gebhart/patrepeval huggingface dataset:
Design of asymmetric DNAzymes for dynamic control of nanoparticle aggregation states in response to chemical stimuli (2006)

Dynamic control of nanomaterial assembly states in response to chemical stimuli is critical in making multi-component materials with interesting properties. Previous work has shown that a Pb2+-specific DNAzyme allowed dynamic control of gold nanoparticle aggregation states in response to Pb2+, and the resulting color change from blue aggregates to red dispersed particles can be used as a convenient way of sensing Pb2+. However, a small piece of DNA (called invasive DNA) and low ionic strength (approximately 30 mM) were required for the process, limiting the scope of application in assembly and sensing. To overcome this limitation, a series of asymmetric DNAzymes, in which one of the two substrate binding regions is longer than the other, has been developed. With such a system, we demonstrated Pb2+-induced disassembly of gold nanoparticle aggregates and corresponding color change at room temperature without the need for invasive DNA, while also making the system more tolerant to ionic strength (33-100 mM). The optimal lengths of the long and short arms were determined to be 14 and 5 base pairs, respectively. In nanoparticle aggregates, the activity of the DNAzyme increased with decreasing ionic strength of the reaction buffer. This simpler and more versatile system allows even better dynamic control of nanoparticle aggregation states in response to chemical stimuli such as Pb2+, and can be used in a wider range of applications for colorimetric sensing of metal ions.
Activation of Phosphatidylinositol 3-Kinase Signaling by the Nonstructural NS1 Protein Is Not Conserved among Type A and B Influenza Viruses (2007)

Recently it has been shown by several laboratories that the influenza A virus nonstructural protein 1 (A/NS1) binds and activates phosphatidylinositol 3-kinase (PI3K). This function of the protein is likely to prevent premature apoptosis induction during viral propagation. Here we show that the B/NS1 protein completely lacks the capacity to induce PI3K signaling. Thus, PI3K activation is another unique function of A/NS1 that is different from the action of its influenza B virus counterpart.
Particle bombardment technology for gene transfer (1994)

Examining the full range and versatility of particle bombardment technology, the contributors to this volume describe the essential protocols, as well as successful applications such as crop improvement and human gene therapy. Hardware design, recombinant DNA and tissue culture techniques, and other technical issues are included. The book brings together recent developments and advancements in the field and unifies plant, microorganism and mammalian systems in a concise volume that enables the reader to access all important theoretical, mechanical and historical aspects of the technology.
Preclinical anti-myeloma activity of EDO-S101, a new bendamustine-derived molecule with added HDACi activity, through potent DNA damage induction and impairment of DNA repair (2017)

These findings provide rationale for the clinical investigation of EDO-S101 in MM, either as a single agent or in combination with other anti-MM drugs, particularly proteasome inhibitors.
Preclinical prediction of factors influencing the elimination of 5,6-dimethylxanthenone-4-acetic acid, a new anticancer drug. (1997)

The glucuronidation of 5,6-dimethylxanthenone-4-acetic acid (DMXAA), a newly developed anticancer drug, was investigated in vitro to determine factors likely to affect the elimination of this compound in patients. Human liver microsomal DMXAA glucuronidation followed Michaelis-Menten kinetics, with a mean apparent Km of approximately 100 microM. Two cDNA-expressed UGT isoforms, UGT1*02 and UGT2B7, had the capacity to glucuronidate DMXAA, although comparative kinetic and inhibitor studies were more consistent with a greater contribution of UGT2B7 to the human hepatic reaction. Microsomal DMXAA glucuronide formation was screened for inhibition by drugs known to be eliminated by glucuronidation. Of the drugs screened, significant inhibition was observed with diclofenac, epirubicin, indomethacin, R,S-ketoprofen, lorazepam, S-naproxen, oxazepam, and temazepam; apparent Ki values ranged from 9.5-318 microM. These values are substantially above unbound concentrations of the individual drugs achieved in vivo. DMXAA glucuronide was found to be unstable at physiological pH values, and the rate of degradation was marginally increased in the presence of albumin. Taken together, these data indicate that the kinetics of DMXAA glucuronidation in vivo are likely to be linear and unaffected by the coadministration of most glucuronidated drugs, but plasma DMXAA clearance may be decreased in patients with renal dysfunction. This study illustrates the utility of in vitro techniques for the prediction of potential drug interactions and other dispositional characteristics of newly developed anticancer drugs before their administration to patients.
Particle Size Determination from X-Ray Line Broadening (1946)

