Alex Sakula
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PROVIDER: S-EPMC341443 | biostudies-literature | 2004 Feb
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Skin cancer is one of most deadly diseases in humans. According to the high similarity between melanoma and nevus lesions, physicians take much more time to investigate these lesions. The automated classification of skin lesions will save effort, time and human life. The purpose of this paper is to present an automatic skin lesions classification system with higher classification rate using the theory of transfer learning and the pre-trained deep neural network. The transfer learning has been applied to the Alex-net in different ways, including fine-tuning the weights of the architecture, replacing the classification layer with a softmax layer that works with two or three kinds of skin lesions, and augmenting dataset by fixed and random rotation angles. The new softmax layer has the ability to classify the segmented color image lesions into melanoma and nevus or into melanoma, seborrheic keratosis, and nevus. The three well-known datasets, MED-NODE, Derm (IS & Quest) and ISIC, are used in testing and verifying the proposed method. The proposed DCNN weights have been fine-tuned using the training and testing dataset from ISIC in addition to 10-fold cross validation for MED-NODE and DermIS-DermQuest. The accuracy, sensitivity, specificity, and precision measures are used to evaluate the performance of the proposed method and the existing methods. For the datasets, MED-NODE, Derm (IS & Quest) and ISIC, the proposed method has achieved accuracy percentages of 96.86%, 97.70%, and 95.91% respectively. The performance of the proposed method has outperformed the performance of the existing classification methods of skin cancer.
| S-EPMC6529006 | biostudies-literature
Project description:Among the advantages of the single-molecule approach when used to study biomolecular structural dynamics and interaction is its ability to distinguish between and independently observe minor subpopulations. In a single-molecule Förster resonance energy transfer (FRET) and alternating laser excitation diffusion experiment, the various populations are apparent in the resultant histograms. However, because histograms are calculated based on the per-burst mean FRET and stoichiometry ratio and not on the internal photon distribution, much of the acquired information is lost, thereby reducing the capabilities of the method. Here we suggest what to our knowledge is a novel statistical analysis tool that significantly enhances these capabilities, and we use it to identify and isolate static and dynamic subpopulations. Based on a kernel density estimator and a proper photon distribution analysis, for each individual burst, we calculate scores that reflect properties of interest. Specifically, we determine the FRET efficiency and brightness ratio distributions and use them to reveal 1), the underlying structure of a two-state DNA-hairpin and a DNA hairpin that is bound to DNA origami; 2), a minor doubly labeled dsDNA subpopulation concealed in a larger singly labeled dsDNA; and 3), functioning DNA origami motors concealed within a larger subpopulation of defective motors. Altogether, these findings demonstrate the usefulness of the proposed approach. The method was developed and tested using simulations, its rationality is described, and a computer algorithm is provided.
| S-EPMC3296060 | biostudies-literature
Project description:XLalphas and ALEX are structurally unrelated mammalian proteins translated from alternative overlapping reading frames of a single transcript. Not only are they encoded by the same locus, but a specific XLalphas/ALEX interaction is essential for G-protein signaling in neuroendocrine cells. A disruption of this interaction leads to abnormal human phenotypes, including mental retardation and growth deficiency. The region of overlap between the two reading frames evolves at a remarkable speed: the divergence between human and mouse ALEX polypeptides makes them virtually unalignable. To trace the evolution of this puzzling locus, we sequenced it in apes, Old World monkeys, and a New World monkey. We show that the overlap between the two reading frames and the physical interaction between the two proteins force the locus to evolve in an unprecedented way. Namely, to maintain two overlapping protein-coding regions the locus is forced to have high GC content, which significantly elevates its intrinsic evolutionary rate. However, the two encoded proteins cannot afford to change too quickly relative to each other as this may impair their interaction and lead to severe physiological consequences. As a result XLalphas and ALEX evolve in an oscillating fashion constantly balancing the rates of amino acid replacements. This is the first example of a rapidly evolving locus encoding interacting proteins via overlapping reading frames, with a possible link to the origin of species-specific neurological differences.
| S-EPMC1186735 | biostudies-literature
Project description:Global lipidomics analysis across large sample sizes produces high-content datasets that require dedicated software tools supporting lipid identification and quantification, efficient data management and lipidome visualization. Here we present a novel software-based platform for streamlined data processing, management and visualization of shotgun lipidomics data acquired using high-resolution Orbitrap mass spectrometry. The platform features the ALEX framework designed for automated identification and export of lipid species intensity directly from proprietary mass spectral data files, and an auxiliary workflow using database exploration tools for integration of sample information, computation of lipid abundance and lipidome visualization. A key feature of the platform is the organization of lipidomics data in "database table format" which provides the user with an unsurpassed flexibility for rapid lipidome navigation using selected features within the dataset. To demonstrate the efficacy of the platform, we present a comparative neurolipidomics study of cerebellum, hippocampus and somatosensory barrel cortex (S1BF) from wild-type and knockout mice devoid of the putative lipid phosphate phosphatase PRG-1 (plasticity related gene-1). The presented framework is generic, extendable to processing and integration of other lipidomic data structures, can be interfaced with post-processing protocols supporting statistical testing and multivariate analysis, and can serve as an avenue for disseminating lipidomics data within the scientific community. The ALEX software is available at www.msLipidomics.info.
