Integration of Modern Molecular Tools with Geological Processes to Reveal Species Phylogeny,Biogeographical Niche Prediction,and Bio-Evolution

Nature is integrated, being simultaneously controlled by different natural aspects. Genetics, bioinformatics, biostatistics and geology are four diverse and broad scientific disciplines. But we believe that these can offer important insights into species distribution and evolution, if integrated. This perspective is grounded on a case study of the family Salvadoraceae, where species distribution and phylogeny show high correlation with the geological records. The results obtained from published and ongoing research indicate that we are pointing toward better visualizing the overlapping boundaries of these specific disciplines, which will be able to more accurately answer key evolutionary questions. We highlight: (1) the combined application of bedrock-soil geological data and bioinformatics to resolve evolutionary questions regarding species eco-distribution, niche prediction and bio-evolution; and (2) signifies the importance of relaxing boundaries between the disciplines to come to a better conclusion on species diversity and distribution-driven controls. Overall, we express and briefly explain our hypothesis to integrate modern analytical tools, viz., statistical correlation of geological data via. geo-statistics (Geo), and spatiotemporal biostatistics via. geo-informatics (Geo), with gene-based paleontological shreds of evidence, and sequence-based bioinformatics, to devise a practical analysis tool, namely “Geo² gene-bioinformatics”. We invoke the development of algorithms through computational-based programs that can provide useful correlations to understand evolutionary systematics and phylogeny, species distribution, and niche prediction.

     

Decision support system for age-related macular degeneration using discrete wavelet transform

Age-related macular degeneration (AMD) affects the central vision and subsequently may lead to visual loss in people over 60 years of age. There is no permanent cure for AMD, but early detection and successive treatment may improve the visual acuity. AMD is mainly classified into dry and wet type; however, dry AMD is more common in aging population. AMD is characterized by drusen, yellow pigmentation, and neovascularization. These lesions are examined through visual inspection of retinal fundus images by ophthalmologists. It is laborious, time-consuming, and resource-intensive. Hence, in this study, we have proposed an automated AMD detection system using discrete wavelet transform (DWT) and feature ranking strategies. The first four-order statistical moments (mean, variance, skewness, and kurtosis), energy, entropy, and Gini index-based features are extracted from DWT coefficients. We have used five (t test, Kullback–Lieber Divergence (KLD), Chernoff Bound and Bhattacharyya Distance, receiver operating characteristics curve-based, and Wilcoxon) feature ranking strategies to identify optimal feature set. A set of supervised classifiers namely support vector machine (SVM), decision tree, \(k\) -nearest neighbor ( \(k\) -NN), Naive Bayes, and probabilistic neural network were used to evaluate the highest performance measure using minimum number of features in classifying normal and dry AMD classes. The proposed framework obtained an average accuracy of 93.70 %, sensitivity of 91.11 %, and specificity of 96.30 % using KLD ranking and SVM classifier. We have also formulated an AMD Risk Index using selected features to classify the normal and dry AMD classes using one number. The proposed system can be used to assist the clinicians and also for mass AMD screening programs.     

Diversity of human lip prints: a collaborative study of ethnically distinct world populations

Background: Cheiloscopy is a comparatively recent counterpart to the long established dactyloscopic studies. Ethnic variability of these lip groove patterns has not yet been explored.

Aim: This study was a collaborative effort aimed at establishing cheiloscopic variations amongst modern human populations from four geographically and culturally far removed nations: India, Saudi Arabia, Spain and Nigeria.

Subjects and methods: Lip prints from a total of 754 subjects were collected and each was divided into four equal quadrants. The patterns were classified into six regular types (A–F), while some patterns which could not be fitted into the regular ones were segregated into G groups (G-0, G-1, G-2). Furthermore, co-dominance of more than one pattern type in a single quadrant forced us to identify the combination (COM, G-COM) patterns.

Results and conclusion: The remarkable feature noted after compilation of the data included pattern C (a bifurcate/branched prototype extending the entire height of the lip) being a frequent feature of the lips of all the populations studied, save for the Nigerian population in which it was completely absent and which showed a tendency for pattern A (a vertical linear groove) and a significantly higher susceptibility for combination (COM) patterns. Chi-square test and correspondence analysis applied to the frequency of patterns appearing in the defined topographical areas indicated a significant variation for the populations studied.     

