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Results for “feature fusion”

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At least 37 records · Page 2Linked to original sources
PubMed1998

Skeletal muscle regeneration mimicking rhabdomyosarcoma: a potential diagnostic pitfall.

AIMS: We report three cases of skeletal muscle regeneration, of which two mimicked a small round cell tumour, especially a rhabdomyosarcoma. METHODS AND RESULTS: One case presented as an intramuscular mass, located in the right quadriceps of a 12-year-old male; the second patient was a 25-year-old football player who complained of painful left peroneus muscles; the third patient was a 22-year-old male who underwent an amputation of the right thigh 5 days after right leg amputation due to limb crush. Histologically, muscle biopsy specimens showed a proliferation of small round cells, either infiltrating the striated muscle in a diffuse manner or growing within and around necrotic myofibres. Immunohistochemically and ultrastructurally, the cellular population was composed of two types of cells: phagocytic cells the nuclei of which occasionally showed a wreathlike arrangement around necrotic myofibres resulting in structures resembling Langhans-type multinucleated giant cells, and proliferating satellite cells showing enlarged nuclei, prominent nucleoli, mitotic figures, myogenic differentiation and fusion features in order to form regenerating myotubes. CONCLUSIONS: Muscle regeneration is a benign process that may occasionally mimic a small round cell proliferation resembling a lymphoma or an alveolar rhabdomyosarcoma with which it should not be confused.

Adult↗
PubMed2025

Leveraging protein language models for cross-variant CRISPR/Cas9 sgRNA activity prediction.

MOTIVATION: Accurate prediction of single-guide RNA (sgRNA) activity is crucial for optimizing the CRISPR/Cas9 gene-editing system, as it directly influences the efficiency and accuracy of genome modifications. However, existing prediction methods mainly rely on large-scale experimental data of a single Cas9 variant to construct Cas9 protein (variants)-specific sgRNA activity prediction models, which limits their generalization ability and prediction performance across different Cas9 protein (variants), as well as their scalability to the continuously discovered new variants. RESULTS: In this study, we proposed PLM-CRISPR, a novel deep learning-based model that leverages protein language models to capture Cas9 protein (variants) representations for cross-variant sgRNA activity prediction. PLM-CRISPR uses tailored feature extraction modules for both sgRNA and protein sequences, incorporating a cross-variant training strategy and a dynamic feature fusion mechanism to effectively model their interactions. Extensive experiments demonstrate that PLM-CRISPR outperforms existing methods across datasets spanning seven Cas9 protein (variants) in three real-world scenarios, demonstrating its superior performance in handling data-scarce situations, including cases with few or no samples for novel variants. Comparative analyses with traditional machine learning and deep learning models further confirm the effectiveness of PLM-CRISPR. Additionally, motif analysis reveals that PLM-CRISPR accurately identifies high-activity sgRNA sequence patterns across diverse Cas9 protein (variants). Overall, PLM-CRISPR provides a robust, scalable, and generalizable solution for sgRNA activity prediction across diverse Cas9 protein (variants). AVAILABILITY AND IMPLEMENTATION: The source code can be obtained from https://github.com/CSUBioGroup/PLM-CRISPR.

CRISPR-Cas Systems↗
PubMed1979

Pseudo-Chediak-Higashi anomaly in acute myeloid leukaemia. An electron microscopical study.

2 cases of acute myeloid leukaemia with inclusion bodies are presented. The inclusions were found mainly in the blast cells but could also be encountered in lymphocytes and plasma cells. Cytochemical and ultrastructural studies showed a great resemblance of these inclusions to the ones found in Chediak-Higashi anomaly, i.e., high acid phosphatase activity, varying in size of inclusions from clusters of small granules to hugh inclusion, sometimes found in vacuoles, featuring fusion of lysosomes.

Acid Phosphatase↗
PubMed2006

Hybrid vision system for online measurement of surface roughness.

A hybrid vision system for online measurement of surface roughness is introduced. The hybrid vision system applies two cameras for capturing the laser speckle pattern and scattering images simultaneously. With the help of advanced image processing, several features of texture and shape are computed for the surface roughness characterization. On the basis of experimental tests, feature fusion to improve measurement range and linearization of the measurement is also discussed.

Journal Article↗
PubMed2000

Giant cell tumor of tendon sheath: a light and electron microscopic study.

