gebhart/patrepeval huggingface dataset:
Preclinical Testing of Recombinant Adenoviral Herpes Simplex Virus-Thymidine Kinase Gene Therapy for Central Nervous System Malignancies (1997)

This study demonstrates the therapeutic efficiency and feasibility of the TK/GCV approach in experimental brain tumors and leptomeningeal metastases. It also demonstrates that the promoter driving the transgene in an adenoviral vector influences toxicity and efficiency of treatment.
Ciliary neurotropic factor, interleukin 11, leukemia inhibitory factor, and oncostatin M are growth factors for human myeloma cell lines using the interleukin 6 signal transducer gp130. (1994)

Interleukin 6 (IL-6) is a major growth factor for tumor plasma cells involved in human multiple myeloma (MM). In particular, human myeloma cell lines (HMCL), whose growth is completely dependent on addition of exogenous IL-6, can be obtained reproducibly from every patient with terminal disease. Four cytokines, ciliary neurotropic factor (CNTF), IL-11, leukemia inhibitory factor (LIF), and oncostatin M (OM), use the same transducer chain (signal transducer gp130) as IL-6 and share numerous biological activities with this IL. We found that these four cytokines stimulated proliferation and supported the long-term growth of two out of four IL-6-dependent HMCL obtained in our laboratory. Half-maximal proliferation was obtained with cytokine concentrations ranging from 0.4 to 1.2 ng/ml for IL-11, LIF, and OM. CNTF worked at high concentrations only (90 ng/ml), but addition of soluble CNTF receptor increased sensitivity to CNTF 30-fold. The growth-promoting effect of these four cytokines was abrogated by anti-gp130 antibodies, contrary to results for anti-IL-6 receptor or anti-IL-6 antibodies. No detectable changes in the morphology and phenotype were found when myeloma cells were cultured with one of these four cytokines instead of IL-6. Concordant with their IL-6-dependent growth, the four HMCL expressed membrane IL-6R and gp130 detected by FACS analysis. LIF-binding chain gene (LIFR) was expressed only in the two HMCL responsive to LIF and OM.
A deficit of detoxification enzymes: pesticide sensitivity and environmental response in the honeybee (2006)

The honeybee genome has substantially fewer protein coding genes ( approximately 11 000 genes) than Drosophila melanogaster ( approximately 13 500) and Anopheles gambiae ( approximately 14 000). Some of the most marked differences occur in three superfamilies encoding xenobiotic detoxifying enzymes. Specifically there are only about half as many glutathione-S-transferases (GSTs), cytochrome P450 monooxygenases (P450s) and carboxyl/cholinesterases (CCEs) in the honeybee. This includes 10-fold or greater shortfalls in the numbers of Delta and Epsilon GSTs and CYP4 P450s, members of which clades have been recurrently associated with insecticide resistance in other species. These shortfalls may contribute to the sensitivity of the honeybee to insecticides. On the other hand there are some recent radiations in CYP6, CYP9 and certain CCE clades in A. mellifera that could be associated with the evolution of the hormonal and chemosensory processes underpinning its highly organized eusociality.
Improved tandem affinity purification tag and methods for isolation of protein heterocomplexes from plants (2004)

A synthetic gene encoding the tandem affinity purification (TAP) tag has been constructed, and the TAP tag assayed for its effects on expression levels and subcellular localization by fusion to green fluorescent protein (GFP) as well as for its effects on steroid-dependent translocation to the nucleus and transcription when fused to a hybrid glucocorticoid receptor. A nuclear localization signal (NLS) was detected in the calmodulin-binding protein (CBP) domain and removed by mutation to improve the usefulness of the TAP tag. Additionally, purification improvements were made, including inhibition of a co-purifying protease, and adding a protein cross-linking step to increase the recovery of interacting proteins. The improved synthetic TAP tag gene and methods were used to isolate proteins interacting with the hybrid glucocorticoid receptor and to identify them by mass spectrometry. The two proteins identified, HSP70 and HSP90, are known to interact with the glucocorticoid receptor in vivo in mammalian cells and in vitro in plants.
A new synthesis of purines (1974)

