gebhart/patrepeval huggingface dataset:
Field emission arrays for medical x-ray imaging (2006)

Experiments demonstrate the feasibility of using microfabricated cold field emission cathodes in x-ray sources for medical imaging. Electron beam currents of 25mA at voltages of 25kV have been used to produce x-ray source focal spot diameters of 0.2mm. Analysis of both filtered and unfiltered x-ray spectra from molybdenum anodes show clear characteristic x-ray lines. These x-ray source characteristics are consistent with the requirements for human breast imaging.
Nuclear changes in necrotic HL-60 cells (2001)

Cell death in eukaryotes can occur by either apoptosis or necrosis. Apoptosis is characterized by well-defined nuclear changes which are thought to be the consequence of both proteolysis and DNA fragmentation. On the other hand, the nuclear modifications that occur during necrosis are largely less known. Here, we have investigated whether or not nuclear modifications occur during ethanol-induced necrotic cell death of HL-60 cells. By means of immunofluorescence staining, we demonstrate that the patterns given by antibodies directed against some nuclear proteins (lamin B1, NuMA, topoisomerase IIalpha, SC-35, B23/nucleophosmin) changed in necrotic cells. The changes in the spatial distribution of NuMA strongly resembled those described to occur during apoptosis. On the contrary, the fluorescent pattern characteristic for other nuclear proteins (C23/nucleolin, UBF, fibrillarin, RNA polymerase I) did not change during necrosis. By immunoblotting analysis, we observed that some nuclear proteins (SAF-A, SATB1, NuMA) were cleaved during necrosis, and in the case of SATB1, the apoptotic signature fragment of 70 kDa was also present to the same extent in necrotic samples. Caspase inhibitors did not prevent proteolytic cleavage of the aforementioned polypeptides during necrosis, while they were effective if apoptosis was induced. In contrast, lamin B1 and topoisomerase IIalpha were uncleaved in necrotic cells, whereas they were proteolyzed during apoptosis. Transmission electron microscopy analysis revealed that slight morphological changes were present in the nuclear matrix fraction prepared from necrotic cells. However, these modifications (mainly consisting of a rarefaction of the inner fibrogranular network) were not as striking as those we have previously described in apoptotic HL-60 cells. Taken together, our results indicate that during necrosis marked biochemical and morphological changes do occur at the nuclear level. These alterations are quite distinct from those known to take place during apoptosis. Our results identify additional biochemical and morphological criteria that could be used to discriminate between the two types of cell death. J. Cell. Biochem. Suppl. 36: 19-31, 2001.
Nonlinear Meissner effect in CuO superconductors (1992)

Recent theories of the NMR in the CuO superconductors are based on a spin-singlet ${\mathit{d}}_{\mathit{x}}^{2}$-${\mathit{y}}^{2}$ order parameter. Since this state has nodal lines on the Fermi surface, nonlinear effects associated with low-energy quasiparticles become important, particularly at low temperatures. We show that the field dependence of the supercurrent, below the nucleation field for vortices, can be used to locate the positions of the nodal lines of an unconventional gap in momentum space, and hence test the proposed ${\mathit{d}}_{\mathit{x}}^{2}$-${\mathit{y}}^{2}$ state.
Mutations in the 5′ Trailer Region of a Respiratory Syncytial Virus Minigenome Which Limit RNA Replication to One Step (2000)