A neoformation has been surgically withdrawn from third finger extensor tendon of the right hand of a 52 year male subject. Light (LM) and electron microscope (EM) observations from a number of tissue fragments allowed the identification of tumor nature, which appeared a giant cell tendon sheath. Moreover, some structural patterns have been described and compared to the previously reported cases. In areas of major cell density, parenchyma does not show lobular or gland-like organization; on the other hand, wide zones characterized by an amorphous matrix, progressively replacing collagen and containing elongated cells, are present. Giant multinucleated cells, mostly localized close to collagen bundles, can also be revealed. Unexpectedly, no foam cells appear and no phagocytized cell debris can be identified in giant multinucleated cells. Engulfed crystals are, differently, evidentiated by electron microscopy, both in mono- and multinucleated cell cytoplasm. Their electron density and their localization within cytoplasmic vacuoles suggest the presence of calcium. A correlation between giant cells and osteoclasts is then proposed. Multiple variously oriented centrioles support the possible mitotic genesis of multinucleated giant cells, which never show, on the other hand, fusion features. Siderosomes and residual bodies are also present. An unusual, diffuse thickening of nuclear lamina, only interrupted at nuclear pore level, is described and discussed.

Giant Cell Tumors↗
PubMed2000

Paratesticular tumor-like lesions.

The diverse non-neoplastic lesions that occur in the paratesticular region and may potentially mimic neoplasms are considered. These include some aspects of normal histology such as a cribriform pattern of the epididymis, bizarre nuclear atypia within epididymal epithelial cells and the presence of Leydig cells outside the testicular parenchyma. Inflammatory changes associated with a hydrocele and a variety of granulomatous and nongranulomatous infectious disorders may mimic a neoplasm on gross evaluation, but should be readily distinguished from them microscopically. This is also the case with malakoplakia and sarcoidosis, which rarely form a paratesticular mass. Other lesions considered are changes associated with vasculitis, the recently described entities inflammatory pseudotumor and fibromuscular hyperplasia and the well-known processes sperm granuloma, spermatocele, vasitis nodosa, fibrous pseudotumor, meconium periorchitis, mesothelial hyperplasia, the testicular tumor of the adrenogenital syndrome, sclerosing lipogranuloma, and splenic-gonadal fusion. Features that aid in the microscopic distinction of these lesions from neoplasms are emphasized.

Diagnosis, Differential↗
PubMed2005

[Treatment of cranial fractures, evaluation of osteosynthesis plates, complications and results].

In recent years, the osteosynthesis plate has became very popular due to its quality during treatment of visceral cranium bone fractures. It is recommended to be used for stabile fusion of multi segment fractures. In the Maxillo-Facial Surgery Clinic of PMA Szczecin the presented method is applied from the mid-80-ies of the last century. Experience and obtained results permit as to state that osteosynthesis plate of visceral cranium posttraumatic fractures provides most efficient method in their treatment. It allows to establish one-time anatomical functional bone fusion, soon return to correct stomatognathic system, shortens hospitalizations time, thus securing speedy return to normal life. Analyzing the complications it was found out that in the majority of cases the decisive significance referred to: the condition of patients, time of reporting after trauma, biomechanical fusion features as wall as skill of the operator. Not always the complications were the results of the applied method.

Adult↗
PubMed2003

[Immunophenotypic features of bcr/abl fusion transcript-positive B-lineage acute lymphoblast leukemia].

