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"HUESOS"
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Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences
2018
Background
The study of ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA preserved in highly degraded, ancient material. However, such material contains large amounts of microbial contamination in addition to DNA fragments from the ancient organism. The resulting mixture of sequences constitutes a challenge for computational analysis, since microbial sequences are hard to distinguish from the ancient sequences of interest, especially when they are short.
Results
Here, we develop a method to quantify spurious alignments based on the presence or absence of rare variants. We find that spurious alignments are enriched for mismatches and insertion/deletion differences and lack substitution patterns typical of ancient DNA. The impact of spurious alignments can be reduced by filtering on these features and by imposing a sample-specific minimum length cutoff. We apply this approach to sequences from four ~ 430,000-year-old Sima de los Huesos hominin remains, which contain particularly short DNA fragments, and increase the amount of usable sequence data by 17–150%. This allows us to place a third specimen from the site on the Neandertal lineage.
Conclusions
Our method maximizes the sequence data amenable to genetic analysis from highly degraded ancient material and avoids pitfalls that are associated with the analysis of ultra-short DNA sequences.
Journal Article
Bone Marrow Pathology
2019
Bone Marrow Pathology has been extensively revised to reflect the significant advances which have occurred in the application of cytogenetics and in particular, molecular genetics in the diagnosis, classification and understanding of haematological disorders.
Bones and cartilage : developmental and evolutionary skeletal biology
2005
Bones and Cartilage provides the most in-depth review ever assembled on the topic. It examines the function, development and evolution of bone and cartilage as tissues, organs and skeletal systems. It describes how bone and cartilage is developed in embryos and are maintained in adults, how bone reappears when we break a leg, or even regenerates when a newt grows a new limb, or a lizard a tail. This book also looks at the molecules and cells that make bones and cartilages and how they differ in various parts of the body and across species. It answers such questions as \"Is bone always bone?\" \"Do bones that develop indirectly by replacing other tissues, such as marrow, tendons or ligaments, differ from one another?\" \"Is fish bone the same as human bone?\" \"Can sharks even make bone?\" and many more. * Complete coverage of every aspect of bone and cartilage* Full of interesting and unusual facts* The only book available that integrates development and evolution of the skeleton* Treats all levels from molecular to clinical, embryos to evolution* Written in a lively, accessible style* Extensively illustrated and referenced* Integrates analysis of differentiation, growth and patterning* Covers all the vertebrates as well as invertebrate cartilages* Identifies the stem cells in embryos and adults that can make skeletal tissues
Development of an easy-to-assemble external fixation system for bone transport
by
GarcIa Alvarez, Jose Jaime
,
Machado Caicedo, Andres
,
Casanova Garcia, Fernando
in
alargamiento de huesos
,
bone elongation
,
bone fractures
2019
We developed a monolateral external fixation system for bone elongation easier to assemble than commercial systems since the clamps can be laterally assembled to the rail in contrast to the commercial systems where the clamps can only be assembled from the ends. The system is formed by clamps, screws, and a rail. The rail is composed of two carbon fiber circular rods of ½” diameter and 42-cm length. The clamps can slide with respect to the rail to allow bone distraction or may be fixed to the rail by using a wedge and a screw. The prototype was mechanically evaluated under the ASTM F1541 standard. The stiffness in axial, Medio Lateral bending (ML), Antero Posterior bending (AP), and flexo-torsional load were 117 N/mm, 46 N/mm, 8.7 N/mm, and 5.8 N-mm/°, respectively, which are on the range of stiffness of commercial systems.
