Miracle-dz/UniFAR-FTUs huggingface dataset:
Physical Incorporation of NADPH-Cytochrome P450 Reductase and Cytochrome P450 into Phospholipid Vesicles Using Glycocholate and Bio-Beads

In a previous study from our laboratory (Drug Metab Dispos 34: 660–666, 2006), we found several limitations with published methods (cholate gel filtration and cholate dialysis) for the incorporation of cytochromes P450 and P450 reductase into phospholipid vesicles. We found that a significant proportion of reductase was not incorporated in the vesicles when the amount of reductase was equal to or greater than that of CYP2B4 in the systems reconstituted with phosphatidylcholine. Furthermore, implementation of these methods compromised the ability of the CYP2B4 to form a ferrous carbon monoxy complex. In the current study, a comparison of results using the detergent-dialysis method with five similar detergents having the “bile salt” ring structure showed that glycocholate results in the greatest incorporation of reductase and the least loss in the ferrous carbon monoxy CYP2B4 complex. The method is further improved by using Bio-Beads SM-2 to remove detergent instead of the lengthy dialysis procedure or size exclusion chromatography that significantly dilutes the protein and lipid concentrations of the preparation. The method is shown to be applicable over a range of lipid/CYP2B4 ratios, and by using assay methods for total lipid, reductase, and CYP2B4, this improved reconstitution method resulted in increased incorporation efficiencies while minimizing the protein degradation inherent with these procedures.
A Fast and Accurate Image-Registration Algorithm Using Prior Knowledge

We propose an iterative image-registration algorithm to estimate the homography between two plane surfaces based on prior information. The difference to established methods using algorithms like SIFT and SURF lies in the kind of features used for the calculation. Instead of patch-based features, the algorithm uses prior information to search for features along 1-D signals and their expected counterparts. This reduces the computational complexity by one dimension and decreases the search space for feature correspondences enormously. The reduction in dimension and the comparison of whole image strips yields better accuracy and lower computational effort, while being able to handle any perspective transformation. Based on a broad variety of test images, an estimation of sufficient prior knowledge and a comparison with the established methods SIFT, SURF and ORB is given. We show that the iterative nature and the strip-based approach makes the algorithm very flexible, thereby achieving high accuracy at low computational effort.
Identification of factors relevant for the estimation of smartphone life cycle

The smartphone industry is a fast-evolving industry with a bright future as smartphones became everyone's daily habit. This paper gathers existing research knowledge and provides the identification of factors that affect the stakeholders and the length of smartphone life cycle. Socio-demographic, economic, technological and psychological factors are found relevant by using comparative and compilation methods. Further aim of this research is to use the identified factors in a following research on life cycle estimation.
Improved Depth Image-Based Rendering Using an Adaptive Compensation Method on an Autostereoscopic 3-D Display for a Kinect Sensor

Depth image-based rendering (DIBR) is a 2-D-3-D view conversion technology in a space domain that corresponds to depth map. DIBR system requires only a single color image and an associated depth map to generate synthesized autostereoscopic 3-D views, but the quality of the result is depreciated due to the disoccluded areas in the depth map. Because of this problem, an improved DIBR method that uses a depth map adaptive compensation method is proposed. Using a fast parallax lookup table, the position of holes is allocated and depth map is split into blocks for statistical analysis and classification in order to estimate the quantity of holes. The result of the classification is used for adaptive multimode filtering to optimize the depth map. The experimental results show that the proposed method not only enhances the quality of depth map by compensating for the bigger and smaller areas of holes referring to analysis results, and by determining the filling method using the type of holes, but also reduces the number of holes that retain better depth map and reduces computation time.
A bare-hand gesture interaction system for virtual environments

