Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of Trigonopsis variabilis D-amino acid oxidase in transgenic rice for cephalosporin production

Transgenic plants have become an effective system to produce recombinant proteins, and there are many examples of transgenic plants that successfully produce functional proteins. In this study, the japonica rice cultivar Taiken 9 was transformed through an Agrobacterium-mediated method to express D-amino acid oxidase (DAAO) from Trigonopsis variabilis. DAAO is a flavoenzyme that catalyzes the oxidation of cephalosporin C to produce the precursor of the cephalosporin antibiotic glutaryl-7-aminocephalosporin acid (Gl-7-ACA). DAAO derived from T. variabilis has the highest catalytic activity for cephalosporin C oxidation of DAAO enzymes that have been characterized. Trigonopsis daao was expressed in rice under the control of either the rice actin 1 (Act1) or maize phosphoenolpyruvate carboxylase (PEPC) promoter. Southern blot analysis demonstrated the integration of Trigonopsis daao gene into the rice genome. Furthermore, northern blot and western blot analysis demonstrated production of the daao transcript and accumulation of its protein in various tissues of transgenic rice plants using either the Act1 or PEPC promoter as compared with the wild type. DAAO activity was detected in both transgenic rice lines with a maximum specific activity of 65.5±7.4 U mg protein^(-1) min^(-1) detected in the leaves of transgenic plants containing the rice Act1 promoter. The transgenic rice plant with the rice Act1 promoter exhibited several fold higher DAAO activity than the plant with the maize PEPC promoter: 5.3-and 3.7-fold higher in the leaves and sheaths, respectively. No DAAO activity was detected in the grains of transgenic rice containing the PEPC promoter. Taken together, these results demonstrate that Trigonopsis daao is stably integrated into the transgenic rice genome, transcribed efficiently, and translated into a functional protein.
Raman-generated pump impact on optical parametric amplification

Continuous-wave (CW) Raman-generated pump impact on a fiber optical parametric amplifier (OPA) is analyzed. Different noise contributions associated to the pump are experimentally and theoretically evaluated. Gain and noise figure of the amplifier are presented and commented for different OPA configurations. By tightly filtering the CW Raman-generated pump an OPA noise figure approaching the 3 dB limit is achieved.
Wavelet-Based Image Registration on Parallel Computers

Digital image registration is very important in many applications such as medical imagery, robotics, and remote sensing. Image registration determines the relative orientation between two or more images. NASA's Mission To Planet Earth (MTPE) program will soon produce enormous Earth data, reaching hundreds of Gbytes per day. Analysis of such data requires accurate and fast registration. We describe a fast algorithm for parallel image registration. Performance of the algorithm is analyzed and experimentally evaluated. It will be shown that the algorithm provides substantial computational savings and the measurements reveal many important characteristics of contemporary high performance computers.
Relationship between Reproductive Allocation and Relative Abundance among 32 Species of a Tibetan Alpine Meadow: Effects of Fertilization and Grazing

Background Understanding the relationship between species traits and species abundance is an important goal in ecology and biodiversity science. Although theoretical studies predict that traits related to performance (e.g. reproductive allocation) are most directly linked to species abundance within a community, empirical investigations have rarely been done. It also remains unclear how environmental factors such as grazing or fertilizer application affect the predicted relationship. Methodology We conducted a 3-year field experiment in a Tibetan alpine meadow to assess the relationship between plant reproductive allocation (RA) and species relative abundance (SRA) on control, grazed and fertilized plots. Overall, the studied plant community contained 32 common species. Principal Findings At the treatment level, (i) RA was negatively correlated with SRA on control plots and during the first year on fertilized plots. (ii) No negative RA–SRA correlations were observed on grazed plots and during the second and third year on fertilized plots. (iii) Seed size was positively correlated with SRA on control plots. At the plot level, the correlation between SRA and RA were not affected by treatment, year or species composition. Conclusions/Significance Our study shows that the performance-related trait RA can negatively affect SRA within communities, which is possibly due to the tradeoffs between clonal growth (for space occupancy) and sexual reproduction. We propose that if different species occupy different positions along these tradeoffs it will contribute to biodiversity maintenance in local communities or even at lager scale.
An Exploratory Study on Agile based Software Development Practices

