gebhart/patrepeval huggingface dataset:
Male reproductive success and population control in the Mediterranean Fruit Fly, Ceratitis capitata (2012)

The traits that determine male reproductive success in Ceratitis capitata (medfly) are largely unknown. This comes despite decades of research into the reproductive behaviour of this agricultural pest. An understanding of what makes a successful male is of great importance in this lekking species, as one male has the ability to dominate access to females. In addition species-specific pest control techniques such as the Sterile Insect Technique (SIT) and Release of Insects carrying a Dominant Lethal (RIDL) rely on the mating competitiveness of mass-reared ‘sterile’ males to disrupt natural mating systems and reduce population numbers. However, it is well known that the mass-rearing process required to generate these individuals produces less competitive males, despite this an understanding of the sexual selection processes that are involved is severely lacking. In this thesis I used the medfly as a model organism to investigate the context-dependent nature of male reproductive success. In Chapters 2 and 3 I investigate the effect of manipulating the adult sex ratio on pre- and post-mating reproductive traits. Chapter 2 uses proximate&#13;\nmanipulation of the adult sex ratio to show how the relationship between pre- and post-mating success is affected by the levels of male competition. Chapter 3 shows that selection lines are unable to select for the traits that predict male reproductive success under altered levels of male competition. Chapter 4 describes the attempts to produce RIDL genetic constructs with embryonic lethality. Chapter 5 demonstrates that RIDL lines of medfly display characteristics that make them suitable for wild population control and may exceed the performance of existing SIT lines. Chapter 6 shows that manipulation of the larval diet can alter the gut microbiota of adults; however these manipulations have no effect on reproductive behaviour. Instead there was a significant effect of high-sugar larval rearing on mating success and body mass. This effect persisted for a single generation in offspring of these flies, even when they were reared on an inferior starch-based larval diet. Finally Chapter 7 summarises the thesis and discusses the implications of this work and future directions for both research in the reproductive behaviour of the medfly, and the future of RIDL technology in medfly population control.
Analysis of birefringent image in the retinal nerve fiber layer by polarization-sensitive optical coherence tomography (2004)

Phase retardation per unit depth (PR/UD) is a physiologically significant parameter which correlates with the orderly arrangement of neurons and neurofibrils within the retinal nerve fiber layer (RNFL) and can vary in glaucoma. The objective of this study is to use Polarization Sensitive Optical Coherence Tomography (PSOCT), to detect both RNFL thickness and depth-resolved birefringence and produce thickness and PR/UD maps of the primate RNFL. RNFL thickness is obtained from the PSOCT intensity image with boundary detection using imaging processing methods. Analysis of PR/UD begins with calculating the Stokes parameters from the horizontal magnitude, vertical magnitude and relative phase difference in the interference fringes of light back scattered from the retina. Computed Stokes parameters are used to determine the fast axis in the RNFL and local phase retardation. PR/UD is calculated by dividing local birefringence by the corresponding RNFL thickness. A three-dimensional map of PR/UD and RNFL thickness is constructed by combining registered B-scans. Three-dimensional maps of thickness and PR/UD from the primate RNFL show that PSOCT is can be used for detecting thickness and PR/UD of the peripapillary RNFL and a very effective modality to diagnose glaucoma.
Controlling nanowire structures through real time growth studies (2010)

