bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epithelial Thickness Profile Changes Induced by Myopic LASIK as Measured by Artemis Very High-frequency Digital Ultrasound
Authors: Reinstein Dan Z. , Srivannaboon Sabong , Gobbe Marine , Archer Timothy J. , Silverman Ronald H. , Sutton Hugo , Coleman D. Jackson 
Published: December 2009

Purpose:
To characterize changes in the corneal epithelial thickness profile induced by myopic LASIK.

Methods:
This was a prospective study of 37 eyes of 19 myopic LASIK patients. Eyes were divided into three groups according to sphere in the maximum myopic meridian: low (−1.00 to −4.00 diopters [D]), moderate (−4.25 to −6.00 D), and high myopia (−6.25 to −13.50 D). The epithelial thickness profile was measured by prototype Artemis very high-frequency (VHF) digital ultrasound scanner (ArcScan Inc) across the central 10-mm corneal diameter preoperatively and between 3 and 6 months postoperatively. The epithelial thickness profile was determined by averaging the epithelial thickness within annular bands centered on the corneal vertex. The change in epithelial thickness profile was calculated as the difference between the preoperative and postoperative epithelial thickness profiles.

Results:
The corneal epithelium thickened after myopic LASIK across the central 6 mm with maximum thickening centrally and progressively less thickening centrifugally in low myopia, and a more homogenous thickening in moderate and high myopia within the 5-mm diameter. The mean epithelial thickening at the corneal vertex was 7.41±1.09 µm, 9.29±1.22 µm, and 12.33±1.05 µm for low, moderate, and high myopia, respectively. The rate of epithelial thickening at the corneal vertex per diopter of myopia treated decreased with increasing myopia.

Conclusions:

Although the magnitude of epithelial thickening increased with increasing ablation depth, in accordance with Barraquer's Law of Thicknesses, the myopic refractive shift due to epithelial thickness profile changes was paradoxically more significant in low myopia than in high myopia. [
J Refract Surg
. 2009;25:444–450.]
Presenilin/γ-Secretase Cleaves CD46 in Response to Neisseria Infection
Authors: Weyand Nathan J. , Calton Christine M. , Higashi Dustin L. , Kanack Kristen J. , So Magdalene 
Published: December 2009

Abstract
CD46 is a type I transmembrane protein with complement and T cell regulatory functions in human cells. CD46 has signaling and receptor properties in immune and nonimmune cells, many of which are dependent on the expression of cytoplasmic tail (cyt) isoforms cyt1 or cyt2. Little is known about how cyt1 and cyt2 mediate cellular responses. We show that CD46-cyt1 and CD46-cyt2 are substrates for presenilin/γ-secretase (PS/γS), an endogenous protease complex that regulates many important signaling proteins through proteolytic processing. PS/γS processing of CD46 releases immunoprecipitable cyt1 and cyt2 tail peptides into the cell, is blocked by chemical inhibitors, and is prevented in dominant negative presenilin mutant cell lines. Two human pathogens, Neisseria gonorrhoeae and Neisseria meningitidis, stimulate PS/γS processing of CD46-cyt1 and CD46-cyt2. This stimulation requires type IV pili and PilT, the type IV pilus retraction motor, implying that mechanotransduction plays a role in this event. We present a model for PS/γS processing of CD46 that provides a mechanism by which signals are transduced via the cyt1 and cyt2 tails to regulate CD46-dependent cellular responses. Our findings have broad implications for understanding the full range of CD46 functions in infection and noninfection situations.
Fos Proteins Suppress Dextran Sulfate Sodium-Induced Colitis through Inhibition of NF-κB
Authors: Takada Yasunari , Ray Neelanjan , Ikeda Eiji , Kawaguchi Tomohiro , Kuwahara Masayoshi , Wagner Erwin F. , Matsuo Koichi 
Published: December 2009

Abstract
The Fos family proteins, c-Fos and Fra-1, are components of the dimeric transcription factor AP-1, which is typically composed of Fos and Jun family proteins. We have previously shown that mice lacking c-Fos (Fos−/− mice) respond more strongly to LPS injection than do wild-type (wt) controls. We then examined the sensitivity of Fos−/− mice to acute inflammatory stress in a dextran sulfate sodium (DSS)-induced colitis model. We found that Fos−/− mice exhibited more severe weight loss, bleeding, diarrhea, and colon shortening than did wt mice, in association with higher TNF-α production and NF-κB activity in colon segments of DSS-treated Fos−/− mice. Furthermore, NF-κB inhibition suppressed severe DSS-induced colitis in Fos−/− mice. In contrast, Fra-1 transgenic (Tg) mice responded poorly to LPS injection, and Fra-1–overexpressing macrophages and fibroblasts showed reduced production of proinflammatory cytokines, NO, and NF-κB activity. Remarkably, in the DSS-induced colitis model, Fra-1 Tg mice showed less severe clinical scores of colitis than did wt mice. Consistently, proinflammatory cytokine production and NF-κB activity in colon segments of DSS-treated Fra-1 Tg mice were lower than in wt controls. These findings reveal that the absence of c-Fos and overexpression of Fra-1 respectively enhance and suppress the activation of NF-κB in DSS-induced inflammatory stress. In this paper, we propose that AP-1 transcription factors containing c-Fos or Fra-1 are negative regulators of NF-κB–mediated stress responses.
EEG Recording in Rodents, with a Focus on Epilepsy
Authors: Martín del Campo C. , Velázquez José L. Pérez , Freire Miguel A. Cortez 
Published: December 2009