Hand-based gestures provide direct mappings of user actions to 3D UI tasks; they are becoming a more attractive interaction alternative than keyboards, mice, controllers, among others. In this paper, we present a fast algorithm for hand gesture recognition for interaction in virtual environments. The method applies mathematical morphology operators (binarization and dilation) to acquire a clean segmented hand image from a depth data stream on which a curvature-metric and K-means algorithm is applied to detect the fingertips, then using fingertip and palm positions together with anthropomorphic metrics and a rule based system we perform gesture recognition. In addition, the intermittence gesture spotting problem is reduced using a digital integrator. Finally, a set of virtual environments were designed to demonstrate the performance, reliability and feasibility of our method.
Predicting query performance in microblog retrieval

Query Performance Prediction (QPP) is the estimation of the retrieval success for a query, without explicit knowledge about relevant documents. QPP is especially interesting in the context of Automatic Query Expansion (AQE) based on Pseudo Relevance Feedback (PRF). PRF-based AQE is known to produce unreliable results when the initial set of retrieved documents is poor. Theoretically, a good predictor would allow to selectively apply PRF-based AQE when performance of the initial result set is good enough, thus enhancing the overall robustness of the system. QPP would be of great benefit in the context of microblog retrieval, as AQE was the most widely deployed technique for enhancing retrieval performance at TREC. In this work we study the performance of the state of the art predictors under microblog retrieval conditions as well as introducing our own predictors. Our results show how our proposed predictors outperform the baselines significantly.
Distributed Architectures and Components for the Virtual Enterprises

A comprehensive solution for enterprise information systems, access to technical or business information, and electronic publishing and commerce for the concurrent enterprising of tomorrow, requires the integration of new sophisticated technologies and systems. This paper presents the research and results achieved in the framework of the VEGA project, establishing an infrastructure supporting the technical and business operations of virtual enterprises, with workflow tools and distributed architectures developed in compliance with product data technology. The VEGA objective is a platform enabling companies to work together, and being the basement for future integration and distribution of business components as promoted in the WONDA 2 project. The WONDA main goal is to specify a scalable 3-Tier component-based architecture for secure and sophisticated access to versatile information systems and electronic content. This paper, which reports on the VEGA’s story and introduces to some WONDA concepts, provides a limited picture of the overall objectives and results achieved in this still experimental area, and should be an incentive for the reader to go further into the projects achievements.
Understanding performance management in schools: a dialectical approach

Purpose – The purpose of this paper is to provide a dialectical framework for the examination of performance management in schools. Design/methodology/approach – The paper is based upon a qualitative study of ten headteachers that involved in-depth semi-structured interviews. Findings – The findings identified four dialectical tensions that underpin performance management in schools: the responsibility to teachers and the responsibility to pupils; external accountability and professional autonomy; discipline of teachers and support of teachers; fixed processes and improvisational practices. Research limitations/implications – This paper provides a means of examining the performance management of teachers from an alternative perspective, one that embraces tensions and contradictions and gives headteachers a richer understanding of how teachers are evaluated and judged. Originality/value – This paper moves beyond the traditional perspective of performance management in schools as a means of subjugation and .
Towards an Areal Typology of Prefixal Perfectivization

Abstract This paper presents the results of an areal-typological study of prefixal perfectivization in Slavic, Baltic, Yiddish, Hungarian, Ossetic and Kartvelian languages based on a uniform set of morphological and functional-semantic parameters. It is shown that there are two clusters of prefixal perfectivization, i.e., Slavic and Kartvelian, while other languages display significant degrees of difference both from each other and from the two clusters. It is further argued on the basis of existing evidence that the development and distribution of the current “landscape” of preverb-based aspectual systems in the languages of Central and Eastern Europe and the Caucasus have been shaped by a complex interplay of genetic, typological and contact factors.
Failure characterization and error detection in distributed web applications