In situ electron microscopy can be used to visualize the physical processes that control the growth of Si and Ge nanowires through the vapor–liquid–solid mechanism. Images and movies are recorded in a transmission electron microscope that has capabilities for depositing catalysts onto a sample and for introducing chemical vapor deposition precursor gases while the sample remains under observation. This technique allows us to measure nucleation, catalyst stability, surface structure and growth kinetics, in some cases confirming existing models and in other cases producing unexpected results and suggesting approaches toward growing novel structures. We will show that nanowire formation provides a unique window into the fundamentals of crystal growth as well as an opportunity to fabricate precisely controlled structures for novel applications.
Role of l-3,4-Dihydroxyphenylalanine in Mussel Adhesive Proteins (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTRole of l-3,4-Dihydroxyphenylalanine in Mussel Adhesive ProteinsMiaoer Yu, Jungyeon Hwang, and Timothy J. DemingView Author Information Departments of Materials and Chemistry University of California, Santa Barbara Santa Barbara, California 93106 Cite this: J. Am. Chem. Soc. 1999, 121, 24, 5825–5826Publication Date (Web):June 5, 1999Publication History Received15 February 1999Published online5 June 1999Published inissue 1 June 1999https://pubs.acs.org/doi/10.1021/ja990469yhttps://doi.org/10.1021/ja990469yrapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views7037Altmetric-Citations558LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Aromatic compounds,Copolymers,Monomers,Nucleic acid structure,Peptides and proteins Get e-Alerts
Molecular characterization of a STreptococcus mutans mutant altered in environmental stress responses (1993)

A mutant defective in aciduricity, GS5Tn1, was constructed following mutagenesis of Streptococcus mutans GS5 with the conjugative transposon Tn916. The mutant grew poorly at acidic pH levels and was sensitive to high osmolarity and elevated temperatures. These properties resulted from a single insertion of Tn916 into the GS5 chromosome, and the DNA fragment harboring the transposon was isolated into the cosmid vector, charomid 9-20. Spontaneous excision of Tn916 from the cosmid revealed that Tn916 inserted into a 8.6-kb EcoRI fragment. On the basis of the restriction analyses of insert fragments, it was found that Tn916 inserted into a 0.9-kb EcoRI-XbaI fragment. Nucleotide sequence analysis of this fragment indicated the presence of two open reading frames, ORF1 and ORF2. By using a marker rescue strategy, a 6.0-kb HindIII fragment including the target site for Tn916 insertion and the 5' end of ORF1 was isolated and sequenced. The deduced amino acid sequences of ORF1 and ORF2 showed significant homology with the diacylglycerol kinase and Era proteins, respectively, from Escherichia coli. Nucleotide sequence analysis of the Tn916 insertion junction region in the GS5Tn1 chromosome revealed that the transposon inserted near the 3' terminus of ORF1. Restoration of ORF1 to its original sequence in mutant GS5Tn1 was carried out following transformation with integration vector pVA891 containing an intact ORF1. The resultant transformant showed wild-type levels of aciduricity as well as resistance to elevated temperatures and high osmolarity. These results suggest that the S. mutans homolog of diacylglycerol kinase is important for adaptation of the organism to several environmental stress signals.
Synthesis and transition-metal complexes of new cross-bridged tetraamine ligands (1996)

New cross-bridged tetraamine ligands (bicyclo[6.6.2],[6.5.2] and [5.5.2] systems ) are synthesized; complexation of CuII and NiII demonstrate that the ligands coordinate selected metals in a cleft.
Stress Shadowing and Microseismic Events: A Numerical Evaluation (2011)

Abstract In horizontal well shale completions, multiple stages, each often with multiple clusters, are used to provide sufficient stimulated area to make an economic well. Each created hydraulic fracture alters the stress field around it. When hydraulic fractures are placed close enough together, the well-known stress shadow effect occurs in which subsequent fractures are affected by the stress field from the previous fractures. The effects include higher net pressures, smaller fracture widths and changes in the associated complexity of the stimulation. The level of microseismicity is also altered by stress shadow effects. For example, it is commonly seen that the number of microseismic events is significantly reduced from the toe to the heal of the well, where the first frac stage is conducted at the toe of the well. In this paper, we present the results of a numerical evaluation of the effect of multiple hydraulic fractures on stress shadowing as a function of fracture spacing, shale rock mechanical properties, and the in-situ stress ratio. In addition, utilizing the inherent ability of discrete element models to evaluate shear and tensile failure along fracture surfaces, shear failure, as a proxy for microseismicity, is evaluated as a function of fracture-induced stress and stress shadowing. The results of the study provide a means to optimize shale completions by understanding the effect of stress ratio, rock mechanical parameters, and hydraulic fracture spacing on the stress shadow effect and the potential for changing fracture complexity.
Post-transcriptional small RNA pathways in plants: mechanisms and regulations (2006)