AbstractThis unit describes the materials, methods, and analytical techniques available for the study of electrical activity of neural tissue in rodents in both homeostatic and disease states, with emphasis on epileptogenesis. A table containing a list of suppliers of relevant materials and equipment is also provided. Curr. Protoc. Neurosci. 49:6.24.1‐6.24.24. © 2009 by John Wiley & Sons, Inc.
Epilepsy
Authors: Spitz Mark C , Dudek F Edward 
Published: December 2009

Abstract
Epilepsy is a chronic neurologic disorder characterized by recent epileptic seizures. It occurs in 0.7% of the population. There are many underlying causes. These include essentially anything that can injure the cerebral cortex and include head trauma, tumors, stroke and infection. However, the most common cause is crytogenic (meaning unknown). Medications are the mainstay of treatment. Surgical treatments are also done. These include ablative procedures, implanted devices and split brain procedures (Dudek's part not included).
DNA
Double‐strand Breaks and Their Consequences in Bacteria
Authors: Kobayashi Ichizo , Handa Naofumi 
Published: December 2009

Abstract

Deoxyribonucleic acid
(DNA) double‐strand breaks, which are caused by many factors such as chemical treatments, radiations and, often, biological factors, are lethal events in organisms carrying DNA as their genome include bacteria. There are various mechanisms that work, sometimes in collaboration or competition with each other, in the processing of these breaks. These include exonucleolytic degradation, end joining and recombination repair. These may bring about death, restoration or recombinational/mutational changes in the genome. Intragenomic collaboration and conflict between various pathways can be a force in their genome evolution. Recent analyses suggest that DNA double‐strand breaks switch on the programme of cell death in bacteria. DNA double‐strand breakage and its consequences in bacteria may provide a good model system to analyse the dynamic relationship between life, death and evolution. Understanding these processes in bacteria is important in medicine, environmental studies and industrial application.

Key concepts:

DNA double‐strand breakage and its consequences in bacteria may provide a model system to analyse the relationship between life, death and evolution.

DNA double‐strand breakage may switch on programmes of cell death in bacteria.
Neonatal Immunity
Authors: Tregoning John S 
Published: December 2009

Abstract

Both our innate and adaptive immune responses are reduced in function at birth. This leads to an increased risk of infection coinciding with a period of maximum exposure to new pathogens, caused by the move from the sterile environment of the womb to the infectious environment of the world. However, not every new antigen seen is dangerous to the newborn and a balance is required to ensure an appropriate immune response and avoid inflammatory responses to benign antigens. To supplement the period of immune immaturity, the mother transfers passive protection, principally antibody, to the child. Vaccines can be used in early life, but the reduced function of the neonatal immune response reduces the efficacy of vaccines which are otherwise effective in adults, necessitating research on infant‐specific formulations.

Key Concepts:

The neonate immune system is reduced in capacity and can be described as hyporesponsive.

The immune system develops in a programmed series of cell maturation events.

Moving from the controlled, sterile environment of the womb to the outside world has a critical impact on the newborn's immune system.

Reduced pattern recognition by neonatal antigen‐presenting cells leads to the observed hyporesponsive phenotype.

The mother provides some immune protection to the child, especially via antibodies in breast milk.
Cell Membrane Features
Authors: Yeagle Philip L 
Published: December 2009

Abstract

The membranes of living cells support much of the functionality of biology. From the subcellular level of organelles to the supercellular level of cell–cell interactions, membranes provide the structures necessary for biological function and organization. Many of those structural and functional features are common among membranes in bacteria, eukaryotic cells and viruses. The lipid bilayer provides the fundamental architecture and some of the properties common to all biological membranes. Membrane proteins confer a myriad of specific functions expressed by cell membranes. Plasma membranes determine the boundary of the cell and many of the interactions of the cell with its environment. Intracellular membranes compartmentalize cells into different functional units with differing internal compositions. The composition of the compartments is maintained by essential transport functions in concert with permeability control. Signal transduction is supported by membranes. Membrane fusion provides a mechanism for intracellular vesicular transport and enveloped virus entry into cells.