The x-ray line broadening method of determining particle size was compared with direct measurement on electron micrographs. By controlled heating of the carbonate, magnesium oxide particles were prepared from 50 to 1000A in diameter. Particle size calculated from x-ray data taken on a Geiger counter spectrometer agreed to ±10 percent with the microscope measurements. Mechanical mixtures of two different sizes were examined by the x-ray method, but the particle sizes could not be determined unless the two maxima of the distribution curve were completely resolved.
Sequence homologies between proteins of bacterial phosphoenolpyruvate-dependent sugar phosphotransferase systems: identification of possible phosphate-carrying histidine residues. (1987)

The DNA sequences for some of the genes involved in the phosphoenolpyruvate-dependent phosphotransferase system (PTS) of Escherichia coli and Salmonella typhimurium have been reported. Comparison of the deduced amino acid sequences of enzyme IIBgi, enzyme IIMtl, and enzyme IIGlc/enzyme IIIGlc, which catalyze the uptake and concomitant phosphorylation of beta-glucosides, mannitol, and glucose, respectively, reveals considerable sequence homology. In particular, the carboxyl-terminal region of enzyme IIBgl is so homologous to the whole of enzyme IIIGlc as to suggest a common function. We postulate that His-547 of enzyme IIBgl receives a phosphate group directly from the cytoplasmic protein HPr and transfers this phosphate to His-306 located in the amino-terminal half of enzyme IIBgl. This latter histidine is conserved in enzyme IIBgl and enzyme IIGlc and, in both proteins, occurs in a region that shows homology with the His-15 region of HPr, which is known to act as the phosphate carrier. An equivalent histidine residue, His-195, is also present in enzyme IIMtl, although here the flanking sequence is different. None of these specified histidine residues is likely to be buried within the membrane.
Growth control in cultured 3T3 fibroblasts II. Molecular properties of a fraction enriched in growth inhibitory activity. (1982)

Treatment of sparse, proliferating cultures of 3T3 cells with medium conditioned by exposure to density-inhibited 3T3 cultures resulted in an inhibition of growth and division in the target cells when compared to similar treatment with unconditioned medium. This growth inhibitory activity was fractionated by ammonium sulfate precipitation and gel filtration, yielding one fraction that was 35-fold enriched in specific activity. Analysis of the chemical and biological properties of this highly active fraction indicated that: (a) it is an endogenous cell product, synthesized by the 3T3 cells and shed into the medium; (b) it is a protein and its activity is sensitive to treatment with pronase; (c) the constituent polypeptide chains have molecular weights of 10,000 and 13,000; and (d) it is not cytotoxic and its effect on target cells are reversible. These results suggest that we have partially purified from conditioned medium an endogenous growth regulatory factor that may play a role in density-dependent inhibition of growth in cultured fibroblasts. We propose the term Fibroblast Growth Regulator to describe this class of molecules.
Mycorrhizal fungi effects on nutrient composition and yield of soybean seeds (1997)

Abstract Nutrient composition and yield of soybean [Glycine max (L.) Merr] seeds are heritable traits affected by environmental factors. This study determined the effects of arbuscular‐mycorrhizal (AM) fungi on seed protein, lipid, and phosphorus (P) composition and yield in soybean grown under a high nitrogen (N) regime. Plants were grown in pot cultures without AM fungi in P‐fertilized (+P) or unfertilized (‐P) soil, or in ‐P soil inoculated with one of the AM fungi Glomus mosseae (Nicol. & Gerd.) Gerd, and Trappe (Gm), Glomus etunicatum Becker and Gerd.(Ge), or Gigaspora rosea Nicol. and Schenck (Gr). Seed yields of+AM plants, as a group, were halfway between those of the +P and ‐P plants. Seed size was highest in Gm plants. Differences in protein concentrations between Ge and Gr and the other treatments were highly significant. Seed P and protein concentrations were not significantly correlated (p=0.162), but a highly significant (r =‐0.949) negative correlation between seed P and lipid concentrations was observed. Phosphorus concentration was highest and that of lipids lowest in +AM plants. Seed yield and nutrient composition were independent of the intensity of root colonization. The seed protein/lipid ratio was highly correlated with seed P concentration and was significantly higher for +AM plants, as a group, than for both +P and ‐P ‐AM plants. Differences in seed dry weight, size, seed/ stem ratio, P content, and protein concentration among +AM plants showed mycorrhiza‐specific host responses. These responses suggest that AM fungi can modify soybean seed development and chemical composition.
Bidirectional RNA Helicase Activity of Eucaryotic Translation Initiation Factors 4A and 4F (1990)

