Reciprocal perspective as a super learner improves drug-target interaction prediction (MUSDTI).

The identification of novel drug-target interactions (DTI) is critical to drug discovery and drug repurposing to address contemporary medical and public health challenges presented by emergent diseases. Historically, computational methods have framed DTI prediction as a binary classification problem (indicating whether or not a drug physically interacts with a given protein target); however, framing the problem instead as a regression-based prediction of the physiochemical binding affinity is more meaningful. With growing databases of experimentally derived drug-target interactions (e.g. Davis, Binding-DB, and Kiba), deep learning-based DTI predictors can be effectively leveraged to achieve state-of-the-art (SOTA) performance. In this work, we formulated a DTI competition as part of the coursework for a senior undergraduate machine learning course and challenged students to generate component DTI models that might surpass SOTA models and effectively combine these component models as part of a meta-model using the Reciprocal Perspective (RP) multi-view learning framework. Following 6 weeks of concerted effort, 28 student-produced component deep-learning DTI models were leveraged in this work to produce a new SOTA RP-DTI model, denoted the Meta Undergraduate Student DTI (MUSDTI) model. Through a series of experiments we demonstrate that (1) RP can considerably improve SOTA DTI prediction, (2) our new double-cold experimental design is more appropriate for emergent DTI challenges, (3) that our novel MUSDTI meta-model outperforms SOTA models, (4) that RP can improve upon individual models as an ensembling method, and finally, (5) RP can be utilized for low computation transfer learning. This work introduces a number of important revelations for the field of DTI prediction and sequence-based, pairwise prediction in general.

Comparison of Laser Doppler Imaging (LDI) and clinical assessment in differentiating between superficial and deep partial thickness burn wounds.

PURPOSE OF PRESENTATION/STUDY: To compare the accuracy of Laser Doppler Imaging (LDI) and clinical assessment in differentiating between superficial and deep partial thickness burns to decide whether early tangential excision and grafting or conservative management should be employed to optimize burn and patient management. STUDY PERIOD: March 2015 to November 2016. METHODS/PROCEDURE DETAILS: Ninety two wounds in 34 patients reporting within 5days of less than 40% burn surface area were included. Unstable patients, pregnant females and those who expired were excluded. The wounds were clinically assessed and LDI done concomitantly Plastic Surgeons blinded to each other's findings. Wound appearance, color, blanching, pain, hair follicle dislodgement were the clinical parameters that distinguished between superficial and deep partial thickness burns. On day 21, the wounds were again assessed for the presence of healing by the same plastic surgeons. The findings were correlated with the initial findings on LDI and clinical assessment and the results statistically analyzed. RESULTS/OUTCOME: The data of 92 burn wounds was analyzed using SPSS (ver. 17). Clinical assessment correctly identified the depth of 75 and LDI 83 wounds, giving diagnostic accuracies of 81.52% and 90.21% respectively. The sensitivity of clinical assessment was 81% and of LDI 92.75%, whereas the specificity was 82% for both. The positive predictive value was 93% for clinical assessment and 94% for LDI while the negative predictive value was 59% and 79% respectively. CONCLUSIONS: Predictive accuracy of LDI was found to be better than clinical assessment in the prediction of wound healing, the gold standard for wound healing being 21 days. As such it can prove to be a reliable and viable cost effective alternative per se to clinical assessment.

Microphthalmia, persistent hyperplastic hyaloid vasculature and lens anomalies following overexpression of VEGF-A188 from the alphaA-crystallin promoter.

PURPOSE: During growth of the embryonic eye, dose- and site-specific expression of heparin-binding growth factors is critical for the formation of an appropriate vascular supply. Overexpression of vascular endothelial growth factor-A(188) (VEGF-A(188)), a strongly heparin-binding, endothelial-specific mitogen, leads to severe disturbance of vascular and overall ocular morphology. This study aimed to evaluate the effects of VEGF-A(188) overexpression on growth of ocular tissue components. METHODS: Stereological and immunohistochemical methods were employed to identify the vascular profiles, ocular tissue proportions, and cell types in VEGF-A(188) transgenic mice and compare them with wild-type mice. RESULTS: In VEGF-A(188) transgenic mice, both lens tissue and total ocular volume were reduced, whereas cross-sectional areas of hyaloid blood vessels, retina, iris, and optic stalk tissues were significantly increased compared to wild-type mice. Endothelial and pericyte cell numbers in the hyaloid vasculature of transgenic mice were increased three fold, with pericytes assuming their characteristic extraluminal position. CONCLUSIONS: Overexpression of VEGF-A(188) in the murine lens results in microphthalmia, in addition to hypertrophy and persistence of the hyaloid vasculature. This is similar to the human disorder persistent hyperplastic primary vitreous (PHPV). The murine model is a useful, experimental paradigm for investigation of this condition.

Unique vascular phenotypes following over-expression of individual VEGFA isoforms from the developing lens.

Formation of a correctly organised vasculature and subsequently embryonic survival is critically dependent on the dosage and site-specific expression of VEGF. Murine VEGF exists in three common isoforms (viz. 120, 164 and 188 amino acids) having different organ specific distribution levels. Gene knock-in studies show that expression of any of the individual isoforms of VEGF extends survival until birth, although each is associated with distinct organ-specific abnormalities. Comparison of the effects of VEGF isoform expression is complicated by the general lethality of mis-expression, in addition to cumulative effects of adjacent tissues from the inappropriately patterned vasculature. Here we investigate the effects of over-expression of individual VEGFA isoforms from the lens-specific alphaA-Crystallin promoter and characterise their effects on the vessel morphology of the hyaloid and developing retinal vasculature. Since the hyaloid vasculature is an anatomically distinct, transient vasculature of the eye, comprising 3 cell types (endothelium, pericytes and macrophages) it is possible to more readily interpret the role of individual VEGF-A isoforms in vascular pattern formation in this model. The severity of the vascular phenotype, characterised by a hyperplastic hyaloid at E13.5 and subsequently retinal vascular patterning and ocular defects, is most severe in transgenics over-expressing the more diffusible forms of VEGFA (120 and 164), whereas in VEGFA(188) transgenics the hyaloid vascular defects partially resolve post-natally. The results of this study indicate that individual isoforms of VEGFA induce distinct vascular phenotypes in the eye during embryonic development and that their relative doses provide instructive cues for vascular patterning.