TEI in LMNL: Implications for Modeling

LMNL (the Layered Markup and Annotation Language) is a small, if ambitious, research project in text encoding. Unlike XML, LMNL markup does not represent document components or constituents (as “elements”) within a structure, but rather simply labels ranges of text within the document for identification and processing. Avoiding choices between structures, any and all structures can be elucidated; this reveals not only new capabilities for the digital processing of humanities texts—simultaneously building on TEI and extending it to new uses—but also something about the way our tools condition our view of our objects of study. This paper presents LMNL and suggests some of its strengths in the context of TEI

The time-dependent rearrangement of the epithelial basement membrane in human skin wounds

In 62 human skin wounds (surgical wounds, stab wounds and lacerations after surgical treatment) we analyzed the immunohistochemical localization of collagen IV in the epithelial basement membrane. In 27 of these wounds the distribution of collagen VII, which represents a specific component of the basement membrane of stratified epithelia, was also analyzed. We were able to demonstrate a virtually identical co-distribution of both collagen IV and VII in the wound area with no significant time-dependent differences in the appearance of both collagen types. Fragments of the epithelial basement membrane could be detected in the wound area from as early as 4 days after wounding and after 8 days a complete restitution of the epithelial basement membrane was observed. In all cases with a wound age of more than 21 days the basement membrane was completely reformed over the former lesional area. The period between 8 and 21 days after wounding was characterized by a wide variability ranging from complete restitution to deposition of basement membrane fragments or total lack of the epidermal basement membrane

Mathematical modeling of the metastatic process

Mathematical modeling in cancer has been growing in popularity and impact since its inception in 1932. The first theoretical mathematical modeling in cancer research was focused on understanding tumor growth laws and has grown to include the competition between healthy and normal tissue, carcinogenesis, therapy and metastasis. It is the latter topic, metastasis, on which we will focus this short review, specifically discussing various computational and mathematical models of different portions of the metastatic process, including: the emergence of the metastatic phenotype, the timing and size distribution of metastases, the factors that influence the dormancy of micrometastases and patterns of spread from a given primary tumor.Comment: 24 pages, 6 figures, Revie

Thermal Transition Properties of Hoki (Macruronus novaezelandiae) and Ling (Genypterus blacodes) Skin Collagens: Implications for Processing

Hoki (Macruronus novaezelandiae) and ling (Genypterus blacodes) are cold-water fish caught in New Zealand waters. Their skins are a major component of the post-processing waste stream. Valuable products could be developed from the skins, as they are primarily composed of collagen, which has many commercial applications. We prepared acid soluble collagens (ASC) from hoki and ling skins, and analyzed their thermal denaturation properties using a Rapid Visco™ Analyzer. At slower heating rates the denaturation temperature (TD) of hoki and ling collagens decreased. This result is consistent with the model of irreversible rate kinetics for the denaturation of collagen. We determined the effects of solvents that disrupt hydrogen bonding on ASC stability. Increasing concentrations of urea from 0.1 M to 1.0 M and acetic acid from 0.1 M to 0.5 M decreased TD. This resulted from the effects of these reagents on the hydrogen bonds that stabilize the collagen triple helix

Banding pattern and fibrillogenesis of ceratotrichia in shark fins

Study by light microscopy, scanning electron microscopy and transmission electron microscopy of the distribution, structure and growth of ceratotrichia in the anterodorsal fin of a lemon shark, Negaprion brevirostris , and in the tailfin of a nurse shark, Ginglymostoma cirratum , shows that the ceratotrichia are large collagen fibers which develop in bilateral rows within the dermis. Surrounding each ceratotrichium is a layer of peritrichial fibroblasts containing secretory vesicles, which appear to be the source of matrix constituents. The peritrichial matrix contains bundles of fine, unbanded collagen fibrils as well as larger, banded fibrils like those in the matrix of ordinary connective tissue. The structure of the peritrichial fibroblasts and of the subjacent peritrichial matrix is the same as that of the fibroblasts and matrix of the conventional connective tissue throughout the fin dermis. Ceratotrichia grow by apposition of collagen fibrils from the peritrichial matrix. In cross section the ceratotrichia appear layered, evidently because of close packing of constituent fibrils in lamellae. In longitudinal section the ceratotrichia exhibit the conventional a, b, c, d and e bands of collagen. The e bands of show two distinct subbands, and the b bands three subbands. Periodicity of the banding pattern is approximately 640 Å like that of conventional collagen fibrils.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/50267/1/1051540202_ftp.pd

