gebhart/patrepeval huggingface dataset:
Apoptosis Techniques and Protocols (1997)

Gene Tools to Study Neuronal Apoptosis Isabelle Martinou Harald Frankowski Marc Missotten Remy Sadoul and Jean-Claude Martinou. Detection of Apoptotic or Necrotic Death in Neuronal Cells by Morphological Biochemical and Molecular Analysis Martin Gschwind and Gerda Huber. Detection of Cell Death in Neural Tissue and Cell Culture Thomas Mahalik Malcolm Wood and Gregory Owens. Cultured Cerebellar Granule Neurons as a Model of Neuronal Apoptosis Guang-Mei Yan and Steven M. Paul. Optimization and Validation of RT-PCR as a Tool to Analyze Gene Expression During Apoptosis Steven Estus. p53 Induction Is a Marker of Neuronal Apoptosis in the Central Nervous System Shahin Sakhi and Steven S. Schreiber. Apoptosis and Ischemia in the Central Nervous System Matthew D. Linnik. Analyses of Apoptosis-Associated DNA Fragmentation In Vivo During Neurodegeneration of the Peripheral Olfactory System in Adult Mammals Emmanuel Moyse and Denis Michel. Both Irreversible Neuronal Death and Reversible Neuronal Stress Are Associated with Increased Levels of Statin a Marker of Cell Cycle Arrest Patricia Boksa Uwe Beffert Doris Dea Richard Alonso Dayan O'Donnell and Judes Poirier. b-Amyloid-Induced Neuronal Cell Death in Transgenic Mice and Alzheimer's Disease Frank M. LaFerla and Gilbert Jay. Use of TUNEL to Measure Retinal Ganglion Cell Apoptosis Lisa Ayn Kerrigan and Donald J. Zack. Methods for Detection of Apoptosis in the CNS Kathrin D. Geiger Floyd E. Bloom and Nora E. Sarvetnick. Techniques for Distinguishing Apoptosis from Necrosis in Cerebrocortical and Cerebellar Neurons Emanuela Bonfoco Maria Ankarcrona Dimitri Krainc Pierluigi Nicotera and Stuart A. Lipton. The Nematode Caenorhabditis elegans as a Model System to Study Neuronal Cell Death Paul Desjardins and St'phane Ledoux. Index.
Pseudorabies virus gene encoding glycoprotein gIII is not essential for growth in tissue culture (1986)

We have established that in the Becker strain of pseudorabies virus (PRV), the glycoprotein gIII gene is not essential for growth in cell culture. This was accomplished by construction and analysis of viral mutants containing two defined deletion mutations affecting the gIII gene. These mutations were first constructed in vitro and introduced into Escherichia coli expression plasmids to verify structure and protein production. Each mutation was then crossed onto PRV by cotransfection of plasmid DNA and parental viral DNA by using gIII-specific monoclonal antibodies as selective and screening reagents. One resultant virus strain, PRV-2, contained an in-frame deletion of a 402-base-pair (bp) SacI fragment contained within the gIII gene. Another virus strain, PRV-10, contained a deletion of a 1,480-bp XhoI fragment removing 230 bp of the upstream, putative transcriptional control sequences and 87% of the gIII coding sequence. The deletion mutants were compared with parental virus by analysis of virion DNA, gIII specific RNA, and proteins reacting with gIII specific antibodies. Upon infection of PK15 cells, the deletion mutants did not produce any proteins that reacted with two gIII specific monoclonal antibodies. However, two species of truncated glycosylated proteins were observed in PRV-2 infected cells that reacted with antiserum raised against bacterially produced gIII protein. PRV-10 produced no detectable gIII-specific RNA or protein. PRV-10 could be propagated without difficulty in tissue culture. Virus particles lacking gIII were indistinguishable from parental PRV virus particles by analysis of infected-cell thin sections in the electron microscope. We therefore conclude that expression of the gIII gene was not absolutely essential for PRV growth in tissue culture.
Synthesis and Antitumor Activity of Novel Benzophenone Derivatives. (1997)

