Next Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are ...significant challenges when dealing with NGS data. Firstly, a huge number of bioinformatics tools for a wide range of uses exist, therefore it is challenging to design an analysis pipeline. Secondly, NGS analysis is computationally intensive, requiring expensive infrastructure, and many medical and research centres do not have adequate high performance computing facilities and cloud computing is not always an option due to privacy and ownership issues. Finally, the interpretation of the results is not trivial and most available pipelines lack the utilities to favour this crucial step.
We have therefore developed a fast and efficient bioinformatics pipeline that allows for the analysis of DNA sequencing data, while requiring little computational effort and memory usage. DNAscan can analyse a whole exome sequencing sample in 1 h and a 40x whole genome sequencing sample in 13 h, on a midrange computer. The pipeline can look for single nucleotide variants, small indels, structural variants, repeat expansions and viral genetic material (or any other organism). Its results are annotated using a customisable variety of databases and are available for an on-the-fly visualisation with a local deployment of the gene.iobio platform. DNAscan is implemented in Python. Its code and documentation are available on GitHub: https://github.com/KHP-Informatics/DNAscan . Instructions for an easy and fast deployment with Docker and Singularity are also provided on GitHub.
DNAscan is an extremely fast and computationally efficient pipeline for analysis, visualization and interpretation of NGS data. It is designed to provide a powerful and easy-to-use tool for applications in biomedical research and diagnostic medicine, at minimal computational cost. Its comprehensive approach will maximise the potential audience of users, bringing such analyses within the reach of non-specialist laboratories, and those from centres with limited funding available.
Purpose
The aim of this study is to estimate the prognostic value of some features documented on preoperative MRI study in patients with acute cervical spinal cord injury.
Methods
The study was ...conducted in patients operated for cervical spinal cord injury (cSCI) from April 2014 to October 2020.
The quantitative analysis on preoperative MRI scans included: length of the spinal cord intramedullary lesion (IMLL the canal diameter at the level of maximal spinal cord compression (MSCC) and the presence of intramedullary hemorrhage. The canal diameter at the MSCC was measured on the middle sagittal FSE-T2W images at the maximum level of injury.
The America Spinal Injury Association (ASIA) motor score was used for neurological assessment at hospital admission. At 12-month follow-up all patients were examined with the SCIM questionnaire.
Results
At linear regression analysis, the length of the spinal cord lesion
β
coefficient −10.35, 95% confidence interval (CI)−13.71 to−6.99;
p
< 0.001, the diameter of the canal at the level of the MSCC (
β
coefficient 6.99, 95% CI 0.65 to 13.33;
p
= 0.032), and the intramedullary hemorrhage (
β
coefficient − 20.76, 95% CI − 38.70 to − 2.82;
p
= 0.025), were significantly associated with the score at the SCIM questionnaire at one year follow-up: shorter spinal cord lesion, greater diameter of the canal at the level of the MSCC, and absence of intramedullary hemorrhage were predictors of better outcome.
Conclusion
According to the findings of our study, the spinal length lesion, canal diameter at the level of spinal cord compression and intramedullary hematoma documented by the preoperative MRI study were associated with the prognosis of patients with cSCI.
The blackbody radiation left over from the Big Bang has been transformed by the expansion of the Universe into the nearly isotropic 2.73 K cosmic microwave background. Tiny inhomogeneities in the ...early Universe left their imprint on the microwave background in the form of small anisotropies in its temperature. These anisotropies contain information about basic cosmological parameters, particularly the total energy density and curvature of the Universe. Here we report the first images of resolved structure in the microwave background anisotropies over a significant part of the sky. Maps at four frequencies clearly distinguish the microwave background from foreground emission. We compute the angular power spectrum of the microwave background, and find a peak at Legendre multipole Ipeak = (197 +/- 6), with an amplitude delta T200 = (69 +/- 8) microK. This is consistent with that expected for cold dark matter models in a flat (euclidean) Universe, as favoured by standard inflationary models.
Recent results from BOOMERANG-98 and MAXIMA-1, taken together with COBE DMR, provide consistent and high signal-to-noise measurements of the cosmic microwave background power spectrum at spherical ...harmonic multipole bands over 2<l less similar to 800. Analysis of the combined data yields 68% (95%) confidence limits on the total density, Omega(tot) approximately 1.11+/-0.07 (+0.13)(-0.12), the baryon density, Omega(b)h(2) approximately 0.032(+0.005)(-0.004) (+0.009)(-0.008), and the scalar spectral tilt, n(s) approximately 1.01(+0.09)(-0.07) (+0.17)(-0.14). These data are consistent with inflationary initial conditions for structure formation. Taken together with other cosmological observations, they imply the existence of both nonbaryonic dark matter and dark energy in the Universe.
