Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning and Transfer of the Salmonella Pathogenicity Island 2 Type III Secretion System for Studies of a Range of Gram-Negative Genera

ABSTRACT The engineering of bacterial strains with specific phenotypes frequently requires the use of blocks or “cassettes” of genes that act together to perform a desired function. The potential benefits of utilizing type III secretion systems in this regard are becoming increasingly realized since these systems can be used to direct interactions with host cells for beneficial purposes such as vaccine development, anticancer therapies, and targeted protein delivery. However, convenient methods to clone and transfer type III secretion systems for studies of a range of different types of bacteria are lacking. In addition to functional applications, such methods would also reveal important information about the evolution of a given type III secretion system, such as its ability to be expressed and functional outside of the strain of origin. We describe here the cloning of the Salmonella enterica serovar Typhimurium pathogenicity island 2 (SPI-2) type III secretion system onto a vector that can be easily transferred to a range of gram-negative bacterial genera. We found that expression of the cloned SPI-2 system in different Gammaproteobacteria and Alphaproteobacteria (as monitored by SseB protein levels) is dependent on the bacterial strain and growth medium. We also demonstrate that the cloned system is functional for secretion, can direct interactions with macrophages, and can be used as a novel tool to analyze the predicted interaction of SseB with host cells. This work provides a foundation for future applications where the cloned SPI-2 region (or other cloned type III systems) can provide a desired function to an engineered gram-negative strain.
Hierarchical face clustering on polygonal surfaces

Many graphics applications, and interactive systems in particular, rely on hierarchical surface representations to efficiently process very complex models. Considerable attention has been focused on hierarchies of surface approximations and their construction via automatic surface simplification. Such representations have proven effective for adapting the level of detail used in real time display systems. However, other applications such as ray tracing, collision detection, and radiosity benefit from an alternative multiresolution framework: hierarchical partitions of the original surface geometry. We present a new method for representing a hierarchy of regions on a polygonal surface which partition that surface dinto a set of face clusters. These clusters, which are connected sets of faces, represent the aggregate properties of the original surface at different scales rather than providing geometric approximations of varying complexity. We also describe the combination of an effective error metric and a novel algorithm for constructing these hierarchies. CR Categories: I.3. 5 [Computer Graphics]: Computational Geometry and Object Modeling—surface and object representations
A Framework for Post-crisis Business Continuity Plans

The traditional risk management literature is oriented towards preventing and decreasing the impact of a crisis on an organization's Business Continuity (BC). This is generally done by identifying, analyzing and assessing the impact that certain anticipated risks would have on the organization. In contrast, there is a relative dearth of literature on what organizations should do once a crisis has occurred. This paper proposes a general framework for post-crisis Business Continuity Planning (BCP). The BCP framework consists of multiple planning aspects, multiple phases and many detailed elements for BC plans. Based on the framework, organizations can design, tailor and/or assess their post-crisis BC plans. Future work will involve industry-specific extensions of the BCP framework.
Green Generative Modeling: Recycling Dirty Data using Recurrent Variational Autoencoders

This paper explores two useful modiﬁcations of the recent variational autoencoder (VAE), a popular deep generative modeling framework that dresses traditional autoencoders with probabilistic attire. The ﬁrst involves a specially-tailored form of conditioning that allows us to simplify the VAE decoder structure while simultaneously introducing robustness to outliers. In a related vein, a second, complementary alteration is proposed to further build invariance to contaminated or dirty samples via a data augmentation process that amounts to recycling. In brief, to the extent that the VAE is legitimately a representative generative model, then each output from the decoder should closely resemble an authentic sample, which can then be resubmitted as a novel input ad inﬁnitum. Moreover, this can be accomplished via special recurrent connections without the need for additional parameters to be trained. We evaluate these proposals on multiple practical outlier-removal and generative modeling tasks, demonstrating considerable improvements over existing algorithms.
The Effects of Singular Value Decomposition on Collaborative Filtering