| S-EPMC3820610 | biostudies-literature
Project description:Miniature Inverted-repeat Transposable Elements (MITEs) are small nonautonomous class-II transposable elements distributed throughout eukaryotic genomes. We identified a novel family of MITEs (named Alex) in the Coffea canephora genome often associated with expressed sequences. The Alex-1 element is inserted in an intron of a gene at the CcEIN4 locus. Its mobility was demonstrated by sequencing the insertion site in C. canephora accessions and Coffea species. Analysis of the insertion polymorphism of Alex-1 at this locus in Coffea species and in C. canephora showed that there was no relationship between the geographical distribution of the species, their phylogenetic relationships, and insertion polymorphism. The intraspecific distribution of C. canephora revealed an original situation within the E diversity group. These results suggest possibly greater gene flow between species than previously thought. This MITE family will enable the study of the C. canephora genome evolution, phylogenetic relationships, and possible gene flows within the Coffea genus.
| S-EPMC3180848 | biostudies-literature
Project description:We characterized the performance, as well as the safety, of a second-generation thin-strut sirolimus-eluting stent with a biodegradable polymer, Alex Plus (Balton, Poland), implanted in patients with type 2 diabetes (DM) with a 4-year follow-up. We defined the primary endpoint as the 48-month rate of major cardiovascular adverse events (MACE), including cardiac death, myocardial infarction (MI), or target lesion revascularization (TLR). The secondary endpoints were all-cause death, cardiac death, MI, and TLR rates at 12, 24, 36, and 48 months. We enrolled 232 patients in whom 282 stents were implanted, including 97 DM and 135 non-DM patients. The mean age of the DM patients was 69.5 ± 10.1 years and females accounted for 30% of the patients. DM patients had higher rates of arterial hypertension (97% vs. 88%, p = 0.016), dyslipidemia (86% vs. 70%, p = 0.005), prior MI (61% vs. 40%, p = 0.002), prior PCI (65% vs. 50%, p = 0.020), and prior CABG (14% vs. 5.9%, p = 0.029). We recorded statistically significant differences for MACE (HR 1.85, 95% CI 1.01-3.41, p = 0.046), cardiac death (HR 4.46, 95% CI 1.44-13.8, p = 0.010), and MI (HR 3.17, 95% CI 1.10-9.12, p = 0.033), but not for TLR, between DM and non-DM patients in terms of the analyzed endpoints at 4 years. Our study showed that Alex Plus was efficient and safe in a contemporary cohort of real-world DM patients undergoing percutaneous revascularization.
| S-EPMC11204307 | biostudies-literature
Project description:BackgroundThe phase III ALEX study in patients with treatment-naive advanced anaplastic lymphoma kinase mutation-positive (ALK+) non-small-cell lung cancer (NSCLC) met its primary end point of improved progression-free survival (PFS) with alectinib versus crizotinib. Here, we present detailed central nervous system (CNS) efficacy data from ALEX.Patients and methodsOverall, 303 patients aged ≥18 years underwent 1:1 randomization to receive twice-daily doses of alectinib 600 mg or crizotinib 250 mg. Brain imaging was conducted in all patients at baseline and every subsequent 8 weeks. End points (analyzed by subgroup: patients with/without baseline CNS metastases; patients with/without prior radiotherapy) included PFS, CNS objective response rate (ORR), and time to CNS progression.ResultsIn total, 122 patients had Independent Review Committee-assessed baseline CNS metastases (alectinib, n = 64; crizotinib, n = 58), 43 had measurable lesions (alectinib, n = 21; crizotinib, n = 22), and 46 had received prior radiotherapy (alectinib, n = 25; crizotinib, n = 21). Investigator-assessed PFS with alectinib was consistent between patients with baseline CNS metastases [hazard ratio (HR) 0.40, 95% confidence interval (CI): 0.25-0.64] and those without (HR 0.51, 95% CI: 0.33-0.80, P interaction = 0.36). Similar results were seen in patients regardless of prior radiotherapy. Time to CNS progression was significantly longer with alectinib versus crizotinib and comparable between patients with and without baseline CNS metastases (P < 0.0001). CNS ORR was 85.7% with alectinib versus 71.4% with crizotinib in patients who received prior radiotherapy and 78.6% versus 40.0%, respectively, in those who had not.ConclusionAlectinib demonstrated superior CNS activity and significantly delayed CNS progression versus crizotinib in patients with previously untreated, advanced ALK+ NSCLC, irrespective of prior CNS disease or radiotherapy.Clinical trial registrationClinicalTrials.gov NCT02075840.
