gebhart/patrepeval huggingface dataset:
Pathological and molecular mechanisms of prostate carcinogenesis: Implications for diagnosis, detection, prevention, and treatment (2003)

Prostate cancer is an increasing threat throughout the world. As a result of a demographic shift in population, the number of men at risk for developing prostate cancer is growing rapidly. For 2002, an estimated 189,000 prostate cancer cases were diagnosed in the U.S., accompanied by an estimated 30,200 prostate cancer deaths [Jemal et al., 2002]. Most prostate cancer is now diagnosed in men who were biopsied as a result of an elevated serum PSA (>4 ng/ml) level detected following routine screening. Autopsy studies [Breslow et al., 1977; Yatani et al., 1982; Sakr et al., 1993], and the recent results of the Prostate Cancer Prevention Trial (PCPT) [Thompson et al., 2003], a large scale clinical trial where all men entered the trial without an elevated PSA (<3 ng/ml) were subsequently biopsied, indicate the prevalence of histologic prostate cancer is much higher than anticipated by PSA screening. Environmental factors, such as diet and lifestyle, have long been recognized contributors to the development of prostate cancer. Recent studies of the molecular alterations in prostate cancer cells have begun to provide clues as to how prostate cancer may arise and progress. For example, while inflammation in the prostate has been suggested previously as a contributor to prostate cancer development [Gardner and Bennett, 1992; Platz, 1998; De Marzo et al., 1999; Nelson et al., 2003], research regarding the genetic and pathological aspects of prostate inflammation has only recently begun to receive attention. Here, we review the subject of inflammation and prostate cancer as part of a "chronic epithelial injury" hypothesis of prostate carcinogenesis, and the somatic genome and phenotypic changes characteristic of prostate cancer cells. We also present the implications of these changes for prostate cancer diagnosis, detection, prevention, and treatment.
Characteristics of PBMC obtained from leukapheresis products and tumor biopsies of patients with non-small cell lung cancer (2009)

The current study characterized peripheral blood mononuclear cells (PBMC) obtained from leukapheresis products of patients with non-small cell lung cancer (NSCLC) for cytokine release, the ability to incorporate tritiated thymidine following stimulation using PHA as well as the levels of both CD4 and CD8 regulatory T cells (Tregs) as defined by FoxP3 expression. Results were compared to normal donor PBMC obtained from buffy coat products. Heterogeneous levels of Th1 (gamma interferon and IL-2), Th2 (IL-10 and IL-13), pro-inflammatory (TNF-alpha and IL-6) and the hematopoietic inducing cytokine GMCSF were detected from both populations of PBMC as measured using ELISA. Overall, we observed that combined levels of Th1 and Th2 cytokines were higher in lung cancer patients compared to that seen in normal donor PBMC. The increased cytokine production was coupled with an observed decrease in the ability of lung cancer patient PBMC to incorporate tritiated thymidine. Furthermore, cytokine containing supernatants obtained from patients inhibited the incorporation of tritiated thymidine from PBMC obtained from normal donors. Thus, the combined cytokines which included high levels of IL-10, appeared to exhibit suppressive functional activity. While not statistically significant, the overall trend toward a Th2 cytokine environment was supported by an increased level of Tregs observed in the leukapheresis products of lung cancer patients. These levels were variable and were accompanied by higher than normal levels of CD8+ cells co-expressing FoxP3. Finally, tumor biopsies were examined from lung cancer patients along with autologous normal adjacent tissue (NAT). In these studies, both gamma interferon and IL-10 were detected. The levels of IL-10 in the LPS stimulated cultures were statistically greater from the cancer biopsies compared to the NAT. The current study confirms many earlier results in a comprehensive manner and extends the analysis to leukapheresis products. An environment is described in cancer patients which is characterized by increased cytokine production and decreased proliferative potential likely under the influence of a significant population of regulatory T cells (Tregs). Taken together, these results are discussed as they relate to the potential implications in lung cancer patients immune response to their disease.
Frequent activation of AKT2 kinase in human pancreatic carcinomas (2002)