The 3' termini of the genomic and antigenomic RNAs of human respiratory syncytial virus (RSV) are identical at 10 of the first 11 nucleotide positions and 21 of the first 26 positions. These conserved 3'-terminal sequences are thought to contain the genomic and antigenomic promoters. Furthermore, the complement of each conserved sequence (i.e., the 5' end of the RNA it encodes) might contain an encapsidation signal. Using an RSV minigenome system, we individually mutated each of the last seven nucleotides in the 5' trailer region of the genome. We analyzed effects of these mutations on encapsidation of the T7 polymerase-transcribed negative-sense genome, its ability to function as a template for RSV-driven synthesis of positive-sense antigenome and mRNA, and the ability of this antigenome to be encapsidated and to function as template for the synthesis of more genome. As a technical complication, mutations in the last five nucleotides of the trailer region were found to affect the efficiency of the adjoining T7 promoter over more than a 10-fold range, even though three nonviral G residues had been included between the core promoter and the trailer to maximize the efficiency of promoter activity. This was controlled in all experiments by monitoring the levels of total and encapsidated genome. The efficiency of encapsidation of the T7 polymerase-transcribed genome was not affected by any of the trailer mutations. Furthermore, neither the efficiency of positive-sense RNA synthesis from the genome nor the efficiency of encapsidation of the encoded antigenome was affected by the mutations. However, nucleotide substitution at positions 2, 3, 6, or 7 relative to the 5' end of the trailer blocked the production of progeny genome, whereas substitution at positions 1 and 5 allowed a low level of genome production and substitutions at position 4 were tolerated. Position 4 is the only one of the seven positions examined that is not conserved between the 3' ends of genomic and antigenomic RNA. The mutations that blocked the synthesis of progeny genome thus limited RNA replication to one step, namely, the synthesis and encapsidation of antigenome. Restoration of terminal complementarity for one of the trailer mutants by making a compensatory mutation in the leader region did not restore synthesis of genomic RNA, confirming that its loss was not due to reduced terminal complementarity. Interestingly, this leader mutation appeared to prevent antigenome synthesis with only a slight effect on mRNA synthesis, apparently providing a dissociation between these two synthetic activities. Genomes in which the terminal 24 or 325 nucleotides of the trailer have been deleted were competent for encapsidation and the synthesis of mRNA and antigenomic RNA, further confirming that terminal complementarity was not required for these functions.
Loop excision of the uterine cervix (1995)

Over the past three years, loop excision has become a standard form of therapy for cervical intraepithelial neoplasia. Clinical trials have found loop excision to be faster and easier than laser ablation for treating cervical intraepithelial neoplasia and to have similar complication and success rates. In addition, loop excision produces a specimen that is suitable for histopathologic evaluation in the majority of patients. As our clinical experience with loop excision has increased, little impact on fertility and pregnancy outcome has been found, but there continues to be concern about overuse of the technique as a method of evaluating women with low-grade abnormal Papanicolaou smears.
Iron-catalyzed hydroxyl radical formation. Stringent requirement for free iron coordination site. (1984)

The catalysis by iron of the formation of reactive oxygen species in biological systems has been well documented. In this present study, we have investigated the hypothesis that iron-catalyzed formation of hydroxyl radical (.OH) from superoxide anion radical (O-.2) and H2O2 requires the availability of at least one iron coordination site that is open or occupied by a readily dissociable ligand such as water. This hypothesis was tested by measuring the catalytic activity of 12 different iron chelates using hypoxanthine and xanthine oxidase to generate O-.2. In these same chelates, we also determined the presence or absence of coordinated water by UV-visible spectroscopy and 1H NMR relaxation measurements. Of all chelates tested, only Fe3+ coordinated to diethylenetriamine pentaacetic acid; ethylenediamine di(o-hydroxyphenylacetic acid), phytate, and Desferal lacked coordination water; and only these four complexes failed to produce hydroxyl radical. Separate determinations of the two redox half-reactions involved (i.e. Fe3+ + O-.2----Fe2+ + O2 and Fe2+ + H2O2----Fe3+ + .OH + OH-) indicate that an available coordination site is necessary for the latter (Fenton) reaction. This principle governing iron reactivity may help advance our understanding of the mechanism of oxidative damage in biological systems and may also permit the design of more effective chelators for the control of iron in biological systems.
Genes and Obesity (1996)

Several twin and adoption studies as well as animal models have confirmed that obesity has a strong genetic component. It is apparent that obesity in humans has a complex polygenic background; that is, the phenotype is determined by an unknown number of genes together with environmental factors. However, there may well be single genes playing a major role within certain families, but the gene may vary from family to family. Two interesting gene candidates have been found in mouse experiments, the ob and the db gene, the products of which are probably a satiety hormone and its receptor, respectively, which regulate food intake. The recent cloning of the ob gene and its human homologue constitute a major breakthrough in this field. The 16-kD protein encoded by the ob gene is called leptin, and is well conserved among vertebrate species. The pig could be a valuable large animal model for human obesity. A fatness locus has been mapped to pig chromosome 4 and most probably a similar locus resides on human chromosome 1q. A more precise definition of the pig-human homology as regards this region is currently being investigated.
The incredible journey: From megakaryocyte development to platelet formation (2013)