Treatment of 6-aminopyrimidines with 4-phenyl-1,2,4-triazoline-3,5-dione gave the Michael-type adducts, 6-amino-5-(4-phenylurazol-1-yl)pyrimidines; fusion of these adducts with several aryl aldehydes gave the corresponding 8-arylpurines.
Overexpression of wild‐type Gαi‐2 suppresses β‐adrenergic signaling in cardiac myocytes (2003)

The role of Galpha(i)-2 overexpression in desensitization of beta-adrenergic signaling in heart failure is controversial. An adenovirus-based approach was used to investigate whether overexpression of Galpha(i)-2 impairs beta-adrenergic stimulation of adenylyl cyclase (AC) activity and cAMP levels in neonatal rat cardiac myocytes (NRCM) and cell shortening of adult rat ventricular myocytes (ARVM). Infection of NRCM with Ad5Galpha(i)-2 increased Galpha(i)-2 by 50-600% in a virus dose-dependent manner. Overexpression was paralleled by suppression of GTP- and isoprenaline-stimulated AC by 10-72% (P<0.001) in a PTX-sensitive manner. Isoprenaline-stimulated shortening of Ad5Galpha(i)-2-infected ARVM was attenuated by 34% (P<0.01). Ad5Galpha(i)-2/GFP (Galpha(i)-2, green fluorescent protein; bicistronic) was constructed to monitor transfection homogeneity and target Galpha(i)-2 overexpression to levels found in heart failure. At Galpha(i)-2 levels of 93% above control, isoprenaline-stimulated AC activity and cAMP levels were reduced by 17% and 40% (P<0.02), respectively. Beta1- and beta2-adrenergic stimulation was reduced similarly. Our results suggest that (a) the Galpha(i)-2 system exhibits tonic inhibition of stimulated AC in cardiac myocytes, (b) Galpha(i)-2-mediated inhibition is concentration-dependent and occurs at Galpha(i)-2 levels seen in heart failure, and (c) Galpha(i)-2-mediated inhibition affects both beta1- and beta2-adrenergic stimulation of AC. The data argue for an important, independent role of the Galpha(i)-2 increase in heart failure.
Regulation of Mitochondrial Morphology by USP30, a Deubiquitinating Enzyme Present in the Mitochondrial Outer Membrane (2008)

Recent studies have suggested that ubiquitination of mitochondrial proteins participates in regulating mitochondrial dynamics in mammalian cells, but it is unclear whether deubiquitination is involved in this process. Here, we identify human ubiquitin-specific protease 30 (USP30) as a deubiquitinating enzyme that is embedded in the mitochondrial outer membrane. Depletion of USP30 expression by RNA interference induced elongated and interconnected mitochondria, depending on the activities of the mitochondrial fusion factors mitofusins, without changing the expression levels of the key regulators for mitochondrial dynamics. Mitochondria were rescued from this abnormal phenotype by ectopic expression of USP30 in a manner dependent on its enzymatic activity. Our findings reveal that USP30 participates in the maintenance of mitochondrial morphology, a finding that provides new insight into the cellular function of deubiquitination.
Morphology and Dynamics of the Endocytic Pathway inDictyostelium discoideum (2002)

Dictyostelium discoideum is a genetically and biochemically tractable social amoeba belonging to the crown group of eukaryotes. It performs some of the tasks characteristic of a leukocyte such as chemotactic motility, macropinocytosis, and phagocytosis that are not performed by other model organisms or are difficult to study. D. discoideum is becoming a popular system to study molecular mechanisms of endocytosis, but the morphological characterization of the organelles along this pathway and the comparison with equivalent and/or different organelles in animal cells and yeasts were lagging. Herein, we used a combination of evanescent wave microscopy and electron microscopy of rapidly frozen samples to visualize primary endocytic vesicles, vesicular-tubular structures of the early and late endo-lysosomal system, such as multivesicular bodies, and the specialized secretory lysosomes. In addition, we present biochemical and morphological evidence for the existence of a micropinocytic pathway, which contributes to the uptake of membrane along side macropinocytosis, which is the major fluid phase uptake process. This complex endosomal compartment underwent continuous cycles of tubulation/vesiculation as well as homo- and heterotypic fusions, in a way reminiscent of mechanisms and structures documented in leukocytes. Finally, egestion of fluid phase from the secretory lysosomes was directly observed.
A method for mild photochemical oxidation; conversion of phenacyl sulfides into carbonyl compounds (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA method for mild photochemical oxidation; conversion of phenacyl sulfides into carbonyl compoundsE. Vedejs and D. A. PerryCite this: J. Org. Chem. 1984, 49, 3, 573–575Publication Date (Print):February 1, 1984Publication History Published online1 May 2002Published inissue 1 February 1984https://pubs.acs.org/doi/10.1021/jo00177a045https://doi.org/10.1021/jo00177a045research-articleACS PublicationsRequest reuse permissionsArticle Views744Altmetric-Citations26LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Can the Heart Repair Itself? (2002)

