amino acid mixtures were absorbed significantly faster from the enzymic hydrolysates. These results suggested that there could be an advantage in using mixtures of peptides rather than free amino acids as the nitrogen source in elemental diets. To test this hypothesis, plasma α-amino nitrogen increments and extent as well as site of absorption of amino acid residues were compared after two liquid test meals containing a protein hydrolysate or its equivalent amino acid mixture had been administered to normal human subjects. The finding of less secretion of fluid into the intestinal lumen, and higher concentrations of α-amino nitrogen in plasma after the protein hydrolysate meal, and the fact that after the two meals amino acid residues were absorbed to the same extent and at the same location, suggest that it would be worth considering the use of peptide mixtures as the nitrogen source in elemental diets.
The conversion of .ALPHA.-aminoisobutyrate decomposing enzyme into simple L-alanine: .ALPHA.-Ketobutyrate aminotransferase by chemical modification. (1978)

Molecular weight of α-aminoisobutyrate (AIB) decomposing enzyme was estimated to be about 180, 000 by the Hedrick-Smith's method and dodecylsulfate-polyacrylamide gel electrophoresis of this enzyme showed a single band having molecular weight of 45, 000. Spectrophotometric titration of the enzyme with pyridoxal 5'-phosphate at pH 7.5 gave four equivalent binding sites per mole. Therefore, AIB decomposing enzyme seemed to be a tetrameric form of a single polypeptide chain. The enzyme was inactivated by phenylglyoxal. In partial inactivation of the enzyme with phenylglyoxal, both AIB decomposing activity and L-alanine: α-ketobutyrate transaminase activity were proportionally lost. This finding was consistent with the concept of a single active site for both activities. The holoenzyme was converted into simple aminotransferase by modification with diethylpyrocarbonate, indicating that only AIB decomposing activity was inactivated. The com-plete inactivation of AIB decomposing activity was achieved by the modification of 1 to 1.5 histidyl residues per monomer of the enzyme. Amino acid specificity and a-keto acid specificity in transamination of the converted simple aminotransferase were not different from those of native enzyme.
Histone Deacetylase Enzymes as Potential Drug Targets in Cancer and Parasitic Diseases (2006)

The elucidation of the mechanisms of transcriptional activation and repression in eukaryotic cells has shed light on the important role of acetylation-deacetylation of histones mediated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), respectively. Another group belonging to the large family of sirtuins (silent information regulators (SIRs)) has an (nicotinamide adenine dinucleotide) NAD(+)-dependent HDAC activity. Several inhibitors of HDACs (HDIs) have been shown to exert antitumor effects. Interestingly, some of the HDIs exerted a broad spectrum of antiprotozoal activity. The purpose of this review is to analyze some of the current data related to the deacetylase enzymes as a possible target for drug development in cancer and parasitic diseases with special reference to protozoan infections. Given the structural differences among members of this family of enzymes, development of specific inhibitors will not only allow selective therapeutic intervention, but may also provide a powerful tool for functional study of these enzymes.
Output characterization of constant bit rate traffic in FIFO networks (2009)

We provide an analytical proof that the departure rate of a CBR flow at an overloaded link with FIFO buffers is proportional to the flow's share of the total offered load at the link. This property of FIFO scheduling was recently validated in in a series of traffic measurement experiments. An extension of the analysis to a multi-node scenario shows that the output rate of a flow in a network with many overloaded FIFO switches approaches the pessimistic values given by blind multiplexing.
Comparative analysis of various tumor-associated antigen-specific t-cell responses in patients with hepatocellular carcinoma (2011)

Cyclophilin B, SART2, SART3, p53, MRP3, AFP, and hTERT were immunogenic targets for HCC immunotherapy. TAA-specific immunotherapy combined with HCC treatments and anti-CTLA-4 antibody has the possibility to produce stronger tumor-specific immune responses.
Arterial Versus Plethysmographic Dynamic Indices to Test Responsiveness for Testing Fluid Administration in Hypotensive Patients: A Clinical Trial (2006)

In the present study, we compared indices of respiratory-induced variation obtained from direct arterial blood pressure measurement with analogous indices obtained from the plethysmogram measured by the pulse oximeter to assess the value of these indices for predicting the cardiac output increase in response to a fluid challenge. Thirty-two fluid challenges were performed in 22 hypotensive patients who were also monitored with a pulmonary artery catheter. Hemodynamic and plethysmographic data were collected before and after intravascular volume expansion. Patients were classified as nonresponders if their cardiac index did not increase by 15% from baseline. Nonresponding patients had both lower arterial pulse variation ([10 +/- 4]% vs [19 +/- 13]%, P = 0.020) and lower plethysmographic pulse variation ([12 +/- 7]% vs [21 +/- 14]%, P = 0.034) when compared with responders. Fluid responsiveness was similarly predicted by arterial and plethysmographic pulse variations (area under ROC curve 0.74 vs 0.72, respectively, P = 0.90) and by arterial and plethysmographic systolic variation (area under ROC curve 0.64 vs 0.72, respectively, P = 0.50). Nonresponders were identified by changes in pulse variation both on arterial and plethysmographic waveform (area under ROC curve 0.80 vs 0.87, respectively, P = 0.40) and by changes in arterial and plethysmographic systolic variations (area under ROC curve 0.84 vs 0.80, respectively, P = 0.76). In the population studied, plethysmographic dynamic indices of respiratory-induced variation were just as useful for predicting fluid responsiveness as the analogous indices derived from direct arterial blood pressure measurement. These plethysmographic indices could provide a noninvasive tool for predicting the cardiac output increase by administering fluid.
Scalable classification over SQL databases (1999)

