bluuebunny/crossref_metadata_2025_split huggingface dataset:
Return of Kosi river induced by Tibet earthquake
Authors: Mukherjee Saumitra 
Published: November 2008

AbstractSeismotectonics and change in river courses were correlated. Following the elastic rebound theory before the occurrence of the earthquake the subsurface rocks accumulate the energy by the tectonic movement. The Kosi river barrage was broken due to the tectonic forces accumulation in the south of Tibet Himalayas. Kosi river originates from Tibetan Himalayas and any disturbance in Tibet plateau has the potential to change the river course.
Voicing a Vision of Translational Research
Authors: Stemple Joseph C. , Thomas Lisa B. 
Published: November 2008

Abstract
Translational research has been characterized as effective translation of new knowledge, mechanisms, and techniques generated by advances in basic science research into new approaches for prevention, diagnosis, and treatment of disease essential for improving health. Research in the area of normal and abnormal voice production has a rich history in both the clinical and basic sciences. This report provides an overview of basic science work in the field of voice and considers the implications and importance of translating this research to the clinical realm.
From Bench to Bedside: Translational Research on Vocal Fold Hydration
Authors: Sivasankar Mahalakshmi , Leydon Ciara 
Published: November 2008

Abstract
The importance of well-hydrated vocal folds in maintaining optimal voice function is widely acknowledged. In this article, we summarize findings from recent bench and bedside research and highlight how use of these experimental techniques has improved our understanding of the physiological mechanisms that regulate vocal fold hydration.
Rheometers, Bioreactors, and Vocalization Forces: Using Basic Science Investigations to Help the Voices of Teachers
Authors: Klemuk Sarah 
Published: November 2008

Abstract
Collaborative studies at the University of Iowa and the National Center for Voice and Speech aim to help the voices of teachers. Investigators study how cells and tissues respond to vibration doses simulating typical vocalization patterns of teachers. A commercially manufactured instrument is uniquely modified to support cell and tissue growth, to subject tissues to vocalization-like forces, and to measure viscoelastic properties of tissues. Through this basic science approach, steps toward safety limits for vocalization and habilitating rest periods for professional voice users will be achieved.
Bench to Bedside: Research Review in Vocal Fold Extracellular Matrix
Authors: Thibeault Susan L. 
Published: November 2008

Abstract
The vocal fold lamina propria is crucial for the production of the vocal fold mucosal wave and quality of voice. Basic science research in this area has increased over the past 10 years secondary to our understanding of this importance. The translational aspects of this research are far reaching as we begin to better understand the development, maintenance, and regeneration of this area. This article serves to present a review of the multi faceted work being completed.
Receptor Mediated Uptake of Pepsin: Significance in Otolaryngology
Authors: Johnston Nikki 
Published: November 2008

Abstract
Reflux of gastric contents into the laryngopharynx contributes to voice disorders, otolaryngological inflammatory disorders, and perhaps even neoplastic diseases of the laryngopharynx. Treatment is currently focuses on increasing the pH of the refluxate because it was thought that the refluxate would not cause injury/symptoms at higher pH. However, many patients with reflux-attributed laryngeal injury/disease have persistent symptoms despite aggressive acid supression therapy. Recent studies using combined multi-channel intraluminal impedance with pH montioring have shown a positive symptom association with non- and weakly-acidic reflux and an association between non-/weakly acidic reflux and refractory symptoms on proton pump inhibitor therapy. Thus, the role of acid alone in the development of reflux related laryngeal pathology has to be questioned and studies examining the effects of the other components of the refluxate are clearly needed. Our data, described herein, supports a role for pepsin in reflux-attributed laryngeal injury/disease independent of the pH of the refluxate and highlights potential novel drug targets.
Tomato (Solanum lycopersicum): A Model Fruit-Bearing Crop
Authors: Kimura Seisuke , Sinha Neelima 
Published: November 2008