Arshad, Fahad A. Ph.D., Purdue University, August 2014. Failure Characterization and Error Detection in Distributed Web Applications . Major Professor: Saurabh Bagchi. We have seen an evolution of increasing scale and complexity of enterprise-class distributed applications, such as, web services for providing anything from critical infrastructure services to electronic commerce. With this evolution, it has become increasingly difficult to understand how these applications perform, when do they fail, and what can be done to make them more resilient to failures, both due to hardware and due to software? Application developers tend to focus on bringing their applications to market quickly without testing the complex failure scenarios that can disrupt or degrade a given web service. Operators configure these web services without the complete knowledge of how the configurations interact with the various layers. Matters are not helped by ad hoc and often poor quality failure logs generated by even mature and widely used software systems. Worse still, both end users and servers sometime suffer from “silent problems” where something goes wrong without any immediate obvious end-user manifestation. To address these reliability issues, characterizing and detecting software problems with some post-detection diagnosticcontext is crucial. This dissertation first presents a fault-injection and bug repository-based evaluation to characterize silent and non-silent software failures and configuration problems in three-tier web applications and Java EE application servers. Second, for detection of software failures, we develop simple low-cost application-generic and applicationspecific consistency checks, while for duplicate web requests (a class of performance problems), we develop a generic autocorrelation-based algorithm at the server end.
Liver stiffness measurement versus liver biopsy to predict survival and decompensations of cirrhosis among HIV/hepatitis C virus-coinfected patients

Objective:To compare the prognostic performance of liver biopsy with that of liver stiffness measurement (LSM) to predict survival and liver decompensations among HIV/hepatitis C virus (HCV)-coinfected patients. Design:Retrospective cohort study. Methods:Cohort of 297 HIV/HCV-coinfected patients, who underwent a liver biopsy and LSM separated by 12 months or less, followed in 10 Spanish tertiary care centers from December 2005 to December 2011 (median follow-up, 5 years; interquartile range, 4.2–5.4 years). Liver biopsies were staged following the Scheuer's score. LSM was obtained by hepatic transient elastometry. A survival analysis was carried out and the integrated discrimination improvement was computed to compare the ability of the survival models to predict outcomes. The incidence of death from any cause and of development of the first decompensation of cirrhosis was calculated. Results:Overall mortality rate was 1.63 [95% confidence interval (CI) 1.06–2.49] per 100 person-years. The adjusted hazard ratio [AHR (95% CI)] of baseline fibrosis (per stage of fibrosis) was 1.52 (1.08–2.15, P = 0.017) and of LSM (per 5 kPa increase) 1.28 (1.12–1.46, P < 0.001). LSM including models yielded a performance 3.9% better than the liver biopsy-based models (P = 0.072). For the prediction of liver decompensations, the AHR (95% CI) of baseline fibrosis by liver biopsy (per stage of fibrosis) was 1.67 (1.15–2.43, P = 0.007) and of LSM (per 5 kPa increase) 1.37 (1.21–1.54, P < 0.001). LSM-based models yielded a performance 8.4% better than the liver biopsy-based models (P = 0.045). Conclusion:LSM-based prediction achieves a similar yield than liver biopsy-based models to predict overall mortality in HIV/HCV-coinfected patients. Models including LSM could predict better liver decompensations than liver biopsy.
Teaching internet algorithmics

We describe an Internet-based approach for teaching important concepts in a Junior-Senior level course on the design and analysis of data structures and algorithms (traditionally called CS7 or DS&amp;A). The main idea of this educational paradigm is twofold. First, it provides fresh motivation for fundamental algorithms and data structures that are finding new applications in the context of the Internet. Second, it provides a source for introducing new algorithms and data structures that are derived from specific Internet applications. In this paper, we suggest some key pedagogical and curriculum updates that can be made to the classic CS7/DS&amp;A course to turn it into a course on Internet Algorithmics. We believe that such a course will stimulate new interest and excitement in material that is perceived by some students to be stale, boring, and purely theoretical. We argue that the foundational topics from CS7/DS&amp;A should remain even when it is taught in an Internet-centric manner. This, of course, should come as no surprise to the seasoned computer scientist, who understands the value of algorithmic thinking.
Security for Future Software Defined Mobile Networks