Novel benzophenone derivatives were synthesized and screened for cytotoxic and antitumor activity. Friedel-Crafts condensation was employed to construct the benzophenone skeleton. Among the compounds synthesized, morpholino and thiomorpholino benzophenones 3a-d exhibited potent cytotoxic activity against P388 murine leukemia and PC-6 human lung carcinoma cells in vitro, and compounds 3a, 3c, and 3j, when administered intraperitoneally, showed significant antitumor activity against the malignant ascites caused by intraperitoneal inoculation of P388 cells in mice.
A Translation Fusion Product of Two Different Insecticidal Crystal Protein Genes of Bacillus thuringiensis Exhibits an Enlarged Insecticidal Spectrum (1990)

Two truncated Bacillus thuringiensis crystal protein genes, belonging to the classes cryIA(b) and cryIC and both coding for insecticidal N-terminal fragments of the corresponding crystal proteins, were translationally fused. Expression of the gene fusion in Escherichia coli showed a biologically active protein with a toxicity spectrum that overlapped those of both contributing crystal proteins.
Using the robust principal component analysis algorithm to remove RF spike artifacts from MR images (2015)

The RPCA despiking algorithm will be a valuable postprocessing method for retrospectively removing stripe artifacts without affecting the underlying signal of interest. Magn Reson Med 75:2517-2525, 2016. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Initial clinical study of indium-111-labeled clone 110 anticarcinoembryonic antigen antibody in patients with colorectal cancer. (1991)

A murine monoclonal antibody directed against carcinoembryonic antigen (CEA) was labeled with indium-111 (111In) by means of a benzylisothiocyanate derivative of diethylenetriamine penta-acetic acid (DTPA) and used for clinical radioimmunodetection studies. Twenty-one patients having a history of surgically resected colorectal cancer and rising serum CEA levels suggestive of tumor recurrence were studied. Patients were infused over 20 minutes with 5, 10, or 20 mg of the monoclonal antibody labeled with 5 mCi of 111In. The mean radiochemical purity was greater than 96%. No toxicity was seen. The stability of the radiolabel on antibody in patient serum was demonstrated by high-performance liquid chromatography (HPLC), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) with autoradiography, and immunoprecipitation for up to 96 hours after infusion. Tumor sites were identified in 20 of 21 patients. Sites of antibody accumulation in 20 patients were confirmed as tumor either by resection at laparotomy (16 patients) or fine-needle biopsy (four patients). Nine patients who had the identified lesion resected or irradiated showed return of the serum CEA antigen level to normal or near normal values. In the absence of high levels of circulating CEA (greater than 500 ng/mL), the disappearance of radioactivity from patient serum demonstrated first order elimination kinetics, with a mean half-life of 38 hours. The serum half-life was not affected by the dose of antibody administered or by serum CEA titers below 500 ng/mL. Despite a mean liver uptake of 18% injected dose (ID) 24 hours after administration, hepatic metastases were easily visualized as areas of increased uptake of radioactivity. Radioimmunodetection of recurrent colorectal cancer, not detected by computed tomographic (CT) scans, appears achievable with this agent. This may allow successful clinical intervention in selected patients.
Endlessly single-mode holey fibers: the influence of core design (2005)

In this paper we evaluate the cut-off properties of holey fibers (HFs) with a triangular lattice of air holes and the core formed by the removal of a single (HF1) or more air holes (HF3 and HF7). With the aid of finite-element simulations we determine the single-mode and multi-mode phases and also find the air hole diameters limiting the endlessly single-mode regime. From calculations of V and W parameters we find that in general HF1 is less susceptible to longitudinal non-uniformities compared to the other designs for equivalent effective areas. As an example we illustrate this general property for the particular case of a macro-bending induced loss.
Rice protein-based infant formula: current status and future development. (2007)