Small RNAs are riboregulators that have critical roles in most eukaryotes. They repress gene expression by acting either on DNA to guide sequence elimination and chromatin remodeling, or on RNA to guide cleavage and translation repression. This review focuses on the various types of post-transcriptional small RNA-directed pathways in plants, describing their roles and their regulations.
TRANSFAC: an integrated system for gene expression regulation (2000)

TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles (http://transfac.gbf.de/TRANSFAC/). Its content has been enhanced, in particular by information about training sequences used for the construction of nucleotide matrices as well as by data on plant sites and factors. Moreover, TRANSFAC has been extended by two new modules: PathoDB provides data on pathologically relevant mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features of scaffold/matrix attached regions (S/MARs) and the proteins binding to them. Additionally, the databases TRANSPATH, about signal transduction, and CYTOMER, about organs and cell types, have been extended and are increasingly integrated with the TRANSFAC data sources.
CD8 T lymphocytes specific for the secreted p60 antigen protect against Listeria monocytogenes infection. (1995)

The ability of Listeria monocytogenes to gain access to the cytoplasm of infected cells results in the processing and presentation of bacterial Ags through the MHC class I pathway. As a result, CD8 T cells are the most effective mediators of acquired immunity in the mouse model of L. monocytogenes infection. CD8 T cells specific for a single nonamer epitope derived from the secreted virulence factor listeriolysin O (LLO) can protect H-2d mice against lethal infection. Bacteria lacking LLO are avirulent and do not elicit protective immunity in mice. Thus, the failure of LLO minus L. monocytogenes to elicit protective immunity could be caused either by their inability to enter the cytoplasm or to the lack of LLO-derived peptide epitopes. In this report we provide evidence that H-2d restricted CD8 T cells with specificity for another L. monocytogenes protein, the secreted p60 molecule, can protect against infection. Our studies further demonstrate that LLO-dependent induction of protective immunity results from access of the bacterium to the cytoplasm. In addition, these studies provide support for the hypothesis that secreted bacterial proteins are the most important targets for protective CD8 T cell-mediated immunity.
Poly(A) elongation during Xenopus oocyte maturation is required for translational recruitment and is mediated by a short sequence element. (1989)

Xenopus oocytes contain several mRNAs that are mobilized into polysomes only at the completion of meiosis (maturation) or at specific times following fertilization. To investigate the mechanisms that control translation during early development, we have focused on an mRNA, termed G10, that is recruited for translation during oocyte maturation. Coincident with its translation, the poly(A) tail of this message is elongated from approximately 90 to 200 adenylate residues. To identify the cis sequence that is required for this cytoplasmic adenylation and recruitment, we have synthesized wild-type and deletion mutant G10 mRNAs with SP6 polymerase. When injected into oocytes that subsequently were induced to mature with progesterone, wild-type G10 mRNA, but not mutant transcripts lacking a 50-base sequence in the 3'-untranslated region, was polyadenylated and recruited for translation. The 50-base sequence was sufficient to confer polyadenylation and translation when fused to globin mRNA, which does not normally undergo these processes during oocyte maturation. Further mutational analysis of this region revealed that a U-rich sequence 5' to the AAUAAA hexanucleotide nuclear polyadenylation signal, as well as the hexanucleotide itself, were both required for polyadenylation and translation. The 50-base cis element directs polyadenylation, but not translation per se, as a transcript that terminates with 3'-deoxyadenosine (cordycepin) is not recruited for translation. The available data suggest that the dynamic process of polyadenylation, and not the length of the poly(A) tail, is required for translational recruitment during oocyte maturation.
Earth: Fourth Edition (1974)

