gebhart/patrepeval huggingface dataset:
Cycloaddition Chemistry on Silicon(001) Surfaces:  The Adsorption of Azo-tert-butane (1998)

The adsorption of azo-tert-butane on the Si(001) surface at 300 K has been investigated using X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FTIR) spectroscopy, scanning tunneling microscopy (STM), and ab initio computational chemistry methods. Although some cleavage of C−H bonds that prevents the formation of a completely ordered layer occurs at room temperature, adsorption onto a 130 K surface occurs molecularly with no bond cleavage. All of the experimental evidence shows that adsorption occurs through the interaction of the NN azo bond with a single SiSi dimer bond, in a manner similar to a [2 + 2] cycloaddition reaction. These results show that the use of [2 + 2] cycloaddition reactions to link organic substituents to the Si(001) surface is not limited to alkenes but can be extended to link compounds which have other types of unsaturated bonds to the Si(001) surface.
The Use ofXenopusOocytes for the Study of Ion Channel (1987)

Recently, in addition to the "traditional" research on meiotic reinitiation and fertilization mechanisms, the oocytes of the African frog Xenopus laevis have been exploited for the study of numerous aspects of ion channel function and regulation, such as the properties of several endogenous voltage-dependent channels and the involvement of second messengers in mediation of neurotransmitter-evoked membrane responses. In addition, injection of these cells with exogenous messenger RNA results in production and functional expression of foreign membranal proteins, including various voltage- and neurotransmitter-operated ion channels originating from brain, heart, and other excitable tissues. This method provides unique opportunities for the study of the structure, function, and regulation of these channels. A multidisciplinary approach is required, involving molecular biology, electrophysiology, biochemistry, pharmacology, and cytology.
Electrochemical Treatment of Cancer. II (1990)

Electrochemical treatment of cancer with DC electrodes changes the microenvironment of the cancer cells by electrophoresis. They may deteriorate and resorb. In larger neoplasms, the effects can be enhanced by electrophoresis of a chemotherapeutic agent. Adriamycin delivered into an electropositive neoplasm electrode will move outwards in the neoplastic area in a high concentration. When given intravenously and the neoplasm electrode is electronegative, the systemic effects may be diminished. The agent is instead accumulated in the neoplastic region in a high concentration. This principle may be used to reduce systemic effects of charged chemotherapeutic compounds. In this preliminary study of cancer in 14 patients, incurable with surgery, radiation treatment, or chemotherapy, beneficial effects were obtained after combined electrochemical treatment and the use of Adriamycin.
Nucleotide sequence of the guaA gene encoding GMP synthetase of Escherichia coli K12. (1985)

GMP synthetase (EC 6.3.4.1), a glutamine amido-transferase encoded by the guaA gene, catalyzes the synthesis of GMP from XMP. The guaA gene was subcloned from the Clarke and Carbon (Clarke, L., and Carbon, J. (1976) Cell 9, 91-99) plasmid pLC34-10, and the nucleotide sequence was determined. The structural gene encodes a protein of 525 amino acid residues having a calculated Mr of 58,604. The amino acid sequence of the NH2 terminus of GMP synthetase was determined and used to verify the translation start site determined from the DNA sequence. A 68-base pair intercistronic region separates guaA from the upstream guaB gene in the polycistronic guaBA operon. The 3' end of the guaA mRNA was determined by S1 nuclease mapping. The 3' end of guaA mRNA is 36-37 nucleotides downstream of the translation stop codon within a region of dyad symmetry that resembles a rho-independent transcription termination site.
Expression of p53, pRB, and p16 in lung tumours: a validation study on tissue microarrays (2003)