As the information on the web increases exponentially, so do the efforts to automatically filter out useless content and to search for interesting content. Through both explicit and implicit actions, users define where their interests lie. Recent efforts have tried to group similar users together in order to better use this data to provide the best overall filtering capabilities to everyone. This thesis discusses ways in which linear algebra, specifically the singular value decomposition, can be used to augment these filtering capabilities to provide better user feedback. The goal is to modify the way users are compared with one another, so that we can more efficiently predict similar users. Using data collected from the PhDs.org website, we tested our hypothesis on both explicit web page ratings and implicit visits data.
An uncertainty reasoning method for abnormal ECG detection

The electrocardiogram (ECG) recognition is important for cardiovascular disease monitoring. It is significant to investigate automatic diagnosis methods related to wearable ECG instruments. This paper introduces Certainty Factor model based an uncertainty reasoning method for abnormal detection. It discusses the application and improvement of Certainty Factor model based on experts' experience in electrocardiogram diagnosis and puts forward the thought of determining the model parameters by machine learning. The experiment results show that the improved Certainty Factor model has better accuracy. The stability of Certainty Factor model is better than that of Bayes when the number of the disease type is increased.
Cutting Edge: Carbohydrate Profiling Identifies New Pathogens That Interact with Dendritic Cell-Specific ICAM-3-Grabbing Nonintegrin on Dendritic Cells

Dendritic cells (DC) are instrumental in handling pathogens for processing and presentation to T cells, thus eliciting an appropriate immune response. C-type lectins expressed by DC function as pathogen-recognition receptors; yet their specificity for carbohydrate structures on pathogens is not fully understood. In this study, we analyzed the carbohydrate specificity of DC-specific ICAM-3-grabbing nonintegrin (SIGN)/CD209, the recently documented HIV-1 receptor on DC. Our studies show that DC-SIGN binds with high affinity to both synthetic mannose- and fucose-containing glycoconjugates. These carbohydrate structures are abundantly expressed by pathogens as demonstrated by the affinity of DC-SIGN for natural surface glycans of the human pathogens Mycobacterium tuberculosis, Helicobacter pylori, Leishmania mexicana, and Schistosoma mansoni. This analysis expands our knowledge on the carbohydrate and pathogen-specificity of DC-SIGN and identifies this lectin to be central in pathogen-DC interactions.
DNA Repair Genes: Alternative Transcription and Gene Expression at the Exon Level in Response to the DNA Damaging Agent, Ionizing Radiation

DNA repair is an essential cellular process required to maintain genomic stability. Every cell is subjected to thousands of DNA lesions daily under normal physiological conditions. Ionizing radiation (IR) is a major DNA damaging agent that can be produced by both natural and man-made sources. A common source of radiation exposure is through its use in medical diagnostics or treatments such as for cancer radiotherapy where relatively high doses are received by patients. To understand the detailed DNA repair gene transcription response to high dose IR, gene expression exon array studies have been performed and the response to radiation in two divergent cell types, lymphoblastoid cell lines and primary fibroblasts, has been examined. These exon arrays detect expression levels across the entire gene, and have the advantage of high sensitivity and the ability to identify alternative transcripts. We found a selection of DNA repair genes, including some not previously reported, that are modulated in response to radiation. Detailed dose and time course kinetics of DNA repair transcription was conducted and results have been validated utilizing PCR methods. Alternative transcription products in response to IR were identified in several DNA repair genes including RRM2B and XPC where alternative initiation sites were found. These investigations have advanced the knowledge about the transcriptional response of DNA repair.
Differential baroreflex control of heart rate in sedentary and aerobically fit individuals.