Synthesis of new piperazinyl-pyrrolo[1,2-a]quinoxaline derivatives as inhibitors of Candida albicans multidrug transporters by a Buchwald–Hartwig cross-coupling reaction

Two series of piperazinyl-pyrrolo[1,2-a]quinoxaline derivatives were prepared via a Buchwald–Hartwig cross-coupling reaction and then evaluated for their ability to inhibit the drug efflux activity of CaCdr1p and CaMdr1p transporters of Candida albicans overexpressed in a Saccharomyces cerevisiae strain. In the initial screening of twenty-nine piperazinyl-pyrrolo[1,2-a]quinoxaline derivatives, twenty-three compounds behaved as dual inhibitors of CaCdr1p and CaMdr1p. Only four compounds showed exclusive inhibition of CaCdr1p or CaMdr1p. Further biological investigations were developed and for example, their antifungal potential was evaluated by measuring the growth of control yeast cells (AD1-8u⁻) and efflux pump-overexpressing cells (AD-CDR1 and AD-MDR1) after exposition to variable concentrations of the tested compounds. The MIC₈₀ values of nineteen compounds ranging from 100 to 901 μM for AD-CDR1 demonstrated that relative resistance index (RI) values were between 8 and 274. In comparison, only seven compounds had RI values superior to 4 in cells overexpressing Mdr1p. These results indicated substrate behavior for nineteen compounds for CaCdr1p and seven compounds for CaMdr1p, as these compounds were transported via MDR transporter overexpressing cells and not by the AD1-8u⁻ cells. Finally, in a combination assay with fluconazole, two compounds (1d and 1f) have shown a synergistic effect (fractional inhibitory concentration index (FICI) values ≤ 0.5) at micromolar concentrations in the AD-MDR1 yeast strain overexpressing CaMdr1p-protein, indicating an excellent potency toward chemosensitization.

Two series of piperazinyl-pyrrolo[1,2-a]quinoxaline derivatives were prepared via a Buchwald–Hartwig cross-coupling reaction and then evaluated for their ability to inhibit the drug efflux activity of two Candida albicans transporters.     

Intrathoracic anastomosis after oesophageal resection for cancer

Cervical anastomosis has been advocated to avoid the pulmonary complications and life-threatening anastomotic disruptions following intrathoracic oesophagogastric anastomosis. This is a retrospective review of 111 oesophageal resections followed by an intrathoracic anastomosis. These resections were performed between September 1993 and August 1994 within a residency training program. The left thoracoabdominal approach was used for distal tumours and the Ivor Lewis technique for more proximal tumours. Squamous cell carcinoma accounted for 72% patients (n = 80), adenocarcinoma for 25% (n = 28), and others for 2.7% patients (n = 3). Of the patients, 69% had pathologic Stage III tumours. Operative mortality rate was 1.8% (two patients). Perioperative complications occurred in 39 patients, including anastomotic leak in 10 patients and myocardial infarction in 2 patients. In the absence of a leak, there were no major pulmonary complications requiring intensive care or ventilatory support. Of those patients with anastomotic disruption, 89% were salvaged by early clinical diagnosis and appropriate treatment. We conclude that transthoracic oesophagectomy with an intrathoracic anastomosis is a safe procedure that can be performed with low mortality and acceptable morbidity. © 1996 Wiley-Liss, Inc.     

How Important is the Tunnel Position in Outcomes Post-ACL Reconstruction: A 3D CT-Based Study

BackgroundDrilling the femoral and tibial tunnels at their anatomical locations are critical for good outcomes and involve seeing the footprints well. We intended to compare two techniques of drilling the tunnels and the patient-reported outcomes and knee stability of patients undergoing single bundle ACL reconstruction using 3D CT to evaluate if the tunnels were anatomical or not.Materials and MethodsSixty single bundle ACL reconstructions were analyzed, 30 each with Technique A and B. Pre-operative and after a minimum 27 month follow-up Lysholm, IKDC, Tegner score, hop test, and Lachman test were noted. 3D CT was done to classify femoral tunnels positions as being well placed, slightly or grossly misplaced and tibial tunnels as optimal or suboptimal and compared.ResultsSixty ACL reconstructions had full follow-up with a mean follow-up of 34 months. There was no significant difference between tunnel positions between the two techniques. Well-placed femoral tunnel had better Lysholm score (62.2 ± 16.2 v/s 48.5 ± 17.2, p 0.002) and IKDC score (62.5 ± 14.3 v/s 52.7 ± 15.1, p 0.012).). Those who had their surgeries within 3 months of their injury had better hop test (4.4 ± 0.9 v/s 3.9 ± 1, p 0.034) and IKDC scores (62.5 ± 15.8 v/s 33.2 ± 13.8, p 0.026) as compared to those that had surgery done after 3 monthsConclusionTibial tunnel positions were optimal in most cases and did not differ between the two techniques. Well-placed femoral tunnels and surgeries done within 3 months of the injury produced best results.     