Activation of AKT/protein kinase B promotes a variety of biological activities important in tumorigenesis, such as cell survival and cell cycle progression. We previously demonstrated amplification and overexpression of the AKT2 gene in a subset of human pancreatic carcinomas. In this investigation, we assessed AKT2 catalytic activity in 50 frozen pancreatic tissues (37 carcinomas, four benign tumors and nine normal pancreata) by in vitro kinase assay. Twelve of 37 (32%) pancreatic carcinomas showed markedly elevated levels of AKT2 activity compared to normal pancreata and begin pancreatic tumors. To delineate mechanisms contributing to AKT2 activation in malignant pancreatic tumors, we examined the status of upstream components of the phosphatilydlinositol 3-kinase (PI3K)/AKT pathway. Western blot analysis revealed loss of PTEN protein expression in two of the 12 pancreatic carcinomas with activated AKT2. In vitro PI3K assays demonstrated high levels of PI3K activity in seven carcinoma specimens that showed AKT2 activation. Immunohistochemical staining confirmed high levels of phosphorylated (active) AKT in malignant pancreatic tumors compared to normal pancreata. Overall, these data suggest that upstream perturbations of the PI3K/AKT pathway contribute to frequent activation of AKT2 in pancreatic cancer, which may contribute to the pathogenesis of this highly aggressive form of human malignancy.
Silicon-Based Lewis Acid Assisted Cinchona Alkaloid Catalysis: Highly Enantioselective Aza-Michael Reaction under Solvent-Free Conditions (2011)

The study showed that a combination of an achiral silicon-based Lewis acid and chiral Lewis base, such as iodotrimethylsilane (TMSI) and cinchonine, generated a highly enantioselective catalyst system under solvent-free conditions which gave aromatic β-amino ketones with up to >99% ee. Mechanistic studies demonstrate the enhanced asymmetric induction may be due to the combined and competitive activation of a carbonyl moiety of chalcone with cinchonine and the silicon-based Lewis acid in the aza-Michael reaction.
Onco‐miR‐155 targets SHIP1 to promote TNFα‐dependent growth of B cell lymphomas (2009)

Non-coding microRNAs (miRs) are a vital component of post-transcriptional modulation of protein expression and, like coding mRNAs harbour oncogenic properties. However, the mechanisms governing miR expression and the identity of the affected transcripts remain poorly understood. Here we identify the inositol phosphatase SHIP1 as a bonafide target of the oncogenic miR-155. We demonstrate that in diffuse large B cell lymphoma (DLBCL) elevated levels of miR-155, and consequent diminished SHIP1 expression are the result of autocrine stimulation by the pro-inflammatory cytokine tumour necrosis factor a (TNFalpha). Anti-TNFalpha regimen such as eternacept or infliximab were sufficient to reduce miR-155 levels and restored SHIP1 expression in DLBCL cells with an accompanying reduction in cell proliferation. Furthermore, we observed a substantial decrease in tumour burden in DLBCL xenografts in response to eternacept. These findings strongly support the concept that cytokine-regulated miRs can function as a crucial link between inflammation and cancer, and illustrate the feasibility of anti-TNFalpha therapy as a novel and immediately accessible (co)treatment for DLBCL.
Alteration in Copy Numbers of Genes as a Mechanism for Acquired Drug Resistance (2004)

Chemoresistance is a major obstacle for successful treatment of cancer. To identify regions of the genome associated with acquired resistance to therapeutic drugs, we conducted molecular cytogenetic analyses of 23 cancer-cell lines, each resistant to either camptothecin, cisplatin, etoposide (VP-16), Adriamycin, or 1-beta-D-arabinofuranosylcytosine, although the parental tumor lines were not. Subtractive comparative genomic hybridization studies revealed regions of gain or loss in DNA-copy numbers that were characteristic of drug-resistant cell lines; i.e., differences from their drug-sensitive parental cell lines. Thirteen ATP-binding cassette (ABC) transporter genes [ABCA3, ABCB1 (MDR1), ABCB6, ABCB8, ABCB10, ABCB11, ABCC1 (MRP1), ABCC4, ABCC9, ABCD3, ABCD4, ABCE1, and ABCF2] were amplified among 19 of the resistant cell lines examined. Three genes encoding antiapoptotic BCL-2 proteins (BCL2L2, MCL1, and BCL2L10) were also amplified and consequently overexpressed in three of the derivative lines. Down-regulation of BCL2L2 with an antisense oligonucleotide sensitized a VP-16 resistant ovarian-cancer cell line (SKOV3/VP) to VP-16. A decrease in copy numbers of genes encoding deoxycytidine kinase, DNA topoisomerase I, and DNA topoisomerase II alpha reduced their expression levels in one cytosine arabinoside-resistant line, two of three camptothecin-resistant lines, and two of five VP-16-resistant cell lines, respectively. Our results indicated that changes in DNA-copy numbers of the genes mentioned can activate or down-regulate them in drug-resistant cell lines, and that such genomic alterations might be implicated in acquired chemoresistance.
Improved gap repair cloning in yeast: treatment of the gapped vector with Taq DNA polymerase avoids vector self‐ligation (2012)