Bone marrow, the liver, and intestinal epithelium can regenerate, but the conventional teaching is that the heart cannot, because cardiac myocytes cannot divide. Consequently, it is generally accepted that the basis of cardiac enlargement and remodeling in response to disease or excessive work is an increase in the size of individual heart cells (hypertrophy) but not in their number (hyperplasia).Hypertrophy is a beneficial response to the demand for increased cardiac work, but it has drawbacks. Since myocytes cannot enlarge indefinitely, the extent to which the heart can adapt through hypertrophy has intrinsic limits. A sustained hemodynamic overload may end . . .
Using Information Extraction to Improve Document Retrieval (1998)

The authors describe an approach to applying a particular kind of Natural Language Processing (NLP) system to the TREC routing task in Information Retrieval (IR). Rather than attempting to use NLP techniques in indexing documents in a corpus, they adapted an information extraction (IE) system to act as a post-filter on the output of an IR system. The IE system was configured to score each of the top 2000 documents as determined by an IR system and on the basis of that score to rerank those 2000 documents. One aim was to improve precision on routing tasks. Another was to make it easier to write IE grammars for multiple topics.
The particle size distribution of emulsions containing diazepam for intravenous use (1976)

The particle size and distribution of size of emulsions intended for intravenous administration is critical for the safety of the patient owing to the dangers of embolism. However, methods of measuring the size are limited in accuracy in the micrometre and sub-micrometre range. The use of a laser centrifugal photosedi-mentometer (LCP) is described which is capable of detecting particles down to 002 m̈m and would appear to be eminently suitable for characterizing emulsion systems in the critical size range. The instrument has been applied to a new drug vehicle containing diazepam which is based on intravenous nutritional emulsions. This emulsion was shown to have a mean particle diameter of 0–2 m̈m, comparable with literature values for chylomicra and similar to previous experimental results on intravenous emulsions. This suggests that the drug formulation is suitable for clinical application, especially as'animal studies indicate that it has a reduced toxicity when compared to propylene glycol injection solutions.
New paradigms in cervical cancer prevention: opportunities and risks (2008)

Testing for the DNA of high-risk types of papilloma virus (HPV) is more sensitive than cytology in detecting pre-cancerous lesions. One of the main advantages will be the possibility of applying prolonged screening intervals. However adequate screening protocols (age of start and stop, screening intervals, management of HPV positive women) need to be applied in order to avoid over-referral to colposcopy and over-treatment and to maintain sustainable costs. Further follow-up of running trials and research on molecular markers will better define these parameters. The new situation will require organised screening programmes with rigorous protocols and monitoring. This will be even more needed when women vaccinated for HPV 16 and 18 will be screened. Research on how to best screen vaccinated women is a priority. This paper proposes an overview of the plausible impact of new technologies in cervical cancer screening in the near future and in the vaccinated cohorts.
Activity of yeast FLP recombinase in maize and rice protoplasts (1993)

We have demonstrated that a yeast FLP/FRT site-specific recombination system functions in maize and rice protoplasts. FLP recombinase activity was monitored by reactivation of beta-glucuronidase (GUS) expression from vectors containing the gusA gene inactivated by insertion of two FRTs (FLP recombination targets) and a 1.31 kb DNA fragment. The stimulation of GUS activity in protoplasts cotransformed with vectors containing FRT inactivated gusA gene and a chimeric FLP gene depended on both the expression of the FLP recombinase and the presence and structure of the FRT sites. The FLP enzyme could mediate inter- and intramolecular recombination in plant protoplasts. These results provide evidence that a yeast recombination system can function efficiently in plant cells, and that its performance can be manipulated by structural modification of the FRT sites.
Synthesis of Highly Modified DNA by a Combination of PCR with Alkyne‐Bearing Triphosphates and Click Chemistry (2007)

