AMR-Diag: Neural network based genotype-to-phenotype prediction of resistance towards ß-lactams in Escherichia coli and Klebsiella pneumoniae.

Antibiotic resistance poses a major threat to public health. More effective ways of the antibiotic prescription are needed to delay the spread of antibiotic resistance. Employment of sequencing technologies coupled with the use of trained neural network algorithms for genotype-to-phenotype prediction will reduce the time needed for antibiotic susceptibility profile identification from days to hours. In this work, we have sequenced and phenotypically characterized 171 clinical isolates of Escherichia coli and Klebsiella pneumoniae from Norway and India. Based on the data, we have created neural networks to predict susceptibility for ampicillin, 3rd generation cephalosporins and carbapenems. All networks were trained on unassembled data, enabling prediction within minutes after the sequencing information becomes available. Moreover, they can be used both on Illumina and MinION generated data and do not require high genome coverage for phenotype prediction. We cross-checked our networks with previously published algorithms for genotype-to-phenotype prediction and their corresponding datasets. Besides, we also created an ensemble of networks trained on different datasets, which improved the cross-dataset prediction compared to a single network. Additionally, we have used data from direct sequencing of spiked blood cultures and found that AMR-Diag networks, coupled with MinION sequencing, can predict bacterial species, resistome, and phenotype as fast as 1-8 h from the sequencing start. To our knowledge, this is the first study for genotype-to-phenotype prediction: (1) employing a neural network method; (2) using data from more than one sequencing platform; and (3) utilizing sequence data from spiked blood cultures.

Artificial Intelligence and Deep Learning: The Future of Medicine and Medical Practice.

ABSTRACT: Artificial Intelligence (AI) and access to "Big Data" together with the evolving techniques in biotechnology will change the medical practice a big way. Many diseases such as type II diabetes will no longer be considered as a single disease. Many familiar cancers such as cancer of liver or pancreas will have hundreds of subtypes whose management will be very different. The way we think about diseases will change. It will no longer be possible for clinicians to make a diagnosis, remember the names of diseases, the names of drugs or management protocols without the help of computers. As computer intelligence becomes more important than human intelligence in deciding diagnosis and treatment there will be a paradigm in the role of doctors. Internet, computers and social media will become more important than individuals in decision making. As a result, medicine will go more and more egalitarian ("wiki") with increasing community participation in health decision making and management. A socialistic pattern will evolve over time globally as an adaptive reaction to the pressures put by artificial intelligence. This is because the individual differences in knowledge or intellect between human beings will become less apparent compared to the super powers of artificial intelligence. Qualities which are unique for humans such as compassion, empathy and emotional care will decide the professional success of future physicians even more than today. Today we are using artificial intelligence in diagnosis and prediction to help clinicians. Clinical algorithms and human experience cannot be replaced by machines. It will take many years to completely merge or replace humans with machines. However, we need to modify our medical education system in order to prepare the medical community and sensitize the society well in advance for a smooth transition.

Design and Validation of an Open-Source, Partial Task Trainer for Endonasal Neuro-Endoscopic Skills Development: Indian Experience.

BACKGROUND: Box trainers are ideal simulators, given they are inexpensive, accessible, and use appropriate fidelity. OBJECTIVE: The development and validation of an open-source, partial task simulator that teaches the fundamental skills necessary for endonasal skull-base neuro-endoscopic surgery. METHODS: We defined the Neuro-Endo-Trainer (NET) SkullBase-Task-GraspPickPlace with an activity area by analyzing the computed tomography scans of 15 adult patients with sellar suprasellar parasellar tumors. Four groups of participants (Group E, n = 4: expert neuroendoscopists; Group N, n =19: novice neurosurgeons; Group R, n = 11: neurosurgery residents with multiple iterations; and Group T, n = 27: neurosurgery residents with single iteration) performed grasp, pick, and place tasks using NET and were graded on task completion time and skills assessment scale score. RESULTS: Group E had lower task completion times and greater skills assessment scale scores than both Group N and R (P ≤ 0.03, 0.001). The performance of Groups N and R was found to be equivalent; in self-assessing neuro-endoscopic skill, the participants in these groups were found to have equally low pretraining scores (4/10) with significant improvement shown after NET simulation (6, 7 respectively). Angled scopes resulted in decreased scores with tilted plates compared with straight plates (30° P ≤ 0.04, 45° P ≤ 0.001). With tilted plates, decreased scores were observed when we compared the 0° with 45° endoscope (right, P ≤ 0.008; left, P ≤ 0.002). CONCLUSIONS: The NET, a face and construct valid open-source partial task neuroendoscopic trainer, was designed. Presimulation novice neurosurgeons and neurosurgical residents were described as having insufficient skills and preparation to practice neuro-endoscopy. Plate tilt and endoscope angle were shown to be important factors in participant performance. The NET was found to be a useful partial-task trainer for skill building in neuro-endoscopy.

Self-assembly: a review of scope and applications.

Self-assembly (SA) is the preferred growth mechanism in the natural world, on scales ranging from the molecular to the macro-scale. It involves the assembling of components, which governed by a set of local interaction rules, lead to the formation of a global minimum energy structure. In this survey, the authors explore the extensive research conducted to exploit SA in three domains; first, as a bottom-up approach to fabricate semiconductor heterostructures and nano-scale devices composed of carbon nanotubes and nanowires; second, for meso-scale assembly to build systems such as three-dimensional electrical networks and microelectromechanical systems by utilising capillary force, external magnetic field and so on as the binding force; and third, as an emerging means to achieve computing via tiling, biomolecular automata and logic gates. DNA, in particular, has been a molecule of choice because of its easy availability, biological importance and high programmability as a result of its highly specific component bases.

