gebhart/patrepeval huggingface dataset:
Biosynthesis and Secretion of Yeast Invertase (1971)

The effect of cycloheximide and 2‐deoxy‐ d ‐glucose on the synthesis and secretion of invertase by yeast cells and protoplasts has been studied. Two yeast strains were used: Saccharomyces 303‐67, whose investase synthesis is repressed by glucose, and a mutant of it, Saccharomyces FH4C, which is only partially affected by high levels of glucose in the incubation media. For both strains the optimum glucose concentration is approximately 10 mM. Cycloheximide inhibited the synthesis of invertase in cells and protoplasts. The secretion of the enzyme by the protoplasts was inhibited to a similar extent. Parallel results were obtained with 2‐deoxy‐ d ‐glucose. Two forms of invertase are present in yeast protoplasts; a light form devoid of carbohydrate and a heavy form which contains carbohydrate and is readily secreted. In all experimental conditions studied the relative amount of both forms remained constant. This indicates that although cycloheximide and 2‐deoxy‐ d ‐glucose exert their action at two different points in the biosynthesis of glycoproteins, either of them can stop the process of synthesis and secretion of yeast invertase.
Path Planning with Adaptive Dimensionality (2021)

Path planning quickly becomes computationally hard as the dimensionality of the state-space increases. In this paper, we present a planning algorithm intended to speed up path planning for high-dimensional state-spaces such as robotic arms. The idea behind this work is that while planning in a high-dimensional state-space is often necessary to ensure the feasibilityof the resulting path, large portions of the path have a lower-dimensional structure. Based on this observation, our algorithm iteratively constructs a state-space of an adaptive dimensionality--a state-space that is high-dimensional only where the higher dimensionality is absolutely necessary for finding a feasible path. This often reduces drastically the size of the state-space, and as a result, the planning time and memory requirements. Analytically, we show that our method is complete and is guaranteed to find a solution if one exists, within a specified suboptimality bound. Experimentally, we apply the approach to 3D vehicle navigation (x, y, heading), and to a 7 DOF robotic arm on the Willow Garage’s PR2 robot. The results from our experiments suggest that ourmethod can be substantially faster than some of the state-of-the-art planning algorithms optimized for those tasks.
Silver-enhanced colloidal gold as a cell surface marker for photoelectron microscopy. (1986)

Colloidal gold labeling in conjunction with silver enhancement was investigated as a labeling technique for photoelectron microscopy (PEM). PEM uses UV-stimulated electron emission to image uncoated cell surfaces, and markers for cell surfaces need to be sufficiently photoemissive to be clearly visible against this background. Label contrast provided by 6 nm or 20 nm colloidal gold markers alone was compared to that provided by 6 nm markers after silver enhancement, using both direct and indirect labeling methods for fibronectin on human fibroblast cell surfaces. In all cases, details of the fibrillar fibronectin labeling distribution which were barely discernible before silver enhancement became highly visible against the cellular surface features. Two factors evidently contribute to the pronounced increase in label contrast with silver enhancement: (1) Increased particle size, which was documented by transmission electron microscopy, and (2) increased photoemission resulting from a silver coating on the enhanced gold markers, compared with the protein coating on the unenhanced gold markers. These data demonstrate that silver enhancement of colloidal gold labeling patterns in PEM images is a highly effective method for localization of specific sites on cell surfaces.
Effects of ammonia on CHO cell growth, erythropoietin production, and glycosylation (2000)