Journal Article
Angiosarcoma óseo en el humero de un paciente pediátrico, un reto diagnóstico: reporte de caso
2022
Resumen El angiosarcoma óseo es una neoplasia maligna rara, agresiva y de mal pronóstico, que es inusual en niños. Esta entidad afecta preferentemente a los huesos tubulares y se puede presentar como lesión solitaria o multicéntrica. Presentamos el caso de una niña de 7 años, sin antecedentes médico quirúrgicos, quien consultó al Instituto Nacional de Cancerología - Colombia, por presentar una lesión tumoral que comprometía la totalidad del húmero, destruyéndolo y deformando el brazo. Para orientar el diagnóstico de la lesión, se realizó un estudio histopatológico minucioso y marcadores de inmunohistoquímica, estos sugirieren una neoplasia vascular maligna. Por el extenso compromiso tumoral, la única opción terapéutica, fue la desarticulación escapulotorácica de la extremidad, seguida de manejo adyuvante con protocolo de quimioterapia. Durante los ciclos de quimioterapia, la paciente presentó lesiones metastásicas en pulmón, que fueron resecadas. En el momento, se encuentra sin lesiones tumorales y en seguimiento estricto.
Journal Article
Ultra-Short Pulse Laser Cleaning of Contaminated Pleistocene Bone: A Comprehensive Study on the Influence of Pulse Duration and Wavelength
by
Miguel Carretero, José
,
Schiavon, Nick
,
de la Fuente, Germán F.
in
Ablation
,
Antiquities
,
archaeological bone
2023
The impact of wavelength and pulse duration in laser cleaning of hard blackish contaminants crust from archaeologically significant Pleistocene bone is investigated in this research. The objective is to determine the practical cleaning procedures and identify adequate laser parameters for cleaning archaeological bone from Sima de los Huesos (Spain) based on conservation and restoration perspectives. Bone surface cleaning was performed utilizing two Q-switched Nd:YAG lasers: sub-nanosecond pulsed lasers with emission wavelengths at 355 nm and 1064 nm, respectively, and a Yb:KGW femtosecond pulsed laser with an emission wavelength in the third harmonic at 343 nm. In all experiments, the laser beam scanning mode was applied to measure cleaning efficiency in removing contaminants and degradation products while assessing the underlying substrate surface damage. Several properties, including wavelength-dependent absorption, pulse repetition rate, and thermal properties of the material, are analyzed when evaluating the ability of these lasers to boost the cleaning efficiency of the deteriorated bone surface. Bone surface morphology and composition were studied and compared before and after laser irradiation, using Optical Microscopy, Scanning Electron Microscopy with Energy Dispersive X-ray Spectrometry (SEM-EDS), Fourier Transform Infrared Spectroscopy (FTIR), and X-ray Photoelectron Spectroscopy (XPS) characterization methods. The results indicate that 238-femtosecond UV laser irradiation with 2.37 TWcm−2 is significantly safer and more efficient toward surface contaminant desorption than sub-nanosecond laser irradiation. The results herein presented suggest that these types of fs lasers may be considered for realistic laser conservation of valuable historic and archaeological museum artifacts.
Journal Article
Oral Manifestations of Histiocytosis of Langerhans Cells: a Pediatric Case Involving Mandible Bone
by
Lecourtois Amézquita, Mariana Gabriela
,
Montero Sánchez, René Abdiel
,
Velázquez Martínez, José Andrés
in
Biopsia
,
Biopsy
,
Bone
2022
Langerhans cells histiocytosis is a rare disease characterized by monoclonal proliferation and migration of special dendritic cells in a variety of organs, most commonly appears eosinophilic granuloma localized, often solitary, and bone lesions that occurs predominantly in pediatric patients. Although is most prevalent in children under the age of 15, this disorder presents in all ages and occurs at a rate of 2 to 5 cases per million per year. LCH is a complex entity; the clinic manifestations can mimic other common conditions and therefore a comprehensive evaluation is indicated. Since oral manifestations are frequent, the early diagnose of this pathology could be detected by dental professionals. The aim of this case report is to describe a case of LCH who initially was misdiagnosed and treated for a dental infection. This disease requires accurate histopathological diagnosis and timely treatment; hence it is necessary to raise awareness among dentists to avoid misdiagnose of oral manifestations of LCH.