Gap repair is a fast and efficient method for assembling recombinant DNA molecules in Saccharomyces cerevisiae. This method produces a circular DNA molecule by homologous recombination between two or more linear DNA fragments, one of which is typically a vector carrying replicative sequences and a selective marker. This technique avoids laborious and costly in vitro purification and ligation of DNA. The DNA repair machinery can also close and ligate the linear vector by mechanisms other than homologous recombination, resulting in an empty vector. The frequency of these unwanted events can be lowered by removing the 5'-phosphate groups using phosphatase, which is the standard method used for in vitro ligation. However, phosphatase treatment is less effective for gap repair cloning than for in vitro ligation, presumably due to the ability of the S. cerevisiae DNA repair machinery to efficiently repair the missing phosphate group to allow religation. We have developed a more efficient method to prevent vector religation, based on treatment of the vector fragment with Taq DNA polymerase and dATP. This procedure prevents vector recircularization almost completely, facilitating the screening for true recombinant clones.
Long‐Term in Vitro Function of Adult Hepatocytes in a Collagen Sandwich Configuration (1991)

In an effort to reconstruct the cellular polarity normally found in the liver, adult rat hepatocytes were sandwiched between two layers of hydrated rat tail tendon collagen matrix. Functionally, sandwiched hepatocytes maintained the secretion of albumin, transferrin, fibrinogen, bile acids, and urea for at least 6 weeks, whereas cells cultured on a single layer of collagen gel ceased such secretion in 1-2 weeks. After 1 week of culture on a single layer of collagen gel, hepatocytes could still recover these lost functions when a second layer of collagen gel was applied. The exact nature of the substrate for constructing the sandwich system appeared to be unimportant as long as it allowed cellular attachment. Hepatocytes cultured in the sandwich system appeared to maintain a distribution of actin filaments similar to the in vivo state, whereas cells cultured on a single layer of collagen gel showed abnormal formation of stress fibers. These studies suggest that simple manipulations of the configuration of extracellular elements can dramatically alter the behavior of cultured hepatocytes.
Cancer cachexia and targeting chronic inflammation: a unified approach to cancer treatment and palliative/supportive care. (2007)

Chronic inflammation often acts as a tumor promoter, resulting in aggressive cancerous growth and spread. Many of the same inflammatory factors that promote tumor growth also are responsible for cancer cachexia/anorexia, pain, debilitation, and shortened survival. A compelling case may be made for mounting an attack on inflammation with other anticancer measures at initial diagnosis, with the consequent probability of improving both patient quality of life and survival. High serum levels of the inflammatory marker C-reactive protein or fibrinogen and an elevated white blood cell count correlate with poor prognosis and may be used as a prognostic index to establish the need for nutritional/metabolic intervention. At the author's institution, a concerted effort is being made to screen all newly diagnosed patients with non-small cell lung cancer for the presence of nutritional problems, inflammatory markers, and related symptoms. Interventions include dietary counseling; nutritional and, if warranted, vitamin supplementation; exercise concordant with the patient's physical condition; a prescription for omega 3 fatty acids if inflammation is present, and general symptom management. To establish the value of early nutritional/metabolic intervention, clinical trials are needed that combine measures that combat cachexia and inflammation with first-line chemotherapy in patients who present with weight loss, fatigue, and deteriorating function.
Postoperative Lumbar Epiduro-Arachnoiditis (1980)