The effect of ammonium chloride was determined on a culture of CHO cells transfected with the human erythropoietin (EPO) gene. Cell growth was inhibited above a culture concentration of 5 mM NH(4)Cl with an IC-50 determined to be 33 mM. The specific production of EPO increased with the addition of NH(4)Cl above 5 mM. At 10 mM NH(4)Cl, the final cell density after 4 days in culture was significantly lower but the final yield of EPO was significantly higher. This appeared to be due to continued protein production after cell growth had ceased. The metabolic effects of added NH(4)Cl included higher specific consumption rates of glucose and glutamine and an increased rate of production of alanine, glycine, and glutamate. The EPO analyzed from control cultures had a molecular weight range of 33-39 kDa and an isoelectric point range of 4.06-4.67. Seven distinct isoforms of the molecule were identified by two-dimensional electrophoresis. This molecular heterogeneity was ascribed to variable glycosylation. Complete enzymatic de-glycosylation resulted in a single molecular form with a molecular mass of 18 kDa. Addition of NH(4)Cl to the cultures caused a significant increase in the heterogeneity of the glycoforms as shown by an increased molecular weight and pI range. Enzymatic de-sialylation of the EPO from the ammonia-treated and control cultures resulted in identical electrophoretic patterns. This indicated that the effect of ammonia was in the reduction of terminal sialylation of the glycan structures which accounted for the increased pI. Selective removal of the N-glycan structures by PNGase F resulted in two bands identified as the O-glycan linked structure (19 kDa) and the completely de-glycosylated structure (18 kDa). The proportion of the O-linked glycan structure was reduced, and its pI increased in cultures to which ammonia was added. Thus, the glycosylation pattern altered by the presence of ammonia included a reduction in terminal sialylation of all the glycans and a reduction in the content of the O-linked glycan. The addition of a sialidase inhibitor to the cultures had no effect on the ammonia-induced increase in EPO heterogeneity. Also, the effect of ammonia on glycosylation could not be mimicked using the weak base chloroquine in our system.
Directed evolution of trimethoprim resistance in Escherichia coli (2007)

Directed evolution is a useful tool in the study of enzymes. It is used in this study to investigate the means by which resistance to the antibiotic trimethoprim develops in dihyrofolate reductase from Escherichia coli. Mutants with clinical levels of resistance were obtained after only three generations. After four generations of directed evolution, several mutants were characterized, along with some point mutants made to investigate amino acid changes of interest. Several mutations were found to grant resistance to trimethoprim, both by reducing the binding affinity of the enzyme for the drug, and by increasing the activity of the enzyme.
Role of neutrophil receptors in opsonophagocytosis of coagulase-negative staphylococci (1991)

The role of neutrophil complement receptors in the opsonophagocytosis of 10 strains of coagulase-negative staphylococci was investigated. Polymorphonuclear leukocytes from adults as well as term and premature newborn infants were tested with normal human serum, adult hypogammaglobulinemic serum, and pooled premature infant serum in an opsonophagocytic assay. Neutrophils from premature infants demonstrated significantly lower killing capacity (62%) than neutrophils from adults (86%) or term infants (84%; P less than 0.02). Maximum inhibition of opsonophagocytosis by adult or infant neutrophils occurred with an FcIII receptor blockade (80%), whereas a blockade of complement receptors produced minimal inhibition. Opsonophagocytic activity for the coagulase-negative staphylococci was not influenced by the serum source but was influenced by reducing the serum concentration below 5%. Abrogation of the complement activity of normal human serum by heating or the addition of ethylenediamine tetraacetate reduced opsonophagocytosis by 100 and 96%, respectively, whereas selective inhibition of the classical complement pathway reduced opsonophagocytosis by only 40%. Thus, opsonophagocytosis of coagulase-negative staphylococci by human sera appears to be mediated primarily by neutrophil Fc receptors, but complement is also required. The inefficiency of these interactions with neutrophils from premature infants may partially explain the enhanced susceptibility of very-low-birth-weight neonates to disseminated, coagulase-negative staphylococcal infections.
Stem cell sources and therapeutic approaches for central nervous system and neural retinal disorders (2008)

In the past decades, stem cell biology has made a profound impact on our views of mammalian development as well as opened new avenues in regenerative medicine. The potential of stem cells to differentiate into various cell types of the body is the principal reason they are being explored in treatments for diseases in which there may be dysfunctional cells and/or loss of healthy cells due to disease. In addition, other properties are unique to stem cells; their endogenous trophic support, ability to home to sites of pathological entities, and stability in culture, which allows genetic manipulation, are also being utilized to formulate stem cell-based therapy for central nervous system (CNS) disorders. In this review, the authors will review key characteristics of embryonic and somatic (adult) stem cells, consider therapeutic strategies employed in stem cell therapy, and discuss the recent advances made in stem cell-based therapy for a number of progressive neurodegenerative diseases in the CNS as well as neuronal degeneration secondary to other abnormalities and injuries. Although a great deal of progress has been made in our knowledge of stem cells and their utility in treating CNS disorders, much still needs to be elucidated regarding the biology of the stem cells and the pathogenesis of targeted CNS diseases to maximize therapeutic benefits. Nonetheless, stem cells present tremendous promise in the treatment of a variety of neurodegenerative diseases.
Prevention of Allogeneic Fetal Rejection by Tryptophan Catabolism (1998)

