ESG: Extended Similarity Group method for automated protein function prediction

We present here the Extended Similarity Group (ESG) method, which annotates query sequences with Gene Ontology (GO) terms by assigning probability to each annotation computed based on iterative PSI-BLAST searches. Conventionally sequence homology based function annotation methods, such as BLAST, retrieve function information from top hits with a significant score (E-values). In contrast, the PFP method, which we have presented previously, goes one step ahead in utilizing a PSI-BLAST result by considering very weak hits even an E-value of up to 100 and also by incorporating the functional association between GO terms (FAM matrix) computed using term co-occurrence frequencies in the UniProt database. PFP is very successful which is evidenced by the top rank in the function prediction category in CASP7 competition. Our new approach, ESG method, further improves the accuracy of PFP by essentially employing PFP in an iterative fashion. An advantage of ESG is that it is built in a rigorous statistical framework: Unlike PFP method that assigns a weighted score to each GO term, ESG assigns a probability based on weights computed using the E-value of each hit sequence on the path between the original query sequence and the current hit sequence

Finite Element Flow Simulations of the EUROLIFT DLR-F11 High Lift Configuration

This paper presents flow simulation results of the EUROLIFT DLR-F11 multi-element wing configuration, obtained with a highly scalable finite element solver, PHASTA. This work was accomplished as a part of the 2nd high lift prediction workshop. In-house meshes were constructed with increasing mesh density for analysis. A solution adaptive approach was used as an alternative and its effectiveness was studied by comparing its results with the ones obtained with other meshes. Comparisons between the numerical solution obtained with unsteady RANS turbulence model and available experimental results are provided for verification and discussion. Based on the observations, future direction for adaptive research and simulations with higher fidelity turbulence models is outlined.Comment: 52nd Aerospace Sciences Meetin

Anisotropic Boundary Layer Adaptivity of Multi-Element Wings

Multi-element wings are popular in the aerospace community due to their high lift performance. Turbulent flow simulations of these configurations require very fine mesh spacings especially near the walls, thereby making use of a boundary layer mesh necessary. However, it is difficult to accurately determine the required mesh resolution a priori to the simulations. In this paper we use an anisotropic adaptive meshing approach including adaptive control of elements in the boundary layers and study its effectiveness for two multi-element wing configurations. The results are compared with experimental data as well as nested refinements to show the efficiency of adaptivity driven by error indicators, where superior resolution in wakes and near the tip region through adaptivity are highlighted.Comment: 52nd Aerospace Sciences Meetin

Review of Concussion and Return-to-Play Guidelines in Sport

Concussion is a form of mild traumatic head injury (TBI) associated with a variety of neurologic signs and symptoms. While historically trivialized in its significance, significant progress has been made in the medical literature and lay understanding of concussion. Severe TBI, long the subject of extensive research, has come under increased scrutiny following experience with blast injuries during the wars in Afghanistan and Iraq. Such experience, grievously earned, has brought significant public attention and funding to the study of head injury. However, for the civilian population, concussion continues to be the most common form of traumatic brain injury, and athletics continues to be the single largest cause of concussion. Concussion in sports has come under substantial scrutiny as a result of widely publicized injuries in major American sports, particularly football and hockey. Media coverage has increased further as understanding of the related yet distinct syndrome of chronic traumatic encephalopathy (CTE), formerly known as dementia pugilistica or punch-drunk syndrome , and its proposed mechanism of repeated sub-concussive trauma has increased. While media attention has focused primarily on concussion in professional athletes, the majority of sports-related concussions occur in youth participants.1 With relative unavailability of physicians trained in on-field assessment of concussed athletes relative to professional sports teams, youth athletes are at significant risk for short- and long-term neurologic injury from concussion. This manuscript aims to outline the natural history of sports concussion and review recent updates in on-field assessment and return-to-play guidelines

An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors.

To address the biological heterogeneity of lung cancer, we studied 199 lung adenocarcinomas by integrating genome-wide data on copy number alterations and gene expression with full annotation for major known somatic mutations in this cancer. This showed non-random patterns of copy number alterations significantly linked to EGFR and KRAS mutation status and to distinct clinical outcomes, and led to the discovery of a striking association of EGFR mutations with underexpression of DUSP4, a gene within a broad region of frequent single-copy loss on 8p. DUSP4 is involved in negative feedback control of EGFR signaling, and we provide functional validation for its role as a growth suppressor in EGFR-mutant lung adenocarcinoma. DUSP4 loss also associates with p16/CDKN2A deletion and defines a distinct clinical subset of lung cancer patients. Another novel observation is that of a reciprocal relationship between EGFR and LKB1 mutations. These results highlight the power of integrated genomics to identify candidate driver genes within recurrent broad regions of copy number alteration and to delineate distinct oncogenetic pathways in genetically complex common epithelial cancers