Thirty-eight patients with the diagnosis of postoperative epiduro-arachnoiditis are reported upon. All had had previous surgery for disc herniation, and the diagnosis of epiduro-arachnoiditis was confirmed at repeat surgery. Massive epidural scarring with no coexistent pathologic condition was found in every patient, and adhesive arachnoiditis was noted in three. The common clinical presentation consisted of low-back pain and sciatica, and radicular pain was usually a continuation or a recurrence of the preoperative sciatic pain. Neurologic deficits were mild, and no patients with the classic picture of adhesive arachnoiditis were found. Myelographic patterns did not disclose any correlation with the clinical symptoms. Five myelograms were normal, while six others simulated a recurrent disc herniation. The results of scar excision were good in 13 patients, fair in eight, and a failure in 17.
Comparative Efficacy of Acustimulation (ReliefBand®) versus Ondansetron (Zofran®) in Combination with Droperidol for Preventing Nausea and Vomiting (2002)

The ReliefBand compared favorably to ondansetron (4 mg intravenously) when used for prophylaxis against postoperative nausea and vomiting. Furthermore, the acustimulation device enhanced the antiemetic efficacy of ondansetron after plastic surgery.
The structural and luminescence properties of porous silicon (1997)

A large amount of work world-wide has been directed towards obtaining an understanding of the fundamental characteristics of porous Si. Much progress has been made following the demonstration in 1990 that highly porous material could emit very efficient visible photoluminescence at room temperature. Since that time, all features of the structural, optical and electronic properties of the material have been subjected to in-depth scrutiny. It is the purpose of the present review to survey the work which has been carried out and to detail the level of understanding which has been attained. The key importance of crystalline Si nanostructures in determining the behaviour of porous Si is highlighted. The fabrication of solid-state electroluminescent devices is a prominent goal of many studies and the impressive progress in this area is described.
Preparation and Characterization of Bidimensional Zeolitic Structures Obtained from Synthetic Beidellite and Hydroxy-Aluminum Solutions (1987)

Abstract Beidellite was synthesized hydrothermally from a noncrystalline gel at 320°C and 130 bar pressure. The beidellitic character of the product was verified by infrared spectroscopy on the NH 4 + -exchanged form. Intercalation was achieved with hydroxy-aluminum solutions having different OH/Al molar ratios. The solutions were investigated by several methods, including 27 Al nuclear magnetic resonance. Essentially, two Al species were detected: monomelic Al and a polymerized form containing Al in four-fold coordination. This latter species was found to be selectively fixed in the interlamellar region, which resulted in a stable spacing of 18 Å at 110°C and 16.2 Å at 700°C. The pillared beidellites had specific surface areas of &gt; 300 m 2 /g, mainly due to micropores. Both Brönsted and Lewis acid sites were evidenced by infrared spectroscopy using pyridine as a probe molecule.
Signaling pathways controlling primordial germ cell migration in zebrafish (2004)

During their migration, zebrafish primordial germ cells (PGCs) rely on directional cues provided by the chemokine SDF-1a, whose receptor is CXCR4b. The molecular mechanisms whereby CXCR4b activation is interpreted intracellularly into directional migration are not known. Here we investigate the role of two important biochemical pathways -- G-protein-dependent and phosphoinositide 3-kinase (PI3K)-dependent signaling -- in directing PGC migration in zebrafish. We show that G proteins of the Gi family are essential for directional migration but not for PGC motility. Inhibition of PI3K signaling in PGCs slows down their migration and leads to abnormal cell morphology as well as to reduced stability of filopodia. Invariably, during directed PGC migration, the distribution of the products of PI3K activity - phosphatidylinositol (3,4,5)-trisphosphate [PtdIns(3,4,5)P(3)] and/or phosphatidylinositol (3,4)bisphosphate [PtdIns(3,4)P(2)] -- is not polarized, and reducing the level of these 3-phosphoinositides does not affect the ability of PGCs to migrate directionally. We therefore conclude that Gi-dependent signaling is essential for directional migration, whereas the PI3K pathway is important for the actual motility of PGCs.
CCR6 Recruits Regulatory T Cells and Th17 Cells to the Kidney in Glomerulonephritis (2010)