PURPOSE We compared arterial, aortic, and carotid-cardiac baroreflex sensitivity in eight average fit (maximal oxygen uptake, VO2max = 42.2+/-1.9 mL x kg(-1) x min(-1)) and eight high fit (VO2max = 61.9+/-2.2 mL x kg(-1) x min(-1)) healthy young adults. METHODS Arterial and aortic (ABR) baroreflex functions were assessed utilizing hypo- and hyper-tensive challenges induced by graded bolus injections of sodium nitroprusside (SN) and phenylephrine (PE), respectively. Carotid baroreflex (CBR) sensitivity was determined using ramped 5-s pulses of both pressure and suction delivered to the carotid sinus via a neck chamber collar, independent of drug administration. RESULTS During vasoactive drug injection, mean arterial pressure (MAP) was similarly altered in average fit (AF) and high fit (HF) groups. However, the heart rate (HR) response range of the arterial baroreflex was significantly attenuated (P < 0.05) in HF (31+/-4 beats x min(-1)) compared with AF individuals (46+/-4 beats x min(-1)). When sustained neck suction and pressure were applied to counteract altered carotid sinus pressure during SN and PE administration, isolating the ABR response, the response range remained diminished (P < 0.05) in the HF population (24+/-3 beats x min(-1)) compared with the AF group (41+/-4 beats x min(-1)). During CBR perturbation, the HF (14+/-1 beats-min(-1)) and AF (16+/-1 beats-min(-1)) response ranges were similar. The arterial baroreflex response range was significantly less than the simple sum of the CBR and ABR (HF, 38+/-3 beats x min(-1) and AF, 57+/-4 beats x min(-1)) in both fitness groups. CONCLUSIONS These data confirm that reductions in arterial-cardiac reflex sensitivity are mediated by diminished ABR function. More importantly, these data suggest that the integrative relationship between the ABR and CBR contributing to arterial baroreflex control of HR is inhibitory in nature and not altered by exercise training.
Evolution of the Ionizing Radiation Background and Star Formation in the Aftermath of Cosmological Reionization

The temporal evolution of the ionizing UV background radiation field at high redshift provides a probe of the evolution of the early star formation rate. By comparing the observed levels of absorption in the highest redshift quasar spectra to the predictions of a hydrodynamic simulation, we determine the evolution of the photoionization rate (Γ) for neutral hydrogen in the intergalactic medium over the redshift range 4.9 ≲ z ≲ 6.1. After accounting for sampling variance, we infer a sharp increase in Γ from z ≃ 6.1 to z ≃ 5.8, probably implying reionization at this redshift. We find a decrease in Γ from z ≃ 5.6 to 5.2 at 3 σ significance. This feature is a generic signature in the aftermath of reionization, entirely consistent with the cosmological reionization process being completed at z ~ 6.1. This generic feature is a result of a significant change in the star formation rate subsequent to the cosmological reionization. There is an abrupt rise of the temperature of the intergalactic medium due to photoheating when it is reionized. This translates to a correspondingly sudden jump in the Jeans mass and a dramatic suppression of gas accretion onto the most abundant (subgalactic) halos at the epochs of interest. The star formation rate suffers a temporary setback in the aftermath of reionization, resulting in a temporary decrease in the amplitude of the ionizing radiation field.
Piezoelectric/magnetostrictive MEMS resonant sensor array for in-plane multi-axis magnetic field detection

This paper reports the demonstration of an array of piezoelectric/magnetostrictive micro electromechanical system (MEMS) magnetic resonant sensors (PM-MRS) for multi-axis magnetic field (H-field) detection. An array of 43 MHz aluminum nitride (AlN) piezoelectric resonators vibrating along different in-plane directions (θ) but coated with a magnetostrictive layer (Fe65.6Co9.4B25) with the same easy axis (EZ) exhibit unique mechanical/ electrical responses as a function of the applied H-field and its direction, enabling a high resolution multi-axis H-field detection. The sensor design yields resonators with a high quality factor (Q ∼ 1500) and electromechanical coupling coefficient (kt2 ∼ 2%) — the highest value ever reported for an AlN PM-MRS. This sensor system paves the way for low power magnetometers that enables single-chip multi-axis H-field detection.
Paradigmas, metáforas e resolução de quebra-cabeças na teoria das organizações

