gebhart/patrepeval huggingface dataset:
Electron Microscopy Reveals the Nucleation Mechanism of Zeolite Y from Precursor Colloids (1999)

The growth of nanoscale crystals of zeolite Y from colloidal aluminosilicate gel particles has been investigated with high-resolution electron microscopy. Each amorphous gel particle nucleates only a single zeolite crystal, with nucleation beginning at the gel-solution interface (see scheme). Further growth of these nanocrystals is possible through the solution-mediated transport of framework building blocks.
The Friedreich ataxia GAA triplet repeat: premutation and normal alleles (1997)

The most common mutation causing Friedreich ataxia (FRDA), an autosomal recessive neurodegenerative disease, is the hyperexpansion of a polymorphic GAA triplet repeat localized within an Alu sequence (GAA-Alu) in the first intron of the frataxin (X25) gene. GAA-Alu belongs to the AluSx subfamily and contains several polymorphisms in strong linkage disequilibrium either with a subgroup of normal alleles, or with hyperexpanded FRDA-associated alleles. GAA repeat sizes in 300 normal chromosomes (97 from carriers and 203 from controls) were distributed in two separate groups: 83% of them contained between six and 10 triplets (small normal alleles), while the remaining 17% had more than 12 triplets, up to 36 (large normal alleles). Sequence analysis showed that no normal, stable allele contained more than 27 uninterrupted GAA triplets. All longer normal alleles were interrupted by a hexanucleotide repeat (GAGGAA). An allele containing an uninterrupted run of 34 GAA triplets was stably transmitted in four instances, but in one case underwent hyperexpansion to 650 triplets. Overall, our results suggest that the FRDA-associated expanded GAA repeats originate from normal alleles by recurrent expansions of alleles at risk.
Use of Ti(III) Complexes To Reduce Ni, Co, and Fe in Water Solutions (1996)

The possibility of using Ti(III) complexes to produce metals of the iron subgroup in aqueous solution at room temperature has been studied. The influence of the solution composition and of the deposition conditions on the process of the reaction has been investigated. The metal reduction was shown to be accompanied by hydrogen generation via the reaction of water reduction with Ti(III) complexes, which is catalyzed with the metal particles formed. The metal powders produced were investigated by X-ray diffraction and transmission electron microscopy methods. The peculiar feature of the reductant used, when compared to conventional hydrogen-containing ones, is that upon employing it ultrafine (10−30 nm) particles of pure polycrystalline highly monodisperse nickel, cobalt, and iron powders are produced, which form chain structures.
ADP-Glucose Pyrophosphorylase, a Regulatory Enzyme for Bacterial Glycogen Synthesis (2003)

The accumulation of alpha-1,4-polyglucans is an important strategy to cope with transient starvation conditions in the environment. In bacteria and plants, the synthesis of glycogen and starch occurs by utilizing ADP-glucose as the glucosyl donor for elongation of the alpha-1,4-glucosidic chain. The main regulatory step takes place at the level of ADP-glucose synthesis, a reaction catalyzed by ADP-Glc pyrophosphorylase (PPase). Most of the ADP-Glc PPases are allosterically regulated by intermediates of the major carbon assimilatory pathway in the organism. Based on specificity for activator and inhibitor, classification of ADP-Glc PPases has been expanded into nine distinctive classes. According to predictions of the secondary structure of the ADP-Glc PPases, they seem to have a folding pattern common to other sugar nucleotide pyrophosphorylases. All the ADP-Glc PPases as well as other sugar nucleotide pyrophosphorylases appear to have evolved from a common ancestor, and later, ADP-Glc PPases developed specific regulatory properties, probably by addition of extra domains. Studies of different domains by construction of chimeric ADP-Glc PPases support this hypothesis. In addition to previous chemical modification experiments, the latest random and site-directed mutagenesis experiments with conserved amino acids revealed residues important for catalysis and regulation.
Seed Mineral Composition of Diverse Peanut Germplasm1 (1983)