The mechanism of ribosome binding to eucaryotic mRNAs is not well understood, but it requires the participation of eucaryotic initiation factors eIF-4A, eIF-4B, and eIF-4F and the hydrolysis of ATP. Evidence has accumulated in support of a model in which these initiation factors function to unwind the 5'-proximal secondary structure in mRNA to facilitate ribosome binding. To obtain direct evidence for initiation factor-mediated RNA unwinding, we developed a simple assay to determine RNA helicase activity, and we show that eIF-4A or eIF-4F, in combination with eIF-4B, exhibits helicase activity. A striking and unprecedented feature of this activity is that it functions in a bidirectional manner. Thus, unwinding can occur either in the 5'-to-3' or 3'-to-5' direction. Unwinding in the 5'-to-3' direction by eIF-4F (the cap-binding protein complex), in conjunction with eIF-4B, was stimulated by the presence of the RNA 5' cap structure, whereas unwinding in the 3'-to-5' direction was completely cap independent. These results are discussed with respect to cap-dependent versus cap-independent mechanisms of ribosome binding to eucaryotic mRNAs.
Improved Plasma Culture System for Production of Erythrocytic Colonies In Vitro: Quantitative Assay Method for CFU-E (1974)

Abstract An improved plasma culture system is described for the production of erythrocytic colonies by mammalian adult hemopoietic cells in vitro under the influence of erythropoietin. The concentration of fetal calf serum in the medium used for dilution of the cells was critical for erythrocytic colony formation when low numbers of cells were plated. Optimal concentrations were found for plasma, fetal calf serum, bovine serum albumin, and L-asparagine in the culture medium, and the colony-forming efficiency was shown to depend on the concentration of erythropoietin. With erythropoietin at plateau concentration, the number of erythrocytic colonies produced was directly proportional to the number of bone marrow or spleen cells plated, over a wide range of cell concentrations. Colony numbers per culture conformed to a Poisson distribution. Thus, the improved plasma culture system may be used for the quantitative assay of CFU-E. The method is rapid (2 days), reliable, convenient, and inexpensive. Since the improved plasma culture system also supports granulocytic colony formation by bone marrow cells in the presence of conditioned medium (CSA), and the number of granulocytic colonies produced is proportional to the number of cells plated, the same hemopoietic cell suspensions can be simultaneously assayed for CFU-E and CFU-C under virtually identical conditions.
Development of an Automated Gangform Climbing System for Apartment Housing Construction - Structural Stability and Tower Crane Lifting Load Analysis - (2012)

갱폼(Gangform)은 기준층 설치 후 반복사용이 가능하여 기존 합판 거푸집에 비해 공기단축이 가능하고 높은 경제성을 확보할 수 있는 시스템 거푸집이다. 또한 거푸집의 처짐량이 작고 외력에 대한 안정성이 높은 장점을 지니고 있다. 그러나 갱폼의 운반 및 인양작업은 타워크레인의 동력에 전적으로 의존하고 있으며, 갱폼 인양작업을 위해 공동주택 골조공사 6~7일 사이클 중 1일의 공기를 차지하는 등 전체 골조 공기에 있어 큰 비중을 차지하고 있다. 이러한 문제점을 해결하기 위해 국내외 관련 업계를 중심으로 갱폼 인양과 관련된 다양한 연구 및 기술개발 노력이 수행되어 왔다. 특히, '공동주택 전용 갱폼 인양 자동화 기술 개발에 관한 연구'는 타워크레인의 동력원에 의존하지 않고 별도의 인양장치에 의해 갱폼의 인양작업을 가능할 수 있도록 하는 개념 디자인을 제안하였다. 이에 대한 후속 연구로써 본 연구에서는 구조해석 프로그램을 활용하여 선행 연구를 통해 제안된 갱폼 인양 자동화 기술의 구조적 안정성을 해석하고, 실제 공동주택 건설현장의 공정데이터를 적용하여 갱폼 인양 자동화 기술 적용 시 기존 타워크레인의 양중부하 감소 효과를 분석함으로써 제안된 공동주택 전용 갱폼 인양 자동화 기술의 기술적 타당성을 제시하고자 한다. Gangform, compared to the traditional forms, is a systemized form which can reduce construction duration and cost by the advantage of using it repeatedly. However, transportation and climbing process of the Gangform is highly dependant on the performance of tower crane. Gangform climbing process takes one day out of six to seven days of a structural work cycle. Tower cranes can not be used in other lifting works when they lift the Gangform during the structural work cycle, causing the delay in the construction project. Numerous efforts and researches have been done in domestic and international industry to solve such limitations of Gangform climbing process. Especially, "A Study on the Development of Automatic Gangform Climbing System for Apartment Housing Construction"has suggested a conceptual model which can climb the Gangform system without a tower crane. In this paper, the technical and economical feasibilities of previously proposed Automatic Gangform climbing system are examined by evaluating its structural stability and lifting load reduction effect.
The Proteome of Native Adult Müller Glial Cells From Murine Retina (2015)