Circulating blood platelets are specialized cells that prevent bleeding and minimize blood vessel injury. Large progenitor cells in the bone marrow called megakaryocytes (MKs) are the source of platelets. MKs release platelets through a series of fascinating cell biological events. During maturation, they become polyploid and accumulate massive amounts of protein and membrane. Then, in a cytoskeletal-driven process, they extend long branching processes, designated proplatelets, into sinusoidal blood vessels where they undergo fission to release platelets. Given the need for platelets in many pathological situations, understanding how this process occurs is an active area of research with important clinical applications.
A review of mathematical models of influenza A infections within a host or cell culture: lessons learned and challenges ahead (2011)

Most mathematical models used to study the dynamics of influenza A have thus far focused on the between-host population level, with the aim to inform public health decisions regarding issues such as drug and social distancing intervention strategies, antiviral stockpiling or vaccine distribution. Here, we investigate mathematical modeling of influenza infection spread at a different scale; namely that occurring within an individual host or a cell culture. We review the models that have been developed in the last decades and discuss their contributions to our understanding of the dynamics of influenza infections. We review kinetic parameters (e.g., viral clearance rate, lifespan of infected cells) and values obtained through fitting mathematical models, and contrast them with values obtained directly from experiments. We explore the symbiotic role of mathematical models and experimental assays in improving our quantitative understanding of influenza infection dynamics. We also discuss the challenges in developing better, more comprehensive models for the course of influenza infections within a host or cell culture. Finally, we explain the contributions of such modeling efforts to important public health issues, and suggest future modeling studies that can help to address additional questions relevant to public health.
Amiodarone Instilled Into the Canine Pericardial Sac Migrates Transmurally to Produce Electrophysiologic Effects and Suppress Atrial Fibrillation (1996)

Amiodarone instilled into the pericardial sac migrates transmurally to produce significant electrophysiologic effects at superficial sites and appears to suppress electrically induced atrial fibrillation.
Novel Type of Staphylococcal Cassette Chromosome mec Identified in Community-Acquired Methicillin-Resistant Staphylococcus aureus Strains (2002)

We identified a new type of staphylococcal cassette chromosome mec (SCCmec) from two community-acquired methicillin-resistant Staphylococcus aureus (MRSA) strains. The novel element, designated type IV SCCmec, had a unique combination of the class B mec gene complex and the type 2 ccr gene complex and was much smaller in size (21 to 24 kb) than previously identified SCCmec elements of hospital-acquired MRSA. Consistent with the strains' susceptibilities to various non-beta-lactam antibiotics, the type IV SCCmec was devoid of any antibiotic resistance genes other than the mecA gene.
Immunocytochemical Localization of the Menkes Copper Transport Protein (ATP7A) to the Trans-Golgi Network (1997)

We have generated polyclonal antibodies against the amino-terminal third of the Menkes protein (ATP7A; MNK) by immunizing rabbits with a histidine-tagged MNK fusion construct containing metal-binding domains 1-4. The purified antibodies were used in Western analysis of cell lysates and in indirect immunofluorescence experiments on cultured cells. On Western blots, the antibodies recognized the approximately 165 kDa MNK protein in CHO cells and human fibroblasts. No MNK signal could be detected in fibroblasts from a patient with Menkes disease or in Hep3B hepatocellular carcinoma cells, confirming the specificity of the antibodies. Immunocytochemical analysis of CHO cells and human fibroblasts showed a distinct perinuclear signal corresponding to the pattern of the Golgi complex. This staining pattern was similar to that of alpha-mannosidase II which is a known resident enzyme of the Golgi complex. Using brefeldin A, a fungal inhibitor of protein secretion, we further demonstrated that the MNK protein is localized to the trans-Golgi network. This data provides direct evidence for a subcellular localization of the MNK protein which is similar to the proposed vacuolar localization of Ccc2p, the yeast homolog of MNK and WND (ATP7B), the Wilson disease gene product. In light of the proposed role of MNK both in subcellular copper trafficking and in copper efflux, these data suggest a model for how these two processes are linked and represent an important step in the functional analysis of the MNK protein.
Strategies for the Solid-Phase Diversification of Poly-l-proline-Type II Peptide Mimic Scaffolds and Peptide Scaffolds Through Guanidinylation (2008)