This edition preserves the classical elements of geology while incorporating current findings and topics such as satellite data, climate change, the eruption of El Chichon, and acid rain. It incorporates the elementary ideas of structural geology and discussions of rock structures. The flow of geological materials between the interior and the surface is developed, and the modern approach of the interactions of the earth and its environmental envelope is discussed.
Automatically Labeling Semantic Classes (2004)

Systems that automatically discover semantic classes have emerged in part to address the limitations of broad-coverage lexical resources such as WordNet and Cyc. The current state of the art discovers many semantic classes but fails to label their concepts. We propose an algorithm labeling semantic classes and for leveraging them to extract is-a relationships using a top-down approach.
Three-dimensional micro-electrode array for recording dissociated neuronal cultures (2009)

This work demonstrates the design, fabrication, packaging, characterization, and functionality of an electrically and fluidically active three-dimensional micro-electrode array (3D MEA) for use with neuronal cell cultures. The successful function of the device implies that this basic concept-construction of a 3D array with a layered approach-can be utilized as the basis for a new family of neural electrode arrays. The 3D MEA prototype consists of a stack of individually patterned thin films that form a cell chamber conducive to maintaining and recording the electrical activity of a long-term three-dimensional network of rat cortical neurons. Silicon electrode layers contain a polymer grid for neural branching, growth, and network formation. Along the walls of these electrode layers lie exposed gold electrodes which permit recording and stimulation of the neuronal electrical activity. Silicone elastomer micro-fluidic layers provide a means for loading dissociated neurons into the structure and serve as the artificial vasculature for nutrient supply and aeration. The fluidic layers also serve as insulation for the micro-electrodes. Cells have been shown to survive in the 3D MEA for up to 28 days, with spontaneous and evoked electrical recordings performed in that time. The micro-fluidic capability was demonstrated by flowing in the drug tetrotodoxin to influence the activity of the culture.
The Submergence Tolerance Regulator SUB1A Mediates Crosstalk between Submergence and Drought Tolerance in Rice (2010)

Submergence and drought are major constraints to rice (Oryza sativa) production in rain-fed farmlands, both of which can occur sequentially during a single crop cycle. SUB1A, an ERF transcription factor found in limited rice accessions, dampens ethylene production and gibberellic acid responsiveness during submergence, economizing carbohydrate reserves and significantly prolonging endurance. Here, we evaluated the functional role of SUB1A in acclimation to dehydration. Comparative analysis of genotypes with and without SUB1A revealed that SUB1A enhanced recovery from drought at the vegetative stage through reduction of leaf water loss and lipid peroxidation and increased expression of genes associated with acclimation to dehydration. Overexpression of SUB1A augmented ABA responsiveness, thereby activating stress-inducible gene expression. Paradoxically, vegetative tissue undergoes dehydration upon desubmergence even though the soil contains sufficient water, indicating that leaf desiccation occurs in the natural progression of a flooding event. Desubmergence caused the upregulation of gene transcripts associated with acclimation to dehydration, with higher induction in SUB1A genotypes. SUB1A also restrained accumulation of reactive oxygen species (ROS) in aerial tissue during drought and desubmergence. Consistently, SUB1A increased the abundance of transcripts encoding ROS scavenging enzymes, resulting in enhanced tolerance to oxidative stress. Therefore, in addition to providing robust submergence tolerance, SUB1A improves survival of rapid dehydration following desubmergence and water deficit during drought.
1,3-disubstituted 2-thioxo-4,5-imidazolidinediones and 2,4,5-imidazolidinetriones and their anticonvulsant activity. (1991)

