gebhart/patrepeval huggingface dataset:
Taking a Toll on human disease: Toll-like receptor 4 agonists as vaccine adjuvants and monotherapeutic agents (2004)

Toll-like receptor (TLR) agonists are being developed for use as vaccine adjuvants and as stand-alone immunomodulators because of their ability to stimulate innate and adaptive immune responses. Among the most thoroughly studied TLR agonists are the lipid A molecules that target the TLR4 complex. One promising candidate, monophosphoryl lipid A, which is a derivative of lipid A from Salmonella minnesota, has proven to be safe and effective as a vaccine adjuvant in > 120,000 human doses. A new class of synthetic lipid A mimetics, the aminoalkyl glucosaminide 4-phosphates (AGPs), have been engineered specifically to target human TLR4 and are showing promise as vaccine adjuvants and as monotherapeutic agents capable of eliciting nonspecific protection against a wide range of infectious pathogens. In this review, the authors provide an update of the preclinical and clinical experiences with the TLR4 agonists, MPL (Corixa Corporation) adjuvant and the AGPs.
Rare cancer-specific mutations in PIK3CA show gain of function (2007)

Fifteen rare cancer-derived mutants of PIK3CA, the gene coding for the catalytic subunit p110alpha of phosphatidylinositol 3-kinase (PI3K), were examined for their biological and biochemical properties. Fourteen of these mutants show a gain of function: they induce rapamycin-sensitive oncogenic transformation of chicken embryo fibroblasts, constitutively activate Akt and TOR-mediated signaling, and show enhanced lipid kinase activity. Mapping of these mutants on a partial structural model of p110alpha suggests three groups of mutants, defined by their location in distinct functional domains of the protein. We hypothesize that each of these three groups induces a gain of PI3K function by a different molecular mechanism. Mutants in the C2 domain increase the positive surface charge of this domain and therefore may enhance the recruitment of p110alpha to cellular membranes. Mutants in the helical domain map to a contiguous surface of the protein and may affect the interaction with other protein(s). Mutants in the kinase domain are located near the hinge of the activation loop. They may alter the position and mobility of the activation loop. Arbitrarily introduced mutations that have no detectable phenotype map either to the interior of the protein or are positioned on a surface region that lies opposite to the exposed surfaces containing gain-of-function mutants. Engineered mutants that exchange acidic or neutral residues for basic residues on the critical surfaces show a gain of function.
Identification and characterization of vlf-1, a baculovirus gene involved in very late gene expression (1994)

We have identified a gene required for strong expression of the polyhedrin gene by characterizing a mutant, tsB837, of the baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV) which is temperature sensitive (ts) for occluded virus production at the nonpermissive temperature. Marker rescue experiments utilizing an overlapping set of AcMNPV genomic clones revealed that the gene responsible for the ts mutant phenotype mapped to a region between 46 and 48 map units. Fragments (2.2 kb) from both wild-type AcMNPV and tsB837 genomes spanning the mutated region were sequenced, and a single nucleotide difference was observed. This mutation is predicted to substitute a single amino acid within a 44.4-kDa polypeptide. Analysis of protein synthesis in wild-type- and mutant-infected cells at the nonpermissive temperature indicated that polyhedrin synthesis was dramatically reduced in the mutant. Northern (RNA) blot analysis revealed that the mutant had markedly reduced levels of polyhedrin transcripts. Transcripts of another very late gene, p10, were also reduced but to a lesser degree. The transcription of two late genes (603 ORF and vp39) was neither reduced nor temporally delayed. Thus, the gene encoding this very late expression factor, designated vlf-1, regulates the levels of very late gene transcripts, and the tsB837 mutation affects the levels of polyhedrin gene transcripts more strongly than those of p10 transcripts. The product of the newly identified gene has a surprising but significant relationship to a family of integrases and resolvases.
Are Stem Cell Characteristics Altered by Disease State? (2005)

