Miracle-dz/UniFAR-FTUs huggingface dataset:
Aminoacylation of Plasmodium falciparum tRNAAsn and Insights in the Synthesis of Asparagine Repeats*

Background: Proteins from the malaria parasite Plasmodium contain extensive asparagine repeats. Results: Plasmodium tRNAAsn concentration and in vitro asparaginylation catalytic parameters were analyzed to explain the frequency of asparagine repeats. Conclusion: The requirement for high levels of asparaginylated tRNAs hinders efficient protein translation. Significance: Limiting the availability of asparaginylated tRNAs represents a plausible regulatory mechanism for the production of properly folded proteins. Genome sequencing revealed an extreme AT-rich genome and a profusion of asparagine repeats associated with low complexity regions (LCRs) in proteins of the malarial parasite Plasmodium falciparum. Despite their abundance, the function of these LCRs remains unclear. Because they occur in almost all families of plasmodial proteins, the occurrence of LCRs cannot be associated with any specific metabolic pathway; yet their accumulation must have given selective advantages to the parasite. Translation of these asparagine-rich LCRs demands extraordinarily high amounts of asparaginylated tRNAAsn. However, unlike other organisms, Plasmodium codon bias is not correlated to tRNA gene copy number. Here, we studied tRNAAsn accumulation as well as the catalytic capacities of the asparaginyl-tRNA synthetase of the parasite in vitro. We observed that asparaginylation in this parasite can be considered standard, which is expected to limit the availability of asparaginylated tRNAAsn in the cell and, in turn, slow down the ribosomal translation rate when decoding asparagine repeats. This observation strengthens our earlier hypothesis considering that asparagine rich sequences act as “tRNA sponges” and help cotranslational folding of parasite proteins. However, it also raises many questions about the mechanistic aspects of the synthesis of asparagine repeats and about their implications in the global control of protein expression throughout Plasmodium life cycle.
Overview: Using Mode of Action and Life Stage Information to Evaluate the Human Relevance of Animal Toxicity Data

A complete mode of action human relevance analysis—as distinct from mode of action (MOA) analysis alone—depends on robust information on the animal MOA, as well as systematic comparison of the animal data with corresponding information from humans. In November 2003, the International Life Sciences Institute's Risk Science Institute (ILSI RSI) published a 2-year study using animal and human MOA information to generate a four-part Human Relevance Framework (HRF) for systematic and transparent analysis of MOA data and information. Based mainly on non-DNA-reactive carcinogens, the HRF features a “concordance” analysis of MOA information from both animal and human sources, with a focus on determining the appropriate role for each MOA data set in human risk assessment. With MOA information increasingly available for risk assessment purposes, this article illustrates the further applicability of the HRF for reproductive, developmental, neurologic, and renal endpoints, as well as cancer. Based on qualitative and quantitative MOA considerations, the MOA/human relevance analysis also contributes to identifying data needs and issues essential for the dose-response and exposure assessment steps in the overall risk assessment.
Mutual Information-Based Modified Randomized Weights Neural Networks

Randomized weights neural networks have fast learning speed and good generalization performance with one single hidden layer structure. Input weighs of the hidden layer are produced randomly. By employing certain activation function, outputs of the hidden layer are calculated with some randomization. Output weights are computed using pseudo inverse. Mutual information can be used to measure mutual dependence of two variables quantitatively based on the probability theory. In this paper, these hidden layer’s outputs that relate to prediction variable closely are selected with the simple mutual information based feature selection method. These hidden nodes with high mutual information values are maintained as a new hidden layer. Thus, the size of the hidden layer is reduced. The new hidden layer’s output weights are learned with the pseudo inverse method. The proposed method is compared with the original randomized algorithms using concrete compressive strength benchmark dataset.
Searching for a “Hidden” Prophage in a Marine Bacterium

ABSTRACT Prophages are common in many bacterial genomes. Distinguishing putatively viable prophages from nonviable sequences can be a challenge, since some prophages are remnants of once-functional prophages that have been rendered inactive by mutational changes. In some cases, a putative prophage may be missed due to the lack of recognizable prophage loci. The genome of a marine roseobacter, Roseovarius nubinhibens ISM (hereinafter referred to as ISM), was recently sequenced and was reported to contain no intact prophage based on customary bioinformatic analysis. However, prophage induction experiments performed with this organism led to a different conclusion. In the laboratory, virus-like particles in the ISM culture increased more than 3 orders of magnitude following induction with mitomycin C. After careful examination of the ISM genome sequence, a putative prophage (ISM-pro1) was identified. Although this prophage contains only minimal phage-like genes, we demonstrated that this “hidden” prophage is inducible. Genomic analysis and reannotation showed that most of the ISM-pro1 open reading frames (ORFs) display the highest sequence similarity with Rhodobacterales bacterial genes and some ORFs are only distantly related to genes of other known phages or prophages. Comparative genomic analyses indicated that ISM-pro1-like prophages or prophage remnants are also present in other Rhodobacterales genomes. In addition, the lysis of ISM by this previously unrecognized prophage appeared to increase the production of gene transfer agents (GTAs). Our study suggests that a combination of in silico genomic analyses and experimental laboratory work is needed to fully understand the lysogenic features of a given bacterium.
Assessing self-reported disability in a low-literate population with chronic low back pain: cross-cultural adaptation and psychometric testing of Igbo Roland Morris disability questionnaire