The purpose of this paper is to present the elements of a radical humanist critique which suggests that the discipline of organization theory has been imprisoned by its metaphors, and to stimulate an awareness through which it can begin to set itself free. The paper explores the relationship among paradigms, metaphors, and puzzle solving showing how organization theory and research is constructed upon a network of assumptions that are taken-for-granted. The metaphorical nature of theory and the implications of metaphor for theory construction are examined. A theoretical and methodological pluralism which allows the development of new perspectives for organizational analysis is suggested. While orthodoxy is based upon a few metaphors characteristic of the functionalist paradigm, metaphors characteristic of other paradigms, which challenge the ground assumptions of orthodoxy, are shown to have much to offer.
Intestinal integrity, endotoxin transport and detoxification in pigs divergently selected for residual feed intake1

ABSTRACT Microbes and microbial components potentially impact the performance of pigs through immune stimulation and altered metabolism. These immune modulating factors can include endotoxin from gram negative bacterial outer membrane component, commonly referred to as lipopolysaccharide (LPS). In this study, our objective was to examine the relationship between intestinal barrier integrity, endotoxin and inflammation with feed efficiency (FE), using pig lines divergently selected for residual feed intake (RFI) as a model. Twelve gilts (62 ± 3 kg BW) from the low RFI (LRFI, more efficient) and 12 from the high RFI (HRFI, less efficient) were used. Individual performance data was recorded for 5 wk. At the end of the experimental period, ADFI of LRFI pigs was less (P < 0.001), ADG not different between the 2 lines (P = 0.72) but the G:F of LRFI pigs was greater than for HRFI pigs (P = 0.019). Serum endotoxin concentration (P < 0.01) and the acute phase protein haptoglobin (P < 0.05) were greater in HRFI pigs. Transepithelial resistance of the ileum, transport of fluorescein isothiocyanate labeled-Dextran and-LPS in ileum and colon, as well as tight junction protein mRNA expression in ileum, did not differ between the lines, indicating the 2 lines did not differ in transport characteristics at the intestinal level. Ileum inflammatory markers, myeloperoxidase (P < 0.05) and IL-8 (P < 0.10), were found to be greater in HRFI pigs. Alkaline phosphatase (ALP) activity was significantly increased in the LRFI pigs in ileum and liver tissues and negatively correlated with blood endotoxin (P < 0.05). Lysozyme activity in the liver was not different between the lines; however, the LRFI pigs had a twofold greater lysozyme activity in ileum (P < 0.05). Despite the difference in their activity, ALP or lysozyme mRNA expression was not different between the lines in either tissue. Decreased endotoxin and inflammatory markers and the enhanced activities of antimicrobial enzymes in the LRFI line may not fully explain the difference in the FE between the lines, but they have the potential to prevent the growth potential in HRFI pigs. Further studies are needed to identify the other mechanisms that may contribute to the greater endotoxin and acute phase proteins in the HRFI pigs and the greater FE in the LRFI pigs.
Inter-language object sharing with the common language runtime: infrastructure for MS.NET

The connection between device integration and large, heterogeneous software systems will be examined. The technology itself will be presented and compared with other middleware, both distributed object and message-oriented, in the context of designing coherent, complex, scalable systems. I'll close with a use case showing that the technology enables rapid, clean software practices, and how these in turn lead to a simplified, yet more powerful, notion of " work flow ". Abstract: The Common Language Runtime (CLR) is language and platform-neutral, and provides the underlying infrastructure for the Microsoft . NET Framework. It consists of several components, including a garbage collector, class loader, metadata engine, just-in-time compiler, and debugging and security services. This talk will introduce the CLR, describe its design, and demonstrate how it enables inter-language object sharing. Abstract: Software development is a collaborative activity involving the sharing of ideas, artifacts, and knowledge among teams of engineers. Many elements are emerging to enhance the importance of collaboration in software development—geographically dispersed teams, more partnering within and across organizations, and leveraging of the Internet as a coordination infrastructure. In particular, the future of software development will be through leveraging the Internet as the base on which collaborative development services will be offered. To be successful requires that the next generation of software development environments be based on the " Three C's "-community, collaboration, and coordination. This presentation examines the requirements for future software development environments, illustrates the kinds of services that must be offered, and examines the challenges that must be overcome in collaborative environments for building the next generation of enterprise scale software solutions. As a result, the presentation explores the current state of collaborative software engineering, analyses the currently available collaborative technologies, and establishes the current state-of-the-practice in collaborative software engineering.
Special Education Eligibility: Developmental Precursors over the First Three Years of Life