Autologous stem cell transplantation combined with gene therapy can potentially be used to treat genetically inherited diseases. However, characterization of multipotential cells from a disease state remains extremely limited. We have characterized adult bone marrow stromal cells (MSCs) derived from three retinal degenerative mouse models and compared them to marrow stromal cells derived from their normal strain counterparts. Despite similar profiles soon after harvest, at 30 days postisolation, marrow stromal cells derived from a disease origin were shown to contain a large pool (approximately 89-99%) of undifferentiated marrow stromal cells (CD90(+)/STRO-1(+)) as compared to their normal counterparts (approximately 19-43%). Fetal bovine serum appeared essential for marrow stromal cell proliferation and was not found to induce differentiation, although it could be substituted with other additives including epidermal growth factor (EGF), platelet-derived growth factor (PDGF), and leukemia inhibitory factor (LIF). We also showed that resulting CD90(+)/STRO(+) cells derived from both states could be directed into desired lineages expressing at the same rate and that they could be transduced with the same efficiency using different viral vehicles. This investigation has shown the existence of a large pool of undifferentiated stem cells derived from the disease state that have the potential to form the desired cell types when appropriately cued.
Tissue MicroArray Analyses of Pancreatic Duodenal Homeobox‐1 in Human Cancers (2005)

In previous studies, we demonstrated that rat insulin promoter (RIP)-driven gene therapy successfully targeted human pancreatic tumor PANC-1 cells and mouse insulinoma NIT-1 cells, which are both pancreatic duodenal homeobox-1 (PDX-1)-positive. The purpose of this study was to perform a human tissue array analysis to determine potential targets for RIP-driven gene therapy. A custom-designed tissue MicroArray analysis of various human cancer specimens was performed using a PDX-1 polyclonal antibody generated in our laboratory. The custom-designed Tissue MicroArray of human tumor specimens consists of human cancer specimens from different origins, such as the pancreas, breast, colon, prostate, kidney, liver, lung, and ovary. A panel of normal human specimens from 20 organs or tissues was used as a control. All tissues were fixed in formalin and embedded in paraffin. The immunohistochemistry studies of the cytoplasm and the nuclear expression levels were compared using the Loda method and blind reviews. Data are presented as the mean +/- SEM (p < 0.05 was considered significant by the unpaired student t-test). PDX-1 expression intensity was elevated in both benign and malignant tissues from the same patient with pancreas, breast, colon, prostate, and kidney cancers, whereas normal human tissues from control subjects without cancer did not express PDX-1. These results suggest that PDX-1 is an early marker for these cancers and could be potentially used as a diagnostic parameter and perhaps could be targeted by PDX-1-activated gene therapies, such as RIP-TK.
Successful Implementation of the ABCDEF Bundle in the MICU through Interprofessional Collaboration and Teamwork (2014)

Earlier this year, members of the medical intensive care unit (MICU) attended an interprofessional workshop that utilized Awakening/Breathing/Choice of Sedation/Delirium/Early Mobility (ABCDE) bundle simulation combined with TeamSTEPPS training to empower care givers to advocate for patient safety while optimizing patient care. The ABCDE bundle is an evidence-based tool designed to implement pain, agitation, and delirium guideline recommendations into routine practice. To further improve patient safety and outcomes and build upon the ABCDE concept, the MICU team developed an interprofession-al practice project by adding routine assessment of need for indwelling Foley catheters to their daily work list, creating the “ABCDEF” bundle.
Packetized Video On MAGNET (1987)

Theoretical analysis of integrated local area network model of MAGNET, an integrated network testbed developed at Columbia University, shows that the bandwidth freed up during video and voice calls during periods of little movement in the images and periods of silence in the speech signals could be utilized efficiently for graphics and data transmission. Based on these investigations, an architecture supporting adaptive protocols that are dynamicaly controlled by the requirements of a fluctuating load and changing user environment has been advanced. To further analyze the behavior of the network, a real-time packetized video system has been implemented. This system is embedded in the real-time multimedia workstation EDDY, which integrates video, voice, and data traffic flows. Protocols supporting variable-bandwidth, fixed-quality packetized video transport are described in detail.
Characterization of Phosphoproteins in Gastric Cancer Secretome (2010)

