Miracle-dz/UniFAR-FTUs huggingface dataset:
Localized Gene Expression in Pseudomonas aeruginosa Biofilms

ABSTRACT Gene expression in biofilms is dependent on bacterial responses to the local environmental conditions. Most techniques for studying bacterial gene expression in biofilms characterize average values across the entire population. Here, we describe the use of laser capture microdissection microscopy (LCMM) combined with multiplex quantitative real-time reverse transcriptase PCR (qRT-PCR) to isolate and quantify RNA transcripts from small groups of cells at spatially resolved sites within biofilms. The approach was first tested and analytical parameters were determined for Pseudomonas aeruginosa containing an isopropyl-β-d-thiogalactopyranoside-inducible gene for the green fluorescent protein (gfp). The results show that the amounts of gfp mRNA were greatest in the top zones of the biofilms, and that gfp mRNA levels correlated with the zone of active green fluorescent protein fluorescence. The method then was used to quantify transcripts from wild-type P. aeruginosa biofilms for a housekeeping gene, acpP; the 16S rRNA; and two genes regulated by quorum sensing, phzA1 and aprA. The results demonstrated that the amount of acpP mRNA was greatest in the top 30 μm of the biofilm, with little or no mRNA for this gene at the base of the biofilms. In contrast, 16S rRNA amounts were relatively uniform throughout biofilm strata. Using this strategy, the RNA amounts of individual genes were determined, and therefore the results are dependent on both gene expression and the half-life of the transcripts. Therefore, the uniform amount of rRNA throughout the biofilms likely is due to the stability of the rRNA within ribosomes. The levels of aprA mRNA showed stratification, with the largest amounts in the upper 30-μm zone of these biofilms. The results demonstrate that mRNA levels for individual genes are not uniformly distributed throughout biofilms but may vary by orders of magnitude over small distances. The LCMM/qRT-PCR technique can be used to resolve and quantify this RNA variability at high spatial resolution.
Explicit Mesh Surfaces for Particle Based Fluids

We introduce the idea of using an explicit triangle mesh to track the air/fluid interface in a smoothed particle hydrodynamics (SPH) simulator. Once an initial surface mesh is created, this mesh is carried forward in time using nearby particle velocities to advect the mesh vertices. The mesh connectivity remains mostly unchanged across time‐steps; it is only modified locally for topology change events or for the improvement of triangle quality. In order to ensure that the surface mesh does not diverge from the underlying particle simulation, we periodically project the mesh surface onto an implicit surface defined by the physics simulation. The mesh surface gives us several advantages over previous SPH surface tracking techniques. We demonstrate a new method for surface tension calculations that clearly outperforms the state of the art in SPH surface tension for computer graphics. We also demonstrate a method for tracking detailed surface information (like colors) that is less susceptible to numerical diffusion than competing techniques. Finally, our temporally‐coherent surface mesh allows us to simulate high‐resolution surface wave dynamics without being limited by the particle resolution of the SPH simulation.
A trust-based information assurance mechanism for military mobile ad-hoc networks

The article presents the concept of a novel mechanism for information assurance provision in tactical mobile ad-hoc networks that operate in disruptive and hostile environment. The authors provide a brief survey of related work and present their own concept, which include surroundings assessment, nodes behaviour classification, advanced inference method and authentication scheme performed at link layer. The concept was examined by simulation experiments and selected results are provided. The proposed system allows to increase the safety of communications and protect against degradation of MANET network resources.
The role of teachers in youth development: reflections of students

Abstract The purpose of this study was to examine the students’ reflections on a subject on leadership and intrapersonal development at The Hong Kong Polytechnic University. Based on 66 personal reflections collected, the data were analyzed using the “framework analysis” methodology. The respondents generally showed positive attitudes toward the subject and the lecturers, and they perceived that the subject promoted their overall development in different domains. With particular reference to their reflections on the instructors teaching the subject, several emerging themes were identified, including (a) caring and supportive attitude, (b) professional pedagogical arrangements and (c) personal engagements and connections. Exemplars are presented in this paper to support the conclusions. The findings are in line with previous research that teachers play an important role in positive youth development programs.
Big Data's Big Unintended Consequences

Businesses and governments exploit big data without regard for issues of legality, data quality, disparate data meanings, and process quality. This often results in poor decisions, with individuals bearing the greatest risk. The threats harbored by big data extend far beyond the individual, however, and call for new legal structures, business processes, and concepts such as a Private Data Commons. The Web extra at http://youtu.be/TvXoQhrrGzg is a video in which author Marcus Wigan expands on his article "Big Data's Big Unintended Consequences" and discusses how businesses and governments exploit big data without regard for issues of legality, data quality, disparate data meanings, and process quality. This often results in poor decisions, with individuals bearing the greatest risk. The threats harbored by big data extend far beyond the individual, however, and call for new legal structures, business processes, and concepts such as a Private Data Commons.
Recent progress on UV lamps for industries