Agile based software development approach is increasingly gaining much interest among software practitioners and researchers due to its ability to produce high quality software in shorter period of time. Even though its importance has been revealed, only few studies were conducted regarding its current practices in the software industry, particularly in Malaysia. Thus, an exploratory study was conducted among software practitioners in Malaysia to study their practices and perceptions on the agile based software development in the real-world projects. Moreover, the practices were covered in a wider perspective by considering the software development, management and documentation practices. This paper discusses the findings from the study, which involved 73 agile practitioners. Structured questionnaire was used for data collection purpose while statistical methods such as frequency, mean, and cross tabulation were used for data analysis. Outcomes from this study reveal that the most implemented agile principles are early delivery and face-to-face communication, whilst the least implemented is self-organizing team. Additionally, majority of the respondents agreed that agile based software development practices are important in order to produce high quality software.
Multiple Comparison Procedures

Multiple comparison procedures (MCPs) are frequently adopted by applied researchers to locate specific differences between treatment groups. That is, omnibus test statistics, such as the analysis of variance F test, can only signify that effects are present, not which specific groups differ from one another (when there are more than two groups). In our paper, we discuss MCPs that can be used to investigate simple pairwise differences between treatment group means, as well as MCPs that can be used to examine complex comparisons (i.e., nonpairwise comparisons) between treatment group means. In particular, we discuss simultaneous as well as stepwise MCPs, emphasizing procedures that can be utilized when the derivational assumptions of the classical procedures of normality and variance homogeneity do not hold. Keywords: pairwise and complex comparisons; simultaneous and stepwise procedures; Type I error rates; robust procedures
Quantitative Microbial Risk Assessment of Pathogenic Vibrios in Marine Recreational Waters of Southern California

ABSTRACT This study investigated the occurrence of three types of vibrios in Southern California recreational beach waters during the peak marine bathing season in 2007. Over 160 water samples were concentrated and enriched for the detection of vibrios. Four sets of PCR primers, specific for Vibrio cholerae, V. parahaemolyticus, and V. vulnificus species and the V. parahaemolyticus toxin gene, respectively, were used for the amplification of bacterial genomic DNA. Of 66 samples from Doheny State Beach, CA, 40.1% were positive for V. cholerae and 27.3% were positive for V. parahaemolyticus, and 1 sample (1.5%) was positive for the V. parahaemolyticus toxin gene. Of the 96 samples from Avalon Harbor, CA, 18.7% were positive for V. cholerae, 69.8% were positive for V. parahaemolyticus, and 5.2% were positive for the V. parahaemolyticus toxin gene. The detection of the V. cholerae genetic marker was significantly more frequent at Doheny State Beach, while the detection of the V. parahaemolyticus genetic marker was significantly more frequent at Avalon Harbor. A probability-of-illness model for V. parahaemolyticus was applied to the data. The risk for bathers exposed to recreational waters at two beaches was evaluated through Monte Carlo simulation techniques. The results suggest that the microbial risk from vibrios during beach recreation was below the illness benchmark set by the U.S. EPA. However, the risk varied with location and the type of water recreation activities. Surfers and children were exposed to a higher risk of vibrio diseases. Microbial risk assessment can serve as a useful tool for the management of risk related to opportunistic marine pathogens.
Reward-Dependent Modulation of Movement Variability