Phosphorylation dysregulation has been implicated in various diseases including cancer. The phosphorylation change of proteins in secretome may be a novel source for the discovery of biomarkers and drug targets. In this study, the phosphoproteins in cancer secretome (phosphosecretome) were globally analyzed for the first time by phosphoproteomics. One hundred forty-two phosphorylation sites on 62 unique phosphopeptides representing 49 nonredundant proteins were identified, several of which are known as secreted proteins involved in carcinogenesis, invasion, and metastasis. Most of them were first found as secreted proteins with no previously known function. Protein sublocation analysis showed that 33 proteins were found to be secreted as phosphoproteins, in which 27 (81.81%) were secreted by a nonclassic, ER/Golgi-independent pathway, suggesting that the phosphorylation modification of these proteins might play an important role in their nonconventional secretion processes. Their protein kinases and regulatory phosphosites involved in the secretion regulation of these phosphoproteins, such as stanniocalcin 2, annexin A2, and HSP90 alphạ, were first identified. The phosphosecretome data enriched the secretome database and phosphoproteome database, and will help us to discover cancer biomarkers and drug targets, illustrating the mystery of the nonclassic protein secretion pathway.
Idiopathic Vertebral Abscess in Pregnancy: Case Report and Literature Review (2007)

Pregnant women are prone to complications from many infections. However, overwhelming soft tissue infections are rarely reported in pregnant women without predisposing factors. A 40-year-old multipara presented with complaints of progressively worsening spinal muscle spasm pain. Because her medical history consisted of preterm deliveries, she was receiving injections of 17-alpha-hydroxyprogesterone caproate (17P). An imaging study revealed replacement of the vertebral marrow with a homogeneous substance. A biopsy stained for gram-positive cocci. Blood culture bottles grew STAPHYLOCOCCUS AUREUS. The lesion was re-aspirated, and grew the same isolate. The patient was treated with antibiotics and had resolution of her pain. Mother and infant did well, and she completed a prolonged course of antibiotics. This study presents an unusual case of idiopathic vertebral osteomyelitis and epidural abscess during pregnancy. Potential reasons for failure to display a systemic response to this infection with associated bacteremia include an innate variation in the patient's immune system and modification in immunity from progesterone therapy. The role that 17P played in this case, if any, is unknown.
Liver X receptors alpha and beta promote myelination and remyelination in the cerebellum (2015)

The identification of new pathways governing myelination provides innovative avenues for remyelination. Liver X receptors (LXRs) α and β are nuclear receptors activated by oxysterols that originated from the oxidation of cholesterol. They are crucial for cholesterol homeostasis, a major lipid constituent of myelin sheaths that are formed by oligodendrocytes. However, the role of LXRs in myelin generation and maintenance is poorly understood. Here, we show that LXRs are involved in myelination and remyelination processes. LXRs and their ligands are present in oligodendrocytes. We found that mice invalidated for LXRs exhibit altered motor coordination and spatial learning, thinner myelin sheaths, and reduced myelin gene expression. Conversely, activation of LXRs by either 25-hydroxycholesterol or synthetic TO901317 stimulates myelin gene expression at the promoter, mRNA, and protein levels, directly implicating LXRα/β in the transcriptional control of myelin gene expression. Interestingly, activation of LXRs also promotes oligodendroglial cell maturation and remyelination after lysolecithin-induced demyelination of organotypic cerebellar slice cultures. Together, our findings represent a conceptual advance in the transcriptional control of myelin gene expression and strongly support a new role of LXRs as positive modulators in central (re)myelination processes.
Regulation of proliferation and osteochondrogenic differentiation of periosteum-derived cells by transforming growth factor-beta and basic fibroblast growth factor. (1995)