INTRODUCTIONTomato (Solanum lycopersicum) is one of the most important vegetable plants in the world. It originated in western South America, and domestication is thought to have occurred in Central America. Because of its importance as food, tomato has been bred to improve productivity, fruit quality, and resistance to biotic and abiotic stresses. Tomato has been widely used not only as food, but also as research material. The tomato plant has many interesting features such as fleshy fruit, a sympodial shoot, and compound leaves, which other model plants (e.g., rice and Arabidopsis) do not have. Most of these traits are agronomically important and cannot be studied using other model plant systems. There are 13 recognized wild tomato species that display a great variety of phenotypes and can be crossed with the cultivated tomato. These wild tomatoes are important for breeding, as sources of desirable traits, and for evolutionary studies. Current progress on the tomato genome sequencing project has generated useful information to help in the study of tomato. In addition, the tomato belongs to the extremely large family Solanaceae and is closely related to many commercially important plants such as potato, eggplant, peppers, tobacco, and petunias. Knowledge obtained from studies conducted on tomato can be easily applied to these plants, which makes tomato important research material. Because of these facts, tomato serves as a model organism for the family Solanaceae and, specifically, for fleshy-fruited plants.
Comb Jellies (Ctenophora): A Model for Basal Metazoan Evolution and Development
Authors: Pang Kevin , Martindale Mark Q. 
Published: November 2008

INTRODUCTIONCtenophores, or comb jellies, are a group of marine organisms whose unique biological features and phylogenetic placement make them a key taxon for understanding animal evolution. These gelatinous creatures are clearly distinct from cnidarian medusae (i.e., jellyfish). Key features present in the ctenophore body plan include biradial symmetry, an oral-aboral axis delimited by a mouth and an apical sensory organ, two tentacles, eight comb rows composed of interconnected cilia, and thick mesoglea. Other morphological features include definitive muscle cells, a nerve net, basal lamina, a sperm acrosome, and light-producing photocytes. Aspects of their development made them attractive to experimental embryologists as early as the 19th century. Recently, because of their role as an invasive species, studies on their role in ecology and fisheries-related fields have increased. Although the phylogenetic placement of ctenophores with respect to other animals has proven difficult, it is clear that, along with poriferans, placozoans, and cnidarians, ctenophores are one of the earliest diverging extant animal groups. It is important to determine if some of the complex features of ctenophores are examples of convergence or if they were lost in other animal branches. Because ctenophores are amenable to modern technical approaches, they could prove to be a highly useful emerging model.
Astyanax mexicanus, the Blind Mexican Cave Fish: A Model for Studies in Development and Morphology: Figure 1.
Authors: Borowsky Richard 
Published: November 2008

INTRODUCTIONThe perpetual darkness of caves has two important consequences for permanent inhabitants. First, eyes and pigmentation lose their primary functions. Second, in the absence of photosynthesis, food is rare. For these reasons, cave-adapted species typically have reduced eyes and pigmentation and increased or more efficient metabolisms. Additionally, other senses are usually augmented to compensate for the loss of vision. Identifying the genetic bases underlying these phenotypic changes will enhance our understanding of the specific pathways involved in control of these phenotypes and, in general, the evolutionary process. Unfortunately, the genetics of most cave animals cannot be studied because they are not easily bred. Blind Mexican tetras, Astyanax mexicanus, are the valuable exception to this rule because fish from the various cave populations are fully interfertile with one another and with eyed sister forms still living in nearby surface streams. Hybrids between surface and cave forms permit genetic analysis of their differences, and study of the pure forms as well as of hybrids allows study of their developmental differences. Quantitative trait loci (QTL) analysis has already identified some specific genes responsible for differences between cave and surface forms as well as other likely candidates; more will be added in the future. This system is a valuable addition to the array of existing models for the study of developmental and evolutionary genetics because cave populations are repositories of numerous naturally occurring mutations affecting development of the eyes and other senses, pigmentation, bone structure, metamerism, and metabolism. These alleles have been prescreened by natural selection for high viability, which simplifies their study. In contrast, new alleles obtained through mutagenesis in other model species are typically burdened with lower viability.
Construction of Nucleic Acid Programmable Protein Arrays (NAPPA) 1: Coating Glass Slides with Amino Silane
Authors: Link Andrew J. , LaBaer Joshua 
Published: November 2008