To investigate the biological features of leukemic cells in bcr/abl fusion transcript-positive B-lineage acute lymphoblastic leukemia (B-ALL), 3- or 4-color flow cytometry with directly conjugated monoclonal antibodies was used to detect the immunophenotype of the cells in 26 patients with bcr/able-positive B-ALL and 32 patients with bcr/abl-negative B-ALL. bcr/abl fusion transcript was detected by RT-PCR. Immunoglobulin heavy chain (IgH) gene rearrangement was detected by PCR. The results showed that all of the B-ALL patients were positive for CD19. There was significant difference in expression of CD34 (96.2% vs 65.6%), CD10 (96.2% vs 71.8%) and CD38 (43.8% vs 95.4%) between bcr/abl-positive and -negative groups. In bcr/abl-positive B-ALL group, the co-expression rates of CD10(+)/CD19(+)/CD34(+), CD10(+)/CD34(+)/HLA-DR(+) and CD10(+)/CD34(+)/CD38(-) were 92.3% (24/26), 73.1% (19/26) and 56.2% (9/16), respectively. In bcr/abl-negative group, co-expression of CD10(+)/CD19(+)/CD34(+) and CD10(+)/CD34(+)/HLA-DR(+) were 43.8% (14/32) and 37.5% (12/32), respectively, there were significant differences (P < 0.05) between bcr/abl-positive and -negative groups, but none of the cases co-expressed CD10(+)/CD34(+)/CD38(-). The detection rate of monoclonal IgH gene rearrangement (58.8%, 10/17) was lower in bcr/abl-positive group than that (85.7%, 12/14) in bcr/able-negative group. It is concluded that the expression rates of CD34 and CD10 are higher, and CD38 and IgH gene rearrangement are lower in bcr/abl-positive B-ALL cases, CD10(+)/CD34(+)/CD38(-) is a unique feature of immunophenotype, and this phenotype of leukemia cells is closer to that of early B-lineage progenitor cells.

Adolescent↗
PubMed1997

Structural features of membrane fusion between influenza virus and liposome as revealed by quick-freezing electron microscopy.

The structure of membrane fusion intermediates between the A/PR/8(H1N1) strain of influenza virus and a liposome composed of egg phosphatidylcholine, cholesterol, and glycophorin was studied using quick-freezing electron microscopy. Fusion by viral hemagglutinin protein was induced at pH 5.0 and 23 degrees C. After a 19-s incubation under these conditions, small protrusions with a diameter of 10-20 nm were found on the fractured convex faces of the liposomal membranes, and small pits complementary to the protrusions were found on the concave faces. The protrusions and pits corresponded to fractured parts of outward bendings of the lipid bilayer or "microprotrusions of the lipid bilayer." At the loci of the protrusions and pits, liposomal membranes had local contacts with viral membranes. In many cases both the protrusions and the pits were aligned in regular polygonal arrangements, which were thought to reflect the array of hemagglutinin spikes on the viral surface. These structures were induced only when the medium was acidic with the virus present. Based on these observations, it was concluded that the microprotrusions of the lipid bilayer are induced by hemagglutinin protein. Furthermore, morphological evidence for the formation of the "initial fusion pore" at the microprotrusion was obtained. The protrusion on the convex face sometimes had a tiny hole with a diameter of <4 nm in the center. The pits transformed into narrow membrane connections <10 nm in width, bridging viruses and liposomes. The structures of the fusion pore and fusion neck with larger sizes were also observed, indicating growth of the protrusions and pits to distinct fusion sites. We propose that the microprotrusion of the lipid bilayer is a fusion intermediate induced by hemagglutinin protein, and suggest that the extraordinarily high curvature of this membrane structure is a clue to the onset of fusion. The possible architecture of the fusion intermediate is discussed with regard to the localization of intramembrane particles at the microprotrusion.

Acids↗
PubMed2006

Determining the ratio of the Gaussian curvature and bending elastic moduli of phospholipids from Q(II) phase unit cell dimensions.

A method is presented for measuring M, the ratio of the Gaussian (saddle splay) elastic modulus to the bending elastic modulus of a lipid monolayer. The ratio M is determined from measurements of the equilibrium bicontinuous inverted cubic (Q(II)) phase unit cell size in excess water as a function of temperature. The analysis includes the effect of a curvature elastic term that is second-order in the Gaussian curvature, K. Preliminary results using data on DOPE-Me validate the method. The fitted value of M is within 8% of the value estimated in an earlier treatment. The method can be used to measure changes in M due to addition of exogenous lipids and peptides to a host lipid system. The Gaussian elastic modulus has a substantial effect on the stability of fusion intermediates (stalks, hemifusion diaphragms, and fusion pores). Studying the effects of peptides and different lipids on M via this method may yield insights into how fusion protein moieties stabilize intermediates in membrane fusion in vivo. The contribution of the K2 curvature elastic term to the free energy of Q(II) phase and fusion pores explains some features of fusion pore stability and dynamics, and some peculiar observations concerning the mechanism of L(alpha)/Q(II) phase transitions.

Animals↗
PubMed1998

The central structural feature of the membrane fusion protein subunit from the Ebola virus glycoprotein is a long triple-stranded coiled coil.