Tissue microarrays have been created from 326 lung tumours, including 173 squamous cell carcinomas (SCCs) and 132 adenocarcinomas (ADs). In order to evaluate the usefulness of this microarray series, the expression of p53, p16, and Rb proteins was compared by immunohistochemistry on both the tissue microarrays and the corresponding whole sections for all 326 tumours. The presence of replicate punches improved both the yield and the concordance of data relative to the whole section results, so that the consensus score from the replicates agreed with the whole section result in more than 90% of informative tumours. The large number of tumours in this series also allowed significant differences in protein expression patterns to be detected between SCC and AD, the major subtypes of non-small cell lung carcinoma (NSCLC). SCC had higher levels of p53 staining (67% vs 52% in AD) and substantially increased p16 loss (SCC 75%, AD 53%) combined with greater retention of pRB expression (SCC 86% vs 67% in AD). The strong inverse correlation between p16 and pRB seen in SCC was essentially absent in AD. This study represents the largest single immunohistochemical survey of protein expression for p53, p16, and RB in NSCLCs.
HLA‐DR, DO AND DP TYPING USING PCR AMPLIFICATION AND IMMOBILIZED PROBES (1991)

A simple, rapid, and precise method of typing HLA class II polymorphism would be valuable in the areas of disease susceptibility, tissue transplantation, individual identification and anthropological genetics. Here we describe a method of analysing class II sequence polymorphism based on polymerase chain reaction (PCR) amplification and hybridization with oligonucleotide probes. One valuable property of sequence-based HLA typing strategies, like oligonucleotide probe hybridization, is that they reveal how and where two alleles differ, not simply that they can be operationally distinguished. The nature and location of HLA polymorphisms appears to be critical in disease association studies and are likely to be important in tissue typing for transplantation. New alleles at the DRB1, DPB1 and DQB1 loci are likely to be identified as this technology is applied to more and more samples, particularly in non-Caucasian ethnic groups. A new allele is uncovered as an unusual pattern of probe binding and then confirmed by sequencing. This pattern is observed because class II polymorphism is localized to specific regions and virtually all 'new' alleles have polymorphisms in the region of probe binding. Obviously, any new allele with a new polymorphic sequence in a region for which typing probes are not available would not be revealed by oligonucleotide typing. With the PCR primers and probes described here, 7 DQA1 alleles, 15 DQB1 alleles, 18 DPB1 alleles, and 32 DRB1 alleles are distinguished. Additional primers and/or probes can, of course, increase the allelic discrimination of oligonucleotide dot blot typing. These horseradish peroxidase (HRP)-labelled oligonucleotide probes are stable (greater than 2 years when stored at 4 degrees C) and the typing system is simple and robust. Over 500 samples from the CEPH pedigrees (unpublished data; A. B. Begovich, et al., manuscript in preparation) and greater than 1000 unrelated samples have been typed by this procedure. Although this dot blot/oligonucleotide hybridization procedure is a powerful and precise method of HLA class II typing, the complexity of the procedure increases as the number of probes required for analysis increases. The reverse dot blot method, based on an array of immobilized probes, allows the typing of individual samples in one single hybridization reaction. In this approach, a panel of unlabelled oligonucleotides are immobilized to a nylon membrane. The PCR product is labelled during the amplification reaction by using biotinylated primers and hybridized to the membrane. The presence of bound PCR product specifically hybridized to a given probe is detected using streptavidin-HRP conjugates and either chromogenic or chemiluminescent substrates.(ABSTRACT TRUNCATED AT 400 WORDS)
Highly Sensitive and Miniaturized Fluorescence Detection System with an Autonomous Capillary Fluid Manipulation Chip (2012)

This paper presents a novel, highly sensitive and ultra-small fluorescent detection system, including an autonomous capillary fluid manipulation chip. The optical detector integrates a LED light source, all necessary optical components, and a photodiode with preamplifier into one package of about 2 cm × 2 cm × 2 cm. Also, the low-cost and simple pumpless microfluidic device works well in sample preparation and manipulation. This chip consists of capillary stop valves and trigger valves which are fabricated by lithography and then bonded with a polydimethylsiloxane-ethylene oxide polymer polydimethylsiloxane (PEO-PDMS) cover. The contact angle of the PEO-PDMS can be adjusted by changing the concentration of the PEO. Hence, the fluidic chip can achieve functionalities such as timing features and basic logical functions. The prototype has been tested by fluorescence dye 5-Carboxyfluorescein (5-FAM) dissolved into the solvent DMSO (Dimethyl Sulfoxide). The results prove a remarkable sensitivity at a pico-scale molar, around 1.08 pM. The low-cost and miniaturized optical detection system, with a self-control capillary-driven microfluidic chip developed in this work, can be used as the crucial parts in portable biochemical detection applications and point of care testing.
Novel Roles of the Chemorepellent Axon Guidance Molecule RGMa in Cell Migration and Adhesion (2012)