Key concepts:

The hydrophobic effect, which governs the behaviour of hydrocarbons in water, controls the structures formed by membrane lipids and membrane proteins.

Many properties of membranes are conferred by fundamental properties of lipid bilayers that form the basic structure for all biological membranes.

Transmembrane proteins have different organizations of amino acids in their primary sequence such that linear sequences of amino acids are available to transit the lipid bilayer.

Integral membrane proteins have a portion of their mass buried in the lipid bilayer.

Peripheral membrane proteins are much like soluble proteins in structure, but are bound to membranes.

Much cellular function is conferred by cell membranes, including compartmentalization, transport, enzyme activity, intracellular trafficking, enveloped viral entry, signal transduction, endocytosis, phagocytosis, action potentials and RNA processing, to name a few.

Specialized cell membranes have specialized functions for cells.
Phospholipases: Degradation of Phospholipids in Membranes and Emulsions
Authors: Fisher Aron B , Jain Mehendra 
Published: December 2009

Abstract

Phospholipases
are enzymes that degrade phospholipids through hydrolytic cleavage of carboxy‐ and phospho‐diester bonds. The enzymes are classified as

phospholipases A
1

, A
2
, C or D depending on the site of hydrolysis at the sn‐1 or sn‐2 acyl ester bond, at the glycerol phosphate bond or at the glycerol phosphate‐base phosphodiester bond, respectively.

Phospholipases A
2

are secreted as components of snake and insect venoms, mammalian digestive juices and inflammatory exudates. Intracellular
phospholipases
participate in a broad spectrum of important physiological functions and pathophysiological processes through modification of phospholipids and generation of products that are potent regulators and messengers. These enzymes have evolved to hydrolyse phospholipids at an organized lipid–aqueous interface. Secreted

phospholipase A
2

can serve as a prototype for interfacial catalysis.

Key Concepts:

Phospholipases are hydrolytic enzymes that cleave at one of the four potential cleavage sites leading to the classification as phospholipase A
1
, A
2
, C or D.

These enzymes function at the interface with organized membranes and serve as models for interfacial catalysis.

Hydrolytic products of catalysis depending on the specific enzyme and substrate include free fatty acids, lysosphospholipids, diacylglycerol, phosphatidic acid and phosphorylated or free base (e.g. choline, ethanolamine, serine and inositol).

Secreted phospholipase A
2
is an important component of snake and insect venoms, mammalian digestive fluids and inflammatory exudates where it leads to degradation of membranes and emulsified lipids.

Intracellular phospholipases have important roles in intracellular signalling through the generation of precursors of signalling molecules such as arachidonic acid, lysosphospholipids and inositol phosphates.

Intracellular phospholipase A
2
activity generates the lysophospholipid substrate that is necessary for remodelling of cellular phospholipids by the deacylation–reacylation pathway.

Phospholipase activity inhibitors include specific agents that act directly on the enzyme and also agents that nonspecifically act by changing the organization of the interface or interfere with interfacial binding of the protein.
Pseudoautosomal Inheritance
Authors: Ellison Jay W 
Published: December 2009

Abstract

Traits encoded by genes on the X‐ and Y‐chromosomes are generally inherited in a specific manner, referred to as sex‐linked. Females receive alleles from their parent's X‐chromosomes, whereas males receive X‐encoded genes from their mother and Y‐encoded genes from their father. However, a small subset of genes on the X‐ and Y‐chromosomes exhibit a pattern of inheritance that is not sex‐linked. That is, genes on the Y‐chromosome are sometimes passed to daughters, and genes on the X‐chromosome are sometimes passed from fathers to their sons. This is possible because the X‐ and Y‐chromosomes share regions of sequence identity, and these regions undergo recombination during male meiosis. Therefore sequences can be transferred from the X to the Y, and vice versa. The resulting transmission pattern resembles that which is seen for sequences on autosomes, and is referred to as pseudoautosomal inheritance.

Key concepts:

The X‐ and Y‐chromosomes contain regions of sequence identity at the ends of their respective short and long arms.

Recombination takes place in male meiosis between the X and Y within these regions of DNA sequence identity.

Traditional patterns of sex‐linked inheritance are sometimes not observed for alleles in these regions of X–Y sequence identity.

The pattern of inheritance observed for alleles in the X–Y identical regions is referred to as pseudoautosomal inheritance, because it resembles the pattern seen for alleles located on autosomes. The areas of sequence identity on the X and Y are thus referred to as the pseudoautosomal regions.