The ectodomain of the Ebola virus Gp2 glycoprotein was solubilized with a trimeric, isoleucine zipper derived from GCN4 (pIIGCN4) in place of the hydrophobic fusion peptide at the N terminus. This chimeric molecule forms a trimeric, highly alpha-helical, and very thermostable molecule, as determined by chemical crosslinking and circular dichroism. Electron microscopy indicates that Gp2 folds into a rod-like structure like influenza HA2 and HIV-1 gp41, providing further evidence that viral fusion proteins from diverse families such as Orthomyxoviridae (Influenza), Retroviridae (HIV-1), and Filoviridae (Ebola) share common structural features, and suggesting a common membrane fusion mechanism.

Amino Acid Sequence↗
PubMed2005

Image mining for investigative pathology using optimized feature extraction and data fusion.

In many subspecialties of pathology, the intrinsic complexity of rendering accurate diagnostic decisions is compounded by a lack of definitive criteria for detecting and characterizing diseases and their corresponding histological features. In some cases, there exists a striking disparity between the diagnoses rendered by recognized authorities and those provided by non-experts. We previously reported the development of an Image Guided Decision Support (IGDS) system, which was shown to reliably discriminate among malignant lymphomas and leukemia that are sometimes confused with one another during routine microscopic evaluation. As an extension of those efforts, we report here a web-based intelligent archiving subsystem that can automatically detect, image, and index new cells into distributed ground-truth databases. Systematic experiments showed that through the use of robust texture descriptors and density estimation based fusion the reliability and performance of the governing classifications of the system were improved significantly while simultaneously reducing the dimensionality of the feature space.

Diagnosis, Differential↗
PubMed2001

Loss at 12p detected by comparative genomic hybridization (CGH): association with TEL-AML1 fusion and favorable prognostic features in childhood acute lymphoblastic leukemia (ALL). A multi-institutional study.

BACKGROUND: Genetic aberrations provide prognostic information in childhood ALL. The proportion of patients with detectable aberrations can be increased by combining G-banding with comparative genomic hybridization (CGH). PROCEDURE: We studied 79 children with ALL by CGH and G-banding, and explored the relationship of these findings to clinical features and outcome. RESULTS: CGH revealed DNA copy number changes in 57 patients (72%), 9 of whom had normal karyotype by G-banding. Gains were more frequent than losses, and changes of whole chromosomes more frequent than partial aberrations. Two frequent partial losses were found; at 9p and 12p. The 9 patients with loss at 12p were studied for the deletion of TEL (ETV6) gene and the fusion of TEL and AML1 genes by fluorescent in situ hybridization (FISH). Eight out of the 9 children with loss at 12p harbored the TEL-AML1 translocation and all 9 had the deletion of a nontranslocated TEL allele. All 9 had precursor-B phenotype and L1 morphology, and 8/9 had WBC below 50 x 10(9)/liter. All children were treated according to Nordic ALL protocols, had a good response to treatment based on day 15 bone marrow morphology, and 7 out of the 9 survived in continuous complete remission (median follow-up 74 months). CONCLUSIONS: CGH is a valuable tool in screening for genetic aberrations in childhood ALL. DNA copy number losses detected at 12p associate with TEL-AML1 fusion as well as with favorable prognostic features.

Adolescent↗
PubMed1998

Conserved structural features of the synaptic fusion complex: SNARE proteins reclassified as Q- and R-SNAREs.

SNARE [soluble NSF (N-ethylmaleimide-sensitive fusion protein) attachment protein receptor] proteins are essential for membrane fusion and are conserved from yeast to humans. Sequence alignments of the most conserved regions were mapped onto the recently solved crystal structure of the heterotrimeric synaptic fusion complex. The association of the four alpha-helices in the synaptic fusion complex structure produces highly conserved layers of interacting amino acid side chains in the center of the four-helix bundle. Mutations in these layers reduce complex stability and cause defects in membrane traffic even in distantly related SNAREs. When syntaxin-4 is modeled into the synaptic fusion complex as a replacement of syntaxin-1A, no major steric clashes arise and the most variable amino acids localize to the outer surface of the complex. We conclude that the main structural features of the neuronal complex are highly conserved during evolution. On the basis of these features we have reclassified SNARE proteins into Q-SNAREs and R-SNAREs, and we propose that fusion-competent SNARE complexes generally consist of four-helix bundles composed of three Q-SNAREs and one R-SNARE.