We report the combination of "click chemistry" with PCR by using alkyne-modified triphosphates for efficient and homogeneous labeling of DNA. A series of modified PCR products of different lengths (300, 900, and 2000 base pairs) were prepared by using a variety of alkyne- and azide-containing triphosphates and different polymerases. After intensive screening of real-time PCR methods, protocols were developed that allow the amplification of genes by using these modified triphosphates with similar efficiency to that of standard PCR. The click reaction on the highly modified PCR fragments provided conversion rates above 90 % and resulted in the functionalization of hundreds of alkynes on large DNA fragments with superb selectivity and efficiency.
Condensation of α-Cyanothioacetamide with Aldehydes Catalyzed by Envirocat EPZG1 (1997)

Abstract Condensation of α-cyanothioacetamide with aldehydes has been carried out in excellent yield under mild conditions by using Envirocat EPZG as a heterogenous reusable catalyst.
Critical closing pressure in cerebrovascular circulation (1999)

Critical closing pressure, although sensitive to variations in ICP and CPP, cannot be used as an accurate estimator of these modalities with acceptable confidence intervals. The difference CCP-ICP significantly correlates with cerebral autoregulation, but it lacks the power to predict outcome after head injury.
Mannan‐binding lectin‐associated serine protease 2 is critical for the development of renal ischemia reperfusion injury and mediates tissue injury in the absence of complement C4 (2014)

Mannan-binding lectin-associated serine protease 2 (MASP-2) has been described as the essential enzyme for the lectin pathway (LP) of complement activation. Since there is strong published evidence indicating that complement activation via the LP critically contributes to ischemia reperfusion (IR) injury, we assessed the effect of MASP-2 deficiency in an isogenic mouse model of renal transplantation. The experimental transplantation model used included nephrectomy of the remaining native kidney at d 5 post-transplantation. While wild-type (WT) kidneys grafted into WT recipients (n=7) developed acute renal failure (control group), WT grafts transplanted into MASP-2-deficient recipients (n=7) showed significantly better kidney function, less C3 deposition, and less IR injury. In the absence of donor or recipient complement C4 (n=7), the WT to WT phenotype was preserved, indicating that the MASP-2-mediated damage was independent of C4 activation. This C4-bypass MASP-2 activity was confirmed in mice deficient for both MASP-2 and C4 (n=7), where the protection from postoperative acute renal failure was no greater than in mice with MASP-2 deficiency alone. Our study highlights the role of LP activation in renal IR injury and indicates that injury occurs through MASP-2-dependent activation events independent of C4.
Large area graphene ion sensitive field effect transistors with tantalum pentoxide sensing layers for pH measurement at the Nernstian limit (2014)

We have fabricated and characterized large area graphene ion sensitive field effect transistors (ISFETs) with tantalum pentoxide sensing layers and demonstrated pH sensitivities approaching the Nernstian limit. Low temperature atomic layer deposition was used to deposit tantalum pentoxide atop large area graphene ISFETs. The charge neutrality point of graphene, inferred from quantum capacitance or channel conductance, was used to monitor surface potential in the presence of an electrolyte with varying pH. Bare graphene ISFETs exhibit negligible response, while graphene ISFETs with tantalum pentoxide sensing layers show increased sensitivity reaching up to 55 mV/pH over pH 3 through pH 8. Applying the Bergveld model, which accounts for site binding and a Guoy-Chapman-Stern picture of the surface-electrolyte interface, the increased pH sensitivity can be attributed to an increased buffer capacity reaching up to 1014 sites/cm2. ISFET response was found to be stable to better than 0.05 pH units over the course of two weeks.
Catabolite repression of the xyl operon in Bacillus megaterium (1992)

