bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automation of Focused Ion Beam (FIB) Sample Preparation
Authors: Young R J 
Published: July 2020

Abstract
The use of focused ion beam (FIB) systems is well established as a sample preparation and imaging tool in a wide range of applications, most notably, in the semiconductor and data storage industries, but also within material and biological sciences (Figs. 1-3). The real benefit of the FIB is that the same ion beam that is used for material removal and deposition is also used for imaging the sample, which results in highly precise and localized sample preparation. In addition, the FIB can be used to prepare samples through multiple layers with different material properties, and allows the rest of specimen to be kept intact for further analysis or processing. FIB is most commonly used to prepare samples for the transmission electron microscope (TEM), the scanning electron microscope (SEM), and for the FIB itself. The FIB, which is an imaging tool in its own right, can produce secondary-electron and -ion images and collect secondary ion mass spectrometry (SIMS) data.
Redeposition Effects in TEM Sample Preparation of Feal-Based Metal Matrix Composites using the Focused Ion Beam Miller
Authors: Cairney Julie M , Munroe Paul R 
Published: July 2020

Abstract
The focused ion beam miller (FIB) has been widely used in the semiconductor industry for many years, but only recently has its potential as a tool for materials science been recognised. The FIB uses a highly energetic beam of gallium ions to sputter material such that it can precisely section, as well as image, areas of interest. The FIB can be used to create crosssections, which can be examined in the FIB or in a scanning electron microscope (SEM). Cross sections can be made from delicate samples or samples in which a specific area needs to be viewed, for example to check the thickness of coatings or for failure analysis.
The FIB may also be used to prepare transmission electron microscope (TEM) specimens [1]. Extremely site-specific thin areas may be prepared with high positional accuracy from heterogeneous samples such as composites or layered structures.
Site Specific TEM Analysis of Micrometer-Sized Particles with the FIB Lift-Out Technique
Authors: Lomness J K , Giannuzzi L A , Hampto M D 
Published: July 2020

Abstract
The focused ion beam (FIB) instrument offers an efficient and reproducible approach for obtaining electron transparent membranes of uniform thickness for TEM analysis. Thus, the use of the FIB to investigate numerous types of materials has grown tremendously recently. Prenitzer et al. demonstrated the ability to acquire TEM specimens from individual Zn powder particles using the FIB lift-out (LO) specimen preparation technique. The 10 μm × 100 μm Zn powders particles were larger than the 5 μrn x 20 μm FIB LO specimen and therefore the LO technique could be directly applied to an individual powder particle. This paper will discuss a novel approach for the preparation of site specific micrometer-sized particles for TEM analysis using the FIB LO technique. The uniqueness of the technique described herein is that site specific TEM LO specimens may be obtained from regions which are smaller than the conventional dimensions of the LO specimen.
FIB Techniques for Analysis of Metallurgical Specimens
Authors: Phaneuf Michael W , Li Jian 
Published: July 2020

Abstract
Focused ion beam (FIB) microscopes, the use of which is well established in the semiconductor industry, are rapidly gaining attention in the field of materials science, both as a tool for producing site specific, parallel sided TEM specimens and as a stand alone specimen preparation and imaging tool.
Both FIB secondary ion images (FIB SII) and FIB secondary electron images (FIB SEI) contain novel crystallographic and chemical information. The ability to see “orientation contrast” in FIB SEI and to a lesser extent SII is well known for cubic materials and more recently stress-free FIB sectioning combined with FIB imaging have been shown to reveal evidence of plastic deformation in metallic specimens. Particularly in hexagonal metals, FIB orientation contrast is sometimes reduced or eliminated by the FIB sectioning process. We have successfully employed FIB gas assisted etching during FIB sectioning using XeF2 for zirconium alloys and Cl2 for zinc coatings on steels to retain orientation contrast during subsequent imaging.
Assessment of Deformation using the Focused Ion Beam Technique
Authors: Burke MG , Duda PT , Botton G , Phaneuf M W 
Published: July 2020