We studied the effects of transforming growth factor-beta and basic fibroblast growth factor on the regulation of proliferation and osteochondrogenic differentiation of periosteum-derived cells, which have the potential to differentiate into bone and hypertrophic cartilage in vitro. Histological observation revealed that transforming growth factor-beta stimulated chondrogenesis of periosteum-derived cells while basic fibroblast growth factor stimulated proliferation of fibroblast-like cells and inhibited osteochondrogenic differentiation. Immunohistochemical studies revealed that basic fibroblast growth factor inhibited the expression of osteocalcin. Transforming growth factor-beta enhanced uronic acid content but decreased DNA content, alkaline phosphatase activity, and calcium content. In contrast, basic fibroblast growth factor enhanced DNA content but decreased alkaline phosphatase activity, calcium content, and uronic acid content. In addition, transforming growth factor-beta shortened the time-course of gene expression of type-X collagen whereas basic fibroblast growth factor inhibited the gene expression. These results indicate that transforming growth factor-beta stimulates osteochondrogenic differentiation of periosteum-derived cells but inhibits proliferation. They also indicate that basic fibroblast growth factor stimulates proliferation of periosteum-derived cells but inhibits osteochondrogenic differentiation.
On modeling of information retrieval concepts in vector spaces (1987)

The Vector Space Model (VSM) has been adopted in information retrieval as a means of coping with inexact representation of documents and queries, and the resulting difficulties in determining the relevance of a document relative to a given query. The major problem in employing this approach is that the explicit representation of term vectors is not known a priori. Consequently, earlier researchers made the assumption that the vectors corresponding to terms are pairwise orthogonal. Such an assumption is clearly unrealistic. Although attempts have been made to compensate for this assumption by some separate, corrective steps, such methods are ad hoc and, in most cases, formally inconsistent. In this paper, a generalization of the VSM, called the GVSM, is advanced. The developments provide a solution not only for the computation of a measure of similarity (correlation) between terms, but also for the incorporation of these similarities into the retrieval process. The major strength of the GVSM derives from the fact that it is theoretically sound and elegant. Furthermore, experimental evaluation of the model on several test collections indicates that the performance is better than that of the VSM. Experiments have been performed on some variations of the GVSM, and all these results have also been compared to those of the VSM, based on inverse document frequency weighting. These results and some ideas for the efficient implementation of the GVSM are discussed.
Xanthomonas campestris pv. campestris Possesses a Single Gluconeogenic Pathway That Is Required for Virulence (2005)

Disruption of ppsA, a key gene in gluconeogenesis, of Xanthomonas campestris pv. campestris resulted in the failure of the pathogen to grow in medium with pyruvate or C4-dicarboxylates as the sole carbon source and a significant reduction in virulence, indicating that X. campestris pv. campestris possesses only the malic enzyme-PpsA route in gluconeogenesis, which is required for virulence.
Cancer statistics, 2018 (2018)

Each year, the American Cancer Society estimates the numbers of new cancer cases and deaths that will occur in the United States and compiles the most recent data on cancer incidence, mortality, and survival. Incidence data, available through 2014, were collected by the Surveillance, Epidemiology, and End Results Program; the National Program of Cancer Registries; and the North American Association of Central Cancer Registries. Mortality data, available through 2015, were collected by the National Center for Health Statistics. In 2018, 1,735,350 new cancer cases and 609,640 cancer deaths are projected to occur in the United States. Over the past decade of data, the cancer incidence rate (2005-2014) was stable in women and declined by approximately 2% annually in men, while the cancer death rate (2006-2015) declined by about 1.5% annually in both men and women. The combined cancer death rate dropped continuously from 1991 to 2015 by a total of 26%, translating to approximately 2,378,600 fewer cancer deaths than would have been expected if death rates had remained at their peak. Of the 10 leading causes of death, only cancer declined from 2014 to 2015. In 2015, the cancer death rate was 14% higher in non-Hispanic blacks (NHBs) than non-Hispanic whites (NHWs) overall (death rate ratio [DRR], 1.14; 95% confidence interval [95% CI], 1.13-1.15), but the racial disparity was much larger for individuals aged <65 years (DRR, 1.31; 95% CI, 1.29-1.32) compared with those aged ≥65 years (DRR, 1.07; 95% CI, 1.06-1.09) and varied substantially by state. For example, the cancer death rate was lower in NHBs than NHWs in Massachusetts for all ages and in New York for individuals aged ≥65 years, whereas for those aged <65 years, it was 3 times higher in NHBs in the District of Columbia (DRR, 2.89; 95% CI, 2.16-3.91) and about 50% higher in Wisconsin (DRR, 1.78; 95% CI, 1.56-2.02), Kansas (DRR, 1.51; 95% CI, 1.25-1.81), Louisiana (DRR, 1.49; 95% CI, 1.38-1.60), Illinois (DRR, 1.48; 95% CI, 1.39-1.57), and California (DRR, 1.45; 95% CI, 1.38-1.54). Larger racial inequalities in young and middle-aged adults probably partly reflect less access to high-quality health care. CA Cancer J Clin 2018;68:7-30. © 2018 American Cancer Society.
Simultaneous analysis of a sequence of paired ecological tables: A comparison of several methods (2011)