We characterized catabolite repression of the genes encoding xylose utilization in Bacillus megaterium. A transcriptional fusion of xylA encoding xylose isomerase to the spoVG-lacZ indicator gene on a plasmid with a temperature-sensitive origin of replication was constructed and efficiently used for single-copy replacement cloning in the B. megaterium chromosome starting from a single transformant. In the resulting strain, beta-galactosidase expression is 150-fold inducible by xylose and 14-fold repressed by glucose, showing that both regulatory effects occur at the level of transcription. Insertion of a kanamycin resistance gene into xylR encoding the xylose-dependent repressor leads to the loss of xylose-dependent regulation and to a small drop in the efficiency of glucose repression to eightfold. Deletion of 184 bp from the 5' part of the xylA reading frame reduces glucose repression to only twofold. A potential glucose-responsive element in this region is discussed on the basis of sequence similarities to other glucose-repressed genes in Bacillus subtilis. The sequence including the glucose-responsive element is also necessary for repression exerted by the carbon sources fructose and mannitol. Their efficiencies of repression correlate to the growth rate of B. megaterium, as is typical for catabolite repression. Glycerol, ribose, and arabinose exert only a basal twofold repression of the xyl operon, which is independent of the presence of the cis-active glucose-responsive element within the xylA reading frame.
Microbial Metagenomics: Beyond the Genome (2010)

Metagenomics literally means "beyond the genome." Marine microbial metagenomic databases presently comprise approximately 400 billion base pairs of DNA, only approximately 3% of that found in 1 ml of seawater. Very soon a trillion-base-pair sequence run will be feasible, so it is time to reflect on what we have learned from metagenomics. We review the impact of metagenomics on our understanding of marine microbial communities. We consider the studies facilitated by data generated through the Global Ocean Sampling expedition, as well as the revolution wrought at the individual laboratory level through next generation sequencing technologies. We review recent studies and discoveries since 2008, provide a discussion of bioinformatic analyses, including conceptual pipelines and sequence annotation and predict the future of metagenomics, with suggestions of collaborative community studies tailored toward answering some of the fundamental questions in marine microbial ecology.
Granulocyte–Macrophage Colony-stimulating Factor to Reverse Sepsis-associated Immunosuppression: A Double-Blind, Randomized, Placebo-controlled Multicenter Trial (2009)

Biomarker-guided GM-CSF therapy in sepsis is safe and effective for restoring monocytic immunocompetence. Use of GM-CSF may shorten the time of mechanical ventilation and hospital/intensive care unit stay. A multicenter trial powered for the improvement of clinical parameters and mortality as primary endpoints seems indicated. Clinical trial registered with www.clinicaltrials.gov (NCT00252915).
Total Synthesis of a Cis-Syn 2-Carbomethoxypsoralen Furan-Side Thymidine Monoadduct (1996)

The first total chemical synthesis of a cis-syn furan-side photoproduct between a psoralen derivative and thymidine is described. The key step in the synthesis was an intramolecular [2 + 2] photocycloaddition, which directed the stereochemical course of the reaction to afford a product equivalent to that formed when a psoralen molecule is allowed to react at a 5‘-TpA-3‘ site in DNA. A model system consisting of a simple benzofuranyl acid tethered to the 5‘ hydroxyl of thymidine showed that it was possible to bias the stereochemical outcome of the photochemical reaction in favor of the desired cis-syn product. Further refinement of the model system allowed for the elaboration of a benzofuran−thymidine photoproduct into a cis-syn 2-carbomethoxypsoralen furan-side thymidine monoadduct. The stereochemistry of all photoproducts as established by NMR and CD spectroscopy indicated that the cycloadditions occurred on the 3‘ face of thymine, the equivalent of a psoralen monoadduct in a 5‘-TpA-3‘ site in DNA. Previously, the inability to program the sequence context of psoralen−DNA adducts has constrained certain biological studies, such as experiments aimed at deciphering the transcriptional effects of adducts at TATA sites. This method is a key step toward overcoming that problem.
Normal Brain Cells Contribute to the Bystander Effect in Suicide Gene Therapy of Malignant Glioma (2007)

Suicide gene transfer using pseudotyped lentiviral vectors was very effective in the treatment of rat glioma and therefore is an attractive therapeutic strategy also in human glioblastoma especially in conjunction with an imaging-guided approach. In addition, high selectivity of gene transfer to tumor cells may not always be desirable for therapeutic genes that exert a clear bystander effect.