The likelihood of observing pseudoautosomal inheritance for a given allele depends on its location within the pseudoautosomal region: the more distal a locus is, the more likely it will demonstrate pseudoautosomal inheritance.
Crystallization of Protein–
DNA
Complexes
Authors: Pakotiprapha Danaya , Jeruzalmi David 
Published: December 2009

Abstract

Determination of atomic resolution structures of protein–
deoxyribonucleic acid
(DNA) complexes using X‐ray crystallography requires preparation of high‐quality crystalline specimens. The preparation of such samples remains an empirical endeavour, more art than science. Nonetheless, decades of experience have yielded a large body of practical strategies and techniques towards this end. Such efforts with protein–DNA complexes enjoy special advantages, but also involve control of a larger set of variables. High purity, chemical and conformational, preparations of both macromolecules are important. Crystallogenesis of protein–DNA complexes is favoured by careful choice of the sequence and the terminal bases and/or base pairs of the DNA target. Modern crystallization screens, which encapsulate the accumulated wisdom of prior investigations, serve as an excellent starting point for experimentation.

Key Concepts

An atomic level analysis of a macromolecule by X‐ray crystallography requires preparation of high‐quality crystals of the entity of interest.

Preparation of crystalline specimens requires highly concentrated solutions of the molecules of interest. Success is favoured when high chemical and conformational purity has been achieved.

Extensive experience in preparation of protein crystals can be applied to growth of protein–DNA crystals. Additionally, the length, composition and identity of the termini of the DNA molecule play significant roles in crystallization.

Initial crystallization trials are set up using a concentrated stock of protein–DNA complex of interest with pre‐made formulations that sparsely sample crystallization space. Precipitation and crystal formation under these conditions are used to direct efforts for further crystallization experiments. The experiments are repeated until crystals suitable for X‐ray diffraction are obtained.
History of Ornithology
Authors: Birkhead T R , Charmantier I 
Published: December 2009

AbstractBefore the seventeenth century, interest in birds centred largely on folklore and their symbolic significance. Ray and Willughby's encyclopaedia, theOrnithology of Francis Willughby(1676 and 1678) marked a turning point in the study of birds by rejecting folklore and focussing especially on biology. Following Ray'sWisdom of God(1691), which addressed ultimate causes, the study of birds developed along two separate strands: (i) systematics, nomenclature and faunistics (inspired byOrnithology) and (ii) natural history (inspired byWisdom). The first of these endeavours dominated ornithology for the next 250 years, and were the main focus of the ornithological Unions founded in the 1800s. The two strands were reunited in the 1920s (central Europe) and 1940s (the UK and the USA). After World War II not only the expansion of higher education resulted in a huge increase in both the number of professional ornithologists, but also our knowledge of avian natural history and evolution.Key conceptsThe study of birds began with Aristotle, but stagnated between the first centuryadand the Renaissance.Ornithology became scientific with the abandonment of emblematics in the 1670s.John Ray initiated two strands of ornithology: systematics and natural history (field ornithology) in the late 1600s.Systematic ornithology focussed on the naming and classification of birds, and later, their geographical distribution.The natural history of birds (field ornithology) focussed on behaviour, ecology and ultimate causes.Ornithological encyclopedias were a product of the Renaissance.After the Renaissance ornithology became increasingly specialized.Charles Darwin's concepts of natural and sexual selection in the mid‐late 1800s were important in encouraging scientific interest in birds.The two strands of ornithology, systematics and natural history, were re‐united in the 1920s (Germany) and 1940s (the UK and the USA).The modernization of ornithology during the twentieth century occurred largely as a result of the conceptual unification of evolutionary thinking in the 1940s and the focus on individual selection in the 1970s.
Palaeoecology: Methods
Authors: Terry Rebecca C 
Published: December 2009

Abstract

Paleoecology is based on the documentation of occurrences and abundances of taxa across time and space. Although methodologically similar to the techniques of neontological ecologists, the discipline is distinct in its integration of a deeper time axis into our understanding of the processes shaping the earth's ecological patterns. Taphonomy is the study of the processes by which organic remains become incorporated into the fossil record. Since this record is both incomplete and biased, multiple taphonomic approaches have been developed to quantify the reliability of the ecological information it preserves. As such, a fundamental issue in paleoecology relates to the sampling and counting of individuals. Although the nature of the preserving sediments often exerts the primary control on how data are collected, techniques exist to standardize sampling and counting strategies to maximize our ability to detect ecological patterns and gain insight into the processes shaping both ancient and modern communities.

Key Concepts:

Paleoecologists study ancient organisms and ecosystem dynamics over evolutionary time scales.

Taphonomic studies have shown that the quality of ecological information preserved in the fossil record is high.

The preservation potential of organic remains is a function of depositional environment as well as structural, chemical and behavioural characteristics of an organism.

Sample standardization is an important consideration for paleoecological data collection and analysis.

Biography information: Rebecca C Terry is a paleoecologist and taphonomist with a research focus on small mammal community dynamics through the Holocene.