Radiation in nature so called daylight dominates only the small region in all wavelengths. UV-ray is located at higher energy region than that of daylight and induces some reactions, which is caused by an act as energetic particles. UV lamps with specific wavelength are controllable for selected reaction in the limited area and the time. They are tried in laboratories at first and applied in industrial plants with great progress of lamp components and their electric circuits. This article reviews the recent progress of industrial discharge lamps radiating UV, VUV, or other specialized wavelength.
Development of a Multimodal Biometric Identification and Verification System using Two Fingerprints

Fingerprint recognition is one of the research hotspots of biometrics techniques. Fingerprints are the most widely used biometric feature for identification and verification in the field of biometrics. [1]. The traditional fingerprint recognition systems have such disadvantages as high computation complexity, low speed, low recognition rate to uncompleted or defiled fingerprints, and not robust[2]. In this paper, we propose a multimodel fingerprint identification and verification method based on pattern recognition, which emphasizes global features of fingerprint. With lots of artificial fingerprint samples, the results show that the proposed method is effective, fast, robust and shows the Improvement in rate of false acceptance and false rejections. Experimental results are analyzed and a fingerprint recognition system is introduced. General Terms Pattern Recognition, Fingerprint classification and verification
A brief overview of population - based optimization techniques and their applications post 2011

Naturally occurring phenomenon serves as an unbiased guide for solving various optimization problems . This paper compiles some of the population - based, sto chastic optimization algorithms including the recently developed social impact theory based optimizer , SITO . The current state of research , including the natural phenomena followed by each and some of their applications to solve various optimization problems is illustrated . The applications after the year 2011 are covered. The efficiency and robustness of various algorithms explored herein , includes particle swarm optimization (PSO) , harmony search (HS) and social impact theory based optimizer (SITO) .
Evaluation of zero-velocity detectors for foot-mounted inertial navigation systems

A study of the performance of four zero-velocity detectors for a foot-mounted inertial sensor based pedestrian navigation system is presented. The four detectors are the acceleration moving variance detector, the acceleration magnitude detector, the angular rate energy detector, and a novel generalized likelihood ratio test detector, refereed to as the SHOE. The performance of each detector is assessed by the accuracy of the position solution provided by the navigation system employing the detector to perform zero-velocity updates. The results show that for leveled ground forward gait at a speed of 5 km/h, the angular rate energy detector and the SHOE give the highest performance, with a position accuracy of 0.14% of the travelled distance. The results also indicate that during leveled ground forward gait, the gyroscope signals hold the most reliable information for zero-velocity detection.
Fuzzy Multicriteria Decision Analysis for Measurement of Document Content Reliability

The objective of the paper is to propose a measurement model for trustworthiness of a document to ensure information security. The definition of trustworthiness in this context refers to the reliability value of the information in the document. the document here refers to an article or a web document. The proposed model relates to an approach for assessing trust of data for use of the information consumer. The model helps to capture multiple factors couple with risk profiles in the determination of the trustworthiness of content. It allows consideration of level of confidence and aggregation of attitude towards risk for normalization of a trust index. We use a fuzzy representation to allow the information consumer to decide their confidence level towards the importance of each criterion. the model enables an automated computation method for a straight forward computation for a unique and personalized trustworthiness. The paper also presents an implementation example for practicality of the proposed model.
Speech enhancement based on deep denoising autoencoder

We previously have applied deep autoencoder (DAE) for noise reduction and speech enhancement. However, the DAE was trained using only clean speech. In this study, we further introduce an explicit denoising process in learning the DAE. In training the DAE, we still adopt greedy layer-wised pretraining plus fine tuning strategy. In pretraining, each layer is trained as a one hidden layer neural autoencoder (AE) using noisy-clean speech pairs as input and output (or transformed noisy-clean speech pairs by preceding AEs). Fine tuning was done by stacking all AEs with pretrained parameters for initialization. The trained DAE is used as a filter for speech estimation when noisy speech is given. Speech enhancement experiments were done to examine the performance of the trained denoising DAE. Noise reduction, speech distortion, and perceptual evaluation of speech quality (PESQ) criteria are used in the performance evaluations. Experimental results show that adding depth of the DAE consistently increase the performance when a large training data set is given. In addition, compared with a minimum mean square error based speech enhancement algorithm, our proposed denoising DAE provided superior performance on the three objective evaluations.
A systematic review of structured sparse learning