5G constitutes the next revolution in mobile communications. It is expected to deliver ultra-fast, ultra-reliable network access supporting a massive increase of data traffic and connected nodes. Different technologies are emerging to address the requirements of future mobile networks, such as Software Defined Networking (SDN), Network Function Virtualization (NFV) and cloud computing concepts. In this paper, we introduce the security challenges these new technologies are facing, inherent to the new telecommunication paradigm. We also present a multitier approach to secure Software Defined Mobile Network (SDMN) by tackling security at different levels to protect the network itself and its users. First, we secure the communication channels between network elements by leveraging Host Identity Protocol (HIP) and IPSec tunnelling. Then, we restrict the unwanted access to the mobile backhaul network with policy based communications. It also protects the backhaul devices from source address spoofing and Denial of Service (DoS) attacks. Finally, we leverage Software Defined Monitoring (SDM) and data collection to detect, prevent and react to security threats.
Hybrid biosynthetic gene therapy vector development and dual engineering capacity

Significance Vaccination is a powerful means of preempting or treating disease. The process depends on successful recognition of a foreign entity (an antigen) to elicit a strong immune response. The delivery of an antigen encoded as a DNA molecule (a genetic antigen) requires the assistance of a vector to facilitate the process of gene expression within immune system sentinels termed antigen-presenting cells (APCs). In this study, two normally distinct vectors (a bacterial cell and a synthetic polymer) were combined to generate a hybrid vector. The new vector coupled synergistic mechanisms to assist and improve gene delivery to APCs. Furthermore, the hybrid vector provides unique and complimentary engineering capabilities that were demonstrated to tailor and improve APC gene delivery further. Genetic vaccines offer a treatment opportunity based upon successful gene delivery to specific immune cell modulators. Driving the process is the vector chosen for gene cargo packaging and subsequent delivery to antigen-presenting cells (APCs) capable of triggering an immune cascade. As such, the delivery process must successfully navigate a series of requirements and obstacles associated with the chosen vector and target cell. In this work, we present the development and assessment of a hybrid gene delivery vector containing biological and biomaterial components. Each component was chosen to design and engineer gene delivery separately in a complimentary and fundamentally distinct fashion. A bacterial (Escherichia coli) inner core and a biomaterial [poly(beta-amino ester)]-coated outer surface allowed the simultaneous application of molecular biology and polymer chemistry to address barriers associated with APC gene delivery, which include cellular uptake and internalization, phagosomal escape, and intracellular cargo concentration. The approach combined and synergized normally disparate vector properties and tools, resulting in increased in vitro gene delivery beyond individual vector components or commercially available transfection agents. Furthermore, the hybrid device demonstrated a strong, efficient, and safe in vivo humoral immune response compared with traditional forms of antigen delivery. In summary, the flexibility, diversity, and potential of the hybrid design were developed and featured in this work as a platform for multivariate engineering at the vector and cellular scales for new applications in gene delivery immunotherapy.
The Need for Salt: Does a Relationship Exist Between Cystic Fibrosis and Exercise-Associated Hyponatremia?

Abstract Lewis, DP, Hoffman, MD, Stuempfle, KJ, Owen, BE, Rogers, IR, Verbalis, JG, and Hew-Butler, TD. The need for salt: Does a relationship exist between cystic fibrosis and exercise-associated hyponatremia? J Strength Cond Res 28(3): 807–813, 2014—Salt replacement is often recommended to prevent exercise-associated hyponatremia (EAH) despite a lack of evidence to support such practice. Exercise-associated hyponatremia is known to be a complex process resulting from the interplay of hydration, arginine vasopressin, and sodium balance. Although evidence suggests overhydration is the dominant pathophysiologic factor in most cases, the contributions of sweat sodium losses remain unclear. A theoretical genetic mechanism producing exuberant sweat sodium loss in athletes is the presence of cystic fibrosis (CF) gene. Individuals with CF develop hypovolemic hyponatremia by sodium loss via sweat through a defective chloride ion transport channel, the CF transmembrane conductance regulator (CFTR). Elevated sweat sodium concentrations in CF single heterozygotes suggest that athletes developing EAH may be CFTR carriers. We targeted the 2010 and 2011 Western States Endurance Run ultramarathon, an event where athletes with EAH regularly present in a hypovolemic state, for a cohort maximizing the potential to document such a relationship. A total of 798 runners started the 2010 (n = 423) and 2011 (n = 375) races. Of the 638 finishers, 373 were screened for EAH by blood draw, 60 (16%) were found to have EAH, and 31 (alpha = 0.05 for n = 9) reported their CF result from a saliva-based genetic testing kit. Neither the 31 EAH-positive athletes nor the 25 EAH-negative comparison cohort athletes tested positive for a CF mutation. This null relationship suggests that CFTR mutations are not associated with the development of EAH and that salt supplementation is unnecessary for such a reason.
Novel Resistance-Nodulation-Cell Division Efflux System AdeDE in Acinetobacter Genomic DNA Group 3

