DNA numerical encoding schemes for exon prediction: a recent history.

Bioinformatics in the present day has been firmly established as a regulator in genomics. In recent times, applications of Signal processing in exon prediction have gained a lot of attention. The exons carry protein information. Proteins are composed of connected constituents known as amino acids that characterize the specific function. Conversion of the nucleotide character string into a numerical sequence is the gateway before analyzing it through signal processing methods. This numeric encoding is the mathematical descriptor of nucleotides and is based on some statistical properties of the structure of nucleic acids. Since the type of encoding extremely affects the exon detection accuracy, this paper is devised for the review of existing encoding (mapping) schemes. The comparative analysis is formulated to emphasize the importance of the genetic code setting of amino acids considered for application related to computational elucidation for exon detection. This work covers much helpful information for future applications.

Imaging following thermal ablation of early lung cancers: expected post-treatment findings and tumour recurrence.

Thermal ablation is a minimally invasive technique that is growing in acceptance and popularity in the management of early lung cancers. Although curative resection remains the optimal treatment strategy for stage I pulmonary malignancies, percutaneous ablative treatments may also be considered for selected patients. These techniques can additionally be used in the treatment of oligometastatic disease. Thermal ablation of early lung tumours can be achieved using several different techniques. For example, microwave ablation (MWA) and radiofrequency ablation (RFA) utilise extreme heat, whereas cryoablation uses extremely cold temperatures to cause necrosis and ultimately cell death. Typically, post-ablation imaging studies are performed within the first 1-3 months with subsequent imaging performed at regular intervals to ensure treatment response and to evaluate for signs of recurrent disease. Surveillance imaging is usually undertaken with computed tomography (CT) and integrated positron-emission tomography (PET)/CT. Typical imaging findings are usually seen on CT and PET/CT following thermal ablation of lung tumours, and it is vital that radiologists are familiar with these appearances. In addition, radiologists should be aware of the imaging findings that indicate local recurrence following ablation. The objective of this review is to provide an overview of the expected post-treatment findings on CT and PET/CT following thermal ablation of early primary lung malignancies, as well as describing the imaging appearances of local recurrence.

Integrated multiplex network based approach for hub gene identification in oral cancer.

Background: The incidence of Oral Cancer (OC) is high in Asian countries, which goes undetected at its early stage. The study of genetics, especially genetic networks holds great promise in this endeavor. Hub genes in a genetic network are prominent in regulating the whole network structure of genes. Thus identification of such genes related to specific cancer types can help in reducing the gap in OC prognosis. Methods: Traditional study of network biology is unable to decipher the inter-dependencies within and across diverse biological networks. Multiplex network provides a powerful representation of such systems and encodes much richer information than isolated networks. In this work, we focused on the entire multiplex structure of the genetic network integrating the gene expression profile and DNA methylation profile for OC. Further, hub genes were identified by considering their connectivity in the multiplex structure and the respective protein-protein interaction (PPI) network as well. Results: 46 hub genes were inferred in our approach with a high prediction accuracy (96%), outstanding Matthews coefficient correlation value (93%) and significant biological implications. Among them, genes PIK3CG, PIK3R5, MYH7, CDC20 and CCL4 were differentially expressed and predominantly enriched in molecular cascades specific to OC. Conclusions: The identified hub genes in this work carry ontological signatures specific to cancer, which may further facilitate improved understanding of the tumorigenesis process and the underlying molecular events. Result indicates the effectiveness of our integrated multiplex network approach for hub gene identification. This work puts an innovative research route for multi-omics biological data analysis.

Genome-wide identification and expression analysis of the plant specific LIM genes in Gossypium arboreum under phytohormone, salt and pathogen stress.