Abstract Quality of peanut (Arachis hypogaea L.) seed is of major concern to the grower, processor, and consumer. Past investigations have mainly focused upon organic compounds, thus basic information pertaining to inorganic elements is relatively sparse. A chemical evaluation study was conducted over a three-year period to determine the concentration of elemental constituents among diverse germplasm and to examine the extent of correlation among element concentrations. Twenty-six distinct genotypes were analyzed for N, K, P, S, Mg, Ca, Fe, Zn, Mn, B, and Cu. Significant differences were found among the germplasm lines for each of the inorganic elements. In general, the means were within the ranges that have been previously reported. Both highly significant positive and negative relationships were observed for several elemental combinations. The largest correlation was negative between seed Ca and K concentrations. These data indicate that careful consideration should be given to the selection method used in a breeding program for improving the compositional balance of peanut seed.
Myasthenia gravis. T epitopes on the delta subunit of human muscle acetylcholine receptor (1991)

Autoimmune T cell lines specific for muscle nicotinic acetylcholine receptor (AChR) were propagated from the blood of three myasthenia gravis patients by the use of a pool of synthetic peptides (delta-pool) corresponding to the complete sequence of the delta-subunit of human muscle AChR. Propagation of AChR-specific T cell lines was attempted unsuccessfully from four other myasthenia gravis patients and from four healthy controls. The lines had CD3+, CD4+, CD8- phenotype, strongly recognized the delta-pool, and cross-reacted vigorously with non-denatured AChR purified from mammalian muscle. They did not cross-react detectably with pools of similar overlapping synthetic peptides corresponding to the complete sequences of the alpha- and gamma-subunits of human muscle AChR. The sequence segments of the delta-subunit that contain T epitopes were identified by investigating the response of the three CD4+ T cell lines to the individual synthetic peptides forming the delta-pool. Each line had an individual pattern of peptide recognition. Although no immunodominant region, recognized in association with different DR haplotypes, could be identified, the sequence segments most strongly recognized by the CD4+ T cell lines were clustered within residues 121-290. One of the peptides more strongly recognized by the T cells corresponded to a sequence segment with high predicted propensity to form an amphipathic alpha-helix, a structural motif proposed to be typical of T epitopes.
SDR architecture refinement for JTRS (2002)

Software-defined radio (SDR) has emerged as a focus of academic research, commercial development, and military investment for future wireless systems. This paper reviews the foundation concepts of the SDR. It characterizes the tradeoffs among core software-radio technologies. These include wideband RF hardware, a flexible digital signal processing platform, and a layered software architecture. Object-oriented analysis by industry participants defined architectures for the Joint Tactical Radio System (JTRS) and the SDR Forum. This paper analyzes those architectures in terms of layered virtual machines. The goal is to clarify technical issues in the cost-effective support of simultaneous hardware and software evolution. Research issues include layering of software objects, and virtual machine efficiency. Layering suggests refinements that would benefit both commercial and military implementations of SDR architecture. Potential benefits for integrated C4ISR are pointed out.
Expression of Inducible Nitric Oxide Synthase in Circulating Neutrophils of the Systemic Inflammatory Response Syndrome and Septic Patients (1998)

There is increasing evidence that nitric oxide (NO) is an important factor in the pathogenesis of septic shock. It is known that polymorphonuclear neutrophils (PMNs) are activated during sepsis or after surgical stress, and they then release various toxic mediators including free radicals. It has not been clear whether NO synthesis can be induced in circulating PMNs. Blood samples were obtained from 11 patients with sepsis, 23 patients with systemic inflammatory response syndrome (SIRS), and 16 patients without SIRS (nonSIRS) who underwent operation. We examined mRNA expression of inducible NO synthase (iNOS) in circulating PMNs from those patients pre- and postoperatively using the reverse transcriptase polymerase chain reaction (RT-PCR) method and measured their serum nitrate (NO2-) + nitrate (NO3-) concentration, peripheral blood white cell (WBC) count, and serum C-reactive protein (CRP) level. The frequency of iNOS expression in PMNs increased in sepsis (100%) and SIRS (70%) patients compared to that in nonSIRS patients (18%) (p < 0.001). The peripheral WBC count and CRP level were significantly higher in iNOS-positive patients than in iNOS-negative patients (p < 0.05 and p < 0.01, respectively). Postoperatively, the serum NO2- + NO3- concentration increased in 87% of septic patients and in 56% of patients with SIRS (p < 0.05 for both). Our study indicated that iNOS mRNA expression is induced in human circulating PMNs of patients with postoperative sepsis and SIRS and may be involved in the pathogenesis of the sepsis syndrome.
Time to recurrence of squamous cell carcinoma of the head and neck (1991)