| S-EPMC6290889 | biostudies-literature
Project description:BackgroundIntimate partner violence (IPV) in pregnancy is a physical, sexual, psychological or economic harm by a current or former partner or spouse on a pregnant woman. It is a global public health problem that is common but underreported. Women are at increased risk of psychiatric illness in pregnancy and after delivery with the risk of major depressive disorder being highest during the postpartum period. Intimate partner violence in pregnancy may worsen this problem.ObjectivesThe objectives of the study were to determine the prevalence of intimate partner violence (IPV) in pregnancy, incidence of postpartum depression and the relationship between intimate partner violence, delivery outcomes and postpartum depression among booked pregnant women at Alex Ekwueme Federal University Teaching Hospital Abakaliki, Ebonyi state, Nigeria (AEFUTHA).Study designThis study was a prospective cohort study.SettingThe antenatal clinic, antenatal ward, labour ward, postpartum clinic and under five clinic of Alex Ekwueme Federal University Teaching Hospital Abakaliki, Ebonyi state, Nigeria were used for the study.MethodOne hundred and thirty-seven booked pregnant women that received antenatal care at AEFUTHA who met the inclusion criteria and consented to the study, were recruited from 37 weeks to 41 weeks gestation and screened for intimate partner violence and depression. Those with depression were referred for treatment while those that met the inclusion criteria were followed up to delivery and the delivery outcomes documented. They were also followed up to six weeks postpartum when they were screened for postpartum depression. Data were collated, tabulated and then statistically analysed using Statistical Package for Social Science (SPSS) software (version 25, Chicago II, USA). Numerical variables including participant's age, parity and gestational age were presented as mean, median, frequencies and standard deviation (Mean ± S.D), while categorical variables including occupation, level of education, social class and family type were presented as numbers and percentages. Chi-square test (X2) and relative risk was used for comparison between groups for categorical variables while Fisher's exact test was used when Chi-square test (X2) was not suitable. Binary regression analysis was used to determine the relationship between intimate partner violence and postpartum depression. A P value of ˂0.05 is considered statistically significant.ResultsThe prevalence of intimate partner violence was 52.6%, as 72 out of the 137 women recruited endured intimate partner violence. The major risk factors for intimate partner violence in the study were low level of education, low social class, polygamy and unemployment. The general incidence of postpartum depression was 29.93% while the incidence among women with intimate partner violence was 56.94%. Women with emotional violence and verbal abuse had a five-fold increase in the incidence of postpartum depression. Sexual violence and physical violence were not statistically significant risk factors for postpartum depression.ConclusionIntimate partner violence is common as seen from the study. It is a significant risk factor for postpartum depression. Women that are emotionally and verbal abused are more likely to have postpartum depression. Screening pregnant women for intimate violence may identify those at risk and allow for proper interventions.
| S-EPMC11468848 | biostudies-literature
Project description:PurposeWe retrospectively assessed prognostic value of circulating cell-free DNA (cfDNA) using data from the phase III ALEX study in treatment-naïve, advanced ALK+ non-small cell lung cancer (NSCLC).Patients and methodsPatients were randomized to receive twice-daily alectinib 600 mg (n = 152) or crizotinib 250 mg (n = 151). cfDNA was quantified from baseline plasma samples, with patients stratified into ≤median and >median cfDNA biomarker-evaluable populations (BEP). Effect of cfDNA concentration on outcomes was analyzed using a Cox regression model with treatment group as covariate, and in multivariate analyses.ResultsMedian cfDNA concentration in the BEP was 11.53 ng/mL (n = 276). A positive correlation was found between cfDNA concentration and number of lesions, organ lesion sites, and tumor size (sum of longest diameter; all P < 0.0001). In both treatment arms, patients in the >median BEP were more likely to experience disease progression than the ≤median BEP [alectinib adjusted HR = 2.04; 95% confidence interval (CI), 1.07-3.89; P = 0.0305 and crizotinib adjusted HR = 1.83; 95% CI, 1.11-3.00, P = 0.0169]. Median progression-free survival was longer with alectinib than crizotinib in both ≤median and >median BEPs (P < 0.0001). Overall survival data remain immature; survival probability was lower in the >median versus ≤median BEP in both treatment arms (alectinib HR = 2.52; 95% CI, 1.08-5.88; P = 0.0333 and crizotinib HR = 2.63; 95% CI, 1.27-5.47; P = 0.0096).ConclusionsThese data suggest that plasma cfDNA concentration may have prognostic value in advanced ALK+ NSCLC. Prospectively designed studies are warranted to investigate this finding.
| S-EPMC9365376 | biostudies-literature