Rice is the world's leading staple cereal food and is the major source of protein for many parts of the world. Rice is among the first solid foods fed to infants in many cultures, in part because of its hypoallergenicity from lack of gluten. Nutritional quality of rice protein compares favorably with other cereal proteins including wheat, oat and barley. It is rich in methionine and cystine, although as is the case for other cereals, it is an incomplete protein source for human infants with lysine and threonine being the primary limiting amino acids. Fortification of rice proteins with these two limiting amino acids improves its protein quality. Rice protein-based infant formulas (RPF) were initially based on high protein rice flours, but more recently are based on rice protein concentrates, isolates or hydrolysates, fortified with lysine and threonine. Hypoallergenicity efficacy, particularly for hydrolyzed rice protein-based formulas, has been reported, and limited data indicated that rice protein based infant formula may provide potentially adequate alternative if standard milk- or soy protein-based formulas are not tolerated. Unlike the rice-protein based infant formula, rice beverage formulas made from rice flour are nutritionally inadequate for infants. Reports have indicated stunted growth in infants/children fed rice beverage formulas. Future development for the RPF include those based on genetically improved rice with high lysine and threonine content, supplementation with appropriate mineral and fat blend, and long-term clinical studies in infants to confirm its efficacy and safety.
Interferon alpha 2b as maintenance therapy in low grade malignant lymphoma improves duration of remission and survival (1996)

We assessed the efficacy and toxicity of interferon alpha 2b (IFN) as maintenance therapy in patients with low grade malignant lymphoma. Between March 1986 and December 1989, 98 patients with low-grade malignant lymphoma in complete remission after conventional chemotherapy were randomly assigned to received IFN, 5.0 MU three times a week for one year, as maintenance therapy (n = 48), or to receive no treatment (control group, n = 50). In March 1994, the median duration of response had not yet been reached in the patients treated with IFN compared to 46 months in the control group. At 9-years 62% of the patients in the IFN arm remain in first complete remission compared to only 25% in the control group (p <.001). In addition, the median duration of survival has not yet been reached in either the IFN arm compared to 74 months in the control group (p <.001). Quality of life was excellent in both groups and severe side effects secondary to IFN treatment were not observed. All patients completed the planned dose of IFN. We conclude that IFN as maintenance therapy in low-grade malignant lymphoma is an excellent therapeutic option because it improves the duration of remission and survival without producing severe side effects or reducing the quality of life.
Demethoxyrapamycin (AY-24,668),a new antifungal antibiotic. (1983)

Demethoxyrapamycin is a new antifungal antibiotic which is co-produced with rapamycin by Streptomyces hygroscopicus. It was isolated as a minor component during recovery of rapamycin. Its antifungal and antitumor activity is compared with that of rapamycin.
Embryos of Artemia Franciscana Survive Four Years of Continuous Anoxia: The Case for Complete Metabolic Rate Depression (1997)

Encysted gastrula embryos of the crustacean Artemia franciscana have acquired an array of adaptations that enable them to survive a wide variety of environmental extremes.The present paper shows that at least 60 % survive 4 years of continuous anoxia at physiological temperatures (20&shy;23 &deg;C) when fully hydrated. Although these embryos appear to carry on a metabolism during the first day of anoxia, no evidence for a continuing metabolism throughout the subsequent 4 years was obtained. During this period, there were no measurable changes in the levels of their stored, mobilizable carbohydrates (trehalose, glycogen, glycerol). Calculations indicate that, if these carbohydrates are being utilized at all during anoxia, the rate is at the least 50 000 times lower than the aerobic rate (lower limit of detection). Indications of proteolysis during prolonged anoxia were sought but not found. Under starvation conditions, the life span of larvae produced from embryos that had undergone 4 years of anoxia was not significantly different from that of larvae produced by embryos that had not experienced anoxia. Thus, all substrates and other metabolites required to support embryonic development to the nauplius, as well as endogenous (unfed) larval growth and molting, are retained during 4 years of anoxia. It is not possible to prove experimentally the absence of a metabolic rate in anoxic embryos under physiological conditions of hydration and temperature. Nevertheless, on the basis of the results presented here, I will make the case that the anoxic embryo brings its metabolism to a reversible standstill. Such a conclusion requires that these embryos maintain their structural integrity in the absence of measurable biosynthesis and free energy flow and are thus an exception to a major biological generality. Potential mechanisms involved in their stability are discussed.
The C-D interhelical domain of the serpin plasminogen activator inhibitor-type 2 is required for protection from TNF-α induced apoptosis (1998)