In 1953 Medawar pointed out that survival of the genetically disparate (allogeneic) mammalian conceptus contradicts the laws of tissue transplantation. Rapid T cell-induced rejection of all allogeneic concepti occurred when pregnant mice were treated with a pharmacologic inhibitor of indoleamine 2,3-dioxygenase (IDO), a tryptophan-catabolizing enzyme expressed by trophoblasts and macrophages. Thus, by catabolizing tryptophan, the mammalian conceptus suppresses T cell activity and defends itself against rejection.
Left main coronary artery occlusion in a patient with solitary coronary ostium in the right aortic sinus (2004)

An 82 year old woman with a history of high blood pressure and chronic atrial fibrillation without oral anticoagulation was admitted to the emergency department because of a syncopal episode followed by chest pain. Until that day she was totally asymptomatic.

On admission the patient was in cardiogenic shock; the ECG …
High Aspect Ragio Silicon Microstructures for Nucleic Acid Extraction (1998)

Silicon fluidic microchips with high surface area to volume ratios have been fabricated using deep reactive ion etching (ORIE) technology [1,2]. These microchips have been used as capture surfaces for nucleic acids (NA). Short (500 bp) and medium size (48,000 bp) DNA have been captured, washed, and eluted with these chips using glass binding chemistries. DNA quantities approaching 40 ng/cm 2 of binding area were captured from input solutions in the 100-1000 ng/mL concentration range, and detected using fluorescence techniques. For low concentration studies, PCR and gel electrophoresis were used as the detection method. Extraction efficiencies of about 50%, and concentration factors of about IO have been demonstrated using bacteriophage lambda DNA as the target. From an input volume of 500 L containing 5 x 10 4 DNA molecules, 2-3 x 10 4 DNA molecules were extracted and eluted into a 25 L volume. These results demonstrate the viability of utilizing such microchips as an element in a compact, disposable cartridge format for the detection of DNA in applications such as clinical diagnostics, biowarfare agent detection, food quality control, and environmental monitoring.
The Turkish Banking System, Financial Crises and the IMF in the Age of Capital Account Liberalization: A Political Economy Perspective (2004)

Recent episodes of financial crises in emerging markets progressively highlighted the importance of a sound and well-functioning banking sector for macroeconomic stability and sustainable economic growth. The Asian crisis of 1997, in particular, drew attention to the fundamental role that a deficient banking system could play in terms of generating major financial crises with devastating repercussions on the real economy and with significant possibilities of contagion in an emerging market context. The recent twin economic crises experienced by Turkey in 2000 and 2001 illustrated in a rather dramatic fashion the strong correspondence between a poorly functioning and under-regulated banking system, on the one hand, and the sudden outbreak of macroeconomic crises on the other. Indeed, the Turkish experience shows that both public and private banks can contribute significantly to the outbreak of economic crises. In retrospect, it may be argued that private commercial banks played an instrumental role in the first of the twin crises experienced in November 2000, whilst, public banks emerged as the central actors in the context of the subsequent crisis of February 2001.
The Regulation of Factor IXa by Supersulfated Low Molecular Weight Heparin (2010)