Movement variability is often considered an unwanted byproduct of a noisy nervous system. However, variability can signal a form of implicit exploration, indicating that the nervous system is intentionally varying the motor commands in search of actions that yield the greatest success. Here, we investigated the role of the human basal ganglia in controlling reward-dependent motor variability as measured by trial-to-trial changes in performance during a reaching task. We designed an experiment in which the only performance feedback was success or failure and quantified how reach variability was modulated as a function of the probability of reward. In healthy controls, reach variability increased as the probability of reward decreased. Control of variability depended on the history of past rewards, with the largest trial-to-trial changes occurring immediately after an unrewarded trial. In contrast, in participants with Parkinson's disease, a known example of basal ganglia dysfunction, reward was a poor modulator of variability; that is, the patients showed an impaired ability to increase variability in response to decreases in the probability of reward. This was despite the fact that, after rewarded trials, reach variability in the patients was comparable to healthy controls. In summary, we found that movement variability is partially a form of exploration driven by the recent history of rewards. When the function of the human basal ganglia is compromised, the reward-dependent control of movement variability is impaired, particularly affecting the ability to increase variability after unsuccessful outcomes.
MyMediaLite: a free recommender system library

MyMediaLite is a fast and scalable, multi-purpose library of recommender system algorithms, aimed both at recommender system researchers and practitioners. It addresses two common scenarios in collaborative filtering: rating prediction (e.g. on a scale of 1 to 5 stars) and item prediction from positive-only implicit feedback (e.g. from clicks or purchase actions). The library offers state-of-the-art algorithms for those two tasks. Programs that expose most of the library's functionality, plus a GUI demo, are included in the package. Efficient data structures and a common API are used by the implemented algorithms, and may be used to implement further algorithms. The API also contains methods for real-time updates and loading/storing of already trained recommender models. MyMediaLite is free/open source software, distributed under the terms of the GNU General Public License (GPL). Its methods have been used in four different industrial field trials of the MyMedia project, including one trial involving over 50,000 households.
Finite-Size Scaling in the transverse Ising Model on a Square Lattice

Energy eigenvalues and order parameters are calculated by exact diagonalization for the transverse Ising model on square lattices of up to 6×6 sites. Finite-size scaling is used to estimate the critical parameters of the model, confirming universality with the three-dimensional classical Ising model. Critical amplitudes are also estimated for both the energy gap and the ground-state energy.
The organized chromatin domain of the repressed yeast a cell‐specific gene STE6 contains two molecules of the corepressor Tup1p per nucleosome

In yeast α cells the a cell‐specific genes STE6 and BAR1 are packaged as gene‐sized chromatin domains of positioned nucleosomes. Organized chromatin depends on Tup1p, a corepressor that interacts with the N‐terminal regions of H3 and H4. If Tup1p functions to organize or stabilize a chromatin domain, the protein might be expected to be present at a level stoichiometric with nucleosomes. Chromatin immunoprecipitation assays using Tup1p antibodies showed Tup1p to be associated with the entire genomic STE6 coding region. To determine stoichiometry of Tup1p associated with the gene, a yeast plasmid containing varying lengths of the STE6 gene including flanking control regions and an Escherichia coli lac operator sequence was constructed. After assembly into chromatin in vivo in Saccharomyces cerevisiae, minichromosomes were isolated using an immobilized lac repressor. In these experiments, Tup1p was found to be specifically associated with repressed STE6 chromatin in vivo at a ratio of about two molecules of the corepressor per nucleosome. These observations strongly suggest a structural role for Tup1p in repression and constrain models for organized chromatin in repressive domains.
Dose Optimization to Minimize Radiation Risk for Children Undergoing CT and Nuclear Medicine Imaging Is Misguided and Detrimental

A debate exists within the medical community on whether the linear no-threshold model of ionizing radiation exposure accurately predicts the subsequent incidence of radiogenic cancer. In this article, we evaluate evidence refuting the linear no-threshold model and corollary efforts to reduce radiation exposure from CT and nuclear medicine imaging in accord with the as-low-as-reasonably-achievable principle, particularly for children. Further, we review studies demonstrating that children are not, in fact, more radiosensitive than adults in the radiologic imaging dose range, rendering dose reduction for children unjustifiable and counterproductive. Efforts to minimize nonexistent risks are futile and a major source of persistent radiophobia. Radiophobia is detrimental to patients and parents, induces stress, and leads to suboptimal image quality and avoidance of imaging, thus increasing misdiagnoses and consequent harm while offering no compensating benefits.
Gastroenteritis in NF-κB-Deficient Mice Is Produced with Wild-Type Camplyobacter jejuni but Not with C. jejuni Lacking Cytolethal Distending Toxin despite Persistent Colonization with Both Strains