Abstract Purpose: Cross-culturally adapt and validate the Igbo Roland Morris Disability Questionnaire. Method: Cross-cultural adaptation, test–retest, and cross-sectional psychometric testing. Roland Morris Disability Questionnaire was forward and back translated by clinical/non-clinical translators. An expert committee appraised the translations. Twelve participants with chronic low back pain pre-tested the measure in a rural Nigerian community. Internal consistency using Cronbach’s alpha; test–retest reliability using intra-class correlation coefficient and Bland–Altman plot; and minimal detectable change were investigated in a convenient sample of 50 people with chronic low back pain in rural and urban Nigeria. Pearson’s correlation analyses using the eleven-point box scale and back performance scale, and exploratory factor analysis were used to examine construct validity in a random sample of 200 adults with chronic low back pain in rural Nigeria. Ceiling and floor effects were investigated in the two samples. Results: Modifications gave the option of interviewer-administration and reflected Nigerian social context. The measure had excellent internal consistency (α = 0.91) and intraclass correlation coefficient (ICC =0.84), moderately high correlations (r > 0.6) with performance-based disability and pain intensity, and a predominant uni-dimensional structure, with no ceiling or floor effects. Conclusions: Igbo Roland Morris Disability Questionnaire is a valid and reliable measure of pain-related disability. Implications for rehabilitation Low back pain is the leading cause of years lived with disability worldwide, and is particularly prevalent in rural Nigeria, but there are no self-report measures to assess its impact due to low literacy rates. This study describes the cross-cultural adaptation and validation of a core self-report back pain specific disability measure in a low-literate Nigerian population. The Igbo Roland Morris Disability Questionnaire is a reliable and valid measure of self-reported disability in Igbo populations as indicated by excellent internal consistency (α = 0.91) and intra-class correlation coefficient (ICC =0.84), moderately high correlations (r > 0.6) with performance-based disability and pain intensity that supports a pain-related disability construct, a predominant one factor structure with no ceiling or floor effects. The measure will be useful for researchers and clinicians examining the factors associated with low back pain disability or the effects of interventions on low back pain disability in this culture. This measure will support global health initiatives concurrently involving people from several cultures or countries, and may inform cross-cultural disability research in other populations.
A standardized kinesin nomenclature

In recent years the kinesin superfamily has become so large that several different naming schemes have emerged, leading to confusion and miscommunication. Here, we set forth a standardized kinesin nomenclature based on 14 family designations. The scheme unifies all previous phylogenies and nomenclature proposals, while allowing individual sequence names to remain the same, and for expansion to occur as new sequences are discovered.
The influence of early hemodynamic optimization on biomarker patterns of severe sepsis and septic shock*

Background:Despite abundant experimental studies of biomarker patterns in early severe sepsis and septic shock, human data are few. Further, the impact of the severity of global tissue hypoxia resulting from resuscitative strategies on these early biomarker patterns remains unknown. Methods:The temporal patterns of interleukin-1 receptor antagonist, intercellular adhesion molecule-1, tumor necrosis factor-&agr;, caspase-3, and interleukin-8 were serially examined over the first 72 hrs of hospitalization after early hemodynamic optimization strategies of early goal-directed vs. standard therapy for severe sepsis and septic shock patients. The relationship of these biomarker patterns to each hemodynamic optimization strategy, severity of global tissue hypoxia (reflected by lactate and central venous oxygen saturation), organ dysfunction, and mortality were examined. Results:Abnormal biomarker levels were present upon hospital presentation and modulated to distinct patterns within 3 hrs based on the hemodynamic optimization strategy. The temporal expression of these patterns over 72 hrs was significantly associated with the severity of global tissue hypoxia, organ dysfunction, and mortality. Conclusion:In early severe sepsis and septic shock, within the first 3 hrs of hospital presentation, distinct biomarker patterns emerge in response to hemodynamic optimization strategies. A significant association exists between temporal biomarker patterns in the first 72 hrs, severity of global tissue hypoxia, organ dysfunction, and mortality. These findings identify global tissue hypoxia as an important contributor to the early inflammatory response and support the role of hemodynamic optimization in supplementing other established therapies during this diagnostic and therapeutic “window of opportunity. ”
Analyzing and managing IT-induced work system changes