The serine proteinase inhibitor (serpin), plasminogen activator inhibitor type 2 (PAI-2), has been reported to inhibit tumor necrosis factor-alpha (TNF) induced apoptosis. In order to begin to understand the molecular basis for this protection, we have investigated the importance of a structural domain within the PAI-2 molecule, the C-D interhelical region, in mediating the protective effect. The C-D interhelical region is a 33 amino acid insertion which is unique among serpins and has been implicated in transglutaminase catalyzed cross-linking of PAI-2 to cell membranes. We have constructed a mutant of PAI-2 wherein 23 amino acids are deleted from the C-D interhelical region generating a structure predicted to be homologous to the closely related, but non-inhibitory serpin, chicken ovalbumin. The PAI-2Delta65/87 deletion mutant retained inhibitory activity against its known serine proteinase target, urokinase-type plasminogen activator (uPA); however expression of this mutant in HeLa cells failed to protect from TNF-induced apoptosis. Analyses of the cellular distribution of PAI-2 showed that intracellular PAI-2, and not secreted or cell-surface PAI-2, was likely responsible for the observed protection from TNF-induced apoptosis. No evidence was found for specific cross-linking of PAI-2 to the plasma membrane in either control or TNF/cycloheximide treated cells. The data demonstrate that the PAI-2 C-D interhelical domain is functionally important in PAI-2 protection from TNF induced apoptosis and suggest a novel function for the C-D interhelical domain in the protective mechanism.
Frequency of Major Molecular Responses to Imatinib or Interferon Alfa plus Cytarabine in Newly Diagnosed Chronic Myeloid Leukemia (2003)

The proportion of patients with CML who had a reduction in BCR-ABL transcript levels of at least 3 log by 12 months of therapy was far greater with imatinib treatment than with treatment with interferon plus cytarabine. Patients in the imatinib group with this degree of molecular response had a negligible risk of disease progression during the subsequent 12 months.
Quantifying genotyping errors in noninvasive population genetics (2004)

The use of noninvasively collected samples greatly expands the range of ecological issues that may be investigated through population genetics. Furthermore, the difficulty of obtaining reliable genotypes with samples containing low quantities of amplifiable DNA may be overcome by designing optimal genotyping schemes. Such protocols are mainly determined by the rates of genotyping errors caused by false alleles and allelic dropouts. These errors may not be avoided through laboratory procedure and hence must be quantified. However, the definition of genotyping error rates remains elusive and various estimation methods have been reported in the literature. In this paper we proposed accurate codification for the frequencies of false alleles and allelic dropouts. We then reviewed other estimation methods employed in hair- or faeces-based population genetics studies and modelled the bias associated with erroneous methods. It is emphasized that error rates may be substantially underestimated when using an erroneous approach. Genotyping error rates may be important determinants of the outcome of noninvasive studies and hence should be carefully computed and reported.
Ocrelizumab: a step forward in the evolution of B-cell therapy (2009)

Recent advances in our understanding of B-cell dysregulation and its important link to autoimmunity have brought about a radical change in the management of autoimmune diseases. Over the past few years, encouraging data from several clinical trials of rituximab, a chimeric anti-CD20 antibody, have led to its approval for use in rheumatoid arthritis (RA). These data, regarding clinical efficacy, safety, improved patient-reported outcomes and cost-effectiveness with the use of rituximab in patients with RA, have led to the exploration of other agents targeting B-cell functions. Ocrelizumab, a novel humanized anti-CD20 antibody, has shown clinical efficacy and safety in a recently reported trial in patients with RA. Future clinical trials will help evaluate further the role of ocrelizumab in RA and its potential use in other autoimmune diseases. This review describes current understanding of B-cell therapy, the role of rituximab in the treatment of RA and the evolving role of ocrelizumab as a B-cell-targeted therapy.
Basic science reviews: Tumor suppressor genes (1992)

Tumor suppressor genes are negative regulators of cell growth. When their normal function is compromised, absence of their inhibitory effects can lead to unrestrained cell cycling and growth. Strong evidence now confirms that loss of proper function of these genes is a common occurrence leading to cancer. Their failure can be caused by alterations in the gene DNA or malfunction of their protein products. The recent extraordinary accumulation of knowledge about these genes reveals that normal carcinogenesis represents breakdown of normal regulatory processes.
Highly efficient elimination of Philadelphia leukemic cells by exposure to bcr/abl antisense oligodeoxynucleotides combined with mafosfamide. (1993)