A personal series of 3,215 patients with proven squamous cell carcinoma of the mucosal surfaces of the upper aerodigestive tract is presented. Of these patients, 515 suffered a recurrence of their primary tumor after a course of radiotherapy. The time from the end of radiotherapy to diagnosis of a primary recurrence was not related to any known host factors, nor to tumor factors except site. However, it was the most significant predictor of survival, both from initial presentation and from the date of recurrence. The time to recurrence did not relate to the size of the tumor at recurrence, suggesting that large recurrences are multicentric. The time to recurrence also predicted response and survival of 67 patients with end-stage disease treated by chemotherapy. The response and survival were better in tumors with a time to recurrence longer than the median; the increased survival was not significant, but the increased response was.
Self-Specific Memory Regulatory T Cells Protect Embryos at Implantation in Mice (2013)

Regulatory T cells (Tregs) play crucial roles in both fetal and tumor development. We recently showed that immunosurveillance by pre-existing CD44(high)CD62L(low) activated/memory Tregs (amTregs) specific for self-Ags protects emergent tumor cells in mice. This Treg response of a memory type is more rapid than and dominates the antitumor response of tumor-specific effector T cells. In this study, we report striking similarities between the early Treg responses to embryo and tumor implantation. Tregs are rapidly recruited to uterus-draining lymph nodes and activated in the first days after embryo implantation in both syngeneic and allogeneic matings; express the markers of the amTreg subset; and are at least in part self-Ag specific, as seen in tumor emergence. Unlike in the tumor emergence setting, however, for which preimmunization against tumor Ags is sufficient for complete tumor eradication even in the presence of Tregs, Treg depletion is additionally required for high frequencies of fetus loss after preimmunization against paternal tissue Ags. Thus, amTregs play a major role in protecting embryos in both naive and preimmune settings. This role and the ensuing therapeutic potential are further highlighted by showing that Treg stimulation, directly by low-dose IL-2 or indirectly by Fms-related tyrosine kinase 3 ligand, led to normal pregnancy rates in a spontaneous abortion-prone model.
Autoradiographic visualization of beta-adrenoceptor subtypes in human lung. (1985)

Adrenoceptor subtypes have been localized in human lung by an autoradiographic method, using [125I]iodocyanopindolol (ICYP) to label beta-receptors in tissue sections. The ICYP was incubated with cryostat sections of microscopically normal human lung method on microscope slides for 2 h at 37 degrees C. Nonspecific binding was determined by incubating adjacent serial sections in the presence of 200 microM (-)-isoproterenol. Specific binding, which accounted for greater than 90% of total counts bound to the sections, was saturable, of high affinity, and stereoselective, having the same pharmacologic characteristics as binding to homogenates prepared from the same lungs. Competition with selective beta-receptor antagonists ICI 118,551 (beta 2-selective) and betaxolol (beta 1-selective) showed that the ratio of beta 2 to beta 1-receptors in the sections was approximately 3:1. Autoradiography revealed that beta-receptors were widely distributed, with dense labeling over airway epithelium, alveolar walls, and submucosal glands, and a lower density of grains over airway and vascular smooth muscle. The beta-receptors of airway smooth muscle from large and small airways were entirely of the beta 2-receptor subtype, which is consistent with functional studies. Similarly, beta-receptors of airway epithelium and vascular smooth muscle were also entirely of the beta 2-receptor subtype. In bronchial submucosal glands and alveolar walls, both receptor subtypes appeared to coexist with beta 2-receptors, making up 10% of the total in glands and 30% in alveoli. The significance of beta 1- and beta 2-receptors in alveolar walls (which account for greater than 90% of total beta-receptors in human lung) remains to be determined.
Synchronization of tumor and normal cells from G1 to multiple cell cycles by lovastatin. (1991)