New unsymmetrically 1,3-disubstituted derivatives of 2-thioxo-4,5-imidazolidinedione (3, 5-7, 9-12) and 2,4,5-imidazolidinetrione (2, 8, 13-15) were synthesized by condensation of the respective thioureas and ureas with oxalyl chloride. They were screened for their central, mainly anticonvulsant activity and only compound 8 revealed antianxiety and antiepileptic properties.
Platelet-derived growth factor (PDGF) in oncogenesis: development of a vascular connective tissue stroma in xenotransplanted human melanoma producing PDGF-BB. (1993)

Human WM9 melanoma cells, previously shown to be devoid of PDGF expression, were stably transfected with a PDGF-B cDNA under the transcriptional control of a cytomegalovirus promoter. Northern blot analysis revealed high expression of an mRNA of the expected size in the PDGF-B-transfected cells. Synthesis and secretion of PDGF-BB was confirmed by immunoprecipitation. Furthermore, conditioned medium from PDGF-B-transfected cells contained a mitogenic activity for fibroblasts. For analysis of tumor growth in vivo, cells of each type were injected subcutaneously into BALB/c nu/nu mice. Tumors from mice injected with WM9 cells transfected with the vector only contained large necrotic areas; only scant blood vessels with narrow lumina were observed. No connective tissue was present. In the tumors from PDGF-B-transfected WM9 cells, nests of tumor were divided by connective tissue septa. An abundance of blood vessels was observed in the connective tissue septa and within the tumor cell nests. There was a complete absence of necrosis in these tumors. The present results suggest that tumor-derived PDGF-BB is a potent mediator of connective tissue stroma formation. The connective tissue framework that is generated in response to PDGF-BB may form a solid support for newly formed blood vessels and, thereby, facilitate the formation of a functional vascular system in the tumor.
Molecular Characterization of Ethoxylates by Complementary Chromatographic Techniques. Evaluation of Efficiency and Reliability (2003)

Article Molecular Characterization of Ethoxylates by Complementary Chromatographic Techniques. Evaluation of Efficiency and Reliability was published on May 1, 2003 in the journal Tenside Surfactants Detergents (volume 40, issue 3).
Cancer Stem Cells (2006)

This review describes cancer stem cells, a topic of considerable biologic and clinical interest in oncology.
The current status of fixation for electron microscopy: A review (1984)

SUMMARY Chemical fixation of cells has been used extensively in different fields of electron microscopy. The type of fixation can be selected to maximize retention of different cell constituents where morphology is of prime interest. For techniques such as immunocytochemistry and autoradiography, a compromise between morphology and retention of antigenicity or radiolabel has to be reached. By careful choice of fixative, buffer and other physical parameters, optimum results can be obtained for both animal and plant tissues. Emphasis has been put on more recent developments in technique.
A Focused Optically Transparent PVDF Transducer for Photoacoustic Microscopy (2019)

This papers reports the development of a novel focused optically-transparent ultrasound transducer with a wide bandwidth for photoacoustic microscopy (PAM). It consists of a 9-μm-thick polyvinylidene fluoride (PVDF) film coated with Indium-tin oxide (ITO) and metal electrodes, which is laminated onto a concave glass lens. A new fabrication process was developed to ensure the formation of continuous ITO coatings on the curved transducer surface without fracturing. Both optical and acoustic experiments were conducted to characterize the performance of the transducer. The testing results show that the transducer has an optical transmittance of 60% (@ 532 nm), an acoustic center frequency of 24 MHz, and an acoustic bandwidth of 26 MHz. With an acoustic numerical aperture (NA) of 0.23, it provides a 0.13-mm acoustic focal spot and a 1.6-mm focal depth. For demonstration, a PAM setup was built for conducting PA imaging on different targets. In contrast to existing PAM systems, the use of the optically-transparent focused transducer allows a simpler and more compact configuration and easier alignment of the optical excitation and acoustic focal points. Such features are especially useful for the development of miniaturized PAM systems for handheld, wearable and even endoscopic applications.