ABSTRACT Campylobacter jejuni continues to be a leading cause of bacterial enteritis in humans. However, because there are no readily available animal models to study the pathogenesis of C. jejuni-related diseases, the significance of potential virulence factors, such as cytolethal distending toxin (CDT), in vivo are poorly understood. Mice deficient in NF-κB subunits (p50−/− p65+/−) in a C57BL/129 background are particularly susceptible to colitis induced by another enterohepatic microaerobe, Helicobacter hepaticus, which, like C. jejuni, produces CDT. Wild-type C. jejuni 81-176 and an isogenic mutant lacking CDT activity (cdtB mutant) were inoculated into NF-κB-deficient (3X) and C57BL/129 mice. Wild-type C. jejuni colonized 29 and 50% of the C57BL/129 mice at 2 and 4 months postinfection (p.i.), respectively, whereas the C. jejuni cdtB mutant colonized 50% of the C57BL/129 mice at 2 p.i. but none of the mice at 4 months p.i. Although the C57BL/129 mice developed mild gastritis and typhlocolitis, they had robust immunoglobulin G (IgG) and Th1-promoted IgG2a humoral responses to both the wild-type strain and the C. jejuni cdtB mutant. In contrast, 75 to 100% of the 3X mice were colonized with both the wild type and the C. jejuni cdtB mutant at similar levels at all times examined. Wild-type C. jejuni caused moderately severe gastritis and proximal duodenitis in 3X mice that were more severe than the gastrointestinal lesions caused by the C. jejuni cdtB mutant. Persistent colonization of NF-κB-deficient mice with the wild type and the C. jejuni cdtB mutant was associated with significantly impaired IgG and IgG2a humoral responses (P < 0.001), which is consistent with an innate or adaptive immune system defect(s). These results suggest that the mechanism of clearance of C. jejuni is NF-κB dependent and that CDT may have proinflammatory activity in vivo, as well as a potential role in the ability of C. jejuni to escape immune surveillance. NF-κB-deficient mice should be a useful model to further study the role of CDT and other aspects of C. jejuni pathogenesis.
Quantum Thermal Transport in Semiconductor Nanostructures

Miao, Kai. Ph.D., Purdue University, May 2017. Quantum Thermal Transport in Semiconductor Nanostructures. Major Professor: Gerhard Klimeck. Modern semiconductor devices scale down to the nanometer range. Heat dissipation becomes a critical issue in the chip design. From a different perspective, energy conservation has attracted much of attention from researchers. The essence of heat dissipation and energy conservation is the heat transport. Thermal properties of semiconductors have been under intense investigation in recent decades. Classical models fail to consider the quantum effects in devices on the scale of nanometers. First-principle methods only can deal with small devices and is computationally intensive. Instead, a modified valence force field (VFF) model is applied to reproduce the phonon properties of different materials and devices. Phonon transport is explored using the Green’s functions. The concept of a Büttiker probe model is first used to mimic the scattering mechanisms in phonon transport. This energy conservation model is straightforward and efficient in describing scattering. In the quasiparticle approximation, phonon scattering will cause a phonon energy shift. This energy shift is represented by the scattering selfenergy in a retarded Green’s function. Phonon lifetime is extracted from the scattering self-energy expression. Different relaxation time approximation (RTA) models are studied and coupled with the phonon Green’s function method for the first time. We prove that the widely used and proven RTA models in the Boltzmann transport equation (BTE) survive in the atomistic Green’s function method. This method can give accurate thermal properties agreeing closely with the experimental results for bulk devices. This atomistic method can also consider quantum confinement effects at the nanoscale. The heat transport across a Si/Ge interface is introduced in this work as an example for this application. The heat transfer across metal/semiconductor (MS) interfaces is investigated as well. Relaxation at the interface
p53 and PCNA Expression in Keratocystic Odontogenic Tumors Compared with Selected Odontogenic Cysts