We identify data-intensive operations that are common to classifiers and develop a middleware that decomposes and schedules these operations efficiently using a backend SQL database. Our approach has the added advantage of not requiring any specialized physical data organization. We demonstrate the scalability characteristics of our enhanced client with experiments on Microsoft SQL Server 7.0 by varying data size, number of attributes and characteristics of decision trees.
MXI1, a putative tumor suppressor gene, suppresses growth of human glioblastoma cells. (1997)

The Mxi1 protein functions in a regulatory network with members of the c-Myc family, in which c-Myc activates transcription and stimulates cell proliferation, and Mxi1 negatively regulates these actions. Inactivation of the MXI1 gene could, therefore, inhibit differentiation and enhance proliferation in the presence of normal levels of c-Myc, and thus MXI1 is a potential tumor suppressor gene. We and others have previously mapped the MXI1 gene to the distal portion of chromosome 10q, a region that is rearranged or affected by allelic loss in many astrocytic brain tumors. Using a newly described polymorphic CA microsatellite repeat in the third MXI1 intron, we show that 7 of 11 informative glioblastomas demonstrated MXI1 allelic loss. Sequence analysis revealed no somatic mutations in any of the six MXI1 coding exons, similar to findings in prostate tumors with MXI1 allelic loss. To determine whether MXI1 can indeed function as a suppressor of growth, we have introduced a steroid-inducible MXI1 expression vector into the U87MG cell line, a glioblastoma cell line lacking endogenous MXI1 expression. Induction of MXI1 expression resulted in a decreased growth rate and distinct morphological changes. Furthermore, cell cycle analysis demonstrated that induction of MXI1 results in accumulation of cells in the G2-M phase. Thus, these studies support the notion that MXI1 normally functions to suppress cell growth and suggest that loss of MXI1 function may play a role in human glioblastoma development.
Phase II study of fluorouracil, leucovorin, and interferon alfa-2a in metastatic colorectal carcinoma. (1993)

PURPOSE To test the activity of a regimen of interferon alfa-2a (IFN alpha-2a) 5 x 10(6) U/m2 subcutaneously (SC) days 1 through 7 combined with leucovorin 500 mg/m2/d intravenously (IV) over 30 minutes and fluorouracil (5-FU) 370 mg/m2/d through IV push 1 hour after leucovorin days 2 through 6 in a phase II study. PATIENTS AND METHODS Forty-six patients with a good performance status (PS) with measurable colorectal cancer and no prior therapy for metastatic disease were entered. Cycles were repeated at 3-week intervals if toxicity had resolved. The 5-FU dose was increased by 15% if toxicity was mild, and decreased by 15% for grade 3 to 4 nonhematologic or grade 4 hematologic toxicity. RESULTS Three complete responses (CRs) and 21 partial responses (PRs) were seen among 44 assessable patients (54%; 95% confidence interval, 39% to 70%). A moderately strong association was noted between PS and response: PS O (n = 26), two CRs and 15 PRs (65%); PS 1 (n = 13), one CR and six PRs (54%); PS 2 (n = 5), zero CRs and zero PRs (0%; two-tailed P = .026). With a median follow-up duration of 18.8 months, the median time to treatment failure (TTF) and survival were 7.8 months and 16.3 months, respectively. Doses were escalated to 425 mg/m2/d 5-FU in 10 patients, but only four tolerated the higher dose. When expressed as the most severe degree of toxicity experienced by each patient across all cycles, grade 3 to 4 toxicity of the following types was observed; mucositis, 37%; diarrhea, 40%; rash, 7%; fatigue, 14%; granulocytopenia, 13%. Dose-limiting toxicity at 370 mg/m2/d 5-FU eventually occurred in 28 patients (61%). Twelve patients (26%) required an IFN alpha-2a dose reduction for constitutional toxicity. CONCLUSION This regimen has promising activity in advanced colorectal cancer, particularly in patients with an Eastern Cooperative Oncology Group (ECOG) PS of 0 to 1.
Sensing the texture of surfaces by anthropomorphic soft fingertips with multi-modal sensors (2004)

This paper describes the development of a human-like multi-modal soft finger and its ability to sense the texture of objects. This fingertip has two silicon rubber layers of different hardness; strain gauges and PVDF films are randomly distributed as tactile sensors. Owing to the dynamics of the silicon between sensors, the fingertip is supposed to have several sensor modalities. Preliminary experiments show that the fingertip can detect the difference between the textures of objects (paper and wood).