The repulsive guidance molecule A (RGMa) is a contact-mediated axon guidance molecule that has significant roles in central nervous system (CNS) development. Here we have examined whether RGMa has novel roles in cell migration and cell adhesion outside the nervous system. RGMa was found to stimulate cell migration from Xenopus animal cap explants in a neogenin-dependent and BMP-independent manner. RGMa also stimulated the adhesion of Xenopus animal cap cells, and this adhesion was dependent on neogenin and independent of calcium. To begin to functionally characterize the role of specific domains in RGMa, we assessed the migratory and adhesive activities of deletion mutants. RGMa lacking the partial von Willebrand factor type D (vWF) domain preferentially perturbed cell adhesion, while mutants lacking the RGD motif affected cell migration. We also revealed that manipulating the levels of RGMa in vivo caused major migration defects during Xenopus gastrulation. We have revealed here novel roles of RGMa in cell migration and adhesion and demonstrated that perturbations to the homeostasis of RGMa expression can severely disrupt major morphogenetic events. These results have implications for understanding the role of RGMa in both health and disease.
Molecular links between cellular mortality and immortality (review). (1996)

Normal diploid cells cultivated in vitro exhibit limited division potential while undergoing ageing during serial passaging. In contrast, cells that have been genetically transformed appear to have lost the regulatory mechanisms of limited growth potential and may continue to divide indefinitely. While cellular mortality is characterised by a progressive cessation of cell growth manifested in cell culture by senescence, immortalisation is the escape from senescence as a result of multiple mechanisms involving the inactivation of tumour suppressor genes, the elevated expression of oncogenes, as well as other genetic and epigenetic changes. The mechanisms governing mortality and immortality are fundamentally linked. The physiological and biochemical features which characterise cellular mortality are examined, herein in the search for markers and timing mechanisms of mortality. The genetic elements involved in the control of mortality and immortality are also discussed, and the fundamental similarities between the molecular and genetic aspects which govern the determination of the phenotypes manifesting the two processes are underlined.
The Influence of Milk Oligosaccharides on Microbiota of Infants: Opportunities for Formulas (2011)

In addition to a nutritive role, human milk also guides the development of a protective intestinal microbiota in the infant. Human milk possesses an overabundance of complex oligosaccharides that are indigestible by the infant yet are consumed by microbial populations in the developing intestine. These oligosaccharides are believed to facilitate enrichment of a healthy infant gastrointestinal microbiota, often associated with bifidobacteria. Advances in glycomics have enabled precise determination of milk glycan structures as well as identification of the specific glycans consumed by various gut microbes. Furthermore, genomic analysis of bifidobacteria from infants has revealed specific genetic loci related to milk oligosaccharide import and processing, suggesting coevolution between the human host, milk glycans, and the microbes they enrich. This review discusses the current understanding of how human milk oligosaccharides interact with the infant microbiota and examines the opportunities for translating this knowledge to improve the functionality of infant formulas.
Ribonucleotide Reductase Inhibitors and Future Drug Design (2006)

Ribonucleotide reductase (RR) is a multisubunit enzyme responsible for the reduction of ribonucleotides to their corresponding deoxyribonucleotides, which are building blocks for DNA replication and repair. The key role of RR in DNA synthesis and cell growth control has made it an important target for anticancer therapy. Increased RR activity has been associated with malignant transformation and tumor cell growth. Efforts for new RR inhibitors have been made in basic and translational research. In recent years, several RR inhibitors, including Triapine, Gemcitabine, and GTI-2040, have entered clinical trial or application. Furthermore, the discovery of p53R2, a p53-inducible form of the small subunit of RR, raises the interest to develop subunit-specific RR inhibitors for cancer treatment. This review compiles recent studies on (1) the structure, function, and regulation of two forms of RR; (2) the role in tumorigenesis of RR and the effect of RR inhibition in cancer treatment; (3) the classification, mechanisms of action, antitumor activity, and clinical trial and application of new RR inhibitors that have been used in clinical cancer chemotherapy or are being evaluated in clinical trials; (4) novel approaches for future RR inhibitor discovery.
The Mechanism of Inhibition of Collagenase by TIMP-1 (1996)