Asiatic cotton (Gossypium arboreum) cultivated as 'desi cotton' in India, is renowned for its climate resilience and robustness against biotic and abiotic stresses. The genome of G. arboreum is therefore, considered as a valued reserve of information for discovering novel genes or gene functions for trait improvements in the present context of cotton cultivation world-wide. In the present study, we carried out genome-wide analysis of LIM gene family in desi cotton and identified twenty LIM domain proteins (GaLIMs) which include sixteen animals CRP-like GaLIMs and four plant specific GaLIMs with presence (GaDA1) or absence (GaDAR) of UIM (Ubiquitin Interacting Motifs). Among the sixteen CRP-like GaLIMs, eleven had two conventional LIM domains while, five had single LIM domain which was not reported in LIM gene family of the plant species studied, except in Brassica rapa. Phylogenetic analysis of these twenty GaLIM proteins in comparison with LIMs of Arabidopsis, chickpea and poplar categorized them into distinct αLIM1, ßLIM1, γLIM2, δLIM2 groups in CRP-like LIMs, and GaDA1 and GaDAR in plant specific LIMs group. Domain analysis had revealed consensus [(C-X2-C-X17-H-X2-C)-X2-(C-X2-C-X17-C-X2-H)] and [(C-X2-C-X17-H-X2-C)-X2-(C-X4-C-X15-C-X2-H)] being conserved as first and/or second LIM domains of animal CRP-like GaLIMs, respectively. Interestingly, single LIM domain containing GaLIM15 was found to contain unique consensus with longer inter-zinc-motif spacer but shorter second zinc finger motif. All twenty GaLIMs showed variable spatio-temporal expression patterns and accordingly further categorized into distinct groups of αLIM1, ßLIM1, γLIM2 δLIM2 and plant specific LIM (DA1/DAR). For the first time, response of GaDA1/DAR under the influence of biotic and abiotic stresses were studied in cotton, involving treatments with phytohormones (Jasmonic acid and Abscisic acid), salt (NaCl) and wilt causing pathogen (Fusarium oxysporum). Expressions patterns of GaDA1/DAR showed variable response and identified GaDA2 as a probable candidate gene for stress tolerance in G. arboreum.

Autologous haematopoietic stem cell transplantation as a first-line disease-modifying therapy in patients with 'aggressive' multiple sclerosis.

BACKGROUND: Autologous haematopoietic stem cell transplantation (AHSCT) is an effective treatment for patients with multiple sclerosis (MS) who have highly active disease, despite the use of standard disease-modifying therapies (DMTs). However, the optimal time for offering AHSCT to patients with 'aggressive' MS is yet to be established. OBJECTIVES: The objective was to explore the safety and efficacy of AHSCT as a first-line DMT in patients with 'aggressive' MS. METHODS: All patients with 'aggressive' MS who received AHSCT as a first-line DMT in five European and North American centres were retrospectively evaluated. RESULTS: Twenty patients were identified. The median interval between diagnosis and AHSCT was 5 (1-20) months. All had multiple poor prognostic markers with a median pre-transplant Expanded Disability Status Scale (EDSS) score of 5.0 (1.5-9.5). After a median follow-up of 30 (12-118) months, the median EDSS score improved to 2.0 (0-6.5, p < 0.0001). No patient had further relapses. Three had residual magnetic resonance imaging (MRI) disease activities in the first 6 months post-transplant, but no further new or enhancing lesions were observed in subsequent scans. CONCLUSION: AHSCT is safe and effective as a first-line DMT in inducing rapid and sustained remission in patients with 'aggressive' MS.

Assessment of cosmesis and quality of life and their correlation using novel, validated methods in breast cancer patients who had undergone breast conservation therapy.

PURPOSE: To assess cosmesis [Breast Cancer Conservation Treatment. Cosmetic Results (BCCT.CORE) software] & QOL [EORTC QLQ (Quality of Life Questionnaire)-C30, BR23 questionnaires] using objective methods &to correlate effect of cosmesis on QOL (Quality of life) in breast cancer patients post BCT (Breast conservation therapy) using a cross-sectional observational study from a tertiary hospital. MATERIALS & METHODS: Cosmesis & QOL had been assessed in all biopsy-proven adult patients of unilateral breast cancer, who had undergone BCT with minimum three months post-BCT & three months post last adjuvant chemotherapy cycle, whichever is delivered last (with just hormonal therapy or followup remaining based on hormone receptor status). Pearson chi-square & Kendall correlation Tau-b tests had been used for testing association between Cosmesis & QOL. Variation of QOL scores between Cosmetic groups had been assessed using Mann-Whitney U-test. RESULTS: Cosmesis was Excellent/Good in 60.4 % of patients. 58.4 % of patients had Excellent/Good Quality of Life. Cosmesis & QOL had a positive correlation (intermediate strength) [Kendall correlation factor-0.484]. QOL-Global scale had better median scores in Excellent/ Good cosmetic group when compared to Fair/Poor group, while for functional & symptomatic scales, contrary had been true. Difference of median-scores between the two groups hadn't been statistically significant in five aspects - being upset over hair loss (p-0.09), sexual-enjoyment (p-0.33), nausea-vomiting (p-0.29), constipation (p0.32) & diarrhea (p-0.72). CONCLUSION: About 2/3rds of patients post-BCT had Excellent/Good Cosmesis & Excellent/Good QOL. Every measure taken before, during & post-BCT to improve Cosmesis might result in better QOL. Future studies must use more accurate three-dimensional methods to assess Cosmesis & its effect on QOL.