Abstract
Focused Ion Beam (FIB) micromachining techniques have gained significant attention over the past few years as a promising method for the preparation of a variety of metallic and nonmetallic materials for subsequent characterization using transmission electron microscopy (TEM) The advantage of the FIB in terms of site specificity and speed for the preparation of uniform electron transparent sections has opened a wide range of potential applications in materials characterization. The ability to image the sample in the FIB can also provide important microstructural data for materials analysis. In this study, both conventionally electropolished and FIB-ed specimens were prepared in order to characterize the microstructure of a commercially-produced tube of Alloy 600 (approximately Ni-15 Cr-10 Fe- 0.05 C). The electropolished samples were prepared using a solution of 20% HClO4 - 80% CH3OH at ∼-40°C. The FIB sections were obtained from a cross-section of the tube that had been mechanically thinned to ∼100 μm. The section was thinned in a Micrion 2500 FIB system with a Ga ion beam at 50 kV accelerating voltage.
A Stress Relief Method to Control Warping of Focused Ion Beam Prepared Membranes for Transmission Electron Microscopy
Authors: Rossie BB , Stevie FA , Shofner TL , Brown SR , Irwin RB 
Published: July 2020

Abstract
The continued decrease in microelectronic feature dimensions has led to a reliance on the focused ion beam (FIB) for site-specific transmission electron microscopy (TEM) specimen preparation. To maximize the capabilities of the FIB, methods must be developed to consistently produce specimens thin enough to generate TEM lattice images. The limiting factor in producing quality TEM specimens by either the traditional or lift-out method is the final thickness of the specimen.
The FIB is used to prepare TEM specimens by removing the bulk material that surrounds a desired feature by sputtering with a focused gallium ion beam. Successively lower beam currents are used to sputter away material until an electron transparent membrane (-0.2 μm) containing the desired feature remains. For a 300 keV TEM, lattice imaging of silicon requires additional membrane thinning to less than 0.05 μm.
The loss of rigidity during the thinning process makes the membrane highly prone to deformation due to residual stresses, linear expansion, and ion beam interaction.
Calibration Method for Elemental Quantification
Authors: Vartuli C B , Stevie F A , Giannuzzi L A , Shofner T L , Purcell B M , Irwin R B , McKinley JM , Wesson R J 
Published: July 2020

Abstract
Energy Dispersive Spectrometry (EDS) is generally calibrated for quantification using elemental standards. This can introduce errors when quantifying non-elemental samples and does not provide an accurate detection limit. In addition, variations between analysis tools can lead to values that differ considerably, especially for trace elements. By creating a standard with an exact trace composition, many of the errors inherent in EDS quantification measurements can be eliminated.
The standards are created by high dose ion implantation. For ions implanted into silicon, a dose of 1E16 cm-2 results in a peak concentration of approximately 1E21 cm-3 or 2% atomic. The exact concentration can be determined using other methods, such as Rutherford Backscattering Spectrometry (RBS) or Secondary Ion Mass Spectrometry (SIMS). For this study, SIMS analyses were made using a CAMECA IMS-6f magnetic sector. Measurement protocols were used that were developed for high concentration measurements, such as B and P in borophosphosilicate glass (BPSG).
Matrix Protein Structural Analysis of Brain Aneurysms by Polarizing Microscopy
Authors: Canham Peter B , Finlay Helen M , Humphrey Jay D 
Published: July 2020

Abstract
The wall of saccular brain aneurysms, lesions that develop at the fork regions of human brain arteries, is a layered multidirectional fabric of fibrous collagen. The wall tissue has the mechanical features of high elastic stiffness and a low tensile strength compared to adjacent arteries. Arterial blood pressure within the sac of an aneurysm stresses the wall in all tangential directions; thus an area of mechanical weakness may be characterized by an area lacking fibre strength, or an area with inadequately aligned fibres.
The collagen fibres of the wall are birefringent, with many fibre types, similar to wound healing skin (types I, III, IV, V, VI) The known correlation between fibre birefringence and tissue strength for dermal wound healing3 provided the opportunity in this research to calculate strength maps to compare one lesion from another, and to make regional comparisons around a single lesion.
Blowing Up the Stiff Balloon: X-Ray Microtomography Reveals Decrease in Arterial Distensibility in Pulmonary Hypertension
Authors: Johnson Roger H , Karau Kelly L , Molthen Robert C , Haworth Steven T , Dawson Christopher A 
Published: July 2020