This teaching case explores the challenges of changing a work system by implementing an information system (IS). The case describes the approach implemented by “The Bank”, a financial service provider, when it implemented a new financial and banking IS “SysOne”, and thus fundamentally changed its work systems. The case is a real business scenario, which bases on case study research conducted by our research team and it adapts recent theoretical advances in the IS implementation literature. Using this teaching case in class should encourage students to discuss IS implementations from a general “system thinking” rather than a “tool thinking” perspective. An IS implementation is not just a new tool, it is a change of employees’ work systems. This teaching case should guide students to extend the efforts implemented to guide employees when implementing an IS beyond the technology to focus on the major IT-induced work system changes and thereby enable successful technochange.
Edge detection using matched filter

For target tracking, automatic target recognition and detection applications, they value edge detection sensibility, precision and location accuracy rather than other criterions. Aimed at these three criterions, this paper presents an edge detection algorithm based on matched filter. Firstly, a matched filter was designed by analyzing the edge model for natural image, then the edge response was computed using the designed matched filter; secondly, the lower and discontinuous filtered responses were further suppressed using a dedicated one-dimension filter; finally, the edge image was obtained by binarizing the edge response with a local adaptive threshold. Experimental results illustrate that the proposed algorithm has more improvement than the Sobel and Canny operators in detection sensibility, precision and location accuracy. Moreover, the algorithm can be implemented with parallel pipeline using FPGA, so it is also rather suitable for real-time applications.
The usage of Discrete Wavelet Transform in voltage and current waveforms analysis in Three-Phase Systems with Balanced or Unbalanced Loads

The balanced and unbalanced three-phase power components definitions contained in the IEEE standard 1459-2010 are obtained by processing the voltage and current signals with the reconstruction of the original signals using Fourier Transform (FT). This method provides only an amplitude-frequency spectrum loosing time-related information and is unable to deal with non-stationary waveforms. This paper proposes an comparative application of IEEE standard definitions and Discrete Wavelet Transform (DWT) definition for the measurement of effective root mean square (RMS) values in Three-Phase Systems with Balanced or Unbalanced Loads. DWT preserves all information on time and frequency in the analysed waveforms and reduces the computational effort by dividing the frequency spectrum into bands or levels.
Analytical model for a geomorphological instantaneous unit hydrograph

The rainfall‐runoff modelling of a river basin can be divided into two processes: the production function and the transfer function. The production function determines the proportion of gross rainfall actually involved in the runoff. The transfer function spreads the net rainfall over time and space in the river basin. Such a transfer function can be modelled using the approach of the geomorphological instantaneous unit hydrograph (GIUH). The effectiveness of geomorphological models is actually revealed in rainfall‐runoff modelling, where hydrologic data are desperately lacking, just as in ungauged basins. These models make it possible to forecast the hydrograph shape and runoff variation versus time at the basin outlet. This article is an introduction to a new GIUH model that proves to be simple and analytical. Its geomorphological parameters are easily available on a map or from a digital elevation model. This model is based on general hypotheses on symmetry that provide it with multiscale versatile characteristics. After having validated the model in river basins of very different nature and size, we present an application of this model for rainfall‐runoff modelling. Since parameters are determined relying on real geomorphological data, no calibration is necessary, and it is then possible to carry out rainfall‐runoff simulations in ungauged river basins. Copyright © 2006 John Wiley & Sons, Ltd.
Truly Nonintrusive Liquid-Level-Sensing Method Based on Lateral Displacement Effect of Light Rays

A truly nonintrusive optical sensing method suitable for accurate and precise measurement of liquid level is proposed and demonstrated in this paper. Sensing principle of the proposed method is based on the phenomenon of lateral displacement effect, which is observed when oblique light rays propagate through material media with different thicknesses and refractive indices. Experimental results of this method demonstrate its ability to measure liquid level very precisely up to a resolution of about 40-50 μm. The proposed method has the potential for use in in situ measurement of liquid level and volume. It can also be exploited for measurement of refractive index of liquid.
The Importance of Respect in Collaborative Work:

This paper argues that respect, defined as esteem for another person’s abilities and character, is an important factor in successful collaborative work. In making this claim, trust is used as the springboard for why interpersonal attitudes are important in the first place. Respect is first differentiated from trust conceptually, and then examined empirically in simulated top management teams. It is argued that respect will affect the group processes of communication, coordination, and conflict in different ways and through alternate mechanisms than trust. Still, both trust and respect will affect group processes and outcomes. The results support this interpretation. The paper concludes by discussing opportunities for future research on respect as well as trust, and the implications this research has for interpersonal factors besides trust and respect.
A Cross-layered Pilot Scheme for IEEE 802.11p