Supersulfated low molecular weight heparin (ssLMWH) inhibits the intrinsic tenase (factor IXa-factor VIIIa) complex in an antithrombin-independent manner. Recombinant factor IXa with alanine substitutions in the protease domain (K126A, N129A, K132A, R165A, R170A, N178A, R233A) was assessed with regard to heparin affinity in solution and ability to regulate protease activity within the factor IXa-phospholipid (PL) and intrinsic tenase complexes. In a soluble binding assay, factor IXa K126A, K132A, and R233A dramatically (10-20-fold) reduced ssLMWH affinity, while factor IXa N129A and R165A moderately (5-fold) reduced affinity relative to wild type. In the factor IXa-PL complex, binding affinity for ssLMWH was increased 4-fold, and factor X activation was inhibited with a potency 7-fold higher than predicted for wild-type protease-ssLMWH affinity in solution. In the intrinsic tenase complex, ssLMWH inhibited factor X activation with a 4-fold decrease in potency relative to wild-type factor IXa-PL. The mutations increased resistance to inhibition by ssLMWH in a similar fashion for both enzyme complexes (R233A > K126A > K132A/R165A > N129A/N178A/wild type) except for factor IXa R170A. This protease had ssLMWH affinity and potency for the factor IXa-PL complex similar to wild-type protease but was moderately resistant (6-fold) to inhibition in the intrinsic tenase complex based on increased cofactor affinity. These results are consistent with conformational regulation of the heparin-binding exosite and macromolecular substrate catalysis by factor IXa. An extensive overlap exists between the heparin and factor VIIIa binding sites on the protease domain, with residues K126 and R233 dominating the heparin interaction and R165 dominating the cofactor interaction.
The Relationship among Structure, Process, and Outcome Dimensions of Nursing Department in Hospitals (2000)

The purpose of this study was to analyze the relationship and the importance of relevant variables among structure, process, and outcome dimensions of nursing department in hospitals. The subject for this study was the registered nurses(N=400) working in medical, intensive care, and surgical units at 5 general hospitals with more than 500beds in Chungnam and Chungbuk. The research design was cross-sectional correlation among the variables based on their self description. The survey instrument was based on eleven structured questionnaires. The data were collected from April 26 to May 26, 1999. The SPSS/PC+ program and LISREL 8.12a program were used to analyze the data. Based on the data collected, the following results were obtained. The relationship among structural, procedural, and outcome dimensions 1. Structural dimension had a relationship with procedural dimension relating to decision-making of caregiving and working conditions, in particular, participation of the problem identification. 2. The extent of participation in decision-making had a relationship with organizational commitment and group effectiveness through the selection process among the total decision-making processes. 3. The structural dimension had a large direct effect rather than indirect effect through decision making processes on organizational commitment and group effectiveness. The relationship of structure, process, outcome dimensions was partially supported by this study. The information obtained from surveys in the field form the basis for the following recommendations for improving organizational effectiveness with in the nursing department in an hospitals. 1) Establishment of decentralized structure, environment, and culture in organizational settings would be desirable so that their members may actively participate in decision-making process. 2) Continuous education and training of nurses with theoretical Knowledge and skill of decision making, practical knowledge, and upright role perception should be highly emphasized for persons in nursing schools and in on-the-job training.
Synthesis of potential inhibitors of hypoxanthine-guanine phosphoribosyltransferase for testing as antiprotozoal agents. 1. 7-Substituted 6-oxopurines (1980)

Biological evidence indicates that the enzyme hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) is vital for cell proliferation in malarial parasites but nonessential for mammalian cells. 7-Substituted guanines and hypoxanthines in which the 7 substituent bears functional or hydrophobic groups were prepared with the aim of finding a suitably constituted compound whose resemblance to the normal substrate allows it to compete for the reversible purine binding site of HGRPTase while allowing a substituent group of the inhibitor molecule to form a covalent bond or strong hydrophobic bond with appropriate sites on the enzyme. Multistep syntheses that began with hydroxyalkylations and alkylations of guanosine led to four key guanines substituted at the 7 position by the following chains: 2-aminoethyl, 3-amino-2-hydroxypropyl, 3-aminobenzyl, and 4-aminobenzyl. Similarly, 7-(4-aminobenzyl)hypoxanthine was prepared. Reactions at the side-chain amino groups with bromoacetic anhydride (or, alternatively, 4-nitrophenyl bromoacetate) and 3- and 4-(fluorosulfonyl)benzoyl chlorides afforded derivatives bearing functional groups capable of forming covalent bonds with enzymes through displacement reactions. 4-Chlorobenzyl derivatives were similarly prepared as potential inhibitors that might act through hydrophobic bonding. Three 7-substituted guanines whose side chains bear other functions (7-guanine-3-propranesulfonic acid, guanine-7-acetaldehyde, and the ethyl ester of 7-guanine-4-crotonic acid) were prepared as potential inhibitors and for possible use as intermediates. None of these compounds extended the life span of P. berghei infected mice or showed significant in vitro inhibition of HGPRTase from H.Ep.-2 cells.
The Leukemia-Lymphoma Cell Line Factsbook (2000)