High dimensional data arising from diverse scientific research fields and industrial development have led to increased interest in sparse learning due to model parsimony and computational advantage. With the assumption of sparsity, many computational problems can be handled efficiently in practice. Structured sparse learning encodes the structural information of the variables and has been quite successful in numerous research fields. With various types of structures discovered, sorts of structured regularizations have been proposed. These regularizations have greatly improved the efficacy of sparse learning algorithms through the use of specific structural information. In this article, we present a systematic review of structured sparse learning including ideas, formulations, algorithms, and applications. We present these algorithms in the unified framework of minimizing the sum of loss and penalty functions, summarize publicly accessible software implementations, and compare the computational complexity of typical optimization methods to solve structured sparse learning problems. In experiments, we present applications in unsupervised learning, for structured signal recovery and hierarchical image reconstruction, and in supervised learning in the context of a novel graph-guided logistic regression.
Novel cross‐linked homogeneous polyacrylamide gels with improved separation properties: Investigation of the cross‐linker functionality

Polyacrylamide (PAAm) gels were synthesized using cross‐linkers with their potential functionality (twice the number of double bonds of a cross‐linker) varying from six to sixteen. Improved electrophoretic separation and highly desirable porosity and sieving properties were observed for most of the PAAm gels containing novel cross‐linkers. An increase in the potential functionality of cross‐linkers used in PAAm gels was an important factor, influencing the pore size and pore size distribution of the network.
An embedded domain-specific language for type-safe server-side web scripting

WASH/CGI is an embedded domain-specific language for server-side Web scripting. Due to its reliance on the strongly typed, purely functional programming language Haskell as a host language, it is highly flexible and---at the same time---it provides extensive guarantees due to its pervasive use of type information.WASH/CGI can be structured into a number of sublanguages addressing different aspects of the application. The document sublanguage provides tools for the generation of parameterized XHTML documents and forms. Its typing guarantees that almost all generated documents are valid XHTML documents. The session sublanguage provides a session abstraction with a transparent notion of session state and allows the composition of documents and Web forms to entire interactive scripts. Both are integrated with the widget sublanguage which describes the communication (parameter passing) between client and server. It imposes a simple type discipline on the parameters that guarantees that forms posted by the client are always understood by the server. That is, the server never asks for data not submitted by the client and the data submitted by the client has the type requested by the server. In addition, parameters are received in their typed internal representation, not as strings. Finally, the persistence sublanguage deals with managing shared state on the server side as well as individual state on the client side. It presents shared state as an abstract data type, where the script can control whether it wants to observe mutations due to concurrently executing scripts. It guarantees that states from different interaction threads cannot be confused.
3D soft tissue warping dynamics simulation based on force asynchronous diffusion model

Soft tissue warping is one of the key technologies of medical dynamics simulation, such as surgical simulation, image guided surgery. In this paper, we present a novel simulation method which is stable and fast like linear models for soft tissue warping simulation. This method performs on the irregular mesh models, and it is able to represent the visual properties of physical processes with low computational complexity using the Force Asynchronous Diffusion Model (FADM) proposed in this paper. It contains three parts: model preprocessing, collision detection and simulation model solution. In model preprocessing, we establish three models based on the triangular mesh: the geometrical model, the physical model and the transitional model. A two‐level collision detection algorithm is presented based on the three models. At every time step of the simulation model solution, to more accurately reflect the internal physical properties of the soft tissue, we divide the springs in physical model into three kinds: tissue springs, connection springs and virtual springs; and we propose the asynchronous regions and active regions to simplify the computing process according to the realistic physical warping. Experimental results show the FAMD can achieve good warping effects on speed and realism. Copyright © 2011 John Wiley & Sons, Ltd.
Working with Twice-Exceptional African American Students: Information for School Counselors.

This qualitative study examined the perceptions, attitudes, and experiences of eight twice-exceptional African American gifted students who attended the same K-12 urban school district in the Midwest. Four major themes emerged—academic supports, personal and social challenges, career worries, and experience with school counselors. Findings revealed that students’ special education status negatively impacted their relationship with peers, educators, and school counselors. Further, students struggled in developing a positive sense of self. Recommendations for school counselors are included.
Community Fisheries in Eastern South Dakota: Angler Demographics, Use, and Factors Influencing Satisfaction

ABSTRACT We surveyed anglers on five community fishing lakes near Brookings, South Dakota to assess angler use and satisfaction. The community lakes attracted younger anglers when compared to statewide and national averages. Overall, satisfaction was generally high (74%) among anglers fishing community lakes. Logistic regression analysis showed that harvest rate, anglers targeting trout, familiarity with the lake, adults fishing with children, and fishing during open water periods were significantly related to angler satisfaction. Angler parties consisting of adults fishing with children were 1.7 times more likely to respond as “satisfied” compared with adults-only angler groups. Fishing opportunities provided by community lakes can enhance participation by younger anglers while simultaneously providing family-oriented recreation (i.e., adults fishing with children) that enhances trip satisfaction.
Regulation of Quinone Oxidoreductase by the Redox-sensing Transcriptional Regulator QorR in Corynebacterium glutamicum*