From the National Institute of Child Health and Development (NICHD) Study of Early Child Care sample, two groups of children at age 36 months were examined—children identified by medical professionals as needing special services and children eligible for special services based on developmental assessments. Demographic information, children's behavioral functioning, mothers' psychological functioning, mother-child interactions, and quality of the home environment were examined. Early home environment and later behavior problems and children's health problems significantly contributed to the prediction model for membership in the group identified by medical professionals. Early home environment and socioeconomic status (SES) significantly contributed to the prediction model for the group identified based on developmental assessments. Results have implications for efforts to screen and detect young children likely to benefit from special education services.
The role of toll-like receptor variants in acute anterior uveitis

Purpose Acute anterior uveitis (AAU) is the most common form of uveitis; however, while it is presumed to have an immunological basis, the precise underlying etiology remains elusive. Toll-like receptors (TLRs) have a key role in linking innate and adaptive immunity, thereby forming a molecular bridge between microbial triggers and the development of AAU. The purpose of this study was to investigate the role of TLR2 and TLR4 gene polymorphisms in the pathogenesis of AAU. Methods The study comprised 225 confirmed cases of idiopathic or human leukocyte antigen (HLA) B27 (subtypes B*2701-2759; HLA-B27)-related AAU and 2,534 population-based controls from the Blue Mountains Eye Study. All participants were of Anglo-Celtic descent. Blood samples were collected for DNA extraction and genotyping. A total of 16 single nucleotide polymorphisms (SNPs) were selected for analysis and either directly genotyped or imputed to cover the common variations within the TLR genes. Data were analyzed at the allelic, genotypic and haplotypic levels. Results Control subjects were significantly older than case subjects (p<0.0001). There was no significant difference in the gender composition between the case and control cohorts (p=0.18). One TLR2 SNP (rs11938228) was found to be associated with AAU at the allelic level (OR=1.28; p=0.017); however this association did not remain following adjustment for age and sex (p=0.067). None of the SNPs at the TLR4 locus were found to differ significantly between cases or controls, irrespective of adjustment for age and gender. Conclusions This study has confirmed that common TLR variants of moderate effect size do not predispose to AAU, undermining the implication of reported mutations in the selective perturbations of TLR expression and function evident in AAU.
Search Based Test Data Generation: A Multi Objective Approach using MOPSO Evolutionary Algorithm

Search based test data generation plays an important role in software testing. Several search based evolutionary algorithms are used to find the optimal test data. Among these algorithms, a meta-heuristic algorithm called Particle Swarm Optimization (PSO) algorithm is adopted for finding the optimal test data for the given Software Under Test (SUT) due to its simplicity and fast convergence. The success of PSO as a single objective optimizer in the literature has motivated to solve multi objective optimization problems. Hence, Multi Objective Particle Swarm Optimization (MOPSO) is adopted for solving more than one objective. This research work consider two objectives which attempts to maximize the branch coverage and reduce the test suite size. A benchmark program is used for the experimental analysis using MOPSO algorithm. The experimental analysis was performed using MOTestGen tool to extract the results. The extracted results portraits the convergence and coverage performance in producing the optimal test data as the population size increases.