BC200 RNA, a small functional RNA that operates as a translational modulator, has been implicated in the regulation of local synaptodendritic protein synthesis in neurons. Cell type-specific ...expression of BC200 RNA is tightly controlled such that the RNA is not normally detected in somatic cells other than neurons. However, the neuron-specific control of BC200 expression is deregulated in a number of tumors. We here report that BC200 RNA is expressed at high levels in invasive carcinomas of the breast. In normal breast tissue or in benign tumors such as fibroadenomas, in contrast, we found that the RNA is not detectable at significant levels. The difference in expression levels between invasive carcinomas and normal/benign tissue was statistically highly significant. Receiver Operating Characteristics analysis of sensitivity and specificity confirmed the diagnostic power of BC200 RNA as a molecular marker of invasive breast cancer. In ductal carcinomas in situ, furthermore, significant BC200 expression was associated with high nuclear grade, suggesting that the presence of BC200 RNA in such tumors may be used as a prognostic indicator of tumor progression. The combined results demonstrate the potential of BC200 expression to serve as a molecular tool in the diagnosis and/or prognosis of breast cancer.
Aims.We present the boomerang-03 experiment, and the maps of the Stokes parameters I, Q, U of the microwave sky obtained during a 14 day balloon flight in 2003. Methods.Using a balloon-borne mm-wave ...telescope with polarization sensitive bolometers, three regions of the southern sky were surveyed: a deep survey (~90 square degrees) and a shallow survey (~750 square degrees) at high Galactic latitudes (both centered at ${\rm RA} \simeq 5.5 h$, ${\rm Dec} \simeq -45\degr$) and a survey of ~300 square degrees across the Galactic plane at ${\rm RA} \simeq 9.1 h$, ${\rm dec} \simeq -47\degr$. All three surveys were carried out in three wide frequency bands centered at 145, 245 and 345 GHz, with an angular resolution of ~$10^{\prime}$. Results.The 145 GHz maps of Stokes I are dominated by Cosmic Microwave Background (CMB) temperature anisotropy, which is mapped with high signal to noise ratio. The measured anisotropy pattern is consistent with the pattern measured in the same region by boomerang-98 and by WMAP. The 145 GHz maps of Stokes Q and U provide a robust statistical detection of polarization of the CMB when subjected to a power spectrum analysis. The amplitude of the detected polarization is consistent with that of the CMB in the ΛCDM cosmological scenario. At 145 GHz, in the CMB surveys, the intensity and polarization of the astrophysical foregrounds are found to be negligible with respect to the cosmological signal. At 245 and 345 GHz we detect ISD emission correlated to the 3000 GHz IRAS/DIRBE maps, and give upper limits for any other non-CMB component. When compared to monitors of different interstellar components, the intensity maps of the surveyed section of the Galactic plane show that a variety of emission mechanisms is present in that region.
We describe a measurement of the angular power spectrum of anisotropies in the cosmic microwave background (CMB) at scales of 0 3 to 5 degrees from the North American test flight of the Boomerang ...experiment. Boomerang is a balloon-borne telescope with a bolometric receiver designed to map CMB anisotropies on a long-duration balloon flight. During a 6 hr test flight of a prototype system in 1997, we mapped more than 200 deg(2) at high Galactic latitudes in two bands centered at 90 and 150 GHz with a resolution of 26 and 16 5 FWHM, respectively. Analysis of the maps gives a power spectrum with a peak at angular scales of 1 degrees with an amplitude 70 µK(CMB).
Usnic acid is a normal component of lichen cells. This natural compound has shown different biological and physiological activities that might have a great relevance in pharmacology and clinics. For ...instance, usnic acid is known for its antibacterial and antiparasitic action. Also, the drug has a potential interest in cancer therapy because of its antimitotic and antiproliferative action. The molecular structure of usnic acid has been validated and further explored in this investigation. Many biological properties of this drug are known; however its potential antiviral action has not yet been evaluated. In this paper, we demonstrate that usnic acid is a potent inhibitor of the proliferation of mouse polyomavirus. Its action is not exerted at the level of virion entry into the host cell. Moreover, the abolition of viral DNA replication is an indirect consequence of the drastic inhibition of RNA transcription.
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