Auto component supply chain: a path to global India

Supply chain management works to bring the supplier, the distributor, and the customer into one cohesive process. The Supply Chain Council defined supply chain as ‘Supply Chain: The flow and transformation of raw materials into products from suppliers through production and distribution facilities to the ultimate consumer., and then Sunil Chopra and Meindl, (2001) have define Supply chain management as ‘Supply Chain Management involves the flows between and among stages in a supply chain to maximize total profitability.’ After 1950, supply chain management got a boost with the production and manufacturing sector getting highest attention. The inventory became the responsibility of the marketing, accounting and production areas. Order processing was part of accounting and sales. Supply chain management became one of the most powerful engines of business transformation. It is the one area where operational efficiency can be gained. It reduces organizations costs and enhances customer service. With the liberalization of world trade, globalization, and emergence of the new markets, many organizations have customers and competitions throughout the world, either directly or indirectly. Business communities are aware that global competitiveness is the key to the success of a business. Competitiveness is ability to produce, distribute and provide products and services for the open market in competition with others. The supply chain, a critical link between supplier, producer and customer is emerged now as an essential business process and a strategic lever, potential value contributor a differentiator for the success of any business. Supply chain management is the management of all internal and external processes or functions to satisfy a customer’s order (from raw materials through conversion and manufacture through logistics delivery.). Goods-either in raw form or processed, whole sale or retailed distribution, business or technology services, in everyday life- in the business or household- directly or indirectly supply chain is ubiquitously associated in expanding socio-economic development. Supply chain growth competitive performance and supporting strong growth impulse at micro as well as micro economic levels. Keeping the India vision at the core of the objective, the role of supply chain is to take up social economic challenges, improve competitive advantages, develop strategies, built capabilities, enhance value propositions, adapt right technology, collaborate with stakeholders and deliver environmentally sustainable outcomes with minimum resources

Simulated spinal cerebrospinal fluid leak repair: an educational model with didactic and technical components.

BACKGROUND: In the era of surgical resident work hour restrictions, the traditional apprenticeship model may provide fewer hours for neurosurgical residents to hone technical skills. Spinal dura mater closure or repair is 1 skill that is infrequently encountered, and persistent cerebrospinal fluid leaks are a potential morbidity. OBJECTIVE: To establish an educational curriculum to train residents in spinal dura mater closure with a novel durotomy repair model. METHODS: The Congress of Neurological Surgeons has developed a simulation-based model for durotomy closure with the ongoing efforts of their simulation educational committee. The core curriculum consists of didactic training materials and a technical simulation model of dural repair for the lumbar spine. RESULTS: Didactic pretest scores ranged from 4/11 (36%) to 10/11 (91%). Posttest scores ranged from 8/11 (73%) to 11/11 (100%). Overall, didactic improvements were demonstrated by all participants, with a mean improvement between pre- and posttest scores of 1.17 (18.5%; P = .02). The technical component consisted of 11 durotomy closures by 6 participants, where 4 participants performed multiple durotomies. Mean time to closure of the durotomy ranged from 490 to 546 seconds in the first and second closures, respectively (P = .66), whereby the median leak rate improved from 14 to 7 (P = .34). There were also demonstrative technical improvements by all. CONCLUSION: Simulated spinal dura mater repair appears to be a potentially valuable tool in the education of neurosurgery residents. The combination of a didactic and technical assessment appears to be synergistic in terms of educational development

Evaluating initial spine trauma response: injury time to trauma center in PA, USA.

Historical perceptions regarding the severity of traumatic spinal cord injury has led to considerable disparity in triage to tertiary care centers. This article retrospectively reviews a large regional trauma database to analyze whether the diagnosis of spinal trauma affected patient transfer timing and patterns. The Pennsylvania Trauma database was retrospectively reviewed. All acute trauma patient entries for level I and II centers were categorized for diagnosis, mechanism, and location of injury, analyzing transportation modality and its influence on time of arrival. A total of 1162 trauma patients were identified (1014 blunt injuries, 135 penetrating injuries and 12 other) with a mean transport time of 3.9 hours and a majority of patients arriving within 7 hours (\u3e75%). Spine trauma patients had the longest mean arrival time (5.2 hours) compared to blunt trauma (4.2 hours), cranial neurologic injuries (4.35 hours), and penetrating injuries (2.13 hours,