INTRODUCTIONFunctional proteomics enables protein activities to be studied in vitro using high-throughput (HT) methods. Protein microarrays are the method of choice because they display many proteins simultaneously and require only small reaction volumes to assess function. Protein microarrays are typically used to (1) measure the abundance of many different analytes in a sample or (2) study the functions or properties of many proteins spotted on the array. Target protein microarrays are usually generated by expressing, purifying, and spotting the proteins onto a solid surface at very close spatial density. An alternative approach is to translate the proteins in situ on the array surface. This approach, termed “Nucleic Acid Protein Programmable Array” (NAPPA), enables the simultaneous expression of proteins in microarray format without the need for individual protein purification. This method uses cell-free extracts that transcribe and translate DNA into proteins which are then captured in situ, thus converting cDNA copies of genes into the desired target proteins. Instead of printing proteins at each feature of the array, the cDNA molecules for the corresponding genes that produce desired proteins are affixed to the array. Chemical treatment of glass slides and DNA isolation can be performed in advance and stored. The plasmid DNA can then be printed to make NAPPA slides, which can be stored dry for use. For experiments, NAPPA slides are expressed followed by detection of proteins and DNA using antibodies and stains. This protocol describes the initial preparation of slides to be used in the method.
Construction of Nucleic Acid Programmable Protein Arrays (NAPPA) 2: Preparing Bacterial Cultures in a 96-Well Format: Figure 1.
Authors: Link Andrew J. , LaBaer Joshua 
Published: November 2008

INTRODUCTIONFunctional proteomics enables protein activities to be studied in vitro using high-throughput (HT) methods. Protein microarrays are the method of choice because they display many proteins simultaneously and require only small reaction volumes to assess function. Protein microarrays are typically used to (1) measure the abundance of many different analytes in a sample or (2) study the functions or properties of many proteins spotted on the array. Target protein microarrays are usually generated by expressing, purifying, and spotting the proteins onto a solid surface at very close spatial density. An alternative approach is to translate the proteins in situ on the array surface. This approach, termed “Nucleic Acid Protein Programmable Array” (NAPPA), enables the simultaneous expression of proteins in microarray format without the need for individual protein purification. This method uses cell-free extracts that transcribe and translate DNA into proteins which are then captured in situ, thus converting cDNA copies of genes into the desired target proteins. Instead of printing proteins at each feature of the array, the cDNA molecules for the corresponding genes that produce desired proteins are affixed to the array. Chemical treatment of glass slides and DNA isolation can be performed in advance and stored. The plasmid DNA can then be printed to make NAPPA slides, which can be stored dry for use. For experiments, NAPPA slides are expressed followed by detection of proteins and DNA using antibodies and stains. This protocol describes preparation of the bacterial cultures in deep-well blocks.
Construction of Nucleic Acid Programmable Protein Arrays (NAPPA) 3: Isolating DNA Plasmids in a 96-Well Plate Format
Authors: Link Andrew J. , LaBaer Joshua 
Published: November 2008

INTRODUCTIONFunctional proteomics enables protein activities to be studied in vitro using high-throughput (HT) methods. Protein microarrays are the method of choice because they display many proteins simultaneously and require only small reaction volumes to assess function. Protein microarrays are typically used to (1) measure the abundance of many different analytes in a sample or (2) study the functions or properties of many proteins spotted on the array. Target protein microarrays are usually generated by expressing, purifying, and spotting the proteins onto a solid surface at very close spatial density. An alternative approach is to translate the proteins in situ on the array surface. This method uses cell-free extracts that transcribe and translate DNA into proteins which are then captured in situ, thus converting cDNA copies of genes into the desired target proteins. Instead of printing proteins at each feature of the array, the cDNA molecules for the corresponding genes that produce desired proteins are affixed to the array. Chemical treatment of glass slides and DNA isolation can be performed in advance and stored. The plasmid DNA can then be printed to make NAPPA slides, which can be stored dry for use. For experiments, NAPPA slides are expressed followed by detection of proteins and DNA using antibodies and stains. This protocol describes a method for isolating the plasmids in a 96-well format.
Construction of Nucleic Acid Programmable Protein Arrays (NAPPA) 4: DNA Biotinylation, Precipitation, and Arraying of Samples
Authors: Link Andrew J. , LaBaer Joshua 
Published: November 2008