Synchronization of mammalian cells is essential for investigations involving cell proliferation. A simple method for obtaining synchrony in all types of cells, through several cycles and with minimal overall metabolic perturbations, has not yet been available. We describe a procedure for synchronizing normal as well as tumor cells reversibly in the G1 phase of the cell cycle using Lovastatin, an inhibitor of 3-hydroxy-3-methylglutaryl-coenzyme A reductase. This method of synchronization was successful with all cell lines tested, including normal and tumor cells of mouse, hamster, and human origins. For example, when MCF-7 human breast cancer cells were synchronized with Lovastatin and released by the addition of mevalonic acid (the product of the reaction catalyzed by 3-hydroxy-3-methylglutaryl-coenzyme A reductase), 3 phases of accelerated thymidine incorporation into DNA corresponding to 3 S phases of the cell cycle occurred during a 90-h period of cell replication. Thymidine incorporation was decreased to less than or equal to 4% during the initial lag of 18 h before the first S phase, and maximum incorporation was then achieved after only 6 h. The antibody Ki-67, which detects a nuclear antigen associated with proliferation, was present in cells arrested with Lovastatin. This fact, together with the lack of thymidine incorporation during the initial lag time, indicates that the cells were arrested in the G1 and not in the G0 phase of the cell cycle. Furthermore, in synchronized tumor-derived human breast epithelial cells, histone H4 RNA was low after Lovastatin release and increased with the onset of DNA synthesis. Concomitant synthesis of DNA and histone H4 RNA expression could be observed for 2 cycles. Minimal perturbations of general metabolic functions occurred since the rate of RNA, protein, and initial DNA synthesis were unaffected by Lovastatin, as evidenced by [3H]uridine, [3H]leucine, and initial [3H]thymidine incorporation. Finally, while the Lovastatin-induced synchronization was overcome by mevalonic acid, addition of squalene or cholesterol-ethanol had no such effect. Thus, Lovastatin appears to prevent formation of an early intermediate in the cholesterol pathway that is essential for progression of cells through early G1 phase.
A Movable Surface: Formation of <i>Yersinia</i> sp. Biofilms on Motile <i>Caenorhabditis elegans</i> (2004)

Bubonic plague is transmitted by fleas whose feeding is blocked by a mass of Yersinia pestis in the digestive tract. Y. pestis and the closely related Y. pseudotuberculosis also block the feeding of Caenorhabditis elegans by forming a biofilm on the nematode head. C. elegans mutants with severe motility defects acquire almost no biofilm, indicating that normal animals accumulate the biofilm matrix as they move through a Yersinia lawn. Using the lectin wheat germ agglutinin as a probe, we show that the matrix on C. elegans contains carbohydrate produced by Yersinia. The carbohydrate is present in bacterial lawns prior to addition of nematodes, indicating that biofilm formation does not involve signaling between the two organisms. Furthermore, biofilm accumulation depends on continuous C. elegans exposure to a lawn of Yersinia bacteria.
p53 Biological Network: At the Crossroads of the Cellular-Stress Response Pathway and Molecular Carcinogenesis (2006)

p53 as a key molecular node in the stress response pathway, including inflammation. p53 is involved in several critical pathways including cell cycle arrest, apoptosis, DNA repair, and cellular senescence, which are essential for normal cellular homeostasis and maintaining genome integrity. The alteration of the TP53 gene or posttranslational modification in the p53 protein can alter its response to cellular stress. The molecular archaeology of the TP53 mutation spectrum generates hypotheses concerning the etiology and molecular pathogenesis of human cancer. The spectrum of somatic mutations in the TP53 gene implicates environmental carcinogens, and both endogenous agents and processes in the etiology of human cancer.
BIOCOMPATIBILITY OF BRILLIANT BLUE G IN A RAT MODEL OF SUBRETINAL INJECTION (2007)

Subretinal injection of the dyes caused retinal cell degeneration at lower concentrations than those reported for intravitreous injection. However, subretinal injection of BBG at 0.25 mg/mL appeared to provide satisfactory biocompatibility.
Effects of gastrin-releasing peptide and analogues on guinea pig nasal mucosal secretion (1993)

The effects of gastrin-releasing peptide (GRP), bombesin, GRP-(1-16) and GRP-(21-27) on guinea pig nasal mucosal secretion were studied in vivo. GRP, bombesin, and GRP-(21-27) induced significant secretion of total protein, albumin, and alkaline phosphatase. GRP induced significant secretion at lower concentrations (10(-11) and 10(-10) M) than were required for bombesin and GRP-(21-27) (10(-7) M). GRP-(1-16) did not stimulate secretion, indicating that the COOH-terminal region of GRP contained the secretagogic principle. Capsaicin, a stimulant of nociceptive sensory nerves, stimulated GRP release into nasal secretions. These data suggest that GRP is present in guinea pig nasal mucosa and that the COOH-terminal region of GRP may regulate mucosal macromolecule secretion.
The Role of Endogenous Hormones in the Etiology and Prevention of Breast Cancer: The Epidemiological Evidence (2004)