Tissue inhibitor of metalloproteinase-I (TIMP-1) is a slow, tight-binding inhibitor of fibroblast-type collagenase. Time-course data from inhibition experiments were analyzed by graphic analysis, by nonlinear regression of the analytic integrals of the rate equations and by nonlinear regression with numeric integration of the rate equations. With the same assumptions, approximations and data, all three methods of analysis produced the same model preferences and values for the kinetic parameters. The time-course data for the inhibition of fibroblast-type collagenase by TIMP-1 are best described by the equations for a noncompetitive two-step mechanism, in which an inactive, rapidly formed, reversible complex slowly forms an inactive, tight complex. However, from the analysis of data from experiments at concentrations of TIMP-1 comparable to that of collagenase, it is apparent that free TIMP-1 also functions in the breakdown of the tight complex. The rapidly formed complex has a dissociation constant of 8 nM and reacts to the tight complex with a first-order rate constant of 0.003 s-1. The back reaction of the tight complex to the rapid complex has a second-order rate constant of 5 x 10(4) M-1 s-1. The resulting global dissociation constant of the tight complex is 0.1 nM at 3 nM TIMP-1 and collagenase concentration. Collagenase without the carboxyl-terminal domain (mini-collagenase) is inhibited by TIMP-1 according to a mechanism, in which the rapidly formed complex has such a high dissociation constant (247 nM) that it effectively constitutes a one-step mechanism, in which TIMP-1 binds with an apparent second-order rate constant of 9.6 x 10(4) mol-1 s-1 and the enzyme-TIMP-1 complex dissociates with a first order rate constant of 0.00026 s-1. The apparent global dissociation constant for the tight complex (2.7 nM) is higher than that for the fibroblast-type collagenase. Participation of TIMP-1 in the dissociation is not demonstrable. Therefore, the carboxyl-terminal domain of fibroblast-type collagenase is important for the initial, rapid binding of TIMP-1 and the initial complex contributes to the overall binding.
Delta F508-CFTR channels: kinetics, activation by forskolin, and potentiation by xanthines (1996)

Trafficking, activation, and kinetics of delta F508-cystic fibrosis transmembrane conductance regulator (CFTR) and CFTR were compared in stably transduced C127I mouse mammary epithelial cells. Western blots detected a small amount of fully glycosylated delta F508-CFTR Efflux of 125I was stimulated by forskolin with the same mean effective concentration (EC50; approximately 0.5 microM) for CFTR and delta F508-CFTR cells, but the maximum response was reduced more than fivefold and its latency increased approximately threefold in delta F508-CFTR cells. In delta F508-CFTR cells, 3-isobutyl-1-methylxanthine (IBMX; EC50 = 1.45 microM) and 8-cyclopentyl-1,3-dipropylxanthine (CPX; EC50 = 58 microM) increased the peak forskolin-stimulated efflux rate approximately 2.5-fold and decreased the time to peak. A sevenfold increase in intracellular adenosine 3',5'-cyclic monophosphate (cAMP) levels accompanied potentiation of forskolin-induced 125I efflux by IBMX but not by CPX. Elevation of intracellular cAMP increased linear voltage-independent whole cell currents 30-fold in CFTR and 4-fold in delta F508-CFTR cells; the response rate in delta F508-CFTR cells was much slower. Single-channel currents were detected in 57 of 68 cell-attached patches from forskolin-prestimulated CFTR cells vs. 6 of 35 patches in delta F508-CFTR cells. Mean number of active channels per patch was 4.1 for CFTR [open probability (Po) = 0.34] and 0.2 for delta F508-CFTR (Po = 0.11). The lower Po of delta F508-CFTR resulted from an approximately threefold longer mean interburst interval. We estimate that forskolin-stimulated chloride conductance of delta F508-CFTR C127I cells is < 5% of CFTR cells. CPX is approximately 25-fold more potent than IBMX in potentiating delta F508-CFTR and may operate by a mechanism other than elevation of cAMP.
Quantifying and Reducing Motion Artifacts in Wearable Seismocardiogram Measurements During Walking to Assess Left Ventricular Health (2016)