Abstract
We are developing nondestructive and non-traumatic imaging methods to quantitatively assess structural and mechanical properties of vascular trees and other complex biological systems. We are applying these methods to studies of vascular remodeling in rodent models of disease. Quantitative vascular tree morphometry has, in the past, been carried out using corrosion casting methods which supply valuable information, but are destructive and tend to be tedious, in particular with regard to associating vessel segment measurements accurately with their positions in the intact tree hierarchy. One of our goals is to refine imaging methods capable of quantifying mechanical, as well as anatomical properties, by virtue of their ability to rapidly acquire multiple image volumes of the same structure under various conditions, all in a nearphysiological state.
Using the micro-CT scanner shown in Figure 1, consisting of a microfocal x-ray tube, specimen stage and image intensifier coupled to a 10242, 12-bit CCD camera, we acquire magnified (3-9X), transmitted x-ray projections of contrast enhanced, excised rat lungs or lung lobes.
Structural Studies of Fibrinolysis: How to Disassemble a Clot
Authors: Weisel John W , Veklich Yuri , Collet Jean-Philippe 
Published: July 2020

Abstract
Fibrin clot formation is necessary for maintaining the integrity of the vasculature via the physiological processes of hemostasis and wound healing and is also involved in pathological processes, such as thrombosis and atherosclerosis. Fibrinolysis, or the dissolution of the clot, is necessary to remove clots so that they do not become obstructive. There must be a dynamic balance between clot formation and fibrinolysis to prevent either bleeding or thrombosis. Although the biochemical process of fibrinolysis is well known, less has been known about the physical process of lysis. In these studies, the surface of digested clots were examined by scanning electron microscopy, the products released were visualized by transmission electron microscopy and the process of lysis was followed in real time by confocal microscopy.
Fibrin is degraded by the fibrinolytic system, in which a plasminogen activator converts plasminogen to plasmin, a serine protease that cleaves specific bonds in fibrin leading to solubilization.
Microvenous Valvular Mapping in the Human Lower Extremity. Valvular Density Alone Cannot Account for Sites of Chronic Venous Stasis and Ulceration.
Authors: Aharinejad S , Nedwed S , Michlits W , Dunn RM , Nourani F , Abraham D , Vernadakis A , Marks SC 
Published: July 2020

Abstract
In the leg venous valves isolate the blood into short columns and thus relieve the vessel wall from the gravitational force of blood columns that would otherwise be several feet in length. Class 6 chronic venous insufficiency is associated with abnormal venous hemodynamics and associated tissue-related abnormalities termed lipodermatosclerosis, accompanied by ulceration. Ingenious surgical techniques have focused on correction of the abnormal hemodynamics by repair, reconstruction, or transplantation of venous valves to the deep venous system of the lower extremity with varying success rates. We have applied free scapular fasciocutaneous flaps to successfully reconstruct recalcitrant grade 6 venous insufficiency ulcers in the lower extremity. We have noticed such ulcers frequently in medial malleolar, lateral malleolar or dorsum pedis but never in the region of the gastrocnemius or peroneus muscles. This fact prompted us to examine the microvenous valvular anatomy in segments of human leg.
Microarchitecture of the Terminal Afferent Vessels in the Rat Liver. A SEM Study of Vascular Corrosion Casts.
Authors: Spornitz Udo M , Bartuskova Irena , Morson Gianni 
Published: July 2020

Abstract
The blood supply of the liver is of dual origin, namely the hepatic artery and the portal vein. The physiological implications of this dual blood supply are well understood (1), the morphological details of the terminal afferent vessels, however, still need to be further investigated. Particularly the various possible types of entry of the terminal afferent vessels into the sinusoids are not yet fully understood. With the aid of a newly developed method, i.e. the combination of detection of a marker substance (with the aid of EDX) and scanning electron microscopy, many of the morphological parameters have been elucidated (2). This new method involves the injection of the liver from two sides (arterial and portal vessels) with methacrylate or Mercox containing either of two different marker substances, both of which can be detected with the aid of an EDX detector. Thus the terminal afferent vessels can easily be told apart (2, 3).
Ultrastructure of a Benign Thymoma
Authors: Siew S 
Published: July 2020