ABSTRACT Resistance-nodulation-cell division type efflux pump AdeDE was identified in acinetobacters belonging to genomic DNA group 3. Inactivation of adeE showed that it may be responsible for reduced susceptibility to amikacin, ceftazidime, chloramphenicol, ciprofloxacin, erythromycin, ethidium bromide, meropenem, rifampin, and tetracycline. However, unlike what was found for other similar efflux systems, the open reading frame for the outer membrane component was not found downstream of the adeDE gene cluster.
16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model

Summary 16GT is a variant caller for Illumina WGS and WES germline data. It uses a new 16-genotype probabilistic model to unify SNP and indel calling in a single variant calling algorithm. In benchmark comparisons with five other widely used variant callers on a modern 36-core server, 16GT ran faster and demonstrated improved sensitivity in calling SNPs, and it provided comparable sensitivity and accuracy in calling indels as compared to the GATK HaplotypeCaller. Availability and implementation https://github.com/aquaskyline/16GT Contact rluo5@jhu.edu Supplementary information Supplementary tables and notes are available at Bioinformatics online.
Metabolism of Sialic Acid by Bifidobacterium breve UCC2003

ABSTRACT Bifidobacteria constitute a specific group of commensal bacteria that inhabit the gastrointestinal tracts of humans and other mammals. Bifidobacterium breve UCC2003 has previously been shown to utilize several plant-derived carbohydrates that include cellodextrins, starch, and galactan. In the present study, we investigated the ability of this strain to utilize the mucin- and human milk oligosaccharide (HMO)-derived carbohydrate sialic acid. Using a combination of transcriptomic and functional genomic approaches, we identified a gene cluster dedicated to the uptake and metabolism of sialic acid. Furthermore, we demonstrate that B. breve UCC2003 can cross feed on sialic acid derived from the metabolism of 3′-sialyllactose, an abundant HMO, by another infant gut bifidobacterial strain, Bifidobacterium bifidum PRL2010.
Plant Production of Vaccine Against HPV: A New Perspectives

Infection by human papilloma virus (HPV) attracted attention in connection with cervical cancer in humans (zur Hausen, 1996). HPV type 16 alone accounts for approximately 50% of all cases of cervical cancer. The virus icosahedral capsid is composed of the L1 major and the L2 minor proteins. L1 alone has the capacity to self-assemble into virus-like particles (VLPs) without participation of L2 or other proteins. Because of similar immunogenicity compared to infectious virions, VLPs can be produced and used as a safe prophylactic vaccine against viral transmission of cervical cancer. During recent years two highly efficient VLP-based HPV vaccines (e.g. Gardasil, Merck MSD and Cervarix, GlaxoSmithKline) become available. For commercial production of vaccines and recombinant therapeutics, plants are often considered as a cost-effective alternative with several benefits. Firstly, production in plants can be easily scaled up in the case of acute demand for production and secondly, produced proteins are unlikely to be contaminated by human or animal pathogens, toxins and oncogenic sequences. Moreover, plants provide a convenient environment for protein expression and storage including the possibility of direct administration as edible vaccine if expressed in the appropriate plant tissue. In this article, we report recent promising advances in the production of prophylactic and therapeutic vaccines against HPV by expression of the relevant antigens in plants, and discuss future prospects for the use of such vaccines.