Gene p16, which drives colorectalcancer, is emerging as a target for potential therapies BCMHouston
. For PCR amplifications, we used DNA isolated from colon tumors as well as healthy tissues . PCR fragments were separated on a 3730 DNA analyzer following the manufacture’s protocol and the raw data were analyzed with GeneMapper 5 software. If the profiles of all markers are identical to those seen in normal tissues, the tumor is classified as microsatellite stable .
were then broken, and cDNAs from each single cell were pooled, cleaned up using Dynabeads MyOne Silane Beads , and amplified by PCR. The amplified products were then fragmented to an optimal size prior to end-repair, A-tailing, and adaptor ligation. The final library was sequenced on the Illumina Novaseq 6000 platform. All scRNA-seq data have been uploaded to GEO and are available at the accession number GSE213568.
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Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data - Genome MedicineBackground The association between microbes and cancer has been reported repeatedly; however, it is not clear if molecular tumour properties are connected to specific microbial colonisation patterns. This is due mainly to the current technical and analytical strategy limitations to characterise tumour-associated bacteria. Methods Here, we propose an approach to detect bacterial signals in human RNA sequencing data and associate them with the clinical and molecular properties of the tumours. The method was tested on public datasets from The Cancer Genome Atlas, and its accuracy was assessed on a new cohort of colorectal cancer patients. Results Our analysis shows that intratumoural microbiome composition is correlated with survival, anatomic location, microsatellite instability, consensus molecular subtype and immune cell infiltration in colon tumours. In particular, we find Faecalibacterium prausnitzii, Coprococcus comes, Bacteroides spp., Fusobacterium spp. and Clostridium spp. to be strongly associated with tumour properties. Conclusions We implemented an approach to concurrently analyse clinical and molecular properties of the tumour as well as the composition of the associated microbiome. Our results may improve patient stratification and pave the path for mechanistic studies on microbiota-tumour crosstalk.
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High-grade gliomas remodel neural circuits: promoting tumor progression and impaired cognitionHigh-grade gliomas remodel neural circuits: promoting tumor progression and impaired cognition Nature UCSF gliomas glioblastoma tumor cognition neuroscience
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EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations - Genome BiologyDeep neural networks (DNNs) hold promise for functional genomics prediction, but their generalization capability may be limited by the amount of available data. To address this, we propose EvoAug, a suite of evolution-inspired augmentations that enhance the training of genomic DNNs by increasing genetic variation. Random transformation of DNA sequences can potentially alter their function in unknown ways, so we employ a fine-tuning procedure using the original non-transformed data to preserve functional integrity. Our results demonstrate that EvoAug substantially improves the generalization and interpretability of established DNNs across prominent regulatory genomics prediction tasks, offering a robust solution for genomic DNNs.
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A fixed reconstruction of fully edentulous patients with immediate function using an apically tapered implant design: a retrospective clinical study - International Journal of Implant DentistryBackground Immediate function has become an accepted treatment modality for fixed restorations in completely edentulous jaws. It is known that implant microtopography (surface) may enhance osseointegration, while implant macrotopography (macrodesign) plays an important role in primary stability in the patient requiring an immediate loading. The aim of this retrospective study was to evaluate the clinical and radiographic outcomes of the edentulous subjects treated with narrow and/or regular diameter, which placed and loaded immediately. Methods Forty-two consecutive patients received 171 implants, including regular and narrow diameter implants (NDIs). Each jaw, 19 mandibles and 24 maxillae, was treated with a fixed-full arch prosthesis according to the Straumann® Pro Arch concept. The majority (95%) of the restorations were supported by four implants, of which the posterior two implants were tilted. A provisional functional acrylic prosthesis was delivered on the day of surgery. All patients were followed up to 55 months. Cumulative survival rate was determined using Kaplan-Meier analysis. Radiological measurement of marginal bone level was performed. Results The overall follow-up time for survival rate was up to 55 months. Four implants (3 implants in maxilla, 1 implant in mandible) were lost, resulting in an overall cumulative implant survival rate of 97.7%. Implant survival rate in the axial and tilted implants was not statistically significant. The mean of interproximal marginal bone loss was 0.15 mm after 24 months. Good soft tissue health was observed in almost 99% of patients. The final prosthesis survival rate was 100%. Conclusions The results of this retrospective pilot study indicated that total edentulous patients requiring an immediate implant placement and loading can be successfully treated with this implant design. The improved mechanical properties of these implants might give a more conservative treatment option for the jaws showing a severe horizon
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Polycyclic aromatic hydrocarbons strongly linked to raised rheumatoid arthritis riskThe amount of environmental exposure to polycyclic aromatic hydrocarbons, or PAH for short, is strongly linked to a person's risk of developing rheumatoid arthritis, suggests research published in the open access journal BMJ Open.
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