bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Orbit and Optic Nerves
Authors: Chakeres Donald William , Bourekas Eric C. 
Published: June 2004

AbstractMagnetic Resonance Imaging (MRI) of the orbits and optic nerves has developed into the “gold standard” of imaging modalities for the evaluation of many soft tissue abnormalities of the orbit. Computed tomography (CT) remains the modality of choice for evaluation of the bony structures of the orbit. MRI is also more flexible, allowing for multiplanar imaging that is not possible with CT. This unit presents a basic protocol for imaging of the orbit. An alternate protocol is presented for the case of dedicated high‐resolution surface coil orbital study.
Herniated Intervertebral Disc
Authors: Jinkins J. Randy , Stark David D. 
Published: June 2004

AbstractOne of the most significant impacts of magnetic resonance imaging (MRI) has been its ability to exquisitely depict normal and pathologic anatomy of the spine. This unit presents a basic protocol for conventional fast spin echo imaging of the spine. An alternate protocol is presented for gradient recalled echo acquisitions that may be used in the sagittal and/or transverse planes to clearly distinguish between discs and soft tissue and to clarify the spinal neural foramen in the cervical region. A second alternate protocol is presented for contrast enhanced MRI acquisitions.
Spinal Canal Stenosis
Authors: Jinkins J. Randy , Stark David D. 
Published: June 2004

AbstractThis unit presents a basic protocol for fast spin echo sequences for imaging to diagnose stenosis of the spinal canal. Spinal stenosis is defined generally as a narrowing of one or more of the following: the central canal, foramina, and lateral recesses of the lumbar spine. Specifically, this stenosis can be classified into three types as defined by location: (a) stenosis of the central spinal canal, (b) stenosis of the intervertebral spinal neural foramen or foramina, and (c) stenosis of the lateral recess(es) of the central spinal canal.
Spondylosis Deformans
Authors: Jinkins J. Randy , Stark David D. 
Published: June 2004

AbstractThis unit presents a basic protocol of conventional and fast spin echo acquisition for detecting spondolysis deformans. The margins of the osteophytosis associated with spondylosis deformans are generally well defined utilizing fast spin echo acquisitions. An alternate protocol is presented for gradient recalled echo acquisitions that may be used in the sagittal and/or transverse planes to clearly distinguish between discs and soft tissue, and to clarify the spinal neural foramen in the cervical region.
Spinal Inflammation
Authors: Jinkins J. Randy , Stark David D. 
Published: June 2004

AbstractThis unit presents a basic protocol for conventional and fast spin echo imaging of spine for evaluation of infections involving the CNS. The epidemic of acquired immunodeficiency syndrome (AIDS) and the frequency of CNS infections has been on the rise. An alternate protocol is presented for coronal acquisition that may be helpful to analyze the perispinal tissues for abscess formation.
Extradural Spinal Cord/Cauda Equina Compression
Authors: Jinkins J. Randy , Stark David D. 
Published: June 2004

AbstractClinical signs and symptoms suggesting acute or subacute compression of the spinal cord or cauda equina constitute a medical emergency requiring urgent diagnosis in order to effect appropriate therapy for alleviating the pathologic process responsible for the compressive phenomenon. The purpose of MR imaging in such cases is to determine the level(s), degree, and, if possible, the type of disease process in order to assist in therapeutic planning gauged toward relieving the neurologic compression. This unit presents a basic protocol for conventional and fast spin echo imaging of spine for such cases. Two alternate protocols are presented for cases where it is necessary to distinguish between the spinal cord and the extradural tissue comprising this structure.
Post Surgical Spinal Evaluation
Authors: Jinkins J. Randy , Stark David D. 
Published: June 2004

AbstractOne of the most challenging areas of diagnosis is to be found in acquiring and interpreting medical images in the patient who has undergone lumbosacral surgery for spinal degenerative disease. The section illustrates the features of expected and abnormal postsurgical spinal imaging. These discussions provide the background, practical information, and graphic examples necessary to enable the medical imaging physician to better approach the clinicoradiologic evaluation of the postsurgical patient.
Cardiac Masses
Authors: Lee Vivian S. 
Published: June 2004