Synthetic oligodeoxynucleotides complementary to the break-point junction of bcr-abl transcripts selectively inhibit the proliferation of Philadelphia-positive leukemic cells, but residual leukemic cells persist in antisense oligodeoxynucleotides-treated cultures. Cyclophosphamide derivatives such as mafosfamide and 4-hydroperoxycyclophosphamide are used at high doses for purging of Philadelphia leukemic cells from marrows but such treatment can be associated with delayed engraftment and prolonged cytopenias. To develop a more effective procedure that might optimize the killing of leukemia cells and the sparing of normal hematopoietic progenitor cells, a 1:1 mixture of Philadelphia leukemic cells and normal bone marrow cells was exposed to a combination of a low dose of mafosfamide and bcr-abl antisense oligodeoxynucleotides and assayed for growth ability in clonogenic assays and in immunodeficient mice. Bcr-abl transcripts were not detected in residual colonies, and cytogenetic analysis of individual colonies revealed a normal karyotype. Normal but not leukemic hematopoietic colonies of human origin were also detected in marrows of immunodeficient mice 1 mo after injection of the treated cells. Our results indicate that a combination of a conventional chemotherapeutic agent and a tumor-specific antisense oligodeoxynucleotide is highly effective in killing leukemic cells and in sparing a much higher number of normal progenitor cells as compared with high-dose mafosfamide treatment. This offers the prospect of a novel and more selective ex vivo treatment of chronic myelogenous leukemia.
Viral Oncolysis (2002)

The concept of using replicating viruses as anticancer agents is not a new one, but the ability to genetically modify these viruses into increasingly potent and tumor-specific vectors is a recent phenomenon. As more is learned about the functions of viral gene products in controlling the mammalian cell cycle and in disabling cellular defense mechanisms, specific viral functions can be augmented or eliminated to enhance antineoplastic efficacy. In this article, general mechanisms by which oncolytic viruses achieve their antitumor efficacy and specificity are reviewed. The paradoxical roles of the immune response are addressed with respect to oncolytic viral therapy, as it, on one hand, impedes the spread of viral infection, and on the other, augments tumor cell destruction through the recruitment of T cells "vaccinated" against tumor antigens. The most commonly used oncolytic viruses are each reviewed in turn, including adenoviruses, herpes simplex viruses, vaccinia viruses, reoviruses, and Newcastle disease viruses. Special attention is focused on the unique biology of each of these viruses as well as the status of several of these mutants in clinical trials.
A General Approach for Receptor and Antibody-Targeted Detection of Native Proteins Utilizing Split-Luciferase Reassembly (2010)

The direct detection of native proteins in heterogeneous solutions remains a challenging problem. Standard methodologies rely on a separation step to circumvent nonspecific signal generation. We hypothesized that a simple and general method for the detection of native proteins in solution could be achieved through ternary complexation, where the conditional signal generation afforded by split-protein reporters could be married to the specificity afforded by either native receptors or specific antibodies. Toward this goal, we describe a solution phase split-luciferase assay for native protein detection, where we fused fragmented halves of firefly luciferase to separate receptor fragments or single-chain antibodies, allowing for conditional luciferase complementation in the presence of several biologically significant protein targets. To demonstrate the utility of this strategy, we have developed and validated assay platforms for the vascular endothelial growth factor, the gp120 coat protein from HIV-1, and the human epidermal growth factor receptor 2 (HER2), a marker for breast cancer. The specificities of the recognition elements, CD4 and the 17b single-chain antibody, employed in the gp120 sensor allowed us to parse gp120s from different clades. Our rationally designed HER2 sensing platform was capable of discriminating between HER2 expression levels in several tumor cell lines. In addition, luminescence from reassembled luciferase was linear across a panel of cell lines with increasing HER2 expression. We envision that the proof of principle studies presented herein may allow for the potential detection of a broad range of biological analytes utilizing ternary split-protein systems.
Nefopam and tramadol for the prevention of shivering during neuraxial anesthesia☆ (2002)

As a pharmacologic means of preventing shivering in patients undergoing neuraxial anesthesia, nefopam may hold the greatest promise.