p53 and PCNA expression in keratocystic odontogenic tumors compared with selected odontogenic cysts Summary: The aim of this study was to evaluate p53 and PCNA expression in different odontogenic lesions regarding their different clinical behaviors. Slices prepared from 94 paraffin-embedded tissue blocks (25 radicular cysts (RC), 23 dentigerous cysts (DC), 23 keratocystic odontogenic tumors (KCOT) and 23 calcifying cystic odontogenic tumors (CCOT)) were stained with p53 and PCNA antibodies using immunohistochemistry procedure. The highest level of p53 expression was in the basal layer of RC, and the highest level of PCNA expression was in the suprabasal layer of KCOT. The differences of p53 expression in basal and suprabasal layers as well as PCNA expression in the suprabasal layer were significant but there was no significant difference in PCNA expression in the basal layer of these lesions. The expression of p53 in the basal layer of RC was higher than in other cysts. This may be due to intensive inflammatory infiltration. Also, the high level of PCNA expression in the suprabasal layer of KCOT may justify its neoplastic nature and tendency to recurrence. KCOT and calcifying cystic odontogenic tumors did not show similar expression of studied biomarkers.
Is It a Baby? Perceived Age Affects Brain Processing of Faces Differently in Women and Men

It is known that infant faces stimulate visual and anterior brain regions belonging to the mesocortical limbic system (orbito-frontal cortex, anterior cingulate cortex, and nucleus accumbens) as well as the fusiform gyrus during face coding, suggesting a preferential response to baby schema. In the present investigation, faces of infants, children, and adults were presented to 40 male and female right-handed university students with technological objects (and inanimate scenarios to serve as targets) in a randomly mixed fashion. EEG was recorded from 128 scalp sites. In both sexes, the N1 response to infant faces was larger than the response to adult faces; however, the baby-specific N1 response was much larger in women than in men across the left hemisphere. The anterior N2 response to infants was greater than the response to children only in women, whereas the response to children of any age was larger than the response to adults in men. LORETA identified the intracranial sources of N2 response to infants in the left fusiform gyrus (FG), as well as the uncus, cingulate, and orbito-frontal cortices. The FG, the limbic, and especially the orbito-frontal sources were much larger in women than in men. The data suggest a sex difference in the brain response to faces of different ages and in the preferential response to infants, especially with regard to activation of the mesocorticolimbic system.
Tropical cyclogenesis and mid-level vorticity

This paper reviews and summarizes our work on the thermodynamics and vorticity dynamics of tropical cyclogenesis with special emphasis on the use of observations from two recent field programs, T-PARC/TCS08 (THORPEX Asian Regional Campaign/Tropical Cyclone Structure experiment) and PREDICT (PRE-Depression Investigation of Cloud systems in the Tropics). Dropsondes deployed from high altitude plus airborne Doppler radar data (in T-PARC/TCS08) allowed examination of candidates for tropical cyclogenesis in unprecedented detail. The subtle interplay of dynamics and thermodynamics, and in particular, the role of the mid-level vortex in enabling spin up of a surface cyclone are elucidated. The interplay between this process and other investigators’ ideas about cyclogenesis is examined also. Finally, those areas of cyclogenesis needing further work are enumerated.
Conformal Coating by Liquid Route on Three-Dimensional Topology

We demonstrated a new approach to the production of three-dimensional-coated patterns using liquid route. Metallic perovskite oxides were coated onto three-dimensional (3D) microstructured substrates with different aspect ratios. The success of the method relies on the solution viscosity monitored by adding viscous liquid. The process of oxide thin films consists in three steps: preparing the precursor solution, coating the solution by spin-coating process onto three-dimensional-Si substrates and post-annealing. The chemical solution 3D-coating is conformal.