Vehicular communication is expected to be a part of the future transportation system and promises to support a plethora of applications for traffic safety, traffic efficiency, and fuel efficiency. Traffic safety applications, such as collision avoidance, demand reliable communications with low latency. To support reliable communications in terms of low frame error rates (FERs), it is necessary to accurately estimate the wireless channel in a receiver. Vehicular wireless channels being highly time- and frequency-variant require the communication systems to accurately estimate the channels for the entire duration of the frames. IEEE 802.11p has been specified as the physical and medium access layers standard for vehicular communications. The pilots in an 802.11p frame are densely concentrated at the beginning of the frame, and as a consequence, accurate channel estimation at later parts of the frame becomes a challenging task. To attain low FERs with the existing pilot pattern, receivers with iterative decoding and equalization strategies have been studied in the literature. These receivers are computationally complex and introduce additional latency in decoding the frames. In this thesis, an alternative solution to overcome the ill-suited pilot pattern is studied. In Paper A, a cross-layered pilot scheme to insert complementary pilots into the 802.11p frame is proposed. The pilot insertion is performed above the physical and medium access layers and therefore does not require modifications to the 802.11p standard. A modified receiver can utilize the complementary pilots for improved channel estimation, while a standard receiver treats the inserted pilots as data and passes them to the higher layers, where they can be removed. A modified receiver that utilizes the complementary training symbols for channel estimation with linear minimum mean squared-error interpolator is described. Numerical results show that FER close to the case with perfect channel state information (CSI) can be obtained with the described receiver for suitably chosen period of pilot insertion. In Paper B, the pilot insertion scheme proposed in Paper A is further improved to support short frames. Hardware implementation feasibility of the proposed scheme is shown by implementing a modified receiver that can utilize the complementary pilots in an field programmable gate array (FPGA) platform. Two low complexity channel estimation schemes are implemented in the modified receiver. Backward compatibility of the proposed scheme is also verified by conducting tests with a commercial transceiver. FER measurements are performed by interfacing the implementation with a channel emulator. The results show that the modified receiver follows the performance of a receiver with perfect CSI with an offset of 3.5 to 4 dB in signal-to-noise ratio and significantly outperforms the commercial 802.11p transceiver we tested.
How to Implement Respondent-Driven Sampling in Practice: Insights from Surveying 24-Hour Migrant Home Care Workers

This article draws on the experience from an ongoing research project employing respondent-driven sampling (RDS) to survey (illicit) 24-hour home care workers. We highlight issues around the preparatory work and the fielding of the survey to provide researchers with useful insights on how to implement RDS when surveying populations for which the method has not yet been used. We conclude the article with ethical considerations that occur when employing RDS.
The Role of Dipeptidyl Peptidase IV (DP IV) Enzymatic Activity in T Cell Activation and Autoimmunity

Abstract Activated T lymphocytes express high levels of dipeptidyl peptidase IV (DP IV)/CD26. Recent studies support the notion that DP IV may play an important role in the regulation of differentiation and growth of T lymphocytes. This article gives a short overview on DP IV/CD26 expression and effects on immune cells in vitro and in vivo. A major focus of this review are clinical aspects of the function of CD26 on hematopoietic cells and the potential usage of synthetic DP IV inhibitors as therapeutics in inflammatory disorders.
CAPR: context-aware participant recruitment mechanism in mobile crowdsourcing

With the advances of sensing, wireless communication, and mobile computing, mobile crowdsourcing has become a new paradigm for data collection and retrieval that has attracted considerable attention. This paper addresses the fundamental research issue in mobile crowdsourcing: Which participants should be selected as winners in each time slot with the aim of maximizing the total utility of the service provider in the long term? First, a double-sided combinatorial auction model is introduced to describe the relationships between the mobile users and requesters from the perspective of supply and demand at a given time. Then, the coupling between the utility values of the system in different time slots is investigated. Based on the aforementioned analyses, this paper proposes a context-aware participant recruitment mechanism, in which the mobile crowdsourcing system dynamically adjusts the participant recruitment mechanism depending on the ratio between the numbers of mobile users and requesters. Context-aware participant recruitment consists of two main components: (1) a heuristic algorithm based on the greedy strategy to determine the winning participants and (2) a critical payment scheme, which guarantees the rationality of the proposed mechanism. Finally, extensive simulations demonstrate that the proposed mechanism achieves high system utility in the long term.