A strategy for the solid-phase diversification of PPII mimic scaffolds through guanidinylation is presented. The approach involves the synthesis N-Pmc-N'-alkyl thioureas as diversification reagents. Analogues of Fmoc-Orn(Mtt)-OH can be incorporated into a growing peptide chain on Wang resin. Side chain deprotection with 1% TFA/CH2Cl2 followed by EDCI-mediated reaction of N-Pmc-N'-alkyl thioureas with the side chain amine affords arginine analogues with modified guanidine head groups. The scope, limitations, and incidental chemistry are discussed.
A comparison of audio-only versus audio-visual second language instruction in first-year university-level Spanish (1998)

During the second half of this century, the study of language acquisition has changed from its original emphasis on language teaching methodologies. Since the late 1960s (Ellis, 1995), a number of studies have focused on second language learning, which "introduced a new research agenda and gave definition to the field that has come to be known as second language acquisition" (Larsen-Freeman &amp; Long, 1991, p. 5). This new research agenda looks closely at learner styles and the learning process. Researchers have learned much of what we know about language acquisition in the three decades since the introduction of the field of second language acquisition, or SLA (Dulay, Burt &amp; Krashen, 1982; Ellis, 1995). Gass (1989) uses Ellis' (1985) definition of second language acquisition, which is "the study of how learners learn an additional language after they have acquired the mother tongue" ( p. 499). The findings of second language research aid foreign language instructors in the classroom because teachers who use these ideas are better able to meet the needs of their students.&#13;\n&#13;\nWhen referring to a language other than the first language, usually a distinction is made between a second language and a foreign language. A second language is a language being acquired in the milieu in which it is the native tongue, such as English being studied by a Korean in England. A foreign language is a language acquired outside of an environment where it is the native tongue, such as a Spaniard's study of French in Spain. Although some researchers choose to differentiate between a second language and a foreign language, "SLA has really come to mean the acquisition of any language(s) other than one's native language" (Larsen-Freeman &amp; Long, 1991, p. 7).
DNA polymerase III holoenzyme of Escherichia coli. Purification and resolution into subunits. (1977)

DNA polymerase III holoenzyme has been purified from Escherichia coli HMS-83, using, as an assay, the conversion of coliphage G4 single-stranded DNA to the duplex replicative form. The holoenzyme consists of at least four different subunits: alpha, beta, gamma, and delta of 140,000, 40,000, 52,000, and 32,000 daltons, respectively. The alpha subunit is DNA polymerase III, the dnaE gene product. The holoenzyme has been resolved by phosphocellulose chromatography into an alpha - gamma - delta complex and a subunit beta (copolymerase III*); neither possesses detectable activity in the G4 system but together reconstitute holoenzyme-like activity. The alpha - gamma - delta complex has been further resolved to yield a gamma - delta complex which reconstitutes alpha - gamma - delta activity when added to DNA polymerase III. The gamma - delta complex contains a product of the dnaZ gene and has been purified from a strain which contains a ColE1-dnaZ hybrid plasmid.
Mechanistic model of cardiac energy metabolism predicts localization of glycolysis to cytosolic subdomain during ischemia (2005)