INTRODUCTIONFunctional proteomics enables protein activities to be studied in vitro using high-throughput (HT) methods. Protein microarrays are the method of choice because they display many proteins simultaneously and require only small reaction volumes to assess function. Protein microarrays are typically used to (1) measure the abundance of many different analytes in a sample or (2) study the functions or properties of many proteins spotted on the array. Target protein microarrays are usually generated by expressing, purifying, and spotting the proteins onto a solid surface at very close spatial density. An alternative approach is to translate the proteins in situ on the array surface. This method uses cell-free extracts that transcribe and translate DNA into proteins which are then captured in situ, thus converting cDNA copies of genes into the desired target proteins. Instead of printing proteins at each feature of the array, the cDNA molecules for the corresponding genes that produce desired proteins are affixed to the array. Chemical treatment of glass slides and DNA isolation can be performed in advance and stored. The plasmid DNA can then be printed to make NAPPA slides, which can be stored dry for use. For experiments, NAPPA slides are expressed followed by detection of proteins and DNA using antibodies and stains. This protocol describes DNA biotinylation, precipitation, and arraying in preparation for protein expression.
Construction of Nucleic Acid Programmable Protein Arrays (NAPPA) 5: Expressing Proteins on NAPPA Slides
Authors: Link Andrew J. , LaBaer Joshua 
Published: November 2008

INTRODUCTIONFunctional proteomics enables protein activities to be studied in vitro using high-throughput (HT) methods. Protein microarrays are the method of choice because they display many proteins simultaneously and require only small reaction volumes to assess function. Protein microarrays are typically used to (1) measure the abundance of many different analytes in a sample or (2) study the functions or properties of many proteins spotted on the array. Target protein microarrays are usually generated by expressing, purifying, and spotting the proteins onto a solid surface at very close spatial density. An alternative approach is to translate the proteins in situ on the array surface. This method uses cell-free extracts that transcribe and translate DNA into proteins which are then captured in situ, thus converting cDNA copies of genes into the desired target proteins. Instead of printing proteins at each feature of the array, the cDNA molecules for the corresponding genes that produce desired proteins are affixed to the array. Chemical treatment of glass slides and DNA isolation can be performed in advance and stored. The plasmid DNA can then be printed to make NAPPA slides, which can be stored dry for use. For experiments, NAPPA slides are expressed followed by detection of proteins and DNA using antibodies and stains. This protocol describes a method for expression of the desired proteins in situ on the printed slides.
Construction of Nucleic Acid Programmable Protein Arrays (NAPPA) 6: Detecting Proteins on NAPPA Slides: Figure 1.
Authors: Link Andrew J. , LaBaer Joshua 
Published: November 2008

INTRODUCTIONFunctional proteomics enables protein activities to be studied in vitro using high-throughput (HT) methods. Protein microarrays are the method of choice because they display many proteins simultaneously and require only small reaction volumes to assess function. Protein microarrays are typically used to (1) measure the abundance of many different analytes in a sample or (2) study the functions or properties of many proteins spotted on the array. Target protein microarrays are usually generated by expressing, purifying, and spotting the proteins onto a solid surface at very close spatial density. An alternative approach is to translate the proteins in situ on the array surface. This method uses cell-free extracts that transcribe and translate DNA into proteins which are then captured in situ, thus converting cDNA copies of genes into the desired target proteins. Instead of printing proteins at each feature of the array, the cDNA molecules for the corresponding genes that produce desired proteins are affixed to the array. Chemical treatment of glass slides and DNA isolation can be performed in advance and stored. The plasmid DNA can then be printed to make NAPPA slides, which can be stored dry for use. For experiments, NAPPA slides are expressed followed by detection of proteins and DNA using antibodies and stains. This protocol describes antibody detection of the arrayed proteins.
Isolation, Culture, and Differentiation of Progenitor Cells from the Central Nervous System
Authors: Hutton Scott R. , Pevny Larysa H. 
Published: November 2008