This book represents an essential reference manual for all of the well-characterized leukemia-lymphoma cell lines currently available. It provides the most important facts, using the succinct and user-friendly format that has made the FactsBooks so popular with scientists and clinical researchers. Introductory chapters provide background and perspective for culturing malignant hematopoietic (blood forming) cell lines. These chapters are followed by over 400 comprehensive individual entries. Each cell line entry highlights essential clinical, immunological, genetic, and functional features and includes a comprehensive listing of references. Key features include: the full spectrum of malignant cell lines from all hematopoietic cell lineages; sister cell lines and relevant subclones; clinical data such as: patient, diagnosis, treatment status, and specimen source; authentication of derivation and availability; immunophenotype; cytogenetic karyotype; translocations and fusion genes; receptor gene rearrangements and genetic alterations; cell cultures aspects: establishment, medium, doubling time, and growth; cytochemical profile; cytokine production and response to cytokines; proto-oncogene and transcription factor expression/alteration; functional features such as: differentiation induction, heterotransplantability; special unique features; and key references.
Development and validation of a T7 based linear amplification for genomic DNA (2003)

We present a T7-based linear amplification protocol for genomic DNA. Validation studies and comparisons with existing methods suggest that incorporation of this protocol will reduce amplification bias in genome mapping experiments.
Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular (2018)

Our results suggest that during human ES cell differentiation, changes in circRNA levels are primarily globally controlled. They also suggest that RMST and FIRRE, genes with established roles in neurogenesis and topological organisation of chromosomal domains respectively, are processed as circular lncRNAs with only minor linear species.
Expression of tumor-associated epitopes on Epstein-Barr virus-immortalized B-cells and Burkitt's lymphomas transfected with epithelial mucin complementary DNA. (1992)

Mucins are among the best described human tumor-associated antigens. At least 73 tumor-reactive anti-mucin antibodies have been described; in addition, we have previously demonstrated the existence of tumor-specific cytotoxic T-lymphocyte epitopes on the mucin produced by breast and pancreatic tumors. To determine whether the appearance of tumor-associated mucin epitopes can be explained by altered post-translational modification of mucin in tumors, or whether the generation of these epitopes requires changes in the mucin gene itself, we studied four Burkitt's lymphomas and six Epstein-Barr virus-immortalized B-cell lines transfected with an expression construct containing the mucin complementary DNA. Transfected cell lines showed stable maintenance of the mucin gene, which comprises 20 or more tandem repeats of a 60-nucleotide sequence. Transfected cells expressed many tumor-associated mucin epitopes, suggesting that the changes in mucin synthesis seen in breast and pancreatic tumors are present in other malignant cell types as well. Furthermore, even though each cell line was transfected with the identical mucin construct, each expressed a different subset of tumor-associated mucin epitopes. This suggests that the specificity of these epitopes for tumors is not due to genetic alterations of the mucin gene in tumors. Incubating transfected cells with phenyl-N-acetyl-alpha-galactosaminide, an inhibitor of O-linked glycosylation, altered cell surface carbohydrate structures and resulted in increased expression of all tumor-associated epitopes, implicating incomplete glycosylation of mucin in the generation of these epitopes. These findings suggest that alterations in the posttranslational modification of normal gene products can result in the expression of novel epitopes. Furthermore, the ability to transfect cancer patients' Epstein-Barr virus-immortalized B-cell lines with mucin will provide an unlimited supply of autologous, mucin-bearing cells with which to study these patients' T-cell response to mucin.