Transarterial chemoembolization for hepatocellular carcinoma: a bibliometric analysis of the most cited articles.

PURPOSE: Bibliometric analysis is a quantitative assessment of the academic literature in a particular field. The aim of our study was to characterize the 100 top-cited articles regarding transarterial chemoembolization (TACE) for the treatment of hepatocellular carcinoma (HCC). MATERIALS AND METHODS: The 'Web of Science' database was used to identify the leading articles regarding TACE for HCC. We determined the top 100 articles according to citations and performed an analysis on year of publication, authorship, department affiliation, publishing journal, institution and country of origin, subject matter and article type. RESULTS: The top-cited articles received between 92 and 2254 citations (median 283.4). The top 100 papers were published in 32 journals between 1983 and 2016. Cancer, Radiology and Hepatology published the most articles (n = 40). Internal medicine was the department affiliation of the first author in 49%. The country providing the most highly cited articles was Japan (n = 24). CONCLUSION: We performed an analysis of the 100 top-cited articles dealing with TACE for HCC, presenting a detailed list of the most influential and historically significant papers. Japan was the country that produced the most top-cited articles, highlighting its key contribution to this field of the literature.

Detection of exon location in eukaryotic DNA using a fuzzy adaptive Gabor wavelet transform.

The existing model-independent methods for the detection of exons in DNA could not prove to be ideal as commonly employed fixed window length strategy produces spectral leakage causing signal noise The Modified-Gabor-wavelet-transform exploits a multiscale strategy to deal with the issue to some extent. Yet, no rule regarding the occurrence of small and large exons has been specified. To overcome this randomness, scaling-factor of GWT has been adapted based on a fuzzy rule. Due to the nucleotides' genetic code and fuzzy behaviors in DNA configuration, this work could adopt the fuzzy approach. Two fuzzy membership functions (large and small) take care of the variation in the coding regions. The fuzzy-based learning parameter adaptively tunes the scale factor for fast and precise prediction of exons. The proposed approach has an immense plus point of being capable of isolating detailed sub-regions in each exon efficiently proving its efficacy comparing with existing techniques.

Hereditary disease prediction in eukaryotic DNA: an adaptive signal processing approach.

Hereditary disease prediction in eukaryotic DNA using signal processing approaches is an incredible work in bioinformatics. Researchers of various fields are trying to put forth a noninvasive approach to forecast the disease-related genes. As diseased genes are more random than the healthy ones, in this work, a comparison of the diseased gene is made against the healthy ones. An adaptive signal processing method like functional link artificial neural network-based Levenberg-Marquardt filter has been proposed in this regard. For parameter upgradation, the algorithm is modified using particle swarm optimization. Here, disease genes are discriminated from healthy ones based on the magnitude of mean square error (MSE), which is calculated through the adaptive filter. The performance of the algorithm is inspected by computing some evaluation parameters. Since accuracy is the prime concern, authors in this work have taken an attempt to improve the accuracy level compared to the existing methods. Taking the reference gene as healthy, the overall process is accomplished by categorizing the diseased and healthy targets with MSE value at a threshold of 0.012. The proposed technique predicts the test gene sets successfully.

Energy saving and Fuzzy-PID position control of electro-hydraulic system by leakage compensation through proportional flow control valve.

In this article, the focus is on the energy efficiency along with the position control of the linear actuator used in heavy earth moving equipment. It is quite evident that linear actuators are one of the critical machinery components used in the construction and mining activities like in booms of excavation equipment. The proposed work employed two different hydraulic circuits and a contrast has been carried out in terms of the energy efficiency. In one hydraulic circuit, the conventional proportional directional control valve (PDCV) is used for the position control. In another one, an innovative solution of using proportional flow control valve (PFCV) by creating artificial leakage between the two ends of the actuator is evaluated according to its energy efficiency. The extra flow coming from the pump during position control is by-passed by PFCV rather than the pressure relief valve in PDCV. This reduces the energy loss in the form of heat and increases the efficiency of the hydraulic circuit. The simulation of the hydraulic circuit is performed using MATLAB/Simulink and results are compared with the experiments and it is found that hydraulic circuit using PFCV is 8.5% more energy efficient than the conventional circuit using PDCV. The position control of the actuator is done using PID controller tuned by the fuzzy controller.

A novel approach for the energy recovery and position control of a hybrid hydraulic excavator.