A pair of ecological tables is made of one table containing environmental variables (in columns) and another table containing species data (in columns). The rows of these two tables are identical and correspond to the sites where environmental variables and species data have been measured. Such data are used to analyze the relationships between species and their environment. If sampling is repeated over time for both tables, one obtains a sequence of pairs of ecological tables. Analyzing this type of data is a way to assess changes in species-environment relationships, which can be important for conservation Ecology or for global change studies. We present a new data analysis method adapted to the study of this type of data, and we compare it with two other methods on the same data set. All three methods are implemented in the ade4 package for the R environment.
Modulation of 5-fluorouracil catabolism in isolated rat hepatocytes with enhancement of 5-fluorouracil glucuronide formation. (1985)

The catabolism of 5-fluorouracil (FUra), which accounts for 90% of the elimination of this antimetabolite in vivo, has recently been characterized in freshly isolated rat hepatocytes in suspension using a highly specific high-performance liquid chromatographic methodology. The present study evaluates the effect of thymine and uracil, which are thought to be catabolized by the same enzymes as FUra, on the metabolism and transmembrane distribution of FUra in isolated rat hepatocytes. Following simulataneous exposure of cells for 5 min to 30 microM [6-3H]FUra and increasing concentrations of either thymine or uracil, dihydrofluorouracil (FUH2) levels decreased in a concentration-dependent manner, and the concentration determined for 50% inhibition of FUra catabolism was 8.0 +/- 0.3 (S.D.) and 67.8 +/- 15.6 microM for thymine and uracil, respectively. Analysis of intracellular and extracellular 3H from 1 min to 2 hr after simultaneous incubation of the hepatocytes with 30 microM FUra and thymine (or uracil) in a 1:7 molar ratio resulted in a decrease of intracellular and extracellular FUH2 and alpha-fluoro-beta-alanine (FBAL), while alpha-fluoro-beta-ureidopropionic acid (FUPA) was enhanced. Unmetabolized FUra (not detected in the absence of thymine or uracil) was detected intracellularly in the presence of thymine or uracil and was accompanied by the appearance of a novel metabolite, preliminarily identified as a glucuronide of the FUra base which reached intracellular levels of 44 +/- 9.76 and 27.45 +/- 1.35 microM in the presence of thymine or uracil, respectively, within 1 hr. This metabolite, which penetrates the cell membrane only slowly, accounted for approximately 60% of the intracellular 3H in the presence of 300 microM FUra and 2 mM thymine, whereas FUra catabolism was inhibited by more than 99% under these conditions. The formation of FUra anabolites was insignificant in the presence of thymine and uracil, and incorporation of FUra into RNA was not enhanced. The lack of anabolism of FUra in isolated hepatocytes exposed to either high initial concentrations of FUra or high intracellular FUra concentrations resulting from modulation (inhibition) of FUra catabolism is consistent with the clinical observation of minimal hepatotoxicity with FUra, despite exposure of the liver to high blood levels. These studies indicate that thymine is a more potent modulator of FUra catabolism in hepatocytes than is uracil. Further studies are needed to clarify the biological importance of the glucuronide of the base FUra which accumulates intracellularly as the concentration of FUra increases within the hepatocytes.