A major limitation in the use of the SCG, a measure of local chest vibrations caused by cardiac ejection of blood in the vasculature, is that a user must remain completely still for high-quality measurements. The motion can create artifacts and practically render the signal unreadable. Addressing this limitation could allow, for the first time, SCG measurements to be obtained reliably during movement-aside from increasing the coverage throughout the day of cardiovascular monitoring, analyzing SCG signals during movement would quantify the cardiovascular system's response to stress (exercise), and thus provide a more holistic assessment of overall health.
Myc oncogenes: the enigmatic family (1996)

The myc family of proto-oncogenes is believed to be involved in the establishment of many types of human malignancy. The members of this family have been shown to function as transcription factors, and through a designated target sequence bring about continued cell-cycle progression, cellular immortalization and blockages to differentiation in many lineages. However, while much of the recent work focusing on the c-myc oncogene has provided some very important advances, it has also brought to light a large amount of conflicting data as to the mechanism of action of the gene product. In this regard, it has now been shown that c-myc is effective in transcriptional repression as well as transcriptional activation and, perhaps more paradoxically, that it has a role in programmed cell death (apoptosis) as well as in processes of cell-cycle progression. In addition, particular interest has surrounded the distinct roles of the two alternative translation products of the c-myc gene, c-Myc 1 and c-Myc 2. The intriguing observation that the ratio of c-Myc 1 to c-Myc 2 increases markedly upon cellular quiescence led to the discovery that the enforced expression of the two proteins individually showed that c-Myc 2 stimulates cell growth, whereas c-Myc 1 appears to be growth suppressing. Clearly, the disparities in the activities of c-Myc, together with the consistent occurrence of mutations of c-myc in human malignancies, means that, although reaching an understanding of the functions of the myc gene family might not be simple, it remains well worthy of pursuit.
Site‐specific transgenesis of the Drosophila melanogaster Y‐chromosome using CRISPR/Cas9 (2018)

Despite the importance of Y-chromosomes in evolution and sex determination, their heterochromatic, repeat-rich nature makes them difficult to sequence (due, in part, to ambiguities in sequence alignment and assembly) and to genetically manipulate. Therefore, they generally remain poorly understood. For example, the Drosophila melanogaster Y-chromosome, one of the most extensively studied Y-chromosomes, is widely heterochromatic and composed mainly of highly repetitive sequences, with only a handful of expressed genes scattered throughout its length. Efforts to insert transgenes on this chromosome have thus far relied on either random insertion of transposons (sometimes harbouring 'landing sites' for subsequent integrations) with limited success or on chromosomal translocations, thereby limiting the types of Y-chromosome-related questions that could be explored. Here, we describe a versatile approach to site-specifically insert transgenes on the Y-chromosome in D. melanogaster via CRISPR/Cas9-mediated homology-directed repair. We demonstrate the ability to insert, and detect expression from, fluorescently marked transgenes at two specific locations on the Y-chromosome, and we utilize these marked Y-chromosomes to detect and quantify rare chromosomal nondisjunction effects. Finally, we discuss how this Y-docking technique could be adapted to other insects to aid in the development of genetic control technologies for the management of insect disease vectors and pests.
Vaccinia virus and oncolytic virotherapy of cancer. (2005)

Vaccinia viruses possess many of the key attributes necessary for an ideal viral backbone for use in oncolytic virotherapy. These include a short lifecycle, with rapid cell-to-cell spread. strong lytic ability, a large cloning capacity and well-defined molecular biology. In addition, although capable of replicating in human cells, they are not considered a natural health problem and are especially well characterized. having been delivered to millions of individuals during the campaign to eradicate smallpox. A variety of tumor-targeting mutations have been described in several different vaccinia strains and the expression of a variety of different transgenes has been studied. Early clinical results using either vaccine strains or genetically modified vaccinia strains have demonstrated antitumor effects. Future prospects for the development of these viruses will be discussed.