Corynebacterium glutamicum cgR_1435 (cg1552) encodes a protein of the DUF24 protein family, which is a novel family of transcriptional regulators. CgR1435 (QorR) is a negative regulator of cgR_1436 (qor2), which is located upstream of cgR_1435 (qorR) in the opposite orientation, and its structural gene. QorR binds to the intergenic region between qor2 and qorR to repress their expression, which is induced by the thiol-specific oxidant diamide. The DNA-binding activity of QorR is impaired by oxidants such as diamide, H2O2, and cumene hydroperoxide in vitro, and its lone cysteine residue (Cys-17) is essential for redox-responsive regulation of QorR activity both in vivo and in vitro. Moreover, a disruptant of qor2, which is a homologue of the ytfG gene of Escherichia coli encoding quinone oxidoreductase, shows increased sensitivity to diamide. It is concluded that the redox-sensing transcriptional regulator QorR is involved in disulfide stress response of C. glutamicum by regulating qor2 expression.
Assembly and Activation of the MotA/B Proton Channel Complex of the Proton-Driven Flagellar Motor of Salmonella enterica

Salmonella enterica can swim by rotating multiple flagella, which arise randomly over the cell surface (Fig. 1A). The flagellum consists of at least three parts: the basal body, the hook, and the filament. The basal body is embedded within the cell membranes and acts as a bidirectional rotary motor powered by an electrochemical potential gradient of protons across the cytoplasmic membrane (Fig. 1B, C). The hook and filament extend outwards in the cell exterior. The filament acts as a helical propeller. The hook exists between the basal body and filament and functions as a universal joint to smoothly transmit torque produced by the motor to the filament. When the motors rotate in counterclockwise direction, the cells can swim smoothly. By quick reversal rotation of the motor to clockwise direction, the cells tumble and change their swimming direction to move toward more favorable environments (Fig. 2) (Berg, 2003; Blair, 2003; Minamino et al., 2008).
JavaGI: The Interaction of Type Classes with Interfaces and Inheritance

The language JavaGI extends Java 1.5 conservatively by a generalized interface mechanism. The generalization subsumes retroactive and type-conditional interface implementations, binary methods, symmetric multiple dispatch, interfaces over families of types, and static interface methods. These features make certain coding patterns redundant, increase the expressiveness of the type system, and permit solutions to extension and integration problems with components in binary form, for which previously several unrelated extensions had been suggested. This article explains JavaGI and motivates its design. Moreover, it formalizes a core calculus for JavaGI and proves type soundness, decidability of typechecking, and determinacy of evaluation. The article also presents the implementation of a JavaGI compiler and an accompanying run-time system. The compiler, based on the Eclipse Compiler for Java, offers mostly modular static typechecking and fully modular code generation. It defers certain well-formedness checks until load time to increase flexibility and to enable full support for dynamic loading. Benchmarks show that the code generated by the compiler offers good performance. Several case studies demonstrate the practical utility of the language and its implementation.
Low-voltage ferroelectric phase shifters from L- to C-band and their applications

This paper describes the design, fabrication and test results of a family of integrated low-voltage ferroelectric phase shifters ranging in frequency of operation from 0.7 GHz to 6 GHz. All devices use a common material system of barium strontium titanate (BaxSr1-x TiO3 or BST) thin-films on a sapphire (Al2O 3) substrate. Thick copper (Cu) metallization is used to allow integration of ferroelectric varactors with high-Q inductors and other passive microwave elements. Novel bias structures have also been developed to reduce the voltages required to tune the materials to less than 20V. The flip-chip mounted devices measure less than 0.080 in. times 0.080 in. Data for an all-pass network BST phase shifter shows that more than 100deg of differential phase shift may be obtained over a 30% fractional bandwidth. To demonstrate the utility of BST phase shifters, a two-element phased array antenna was designed and tested in conjunction with a wireless local area network (WLAN). Field tests showed that the data throughput of the WLAN was significantly improved in the presence of strong interference by use of the BST phased array antenna
Time-varying periodic convolutional codes with low-density parity-check matrix

We present a class of convolutional codes defined by a low-density parity-check matrix and an iterative algorithm for decoding these codes. The performance of this decoding is close to the performance of turbo decoding. Our simulation shows that for the rate R=1/2 binary codes, the performance is substantially better than for ordinary convolutional codes with the same decoding complexity per information bit. As an example, we constructed convolutional codes with memory M=1025, 2049, and 4097 showing that we are about 1 dB from the capacity limit at a bit-error rate (BER) of 10/sup -5/ and a decoding complexity of the same magnitude as a Viterbi decoder for codes having memory M=10.