A new multidomain mathematical model of cardiac cellular metabolism was developed to simulate metabolic responses to reduced myocardial blood flow. The model is based on mass balances and reaction kinetics that describe transport and metabolic processes of 31 key chemical species in cardiac tissue. The model has three distinct domains (blood, cytosol, and mitochondria) with interdomain transport of chemical species. In addition to distinguishing between cytosol and mitochondria, the model includes a subdomain in the cytosol to account for glycolytic metabolic channeling. Myocardial ischemia was induced by a 60% reduction in coronary blood flow, and model simulations were compared with experimental data from anesthetized pigs. Simulations with a previous model without compartmentation showed a slow activation of glycogen breakdown and delayed lactate production compared with experimental results. The addition of a subdomain for glycolysis resulted in simulations showing faster rates of glycogen breakdown and lactate production that closely matched in vivo experimental data. The dynamics of redox (NADH/NAD+) and phosphorylation (ADP/ATP) states were also simulated. These controllers are coupled to energy transfer reactions and play key regulatory roles in the cytosol and mitochondria. Simulations showed a similar dynamic response of the mitochondrial redox state and the rate of pyruvate oxidation during ischemia. In contrast, the cytosolic redox state displayed a time response similar to that of lactate production. In conclusion, this novel mechanistic model effectively predicted the rapid activation of glycogen breakdown and lactate production at the onset of ischemia and supports the concept of localization of glycolysis to a subdomain of the cytosol.
HCV Persistence and Immune Evasion in the Absence of Memory T Cell Help (2003)

Spontaneous resolution of hepatitis C virus (HCV) infection in humans usually affords long-term immunity to persistent viremia and associated liver diseases. Here, we report that memory CD4+ Tcells are essential for this protection. Antibody-mediated depletion of CD4+ Tcells before reinfection of two immune chimpanzees resulted in persistent, low-level viremia despite functional intra-hepatic memory CD8+ Tcell responses. Incomplete control of HCV replication by memory CD8+ Tcells in the absence of adequate CD4+ Tcell help was associated with emergence of viral escape mutations in class I major histocompatibility complex-restricted epitopes and failure to resolve HCV infection.
Quantitation of microsomal alpha-hydroxylation of the tobacco-specific nitrosamine, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone. (1991)

4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is activated to DNA alkylating species via two different alpha-hydroxylation pathways. Methylene hydroxylation leads to DNA methylation, whereas methyl hydroxylation yields DNA pyridyloxobutylation. We have developed a high-pressure liquid chromatography assay utilizing radiochemical detection that permits the determination of the extent of metabolism through each pathway in microsomal preparations. Levels of 4-hydroxy-1-(3-pyridyl)-1-butanone (HPB) were used to measure the extent of methyl hydroxylation, whereas levels of the aldehyde, 4-oxo-1-(3-pyridyl)-1-butanone (OPB), were used to quantify the extent of methylene hydroxylation. Incubations of [5-3H]NNK with microsomes and cofactors were conducted in the presence of 5 mM sodium bisulfite to trap the reactive OPB. The inclusion of bisulfite did not affect the rate of NNK metabolism. Trapping the aldehyde also inhibited its further oxidation to the corresponding acid or reduction to HPB. Furthermore, the conversion of HPB to OPB made only a minor contribution to the OPB levels under our incubation conditions. Analysis of incubation mixtures containing [5-3H]NNK, cofactors, and either A/J mouse liver or lung microsomes demonstrated that OPB was a significant metabolite of NNK. The OPB:HPB ratio was greater in liver (1.5) than in lung (0.2-1) microsomal preparations. Apparent Km values for OPB and HPB formation in lung microsomes were 23.7 and 3.6 microM, respectively, whereas the corresponding values for liver microsomes were 19.1 and 73.8 microM, respectively. These data are consistent with the involvement of more than one cytochrome P-450 isozyme in the activation of NNK to DNA reactive species.
Passivation, structural modification, and etching of amorphous silicon in hydrogen plasmas (1997)

Atomic hydrogen from plasma discharges dissolves in silicon previously amorphized by ion implantation (aSi) in the form of Si–H bonds, giving rise to infrared (IR) absorption at ∼1990 cm−1 and causing partial activation of implanted dopants. Passivation of aSi does not affect the rate at which the material subsequently undergoes solid phase epitaxy. Exposure giving rise to [H]&amp;gt;6 at. % causes the appearance of an additional IR absorption band at ∼2080 cm−1 and coloration of the layer. Despite annealing, the Si–H defects, normal solid phase epitaxy does not occur during subsequent heat treatment. The structural modification by H-plasma exposure coincides with etching of the layer. The observations can be understood in terms of void formation in aSi resulting from the clustering of Si–H.