Amino Acid Sequence↗
PubMed1987

Osmotic swelling allows fusion of sendai virions with membranes of desialyzed erythrocytes and chromaffin granules.

Sendai virus particles are able to fuse with Pronase-neuraminidase-treated human erythrocyte membranes as well as with vesicles obtained from chromaffin granules of bovine medulla. Fusion is inferred either from electron microscopic studies or from the observation that incubation of fluorescently labeled (bearing octadecyl Rhodamine B chloride) virions, with right-side-out erythrocyte vesicles (ROV) or with chromaffin granule membrane vesicles (CGMV), resulted in fluorescence dequenching. Fusion of Sendai virions with virus receptor depleted ROV was observed only under hypotonic conditions. Fusion with virus receptor depleted ROV required the presence of the two viral envelope glycoproteins, namely, the HN and F polypeptides. A 3-fold increase in the degree of fluorescence dequenching (virus-membrane fusion) was also obtained upon incubation of Sendai virions with CGMV in medium of low osmotic strength. This increase was not observed with inactivated, unfusogenic Sendai virions. The results of the present work demonstrate that, under hypotonic conditions, fusion between Sendai virions and biological membranes does not require the presence of specific receptors. Such fusion is characterized by the same features as fusion with and infection by Sendai virions of living cultured cells.

Chromaffin Granules↗
PubMed1999

Membrane fusion induced by a short fusogenic peptide is assessed by its insertion and orientation into target bilayers.

To clarify the molecular mechanism by which an amphipathic negatively charged peptide consisting of 11 residues (WAE) induces fusion, and the relevance of these features for fusion, its mode of insertion and orientation into target bilayers were investigated. Using attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) in combination with techniques based on tryptophan fluorescence, the peptide was found to form an alpha-helix, shallowly inserted into the membrane to which it is anchored. Interestingly, in the presence of target membranes, WAE inserts into the target bilayer as an alpha-helix oriented almost parallel to the lipid acyl chains. The accessibility of the peptide to either acrylamide (as an aqueous quencher of Trp fluorescence) or deuterium oxide (on the course of an FTIR deuteration kinetics) was lower in the presence than in the absence of target membranes, confirming that under those conditions, the peptide was shielded from the aqueous environment. Since fusion experiments have shown a temperature dependence, the effect of this later parameter on the structure and mode of insertion of the peptide was also analyzed. In the presence of target membrane, but not in their absence, the amount of alpha-helical structure increased with temperature, reflecting a similar temperature-dependent increase in the rate and extent of WAE-induced fusion. Also, the extent of penetration of the helix into the target membrane was greater at 37 degrees C than at lower temperatures. This temperature-dependent distinction was revealed by a decreased accessibility of the peptide to deuterium oxide and acrylamide at 37 degrees C as compared to that at lower temperatures. These data underscore the role of peptide structure, peptide penetration, and orientation in the mechanism of protein-induced membrane fusion.

Cholesterol↗
PubMed2003

Allogeneic interactions in Hydractinia: is the transitory chimera beneficial?

The colonial marine hydroid, Hydractinia, exhibits four possible outcomes to allogeneic contacts: passive rejection, aggressive rejection, stable fusion and transitory fusion. In the special case of transitory fusion, Hydractinia colonies undergo tissue fusion, followed by tissue death at the original contact area, and colony separation. This type of rejection is different in several aspects from the rejection process that accompanies incompatible encounters. It has been suggested that in transitory fusion, the colonies gain immediate benefits from fusion, mainly due to size increase, without succumbing to costs associated with fusion (germ line parasitism). We report a long-term observation of repeated fusion and separation cycles in clones featuring transitory fusion that revealed a slow-down of specific growth rates following fusion, and recovery in growth rates following separation. Very rapid transfer of stained material between partners in transitory chimeras provides suggestive evidence that protection against germ line parasitism is far from being guaranteed by separation. Our data cast doubt as to whether the benefits considered for transitory fusion are sustainable and support the already made suggestion that fusion with self, rather than fusion with kin, has been the major selective force governing the evolution of allorecognition in colonial invertebrates.

Animals↗