La histiocitosis de las células de Langerhans es una enfermedad poco frecuente que se caracteriza por la proliferación monoclonal y la migración de células dendríticas especiales en una variedad de órganos; lo más común es que aparezca un granuloma eosinofílico localizado, a menudo solitario, así como lesiones óseas que se producen predominantemente en pacientes pediátricos. Aunque es más frecuente en los niños menores de 15 años, este trastorno se presenta en todas las edades y se produce a una tasa de 2 a 5 casos por millón al año. La HCL es una entidad compleja; las manifestaciones clínicas pueden imitar otras afecciones comunes y, por lo tanto, se indica una evaluación exhaustiva. Dado que las manifestaciones orales son frecuentes, el diagnóstico precoz de esta patología podría ser detectado por los profesionales de la odontología. El objetivo de este reporte de caso es describir un caso de HCL que inicialmente fue mal diagnosticado y tratado por una infección dental. Esta enfermedad requiere un diagnóstico histopatológico preciso y un tratamiento oportuno; por lo tanto, es necesario sensibilizar a los dentistas para evitar un diagnóstico erróneo de las manifestaciones orales de la HCL.
Journal Article
Fabrication of a Promising Hierarchical Porous Surface on Titanium for Promoting Biocompatibility
2020
The effects of the nano-titanium hydrides (nano-γ-TiH) phase on the formation of nanoporous Ti oxide layer by the potential approach (hydrogen fluoride (HF) pretreatment and sodium hydroxide (NaOH) anodization) were investigated using scanning electron microscopy, X-ray photoelectron spectroscopy, X-ray diffractometry, and transmission electron microscopy. The nano-γ-TiH phase was formed by the HF pretreatment with various current densities. After the NaOH anodization, the nano-γ-TiH phase was dissolved and transformed into nanoporous rutile-Ti dioxide (R-TiO2). As the Ti underwent HF pretreatment and NaOH anodization, the microstructure on the surface layer was transformed from α-Ti → (α-Ti + nano-γ-TiH) → (α-Ti + R-TiO2). In-vitro biocompatibility also indicated that the Ti with a hierarchical porous (micro and nanoporous) TiO2 surface possessed great potential to enhance cell adhesion ability. Thus, the potential approach can be utilized to fabricate a promising hierarchical porous surface on the Ti implant for promoting biocompatibility.
Journal Article
Denisovans, Melanesians, Europeans, and Neandertals: The Confusion of DNA Assumptions and the Biological Species Concept
A number of recent articles have appeared on the Denisova fossil remains and attempts to produce DNA sequences from them. One of these recently appeared in
Science
by Vernot et al. (Science 352:235–239, 2016). We would like to advance an alternative interpretation of the data presented. One concerns the problem of contamination/degradation of the determined DNA sequenced. Just as the publication of the first Neandertal sequence included an interpretation that argued that Neandertals had not contributed any genes to modern humans, the Denisovan interpretation has considerable influence on ideas regarding human evolution. The new papers, however, confuse established ideas concerning the nature of species, as well as the use of terms like premodern, Archaic Homo, and
Homo heidelbergensis
. Examination of these problems presents a solution by means of reinterpreting the results. Given the claims for gene transfer among a number of Mid Pleistocene hominids, it may be time to reexamine the idea of anagenesis in hominid evolution.
Journal Article
Immediate Loaded Post Extraction Implant and Connective Graft-Guided Bone Regeneration: A Case Report
by
Mayta-Tovalino, Frank
,
Alvitez-Temoche, Daniel
,
Espinoza-Carhuancho, Fran
in
Aesthetics
,
Allografts
,
Bone grafts
2024
This case report describes the clinical and therapeutic approach used in a 32-year-old female patient with a tooth fracture in tooth 22. The patient, with no history of systemic disease, presented with a chronic periapical lesion and a cervical fracture in the affected tooth. Treatment included atraumatic extraction of the tooth, followed by placement of a 3.75 x 10mm post-extraction implant with immediate loading and guided bone regeneration. The minimally invasive surgical technique was employed using the Dentoflex® drilling sequence. The primary stability of the implant, measured in 37 Newtons of torque, allowed the placement of a prefabricated metal abutment for the subsequent cemented crown. Bone regeneration of the interimplant space was successfully performed, supplemented by connective grafting due to the patient's thin gingival phenotype. Postoperative follow-up, including controls at 7, 14 days and four months, showed a satisfactory conformation of the gingival margin and papillary tissue, consolidating the success of the treatment.
Journal Article