AbstractMagnetic Resonance Imaging (MRI) may be indicated in patients who have poor acoustic windows or in whom lesions are incompletely characterized by echocardiography. This unit presents a basic technique for evaluating cardiac masses, with optional contrast‐enhanced sequences for specific indications. The parameters are based on experience on a Siemens 1.5 T Vision or Symphony and should be altered accordingly for different field strengths and machines from different manufacturers.
Aortic Aneurysm and Pseudoaneurysm Assessment
Authors: Contreras Maricela , Amin Rajesh S. , Yucel E. Kent 
Published: June 2004

AbstractAlthough contrast angiography is still considered the “gold standard” for evaluation of the aorta and its major branches, Magnetic Resonance Angiography (MRA) has quickly gained popularity as an imaging tool for the assessment of the entire aorta. MRA serves as an alternative imaging modality that can be utilized in patients with impaired renal function and with allergies to iodinated contrast medium (iodinated contrast medium is required in contrast angiography and computed tomography, CT). The purpose of this unit is to present fundamental MRA techniques useful in the evaluation of the thoracic and abdominal aorta based on experience on a 1.5 T GE LX scanner.
Pulmonary Embolism
Authors: Bis Kostaki G. , Shetty Anil N. 
Published: June 2004

AbstractThere have been a number of approaches taken to image the pulmonary vasculature. This unit presents basic protocols based on black blood spin echo and/or gradient echo techniques for detection of pulmonary embolisms and deep vein thrombosis. Bright blood magnetic resonance angiography (MRA), 2‐D time‐of‐flight (TOF), and 3‐D contrast‐enhanced MRA is also presented for visualizing the entire vascular tree. The parameters provided in this unit are acquired from Siemens 1.5T Vision Scanner. These parameters may need to be altered depending on the field strength and equipment manufacturer.
Deep Vein Thrombosis Detection
Authors: Bis Kostaki G. , Shetty Anil N. 
Published: June 2004

AbstractMagnetic Resonance Angiography (MRA) is a robust and noninvasive technique for evaluating the vascular system with respect to deep venous thrombosis (DVT) of the lower extremities. This unit presents basic protocols for imaging the pelvic and lower extremity veins for evaluating DVT. A protocol is also provided for defining the sequence for imaging the pelvic and lower extremity veins with a stepping table.
Brachial Plexus
Authors: Takahashi Naoki , Narra Vamsidhar 
Published: June 2004

AbstractMRI is the primary imaging modality used to diagnose the cause of brachial plexopathy. This unit presents protocols to diagnose the cause of brachial plexus. The provides the core component of this procedure and an alternate protocol is presented for the case of avulsion injury from trauma. A second alternate protocol is presented for the case where neoplastic involvement of the brachial plexus is suspected or any abnormalities are seen. A third alternate protocol is presented for the cases when the patient has symptoms of thoracic outlet syndrome and vascular compression is suspected.
MRI of the Female Pelvis
Authors: Wilber Kathy , Semelka Richard , Fisher Laurie 
Published: June 2004

AbstractMRI provides an effective means for evaluating the female pelvis. This unit present a basic protocol for imaging the female pelvis. The protocol is designed to evaluate for the presence of fibroids or adenomyosis, uterine anomalies, and endometriosis. This protocol also provides limited evaluation of adnexal disease processes including: identification of ovaries, hemorrhagic ovarian cysts, and dermoid tumors.
Silicone Breast Implants
Authors: Gorczyca David P. 
Published: June 2004

AbstractMagnetic resonance imaging is a powerful noninvasive means by which to study the integrity of silicone breast implants. Silicone has a unique MR frequency and long T1 and T2 relaxation times that allow for several MR sequences to provide excellent diagnostic images. This unit presents a basic protocol for imaging of silicon breast implants.
Rotator Cuff Disease
Authors: Gigena Leopoldo M. , Chung Christine B. , Resnick Donald 
Published: June 2004

AbstractShoulder pain is a common clinical presentation. Though the spectrum of disorders affecting the shoulder is quite diverse, emphasis is often placed on abnormalities of the rotator cuff and glenohumeral joint instability. The rotator cuff plays an important role in both the function and stability of the shoulder. Moreover, its pathology, with early and accurate diagnosis, is amenable to treatment, which can markedly affect patient outcome. This unit presents an MR imaging protocol for evaluation of the glenohumeral joint. Though specific emphasis is placed on the rotator cuff, it can also be used for global assessment of the shoulder.
MR Arthrography of Shoulder
Authors: Chung Christine B. , Gigena Leopoldo M. , Resnick Donald 
Published: June 2004