Nanoscale structure of type I collagen fibrils: Quantitative measurement of D‐spacing

This article details a quantitative method to measure the D‐periodic spacing of type I collagen fibrils using atomic force microscopy coupled with analysis using a two‐dimensional fast fourier transform approach. Instrument calibration, data sampling and data analysis are discussed and comparisons of the data to the complementary methods of electron microscopy and X‐ray scattering are made. Examples of the application of this new approach to the analysis of type I collagen morphology in disease models of estrogen depletion and osteogenesis imperfecta (OI) are provided. We demonstrate that it is the D‐spacing distribution, not the D‐spacing mean, that showed statistically significant differences in estrogen depletion associated with early stage osteoporosis and OI. The ability to quantitatively characterize nanoscale morphological features of type I collagen fibrils will provide important structural information regarding type I collagen in many research areas, including tissue aging and disease, tissue engineering, and gene knockout studies. Furthermore, we also envision potential clinical applications including evaluation of tissue collagen integrity under the impact of diseases or drug treatments. The distribution of Type I collagen fibril D‐spacing provides important morphological information regarding Type I collagen in diseases such as early stages of osteoporosis and osteogenesis Imperfecta . In this article, the authors use Atomic Force Microscopy (AFM) imaging combined with two Dimensional Fast Fourier Transform (2D FFT) analysis to quantitatively assess Type I collagen fibril D‐spacing. This methodology allows imaging and characterization of Type I collagen constituted biological tissues, hydrogels, and other collagen based biomaterials.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94732/1/117_ftp.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/94732/2/biot_201200174_sm_suppinfo.pd

Bioinformatics in crosslinking chemistry of collagen with selective cross linkers

<p>Abstract</p> <p>Background</p> <p>Identifying the molecular interactions using bioinformatics tools before venturing into wet lab studies saves the energy and time considerably. The present study summarizes, molecular interactions and binding energy calculations made for major structural protein, collagen of Type I and Type III with the chosen cross-linkers, namely, coenzyme Q₁₀, dopaquinone, embelin, embelin complex-1 & 2, idebenone, 5-O-methyl embelin, potassium embelate and vilangin.</p> <p>Results</p> <p>Molecular descriptive analyses suggest, dopaquinone, embelin, idebenone, 5-O-methyl embelin, and potassium embelate display nil violations. And results of docking analyses revealed, best affinity for Type I (- 4.74 kcal/mol) and type III (-4.94 kcal/mol) collagen was with dopaquinone.</p> <p>Conclusions</p> <p>Among the selected cross-linkers, dopaquinone, embelin, potassium embelate and 5-O-methyl embelin were the suitable cross-linkers for both Type I and Type III collagen and stabilizes the collagen at the expected level.</p

The distribution of structures in evolving protein populations

Proteins exhibit a nonuniform distribution of structures. A number of models have been advanced to explain this observation by considering the distribution of designabilities, that is, the fraction of all sequences that could successfully fold into any particular structure. It has been postulated that more designable structures should be more common, although the exact nature of this relationship has not been addressed. We find that the nonuniform distribution of protein structures found in nature can be explained by the interplay of evolution and population dynamics with the designability distribution. The relative frequency of different structures has a greater-than-linear dependence on designability, making the distribution of observed protein structures more uneven than the distribution of designabilities. The distribution of structures is also affected by additional factors such as the topology of the sequence space and the similarity of other structures. © 2000 John Wiley & Sons, Inc. Biopoly 53: 1–8, 2000Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34324/1/1_ftp.pd

The Circular Dichroism Spectrum and Structure of Unordered Polypeptides and Proteins

The evidence bearing on our revision of the early assignment of the circular dichroism spectrum of the maximally unordered polypeptide chain is reviewed. Our initial, as well as subsequent, studies are believed to support the proposed revision in assignment. This conclusion need not be modified in the light of recent work on water‐soluble, non‐ionizable polymers.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/101811/1/197400018_ftp.pd