Quantitative analysis of the Kawase versus the modified Dolenc-Kawase approach for middle cranial fossa lesions with variable anteroposterior extension.

OBJECT: The surgical corridor to the upper third of the clivus and ventral brainstem is hindered by critical neurovascular structures, such as the cavernous sinus, petrous apex, and tentorium. The traditional Kawase approach provides a 10 × 5-mm fenestration at the petrous apex of the temporal bone between the 5th cranial nerve and internal auditory canal. Due to interindividual variability, sometimes this area proves to be insufficient as a corridor to the posterior cranial fossa. The authors describe a modification to the technique of the extradural anterior petrosectomy consisting of additional transcavernous exploration and medial mobilization of the cisternal component of the trigeminal nerve. This approach is termed the modified Dolenc-Kawase (MDK) approach. METHODS: The authors describe a volumetric analysis of temporal bones with 3D laser scanning of dry and drilled bones for respective triangles and rhomboid areas, and they compare the difference of exposure with traditional versus modified approaches on cadaver dissection. Twelve dry temporal bones were laser scanned, and mesh-based volumetric analysis was done followed by drilling of the Kawase triangle and MDK rhomboid. Five cadaveric heads were drilled on alternate sides with both approaches for evaluation of the area exposed, surgical freedom, and angle of approach. RESULTS: The MDK approach provides an approximately 1.5 times larger area and 2.0 times greater volume of bone at the anterior petrous apex compared with the Kawase's approach. Cadaver dissection objectified the technical feasibility of the MDK approach, providing nearly 1.5-2 times larger fenestration with improved view and angulation to the posterior cranial fossa. Practical application in 6 patients with different lesions proves clinical applicability of the MDK approach. CONCLUSIONS: The larger fenestration at the petrous apex achieved with the MDK approach provides greater surgical freedom at the Dorello canal, gasserian ganglion, and prepontine area and better anteroposterior angulation than the traditional Kawase approach. Additional anterior clinoidectomy and transcavernous exposure helps in dealing with basilar artery aneurysms.

Quantitative analysis of variable extent of anterior clinoidectomy with intradural and extradural approaches: 3-dimensional analysis and cadaver dissection.

BACKGROUND: Drilling of the anterior clinoid process (ACP) is an integral component of surgical approaches for central and paracentral skull base lesions. The technique to drill ACP has evolved from pure intradural to extradural and combined techniques. OBJECTIVE: To describe the computerized morphometric evaluation of exposure of optic nerve and internal carotid artery with proposed tailored intradural (IDAC) and complete extradural (EDAC) anterior clinoidectomy. METHODS: We describe a morphometric subdivision of ACP into 4 quadrangles and 1 triangle on the basis of fixed bony landmarks. Computerized volumetric analysis with 3-dimensional laser scanning of dry-drilled bones for respective tailored IDAC and EDAC was performed. Both approaches were compared for the area and length of the optic nerve and internal carotid artery. Five cadaver heads were dissected on alternate sides with intradural and extradural techniques to evaluate exposure, surgical freedom, and angulation of approach. RESULTS: Complete anterior clinoidectomy provides a 2.5-times larger area and 2.7-times larger volume of ACP. Complete clinoidectomy deroofed the optic nerve to an equal extent as by proposed the partial tailored clinoidectomy approach. Tailored IDAC exposes only the distal dural ring, whereas complete EDAC exposes both the proximal and distal dural rings with complete exposure of the carotid cave. CONCLUSION: Quantitative comparative evaluation provides details of exposure and surgical ease with both techniques. We promote hybrid/EDAC technique for vascular pathologies because of better anatomic orientation. Extradural clinoidectomy is the preferred technique for midline cranial neoplasia. An awareness of different variations of clinoidectomy can prevent dependency on any particular approach and facilitate flexibility.

Free-access open-source e-learning in comprehensive neurosurgery skills training.

BACKGROUND: Since the end of last century, technology has taken a front seat in dispersion of medical education. Advancements of technology in neurosurgery and traditional training methods are now being challenged by legal and ethical concerns of patient safety, resident work-hour restriction and cost of operating-room time. To supplement the existing neurosurgery education pattern, various e-learning platforms are introduced as structured, interactive learning system. MATERIALS AND METHODS: This study focuses on the concept, formulation, development and impact of web based learning platforms dedicated to neurosurgery discipline to disseminate education, supplement surgical knowledge and improve skills of neurosurgeons. 'Neurosurgery Education and Training School (NETS), e-learning platform' has integration of web-based technologies like 'Content Management System' for organizing the education material and 'Learning Management System' for updating neurosurgeons. NETS discussion forum networks neurosurgeons, neuroscientists and neuro-technologists across the globe facilitating collaborative translational research. RESULTS: Multi-authored neurosurgical e-learning material supplements the deficiencies of regular time-bound education. Interactive open-source, global, free-access e-learning platform of NETS has around 1) 425 visitors/month from 73 countries; ratio of new visitors to returning visitors 42.3; 57.7 (2); 64,380 views from 190 subscribers for surgical videos, 3-D animation, graphics based training modules (3); average 402 views per post. CONCLUSION: The e-Learning platforms provide updated educational content that make them "quick, surf, find and extract" resources. e-Learning tools like web-based education, social interactive platform and question-answer forum will save unnecessary expenditure of time and travel of neurosurgeons seeking knowledge. The need for free access platforms is more pronounced for the neurosurgeons and patients in developing nations.