To date, the proteomic profiling of Müller cells, the dominant macroglia of the retina, has been hampered because of the absence of suitable enrichment methods. We established a novel protocol to isolate native, intact Müller cells from adult murine retinae at excellent purity which retain in situ morphology and are well suited for proteomic analyses. Two different strategies of sample preparation - an in StageTips (iST) and a subcellular fractionation approach including cell surface protein profiling were used for quantitative liquid chromatography-mass spectrometry (LC-MSMS) comparing Müller cell-enriched to depleted neuronal fractions. Pathway enrichment analyses on both data sets enabled us to identify Müller cell-specific functions which included focal adhesion kinase signaling, signal transduction mediated by calcium as second messenger, transmembrane neurotransmitter transport and antioxidant activity. Pathways associated with RNA processing, cellular respiration and phototransduction were enriched in the neuronal subpopulation. Proteomic results were validated for selected Müller cell genes by quantitative real time PCR, confirming the high expression levels of numerous members of the angiogenic and anti-inflammatory annexins and antioxidant enzymes (e.g. paraoxonase 2, peroxiredoxin 1, 4 and 6). Finally, the significant enrichment of antioxidant proteins in Müller cells was confirmed by measurements on vital retinal cells using the oxidative stress indicator CM-H2DCFDA. In contrast to photoreceptors or bipolar cells, Müller cells were most efficiently protected against H2O2-induced reactive oxygen species formation, which is in line with the protein repertoire identified in the proteomic profiling. Our novel approach to isolate intact glial cells from adult retina in combination with proteomic profiling enabled the identification of novel Müller glia specific proteins, which were validated as markers and for their functional impact in glial physiology. This provides the basis to allow the discovery of novel glial specializations and will enable us to elucidate the role of Müller cells in retinal pathologies - a topic still controversially discussed.
Isolation of genomic clones containing the amdS gene of Aspergillus nidulans and their use in the analysis of structural and regulatory mutations. (1983)

Previous analysis of the amdS gene of Aspergillus nidulans has identified multiple regulatory circuits mediated by trans-acting regulatory genes, cis-acting mutations have been identified and shown to specifically affect individual regulatory circuits. Fine-structure genetic mapping of the amdS regions showed that these cis-acting mutations occur in a complex controlling region adjacent to the amdS structural gene. The amdS gene was cloned by differential hybridization, using cDNA probes derived from a high-level-producing strain and from a strain with a large amdS deletion mutation. RNA blotting experiments showed that a single RNA species of 1,600 to 1,700 base pairs is transcribed from the amdS gene. DNA blotting experiments on a large number of amdS mutant strains, including deletions and translocations, allowed the genetic and physical maps of the gene to be correlated. The controlling region of the gene is situated at the 5' end of the gene and the direction of transcription is toward the centromere of chromosome III. The regulatory mutations in the controlling region were found to be due to small-scale alterations in the DNA rather than to large-scale rearrangements resulting in gene fusions.
Cell Research Fused (2007)