The heavy earth moving machineries (HEMM) like hydraulic excavator play a major role in construction and mining industries. In this context, the energy saving strategies in hydraulic excavator needs to be addressed considering its vital importance. Since the hydraulic excavators are subjected to heavy loads, hence the opportunity to harness the potential gravitational energy (GPE) remains a key area which can be effectively explored in order to minimize the energy consumption in consideration with hydraulic excavator. In the projected system, the potential energy is stored as pressure energy in hydro-pneumatic accumulator. The upward movement of the boom is executed with the help of prime mover during the starting of the first duty cycle. In the latter duty cycles, the stored pressurized energy is utilized together with the prime mover energy capable to execute the upward movement of the boom. The position of the boom cylinder is controlled by using the conventional PID controller using proportional flow control valve (PFCV) and accumulator. The error between the actual position and demand position of the linear actuator is minimized along with attainment of superior controlled performance while utilizing Model Predictive Controller (MPC). The pressurized accumulator with PFCV has been utilized to cater the different position demands. This has been also justified both experimentally and analytically with the error in the permissible range of 2%. It has been observed that the proposed system is 10% more efficient in contrast to the conventional system.

Congenital Eventration of Diaphragm Presenting As Diaphragmatic Hernia: A Case Report.

Eventration of diaphragm is an abnormal elevation of diaphragmatic musculature while retaining normal attachments to the sternum, ribs and dorsolumber spine. It is a rare anomaly where the continuity of diaphragm remains intact. Pathological process can affect either all or only a portion of hemidiaphragm. Symptoms vary according to size of the defect. Large defect may mimic diaphragmatic hernia. The present case represents a full term female newborn that developed respiratory distress, cyanosis and feeding difficulties since 1st day of life. Clinical features and chest imaging of this case was assumed to be left sided diaphragmatic hernia which was found wrong in the operation theater. She was found to have left sided eventration of diaphragm to create symptom. Successful plication of ipsilateral diaphragm was done on 13th day of life. Supervised post operative ventilatory support along with other postoperative care improved the condition of this neonate. A large defect with eventration of diaphragm may be life threatening but a timely good management can save neonate from such condition.

Organophosphorus Compounds Poisoning in a Neonate: A Case Report.

Organophosphorus compounds (OPC) are widely used insecticides. Such poisoning is very rare in neonate. A 23 days old infant was admitted with severe respiratory distress, excessive secretion from nose and mouth, bluish discoloration of extremities and poor feeding for 4 hours. He was pale, cyanosed and lethargic with gasping respiration. Frothing was coming through mouth and nose. There was watering of eyes, pupils were pin pointed and light reflex was sluggish. The baby was hypothermic, hypotonic with altered sensorium. Capillary refill time was <3 sec. The neonate was gasping; there was crepitation over lung fields. Precordium and abdomen was normal. An odor of OPC was smelt on clothing and secretions of the infant. The baby was wrapped with a cloth that was ware during pesticide spraying in the field. In addition to general measures, decontamination of skin and clothing and gastric lavage was done. Empirical antibiotic, injection atropine and pralidoxime were given. Patient showed clinical improvement with disappearance of cholinergic signs. The baby was discharged on 7th day of admission after full recovery.

An integrated approach for identification of exon locations using recursive Gauss Newton tuned adaptive Kaiser window.

Identification of exon location in a DNA sequence has been considered as the most demanding and challenging research topic in the field of Bioinformatics. This work proposes a robust approach combining the Trigonometric mapping with Adaptive tuned Kaiser Windowing approach for locating the protein coding regions (EXONS) in a genetic sequence. For better convergence as well as improved accurateness, the side lobe height control parameter (ß) of Kaiser Window in the proposed algorithm is made adaptive to track the changing dynamics of the genetic sequence. This yields better tracking potential of the anticipated Adaptive Kaiser algorithm as it uses the recursive Gauss Newton tuning which in turn utilizes the covariance of the error signal to tune the ß factor which has been shown through numerous simulation results under a variety of practical test conditions. A detailed comparative analysis with the existing mapping schemes, windowing techniques, and other signal processing methods like SVD, AN, DFT, STDFT, WT, and ST has also been included in the paper to focus on the strength and efficiency of the proposed approach. Moreover, some critical performance parameters have been computed using the proposed approach to investigate the effectiveness and robustness of the algorithm. In addition to this, the proposed approach has also been successfully applied on a number of benchmark gene sets like Musmusculus, Homosapiens, and C. elegans, etc., where the proposed approach revealed efficient prediction of exon location in contrast to the other existing mapping methods.

Off-Label Medication in Children: Responsibilities of Pediatrician and Neonatologist.