INTRODUCTIONThe ability to prospectively identify and characterize neural progenitor cells in vivo has been difficult due to a lack of cell-surface markers specific for these cell types. A widely used in vitro culture method, known as the Neurosphere Assay (NSA), has provided a means to retrospectively identify neural progenitor cells as well as to determine both their self-renewal capacity and their ability to generate the three primary cell types of the nervous system: neurons, astrocytes, and oligodendrocytes. Today, combined with the establishment of multiple transgenic mouse strains expressing fluorescent markers and advances in cell isolation techniques such as fluorescence-activated cell sorting (FACS), the NSA provides a powerful system to prospectively elucidate neural progenitor characteristics and functions. Here we describe methods for the isolation, culture, and differentiation of neural progenitors from the developing mouse and adult cortex.
Preparing Recombinant Gonad Organ Cultures
Authors: Capel Blanche , Batchvarov Jordan 
Published: November 2008

INTRODUCTIONIt can be useful to assay migration between any two adjacent tissues during development. This protocol assays cell migration between the gonad and mesonephros using tissue recombination between genetically marked and unmarked tissue, combined with an organ culture technique. First, agar blocks are prepared in a custom-built mold. The size and shape of the wells are important to maintain the authentic three-dimensional morphology of the organ; the molds here are designed specifically to accommodate the gonad/mesonephros complex. Freshly dissected organs are then transferred to grooves within the agar blocks, where they are allowed to grow over 24-48 h. Using this protocol, organs develop with good morphology, and show only an ~12-h delay relative to in vivo development.
How to Grow Tomatoes
Authors: Kimura Seisuke , Sinha Neelima 
Published: November 2008

INTRODUCTIONTomatoes can be easily grown in a field, in a greenhouse, or in a growth cabinet. They need acidic soil (pH 6.0-6.8), a lot of light, and water. The optimum temperature for growing tomato plants and fruit is 18°C-24°C. This protocol describes how to germinate tomato seeds, cultivate adult plants, and harvest seeds from fruit.
Crossing Tomato Plants
Authors: Kimura Seisuke , Sinha Neelima 
Published: November 2008

INTRODUCTIONThis protocol describes how to cross tomato plants. Crossing is important for the genetic analysis and breeding of tomatoes. Tomatoes are self-pollinating plants; thus, emasculation (removal of the anthers from the female parent) is essential. All wild tomato species can be crossed with cultivated tomatoes (although it may be difficult); this is useful because wild tomatoes are a great source of desirable traits. Most commercial tomatoes are F1 hybrids, and the seeds for them were produced by crossing two parent tomatoes.
Mnemiopsis leidyi Spawning and Embryo Collection
Authors: Pang Kevin , Martindale Mark Q. 
Published: November 2008

INTRODUCTIONCtenophores, or comb jellies, are a group of marine animals whose unique biological features and phylogenetic placement make them a key taxon for understanding animal evolution. Because of its large size, fecundity, abundance in coastal areas, and recent introduction to European waters, Mnemiopsis leidyi (commonly called “sea walnuts”) is the most highly studied ctenophore. Under optimal conditions, these self-fertile hermaphrodites are capable of reproduction at 2 wk of age and can release up to 10,000 eggs per day. Adults can be maintained in large aquaria with gentle aeration as long as they are well fed and can be spawned daily; multiple generations can be raised in the laboratory. This protocol describes how to collect embryos from M. leidyi. Under natural conditions, spawning normally occurs ~8 h after sunset, such that eggs are released under the cover of darkness. Because spawning is triggered by the onset of darkness, keeping animals under an artificial light regimen in the laboratory can alter the time of spawning. This protocol is designed to induce animal spawning at approximately 11:00 a.m.; however, it can be adjusted for other times. The duration from spawning to hatching of larvae is 18-24 h.