AbstractThe glenohumeral joint boasts the greatest range of motion of any peripheral joint in the body, but not without cost; it is also the most frequently dislocated joint in the body. Stability of this articulation is limited for two major reasons. The articulating surface of the glenoid is significantly smaller than that of the humeral head, and the joint capsule is redundant and provides little support. This unit presents a basic MR arthrography protocol for evaluation of glenohumeral joint instability.
Bone Stress Injuries
Authors: Bergman Gabrielle , Jones Timothy R. 
Published: June 2004

AbstractThis unit outlines basic MRI protocols for evaluating the most common bone stress injuries including those of the tibia, femoral neck, femoral shaft, metatarsal, and navicular bone. The protocols concentrate on the lower extremity, as the majority of stress injures occur in this region. These protocols were developed using a 1.5 T system (Signa, General Electric Medical Systems). However, the sequences described could be adapted to low‐ or mid‐field scanners using STIR (short tau inversion recovery) sequences to acquire the T2‐weighted images. This technique would thus require longer scan times and lower resolution matrices.
Abnormalities of the Osseous Structures of the Hip and Peri‐Articular Soft Tissues
Authors: Kneeland J. Bruce , Kaut Roth Carolyn , Garrison James , Testa Anthony 
Published: June 2004

AbstractThis unit presents a basic protocol for detection and assessment of a large number of disorders arising in the bones of the hip or the surrounding soft tissues, including osteonecrosis, transient osteopenia, fractures, soft tissue injuries, and tumors. All of these disorders can be readily assessed without the use of a contrast agent. The evaluation of intra‐articular structures, in particular the acetabular labrum, however, is probably best accomplished with the use of the direct injection of a Gd‐chelate contrast agent into the hip joint. The protocol is presented for a 1.5‐Tesla system for evaluation of disease in the region of the hip. Modifications for low‐field (0.23 to 0.3 T) systems are also discussed.
Magnetic Resonance Imaging of the Gastrointestinal Tract
Authors: Low Russell N. 
Published: June 2004

AbstractMRI provides comprehensive information on gastrointestinal diseases, including infectious, inflammatory, and malignant processes. We employ a set protocol incorporating breath‐hold SS RARE imaging combined with gadolinium‐enhanced, fat‐suppressed SPGR imaging in the transverse and coronal planes. Bowel distension is accomplished with inexpensive water‐soluble intraluminal contrast agents.
Short‐TR, Coherent, Gradient Echo Imaging
Authors: Norman Cheng Yu‐Chung , Haacke E. Mark 
Published: June 2004

AbstractWhen a spin system is repeatedly disturbed by a fast repetition of RF pulses, the transverse magnetization after each new RF pulse approaches a steady‐state value which is smaller than the thermal equilibrium value. The spin system takes a finite number of pulses before this steady‐state is reached in a time that depends on both the T1 of the tissue and the flip angle of the RF pulse. The focus of this unit is on understanding the build‐up of the magnetization to steady‐state and the practical implementation of the simplest forms of imaging in the steady‐state. Sequences utilizing a steady‐state approach can be broadly classified as steady‐state coherent (SSC) and steady‐state incoherent (SSI) sequences. The SSC behavior is the subject of this unit.
Contrast
Authors: Celik Azim , Lin Weili 
Published: June 2004

AbstractContrast (Azim Celik, General Electric Company, Milwaukee, Wisconsin and Weili Lin, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina). SNR (signal‐to‐noise ratio) determines the effectiveness of an imaging experiment. However, even the highest SNR does not guarantee the usefulness of an image. An important aim of imaging for diagnostic purposes is to be able to distinguish between diseased and neighboring normal tissues. If the imaging method used does not have a signal‐manipulating mechanism which produces different signals for the diseased and normal tissues, then distinguishing the two tissues is not possible. This unit provides a detailed discussion of the contrast‐producing mechanisms that arise from the signal dependence on a wide variety of tissue parameters.
Contrast Agents
Authors: Celik Azim , Lin Weili 
Published: June 2004