Use of drug in pediatrics and neonatology should be rational. There are clinical situations when the use of unlicensed medicines or use of medicines outside the terms of license (i.e., 'off-label') may be judged by prescriber in the best interest of the patient. Off-label prescribing is clinically appropriate when the benefits outweigh the potential risks. Such practice is particularly common in pediatrics and neonatology where development of age-appropriate formulations is difficult. Before going to prescribe a drug on off-label basis, the clinician should be satisfied that an alternative medicine would not meet the patient's needs. The clinician should be satisfied that there is sufficient evidence base safety and efficacy on off-label drug use. Communication with legal guardian with sufficient information about proposed treatment is needed. The clinician has a responsibility to monitor the off-label use of drug. He should submit a report on suspected adverse drug reactions if he observes to the authorized body.

Studies on the interaction of a synthetic nitro-flavone derivative with DNA: A multi-spectroscopic and molecular docking approach.

Interaction of a ligand with DNA is often the basis of drug action of many molecules. Flavones are important in this regard as their structural features confer them the ability to bind to DNA. 2-(4-Nitrophenyl)-4H-chromen-4-one (4NCO) is an important biologically active synthetic flavone derivative. We are therefore interested in studying its interaction with DNA. Absorption spectroscopy studies included standard and reverse titration, effect of ionic strength on titration, determination of stoichiometry of binding and thermal denaturation. Spectrofluorimetry techniques included fluorimetric titration, quenching studies and fluorescence displacement assay. Assessment of relative viscosity and estimation of thermodynamic parameters from CD spectral studies were also undertaken. Furthermore, molecular docking analyses were also done with different short DNA sequences. The fluorescent flavone 4NCO reversibly interacted with DNA through partial intercalation as well as minor-groove binding. The binding constant and the number of binding sites were of the order 104 M-1 and 1 respectively. The binding stoichiometry with DNA was found to be 1:1. The nature of the interaction of 4NCO with DNA was hydrophobic in nature and the process of binding was spontaneous, endothermic and entropy-driven. The flavone also showed a preference for binding to GC rich sequences. The study presents a profile for structural and thermodynamic parameters, for the binding of 4NCO with DNA. DNA is an important target for ligands that are effective against cell proliferative disorders. In this regard, the molecule 4NCO is important since it can exert its biological activity through its DNA binding ability and can be a potential drug candidate.

The Structure of Speed of Processing Across Cultures.

We examined whether a general processing factor emerges when using response times for cognitive processing tasks and whether such a factor is valid across three different cultural groups (Chinese, Canadian, and Greek). Three hundred twenty university students from Canada (n = 115), China (n = 110), and Cyprus (n = 95) were assessed on an adaptation of the Das-Naglieri Cognitive Assessment System (D-N CAS; Naglieri & Das, 1997). Three alternative models were contrasted: a distinct abilities processing speed model (Model 1) that is dictated by the latent four cognitive factors of planning, attention, simultaneous and successive (PASS) processing, a unitary ability processing speed model (Model 2) that is dictated by the response time nature of all measures, and a bifactor model (Model 3) which included the latent scores of Models 1 and 2 and served as the full model. Results of structural equation modeling showed that (a) the model representing processing speed as a collection of four cognitive processes rather than a unitary processing speed factor was the most parsimonious, and (b) the loadings of the obtained factors were invariant across the three cultural groups. These findings enhance our understanding of the nature of speed of processing across diverse cultures and suggest that even when cognitive processes (i.e., PASS) are operationalized with response time measures, the processing component dominates speed.

Isolation, culture, characterization, and osteogenic differentiation of canine endometrial mesenchymal stem cell.

AIM: In this study, the canine endometrium tissue is characterized for its stem cell properties such as adherence to tissue culture plate (plasticity), short population doubling time, serial clonal passaging, long-term culturing properties, stem cell marker expression, and multilineage differentiation potential. MATERIALS AND METHODS: The present work describes a novel isolation protocol for obtaining mesenchymal stem cells from the uterine endometrium and is compared with cells derived from umbilical cord matrix as a positive control. These cells are clonogenic, can undergo several population doublings in vitro, and can be differentiated to the osteocytes in mature mesenchymal tissues when grown in osteogenic differentiation media as detected by Alizarin Red-S staining. RESULTS: It is reported for the first time that the cells derived from the canine endometrium (e-multipotent stem cells [MSCs]) were able to differentiate into a heterologous cell type: Osteocytes, thus demonstrating the presence of MSCs. Thus, the endometrium may be told as a potential source of MSCs which can be used for various therapeutic purposes. CONCLUSION: The endometrium can be used as a potential source of MSCs, which can be used for various therapeutic purposes.