Breast cancer is the most common cause of cancer death in women worldwide. Rates vary about fivefold around the world, but they are increasing in regions that until recently had low rates of the disease. Despite the numerous uncertainties surrounding the etiology of breast cancer, intensive epidemiological, clinical, and genetic studies have identified a number of biologic and social traits as risk factors associated with it. Principal among them are the evidence of BRCA1 and BRCA2 susceptibility genes, familial history of breast cancer, age, higher socioeconomic status, ionizing radiation, tallness in adult life, alcohol consumption, and a variety of hormonal and metabolic factors. Among the hormonal influences, a relevant etiological function has been ascribed to unopposed exposure to elevated levels of estrogens and androgens. In addition, new epidemiological evidence indicates that among the metabolic factors, glucose metabolism, hyperinsulinemic insulin resistance, and insulin-like growth factor bioavailability may also play a role in breast cancer. These endocrine and metabolic factors may represent future targets for breast cancer prevention.
Integrated Sequential As-Built and As-Planned Representation with D4AR Tools in Support of Decision-Making Tasks in the AEC/FM Industry (2011)

The significant advancement in digital imaging and widespread popularity of digital cameras for capturing a comprehensive visual record of construction performance in the architecture, engineering, construction, and facility management (AEC/FM) industries have triggered an extensive growth in the rate of site photography, allowing hundreds of images to be stored for a project on a daily basis. Meanwhile, collaborative AEC technologies centering around building information models (BIMs) are becoming widely applied to support various architectural, structural, and preconstruction decision-making tasks. These models, if integrated with the as-built perspective of a construction, have great potential to extensively add value during the construction phase of a project. This paper reports recent developments from research efforts in (1) automated acquisition of as-built point-cloud models from unordered daily site photo collections and geo-registration of site images, (2) automated generation of four-dimensional (4D) as-built point-cloud models, and (3) semiautomated superimposition of the integrated as-built model over 4D (three dimensions plus time) BIMs to generate integrated 4D as-built and as-planned visualizations. The limitations and benefits of each modeling approach, the motivations for development of 4D augmented-reality (D4AR) environments for integrated visualization of as-built and as-planned models, the perceived and observed applications, and the benefits in seven case studies are discussed. Not only does a D4AR model visualize construction processes and performance deviations, it can also be used as a tool for automated and remote monitoring of progress and safety, quality control, and site layout management, and enables enhanced coordination and communication.
Requirement for the Expression of Poly(ADP-ribose) Polymerase during the Early Stages of Differentiation of 3T3-L1 Preadipocytes, as Studied by Antisense RNA Induction (1995)

Poly(ADP-ribose) polymerase (PADPRP) is biologically significant in the rejoining of DNA strand breaks. Post confluent cultures of 3T3-L1 preadipocytes showed marked increases in PADPRP protein and activity when the cells were induced to differentiate into adipocytes. When this increase in PADPRP expression was prevented in stably transfected 3T3-L1 cells by induction of PADPRP antisense RNA synthesis, the cells did not differentiate nor undergo the two or three rounds of DNA replication that are required for initiation of the differentiation process. 3T3-L1 cells expressing PADPRP antisense RNA under differentiation conditions were easily detached from plates and in some cases eventually died. When newly expressed PADPRP protein and DNA synthesis was assessed in cells at zero time or at 24 h after induction of differentiation by incorporation of bromodeoxyuridine or [3H]thymidine into DNA, significant incorporation was shown to occur in control cells after 24 h, but not in antisense cells. Furthermore, during the first 24 h, the co-immunoprecipitation of PADPRP and DNA polymerase alpha was observed in control cells, whereas no such complex formation was noted in the induced antisense cells, nor in uninduced control cells.
Label-free quantitative proteomics of CD133-positive liver cancer stem cells (2012)

These findings confirmed that mass spectrometry-based label-free quantitative proteomics can be used to gain insights into liver cancer stem cells.