Abstract
A thymoma is a tumor which arises from the epithelial cells of the thymus. Despite the progressive involution of the thymus post-puberty, the peak incidence of thymomas is in adults, after the age of 40. Owing to the normal anatomic location of the thymus in the antero-superior mediastinum, thymomas account for 20-30% of masses in that situation, and, they have to be differentiated from other neoplasms which may be found in the anterior mediastinam, such as, lymphocytic lymphoma, Hodgkin's disease, Germinoma (seminoma), Thymic carcinoid tumor, oat cell carcinoma and parathyroid adenoma.
Embryologically, the thymus develops as an outgrowth of epithelial cells from the third pharyngeal pouches in association with the inferior parathyroid glands and migrates from the neck to the mediastinum. In embryonic life, blood borne stem cells from the yolk sac are seeded into the thymus which becomes the primary lymphoid organ. Within the thymus, the primitive stem cells differentiate into lymphocytes, which proliferate and differentiate into T-lymphocytes (thymus-dependent, thymocytes). Some of the T-lymphocytes are released into the blood stream and populate peripheral lymphoid organs. They constitute 60-70% of circulating lymphocytes.
Immunogold Labeling for Igg, Immunoglobulin Light Chains and P-Component in Fibrillary and Immunotactoid Glomerular Nephritis
Authors: Hearn S , Walton J , Moussa M , Rieckenberg Mark , Hutcheson K 
Published: July 2020

Abstract
Fibrillary and immunotactoid glomerulonephritis (FGN & IGN) are uncommon glomerular diseases, diagnosed by electron microscopic identification of fibril deposits which are negative by the Congo red stain. Micro-fibrils are similar to normal structures in glomerular basement membrane and matrix and they can be missed by EM. Pathogenesis of these glomerulopathies is unclear but they are not believed to be associated with monoclonal gammopathies as in AL amyloidosis. Immunofluorescense (IF) on FGN indicates the fibrils typically are positive for IgG and both immunoglobulin light chains while IGN fibrils are light chain monoclonal. We did immunogold labeling on four cases of FIGN in to improve the diagnosis of these diseases and investigate fibril protein composition.
Renal biopsies from four patients consisted of one IGN and 3 FGN. Tests included frozen section IF (IgG, IgA, IgM, C3), paraffin section histology (Congo Red) and conventional EM (osmium fixation and epoxy embedding).
Predictive Value of P53-Positive Cells for Esophageal Cancer Micrometastasis
Authors: Bailey GW , McKernan S , Price RL , Walck SD , Charest P-M , Gauvin R , Wei C , Mao Y , Krasna M 
Published: July 2020

Abstract
Esophageal cancer is the fastest growing malignancy of any tumor in the United States with an increased incidence of adenocarcinoma across all socioeconomic boundaries. The stage and the residual tumor classification are the most important prognostic factors. However, patients with similar stage of disease show a marked difference in survival. Therefore, there are needs to identify new molecular prognostic markers that may help to better assess the survival probability.
The recently introduced genetic diagnosis of cancer micrometastasis is quite attractive because of its high detection sensitivity. Not infrequently, however, there are marked discrepancies between genetic and conventional histologic diagnoses, especially concerning lymph nodes from carcinoma patients. Alterations in the p53 tumor suppressor gene are the most frequent genetic changes found in breast and lung cancer. The p53 gene functions as a negative regulator of cell growth. Alterations in the gene lead to loss of its usual negative growth regulation and more rapid cell proliferation.
Increase Transforming Growth Factor-Beta and its Receptors in Human Renal Tissue with Rejection
Authors: Song H , Papadimitriou J , Drachenberg C , Weir M R , Wei C 
Published: July 2020

Abstract
Transforming growth factor-bate (TGF-β) is a growth-relating peptide that has been shown to enhance collagen production in vivo and in vitro. TGF-β isoforms include TGF-β 1, β2 and β3. TGF-β receptors subtypes include type I (TGFβRI) and type II (TGFβRII) receptors. Overproduction of TGF-β can lead to real damage.
Renal graft rejection is major problem after kidney transplantation with severe renal damage. We hypothesized that renal tissue level of TGF-β may increase in renal rejection after kidney transplantation. Therefore, the current study was designed to determine the TGF-β 1 isoform and its receptor TGFβRI in human renal tissue with rejection by immunohistochemical staining (IHCS) and compared with normal human renal tissue. The results of IHCS was evaluated by IHCS staining density scores (0, no staining; 1, minimal staining; 2, mild staining; 3, moderate staining; and 4, strong staining). The positive staining area (+%) in entire section was also determined. The sections treated with preabsorbed blocking peptide or nonimmune rabbit serum demonstrated no immunoperoxidase activity.
Increasing Nitric Oxide Synthase in Human Renal Graft Rejection after Kidney Transplantation
Authors: Seta K , Papadimitriou J , Drachenberg C , Weir M R , Wei C 
Published: July 2020