T cells recruited to the kidney contribute to tissue damage in crescentic and proliferative glomerulonephritides. Chemokines and their receptors regulate T cell trafficking, but the expression profile and functional importance of chemokine receptors for renal CD4+ T cell subsets are incompletely understood. In this study, we observed that renal FoxP3+CD4+ regulatory T cells (Tregs) and IL-17-producing CD4+ T (Th17) cells express the chemokine receptor CCR6, whereas IFNgamma-producing Th1 cells are CCR6-. Induction of experimental glomerulonephritis (nephrotoxic nephritis) in mice resulted in upregulation of the only CCR6 ligand, CCL20, followed by T cell recruitment, renal tissue injury, albuminuria, and loss of renal function. CCR6 deficiency aggravated renal injury and increased mortality (from uremia) among nephritic mice. Compared with wild-type (WT) mice, CCR6 deficiency reduced infiltration of Tregs and Th17 cells but did not affect recruitment of Th1 cells in the setting of glomerulonephritis. Adoptive transfer of WT but not CCR6-deficient Tregs attenuated morphologic and functional renal injury in nephritic mice. Furthermore, reconstitution with WT Tregs protected CCR6-/- mice from aggravated nephritis. Taken together, these data suggest that CCR6 mediates renal recruitment of both Tregs and Th17 cells and that the reduction of anti-inflammatory Tregs in the presence of a fully functional Th1 response aggravates experimental glomerulonephritis.
Performance- and safety-enhanced lentiviral vectors containing the human interferon-β scaffold attachment region and the chicken β-globin insulator (2003)

Retroviral vectors are the most efficient means of stable gene delivery to hematopoietic stem cells (HSCs). However, transgene expression from retroviral vectors is frequently subject to the negative influence of chromosomal sequences flanking the site of integration. Toward the development of autonomous transgene expression cassettes, we inserted the human interferon-beta scaffold attachment region (IFN-SAR) and the chicken beta-globin 5' DNase I hypersensitive site 4 (5'HS4) insulator both separately and together into a series of self-inactivating (SIN) lentiviral vector backbones. Transduced cells of the human CD34+ hematopoietic progenitor line KG1a-pooled populations as well as individual clones harboring single integrants--were analyzed for reporter expression during culture periods of up to 4 months. Vectors carrying both the 5'HS4 insulator and the IFN-SAR consistently outperformed control vectors without inserts as well as vectors carrying either element alone. The performance of a set of vectors containing the murine stem cell virus long terminal repeat as an internal promoter was subsequently assessed during in vitro monocytic differentiation of transduced primary human CD34+ cord blood cells. Similar to what was observed in the KG1a hematopoietic progenitor cell model, optimal reporter expression in primary monocytes was obtained with the vector bearing both regulatory elements. These findings indicate that the 5'HS4/IFN-SAR combination is particularly effective at maintaining open chromatin domains permissive for high-level transgene expression at early and late stages of hematopoietic development, and thus could be of utility in HSC-directed retroviral vector-mediated gene transfer applications.
A Salmonella typhi OmpC fusion protein expressing the CD154 Trp140–Ser149 amino acid strand binds CD40 and activates a lymphoma B‐cell line (2003)

CD154 is a type II glycoprotein member of the tumour necrosis factor (TNF) ligand family, which is expressed mainly on the surface of activated T lymphocytes. The interaction with its receptor CD40, plays a central role in the control of several functions of the immune system. Structural models based on the homology of CD154 with TNF and lymphotoxin indicate that binding to CD40 involves three regions surrounding amino acids K143, R203 and Q220, and that strands W140-S149 and S198-A210 are critical for such interactions. Also, it has been reported that two recombinant CD154 fragments, including amino acid residues Y45-L261 or E108-L261 are biologically active, whereas other polypeptides, including S149-L261, are not. Therefore, we decided to construct a fusion protein inserting the W140-S149 amino acid strand (WAEKGYYTMS) in an external loop of the outer membrane protein C (OmpC) from Salmonella enterica serovar Typhi and assess its ability to bind CD40 and activate B cells. The sodium dodecyl sulphate-polyacrylamide gel electrophoresis demonstrated that the chimeric OmpC-gp39 protein conserved its ability to form trimers. Binding to CD40 was established by three variants of enzyme-linked immunosorbent assay, a direct binding assay by coating plates with a recombinant CD40-Fc protein and through two competition assays between OmpC-gp39 and recombinant CD154 or soluble CD40-Fc. Flow cytometry analysis demonstrated that OmpC-gp39 increased the expression levels of major histocompatibility complex II, CD23, and CD80, in Raji human B-cell lymphoma similarly to an antibody against CD40. These results further support that the CD154/CD40 interaction is similar to the TNF/TNF receptor. This is the first report of a bacterial fusion protein containing a small amino acid strand form a ligand that is able to activate its cognate receptor.