AbstractContrast agents in general are exogeneous substances employed to alter natural tissue contrast. The motivation behind the use of contrast agents in MR imaging is to further enhance contrast between normal and diseased tissue types and indicate functionality of an organ. The focus of this unit is to give to the basic mechanisms of contrast agents in MR without going into their clinical applications.
Diffusion Tensor MR Imaging
Authors: Chenevert Thomas L. , Welsh Robert C. 
Published: June 2004

AbstractThis unit reviews the physical principles and methodologies involved in diffusion‐weighted imaging (DWI) and diffusion tensor imaging (DTI) for clinical applications. Diffusion‐sensitive MRI noninvasively provides insight into processes and microscopic cellular structures that alter molecular water mobility. Formalism to extend the Bloch equation to include effects of random translational motion through field gradients is reviewed. Definition of key acquisition parameters is also reviewed along with common methods to calculate and display tissue diffusion properties in a variety of image formats. Characterization of potential directional‐dependence of diffusion (i.e., anisotropy), such as that which exists in white matter, requires DTI. Diffusion tensor formalism and measurement techniques then reduce the diffusion tensor into standard anisotropy quantities that are summarized along with commonly used methods to depict directional information in an image format.
Large‐Scale Preparation of Plasmid DNA
Authors: Heilig J.S. , Elbing Karen L. , Brent Roger 
Published: June 2004

AbstractAlthough the need for large quantities of plasmid DNA has diminished as techniques for manipulating small quantities of DNA have improved, occasionally large amounts of high‐quality plasmid DNA are desired. This unit describes the preparation of milligram quantities of highly purified plasmid DNA. The first part of the unit describes three methods for preparing crude lysates enriched in plasmid DNA from bacterial cells grown in liquid culture: alkaline lysis, boiling, and Triton lysis. The second part describes four methods for purifying plasmid DNA in such lysates away from contaminating RNA and protein: CsCl/ethidium bromide density gradient centrifugation, polyethylene glycol (PEG) precipitation, anion‐exchange chromatography, and size‐exclusion chromatography.
Introduction to Lambda Phages
Authors: Lech Karen , Brent Roger 
Published: June 2004

AbstractThe biology of lambda‐derived vectors is extremely well understood. This introduction to the biology of lambda and related phages is included to help readers use the lambda vectors that are employed in the manual and to help readers understand new lambda vectors that are being developed. Specific topics include a discussion of lytic growth (i.e., requirements for DNA replication, packaging and lysis) and lysogenic growth (i.e., requirements for lysogenization and induction of a lysogen).
Introduction to Vectors Derived from Filamentous Phages
Authors: Greenstein David , Brent Roger 
Published: June 2004

AbstractMany vectors in current use are derived from filamentous phages. These vectors are used because DNA inserted into them can be recovered in two forms: double‐stranded circles and single‐stranded circles. This overview unit describes the lifecycle of filamentous phages along with the development and use of filamentous phage vectors.
Purification and Concentration of DNA from Aqueous Solutions
Authors: Moore David , Dowhan Dennis 
Published: June 2004

AbstractThis unit presents basic procedures for manipulating solutions of single‐ or double‐stranded DNA through purification and concentration steps. These techniques are useful when proteins or solute molecules need to be removed from aqueous solutions, or when DNA solutions need to be concentrated. The , using phenol extraction and ethanol (or isopropanol) precipitation, is appropriate for purification of DNA from small volumes (<0.4 ml) at concentrations lower than 1 mg/ml. Three support protocols outline methods to buffer the phenol used in extractions, concentrate DNA using butanol, and extract residual organic solvents with ether. An alternative to these methods is nucleic acid purification using glass beads and this is also presented. These protocols may also be used for purifying RNA. The final two alternate protocols are used for concentrating RNA and extracting and precipitating DNA from larger volumes and from dilute solutions, and for removing low‐molecular‐weight oligonucleotides and triphosphates.
Purification of DNA by Anion‐Exchange Chromatography
Authors: Budelier Kim , Schorr Joachim 
Published: June 2004