Abstract
Nitric oxide (NO) is a potent endothelial-drived vasorelaxing factor and may involved in salt sensitive hypertension and renal damage. Nitric oxide is produced from L-arginine by activation of nitric oxide synthase (NOS). Three NOS has been identified which are brain NOS (bNOS), inducible NOS (iNOS) and endothelial NOS (eNOS). On the other hand, renal graft rejection is major problem after kidney transplantation with severe renal damage and renal vasoconstriction. While NOS has been reported localized in human and animal kidney, the status of three NOS in human renal tissue with rejection remains poorly defined. Therefore, the present study was designed to determine the expression of bNOS, iNOS and eNOS by immunohistochemical staining (IHCS) in human renal tissue with rejection and compared with that in normal human renal tissue.
Human renal biopsy (n=5) were obtained after kidney transplantation with mild and moderate renal rejection. Normal kidney biopsy was obtained during nephrectomy.
The Effects of Cyclosporin-A on Human Vascular Smooth Muscle Cells Apoptosis
Authors: Kinjo M , McLaughlin J S , Wei. C 
Published: July 2020

Abstract
Cyclosporine-A is the one of the most effective immunosuppressant drug in organ transplantation. However, cyclosporine-A has a potent cytotoxic effect. Cellular apoptosis is being suggested may contribute to the cyclosporine A-mediated cytotoxic action. To date, regarding the effects of cyclosporine-A on apoptosis and apoptosis-related genes expression in vascular smooth muscle cells remain unclear. Therefore, the current study was designed to investigate the actions of cyclosporine-A on apoptosis and p53 expression in human vascular smooth muscle cells.
Human saphenous vein was obtained from coronary artery bypass surgery (n=5). After saphenous vein removed, the tissue was minced and incubated in the special tissue culture system for 24 hours in the absence or presence of cyclosporine-A (10-6M). To detect the DNA fragmentation, in situ terminal deoxymucleotidyl transferase dUTP nick end labeling (TUNEL) was performed. The p53 level in human vascular smooth muscle cells was determined by immunohistochemical staining (IHCS). An average of 1000 nuclei was analyzed for both TUNEL and p53 EHCS studies.
Renal Manifestations of Hepatitis C Virus Infection: Extremity at a Distance
Authors: Howell D N , Miller S E 
Published: July 2020

Abstract
Hepatitis C virus (HCV) is an RNA virus of the family Flaviviridae. In the decade since its identification,1 it has emerged as a leading cause of chronic hepatitis and cirrhosis. Easily transmissible by parenteral and sexual routes, fastidious in culture, highly limited in host range, and difficult to detect by most microscopic and immunohistochemical methods, HCV qualifies as an extreme pathogen. Another form of extremity exhibited by HCV is the bewildering array of renal disorders that occur in the setting of HCV-induced hepatitis.
Several different mechanisms may underlie the development of renal disease in patients infected with HCV. Immune complexes of anti-HCV antibodies and viral components, frequently bound to anti-immunoglobulin rheumatoid factors, can form in the circulation and be deposited in the kidney. HCV has also been shown to induce immune responses to a variety of autoantigens, some of which are expressed in the kidney. Hepatic injury caused by HCV may produce downstream effects on other organs, including the kidney.
Multiple Microscopic Approaches to the Study of Oral Bacterial Biofilms.
Authors: Palmer Robert J , Kazmerzak Karen , Wu Rosemary , Kolenbrander Paul E 
Published: July 2020

Abstract
Biofilms are collections of microorganisms at interfaces. Because of the high proportion of interfacial regions in the natural environment, biofilms are likely to be the repository for most of the world's microbial biomass. The close proximity of organisms within the biofilm presents the opportunity for intra- and interspecies signaling on a physical level through direct contact of organisms with one another, and on a metabolic level through production/excretion of intermediary molecules of metabolism and of specific cell signaling molecules. One of the best studied biofilms is dental plaque, which has been investigated from a microscopy standpoint since the time of van Loewenhouk and from a classical bacteriological standpoint since the relatively recent (20th century) development of anaerobic culture techniques. Through the even more recent (the last decade) application of molecular methods, it has been shown that perhaps half of all bacteria present in plaque are culturable and, at present, this consists of some 500 species.