Cervicofacial actinomycosis

Cervicofacial actinomycosis is an uncommon, chronic, suppurative, and granulomatous bacterial infection. It is often of dental origin and tends to mimic other dental infections, granulomatous disorders, and cancers. The initial diagnostic workup, predicated upon imaging and tissue biopsies, is frequently nonspecific. A definitive diagnosis is usually rendered only after surgical excision and histologic examination of the cervicofacial mass. We propose a classification of three stages: localized infection without sinus involvement, localized infection with sinus involvement, and disseminated infection, to facilitate recognition, diagnosis, and early aggressive treatment. Untreated infection may be life-threatening. Therapy may require long-term antibiotics; however, many cases may also necessitate complete surgical excision.     

ENIGMA-DTI: Translating reproducible white matter deficits into personalized vulnerability metrics in cross-diagnostic psychiatric research

The ENIGMA-DTI (diffusion tensor imaging) workgroup supports analyses that examine the effects of psychiatric, neurological, and developmental disorders on the white matter pathways of the human brain, as well as the effects of normal variation and its genetic associations. The seven ENIGMA disorder-oriented working groups used the ENIGMA-DTI workflow to derive patterns of deficits using coherent and coordinated analyses that model the disease effects across cohorts worldwide. This yielded the largest studies detailing patterns of white matter deficits in schizophrenia spectrum disorder (SSD), bipolar disorder (BD), major depressive disorder (MDD), obsessive–compulsive disorder (OCD), posttraumatic stress disorder (PTSD), traumatic brain injury (TBI), and 22q11 deletion syndrome. These deficit patterns are informative of the underlying neurobiology and reproducible in independent cohorts. We reviewed these findings, demonstrated their reproducibility in independent cohorts, and compared the deficit patterns across illnesses. We discussed translating ENIGMA-defined deficit patterns on the level of individual subjects using a metric called the regional vulnerability index (RVI), a correlation of an individual's brain metrics with the expected pattern for a disorder. We discussed the similarity in white matter deficit patterns among SSD, BD, MDD, and OCD and provided a rationale for using this index in cross-diagnostic neuropsychiatric research. We also discussed the difference in deficit patterns between idiopathic schizophrenia and 22q11 deletion syndrome, which is used as a developmental and genetic model of schizophrenia. Together, these findings highlight the importance of collaborative large-scale research to provide robust and reproducible effects that offer insights into individual vulnerability and cross-diagnosis features.     

Emergency subtotal hepatectomy: a new concept for acetaminophen-induced acute liver failure: temporary hepatic support by auxiliary orthotopic liver transplantation enables long-term success

INTRODUCTION: Acetaminophen (paracetamol) overdose (AOD) has recently emerged as the leading cause of acute liver failure (ALF) in the United States, with an incidence approaching that seen in the United Kingdom. We describe a new way to treat AOD ALF patients fulfilling King's College criteria for "super-urgent" liver transplantation. METHODS: Beginning in June 1998, we have been piloting a clinical program of subtotal hepatectomy and auxiliary orthotopic liver transplantation (ALT) for AOD ALF. Our technique is based on the following principles: (1) subtotal hepatectomy; (2) auxiliary transplantation of a whole liver graft; (3) gradual withdrawal of immunosuppression after recovery. Results were compared with patients who had undergone an orthotopic liver transplantation (OLT) for AOD ALF in the same period. Quality of life comparisons were made using the SF36 questionnaire. RESULTS: Thirteen patients underwent this procedure between June 1998 and March 2005. Median survival is 68 months (range, 0-102 m). Actual survival data show that 9 of 13 patients are alive (69%) compared with 7 of 13 OLT patients (54%). One ALT patient required a retransplantation with an OLT due to hepatic vein thrombosis, and immunosuppression is therefore maintained. The other 8 surviving ALT patients are off immunosuppression. These 8 ALT patients have normal liver function and have a better quality of life compared with the 7 surviving OLT patients. CONCLUSION: Our results with this new technique are encouraging: 69% actual survival, no long-term immunosuppression requirement, and improved quality of life in the 62% successful cases.