AbstractColumn chromatography has evolved to provide a rapid and effective alternative to more laborious methods for preparing high‐quality DNA, such as CsCl‐gradient centrifugation. This unit describes the use of a column made of a unique anion‐exchange resin that selectively binds nucleic acids, allowing rapid separation of DNA from contaminating RNA, proteins, carbohydrates, and metabolites. The procedure employs columns supplied by QIAGEN; other preparation methods are available from other suppliers. A crude nucleic acid sample (usually a cleared cell lysate) is applied to the QIAGEN tip under conditions that favor binding. Contaminants in the sample are washed from the column with a moderate‐salt buffer, and DNA is eluted using a high‐salt buffer.
Agarose Gel Electrophoresis
Authors: Voytas Daniel 
Published: June 2004

AbstractAgarose gel electrophoresis is a simple and highly effective method for separating, identifying, and purifying 0.5‐ to 25‐kb DNA fragments. The protocol can be divided into three stages: (1) a gel is prepared with an agarose concentration appropriate for the size of DNA fragments to be separated; (2) the DNA samples are loaded into the sample wells and the gel is run at a voltage and for a time period that will achieve optimal separation; and (3) the gel is stained or, if ethidium bromide has been incorporated into the gel and electrophoresis buffer, visualized directly upon illumination with UV light.
Pulsed‐Field Gel Electrophoresis
Authors: Finney Michael 
Published: June 2004

AbstractDNA molecules longer than 25 kb are poorly resolved by standard agarose gel electrophoresis. These longer molecules can be resolved using several techniques that periodically change the direction of the electric field in the gel. This unit describes the simplest and most generally useful of the pulsed‐field techniques, field inversion electrophoresis, which can be tuned to resolve molecules from ˜10 to 2000 kb (or more with specialized equipment). To resolve molecules beyond the range of field inversion, it is necessary to use some sort of field‐angle alternation electrophoresis such as CHEF (contour‐clamped homogeneous electric field; described in an ). A method is also provided for preparing high‐molecular‐weight DNA samples and size markers embedded in agarose blocks.
Isolation and Purification of Large DNA Restriction Fragments from Agarose Gels
Authors: Moore David , Dowhan Dennis , Chory Joanne , Ribaudo Randall K. 
Published: June 2004

AbstractThis unit describes methods for recovering and purifying DNA restriction fragments from agarose gels. The first protocol describes electroelution of the fragment of interest from standard agarose gels using buffer‐filled dialysis bags, followed by concentration and purification using an Elutip column. This approach can be used effectively for fragments of all sizes from 50 to 20,000 bp. Electrophoresis directly onto NA‐45 paper (second protocol) provides relatively high yields for fragments <2000 bp. Fragments >1000 bp can also be separated on low gelling/melting agarose gels and purified by phenol extraction (third protocol), b‐agarase digestion of the gel (first alternate protocol), or via glass beads extraction (second alternate protocol). Removing linkers from a fragment using a column rather than a gel is described, followed by a method for estimating DNA concentrations in solution.
Southern Blotting
Authors: Brown Terry 
Published: June 2004

AbstractSouthern blotting is the transfer of DNA fragments from an electrophoresis gel to a membrane support (the properties and advantages of the different types of membrane, transfer buffer, and transfer method are discussed in detail), resulting in immobilization of the DNA fragments, so the membrane carries a semipermanent reproduction of the banding pattern of the gel. After immobilization, the DNA can be subjected to hybridization analysis, enabling bands with sequence similarity to a labeled probe to be identified. This unit presents several protocols for DNA transfer to nylon and nitrocellulose membranes, and for calibrating a UV transilluminator to cross‐link the transferred DNA to the membrane.
Dot and Slot Blotting of DNA
Authors: Brown Terry 
Published: June 2004

AbstractDot and slot blotting are simple techniques for immobilizing bulk unfractionated DNA on a nitrocellulose or nylon membrane. Hybridization analysis can then be carried out to determine the relative abundance of target sequences in the blotted DNA preparations. Dot and slot blots differ only in the geometry of the blot, a series of spots giving a hybridization pattern that is amenable to analysis by densitometric scanning. Samples are usually applied to the membrane using a manifold attached to a suction device. The describes such a procedure for dot or slot blotting on an uncharged nylon membrane; annotations to the steps detail the minor modifications that are needed if blotting onto nitrocellulose. The first alternate protocol describes the more major changes required for blotting with a positively charged nylon membrane. A second alternate protocol describes preparation of dot blots by spotting the samples onto the membrane by hand.