Chinese and Australian scientists are combining their stem cell expertise in a new partnership. The $1 million Australia-China Centre for Excellence in Stem Cells, announced this week, will forge a link between Peking University Stem Cell Research Center and Monash University Immunology and Stem Cell Laboratories. The new center's initial push will be using adult mesenchymal stem cells to treat cancer and diseases of the lung and liver, says Richard Boyd, director of the Monash lab. “Combining stem cell biology and immunology will push the field forward,” adds Peking lab chief Li Lingsong.
Modulation of Fc gamma and complement receptor function by the glycosyl-phosphatidylinositol-anchored form of Fc gamma RIII. (1994)

Human neutrophils express two structurally distinct receptors for IgG, the transmembrane Fc gamma RII (CD32) and the glycosyl-phosphatidylinositol-linked Fc gamma RIII (CD16). To explore the respective functional roles of Fc gamma RII and Fc gamma RIII, we have used anti-receptor mAb fragments coupled with erythrocytes to quantify both individual and cooperative receptor functions. With individual receptor engagement, Fc gamma RII (E-IV.3) was much more efficient than Fc gamma RIIIB (E-3G8) in initiating phagocytosis (p < 0.001). However, when identical total numbers of receptors were engaged, co-ligation of Fc gamma RII and Fc gamma RIIIB resulted in a phagocytic response, which was: 1) greater than that for either receptor alone (> twofold Fc gamma RII alone (p < 0.001) and > 20-fold Fc gamma RIIIB alone (p < 0.001)); 2) greater than the sum of Fc gamma RII and Fc gamma RIIIB (p < 0.001); and 3) comparable to the phagocytic potential of Fc gamma RII in FMLP pre-activated neutrophils. This synergistic capacity of Fc gamma RIIIB also enabled CR phagocytosis. Furthermore, the capacity for Fc gamma RIIIB to interact synergistically with Fc gamma RII was preserved in FMLP-preactivated neutrophils. The activation of Fc gamma RII by Fc gamma RIIIB was associated with tyrosine phosphorylation of the Fc gamma RII cytoplasmic domain, which is essential for Fc gamma RII function and which, by analogy to the Ig alpha-chain of the B cell Ag receptor complex, the zeta-chain of CD3, and the gamma-chain of some Fc epsilon Rs and Fc gamma Rs, may enhance the binding and activation of Src or Syk family tyrosine kinases. Thus, Fc gamma RIIIB can affect multiple receptor families and play a role in achieving maximal Fc gamma R capacity, even in stimulated neutrophils in inflammatory sites.
Group communication in differentiated services networks (2002)

The Differentiated Services (DiffServ) approach will also bring benefits for multicast applications which need quality of service support. For instance, a highly reliable multicast service can be provided based on the proposed expedited forwarding behavior. Such a service may also be used advantageously in a global computing cluster infrastructure, e.g., for distribution of synchronization messages. However, DiffServ multicast services have not been addressed in a very detailed manner yet. This paper illustrates some of the problems which will arise when IP Multicast is used in DiffServ networks without taking special precautions into account for providing it. Those problems mainly lead to situations in which other service users are affected adversely. In order to retain the benefits of the DiffServ approach, a quite simple and scalable solution for those problems is needed, not resulting in additional complexity or costs in a DiffServ domain. The proposed architecture in this paper requires only an additional entry for the DiffServ Codepoint in multicast routing tables and some support by management mechanisms. The discussion of the related problems and presentation of the solution is illustrated and confirmed by some measurements performed with a Linux implementation of DiffServ, and an adapted Linux multicast router.
Herpes Zoster in Children With Cancer (1973)

Of 1,132 children treated for malignant neoplasias at St. Jude Children's Research Hospital, 101 developed herpes zoster. This population was studied retrospectively to determine frequency of infection, relationship to cancer therapy, clinical course, complications, and results of treatment. The incidence of infection was highest (22%) in patients with Hodgkin disease and lowest (0.7%) in patients with acute myelogenous leukemia. The overall incidence was 9%. Mortality was low in these children—3% for those with infection and 0.3% for the total population. Complications included pneumonitis, meningoencephalitis, chronic thrombocytopenia, iritis, keratitis, and progressive and prolonged cutaneous zoster. Cobalt-60 irradiation produced no significant changes in zoster incidence, and no specific chemotherapeutic drugs could be implicated as instigating factors in infection. Rates of survival and recurrence of malignant neoplasm were not affected by the presence of herpes zoster infection.