Miracle-dz/UniFAR-FTUs huggingface dataset:
Grassland Management Regimens Reduce Small-Scale Heterogeneity and Species Diversity of β-Proteobacterial Ammonia Oxidizer Populations

ABSTRACT The impact of soil management practices on ammonia oxidizer diversity and spatial heterogeneity was determined in improved (addition of N fertilizer), unimproved (no additions), and semi-improved (intermediate management) grassland pastures at the Sourhope Research Station in Scotland. Ammonia oxidizer diversity within each grassland soil was assessed by PCR amplification of microbial community DNA with both ammonia oxidizer-specific, 16S rRNA gene (rDNA) and functional, amoA, gene primers. PCR products were analysed by denaturing gradient gel electrophoresis, phylogenetic analysis of partial 16S rDNA and amoA sequences, and hybridization with ammonia oxidizer-specific oligonucleotide probes. Ammonia oxidizer populations in unimproved soils were more diverse than those in improved soils and were dominated by organisms representing Nitrosospira clusters 1 and 3 and Nitrosomonas cluster 7 (closely related phylogenetically to Nitrosomonas europaea). Improved soils were only dominated by Nitrosospira cluster 3 and Nitrosomonas cluster 7. These differences were also reflected in functional gene (amoA) diversity, with amoA gene sequences of both Nitrosomonas and Nitrosospira species detected. Replicate 0.5-g samples of unimproved soil demonstrated significant spatial heterogeneity in 16S rDNA-defined ammonia oxidizer clusters, which was reflected in heterogeneity in ammonium concentration and pH. Heterogeneity in soil characteristics and ammonia oxidizer diversity were lower in improved soils. The results therefore demonstrate significant effects of soil management on diversity and heterogeneity of ammonia oxidizer populations that are related to similar changes in relevant soil characteristics.
Excavatolide B Attenuates Rheumatoid Arthritis through the Inhibition of Osteoclastogenesis

Osteoclasts are multinucleated giant cells of macrophage/monocyte lineage, and cell differentiation with the upregulation of osteoclast-related proteins is believed to play a major role in the destruction of the joints in the course of rheumatoid arthritis (RA). Pro-inflammatory cytokines, such as interleukin-17A (IL-17A) and macrophage colony-stimulating factor (M-CSF), can be overexpressed in RA and lead to osteoclastogenesis. In a previous study, we found that cultured-type soft coral-derived excavatolide B (Exc-B) exhibited anti-inflammatory properties. In the present study, we thus aimed to evaluate the anti-arthritic activity of Exc-B in in vitro and in vivo models. The results demonstrated that Exc-B inhibits LPS-induced multinucleated cell and actin ring formation, as well as TRAP, MMP-9, and cathepsin K expression. Additionally, Exc-B significantly attenuated the characteristics of RA in adjuvant (AIA) and type II collagen-induced arthritis (CIA) in rats. Moreover, Exc-B improved histopathological features, and reduced the number of TRAP-positive multinucleated cells in the in vivo AIA and CIA models. Immunohistochemical analysis showed that Exc-B attenuated the protein expression of cathepsin K, MMP-2, MMP-9, CD11b, and NFATc1 in ankle tissues of AIA and CIA rats. Level of interleukin-17A and macrophage colony-stimulating factor were also decreased by Exc-B. These findings strongly suggest that Exc-B could be of potential use as a therapeutic agent by inhibiting osteoclast differentiation in arthritis. Moreover, this study also illustrates the use of the anti-inflammatory marine compound, Exc-B, as a potential therapeutic strategy for RA.
A review of Bayesian neural networks with an application to near infrared spectroscopy

MacKay's (1992) Bayesian framework for backpropagation is a practical and powerful means to improve the generalization ability of neural networks. It is based on a Gaussian approximation to the posterior weight distribution. The framework is extended, reviewed, and demonstrated in a pedagogical way. The notation is simplified using the ordinary weight decay parameter, and a detailed and explicit procedure for adjusting several weight decay parameters is given. Bayesian backprop is applied in the prediction of fat content in minced meat from near infrared spectra. It outperforms "early stopping" as well as quadratic regression. The evidence of a committee of differently trained networks is computed, and the corresponding improved generalization is verified. The error bars on the predictions of the fat content are computed. There are three contributors: The random noise, the uncertainty in the weights, and the deviation among the committee members. The Bayesian framework is compared to Moody's GPE (1992). Finally, MacKay and Neal's automatic relevance determination, in which the weight decay parameters depend on the input number, is applied to the data with improved results.
Personal Exposure to Polycyclic Aromatic Hydrocarbons in Newsagents in Tehran, Iran

Background: Vehicle exhaust is a major source of exposure to Polycyclic Aromatic Hydrocarbons (PAHs) found in the urban atmosphere. Newsagents usually work close to heavy traffic flow. The purpose of this study was to assess the breathing zone exposure of newsagents to PAHs found in the urban atmosphere of Tehran City during summer and autumn seasons and comparing the levels of exposure in both seasons. Methods: Fifteen non-smoking newsagents were randomly selected from north, south, east, west, and center of Tehran. Particle and gas phases PAHs were collected on polytetrafluoroethylene (PTFE) filter and XAD-2 adsorbent. Gas chromatography–mass spectrometry (GC/MS) was used to determine PAHs concentrations in newsagent’s breathing zone samples. Results: The highest and lowest values of exposures during summer and autumn in all sampling stations were recorded for benzo[a]anthracene and benzo[ghi]perylene, respectively. Mann-Whitney test results showed that seasonal variation had significant influence on concentrations of all studied PAHs (P= 0.001) except benzo[ghi]perylene (P= 0.089). An increase in concentrations of PAHs was observed in autumn. Conclusion: The workers of the newsstands in the south area of Tehran City were experiencing higher levels of exposures to PAHs. Newsagents’ breathing zone exposures to PAHs during the cold period were two to three folds higher than those during the warm period were. The levels of exposures in all sampling stations were below the OSHA and NIOSH’s recommended exposure limits.
The Number Density of 0.6 < z < 1.7 Mg II Systems from CORALS: Observational Biases at Intermediate Redshift

The goal of the Complete Optical and Radio Absorption Line System (CORALS) survey is to quantify the potential impact on QSO absorber statistics from dust in intervening galaxies. Dust may introduce a selection bias in surveys that are based on magnitude-limited QSO samples, leading to an underestimate of absorber number density, n(z). Here we present the results of the second phase of the CORALS survey, which extends our previous work on z > 1.8 damped Lyα systems (DLAs) to search for strong metal line systems (candidate DLAs) in the range 0.6 < z < 1.7. We have identified 47 Mg II systems with rest-frame equivalent widths EW(Mg λ2796) > 0.3 Å in our sample of 75 radio-selected quasars. The total redshift path covered by the survey is Δz = 35.2, 58.2, and 63.8 for EW(Mg λ2796) > 0.3, 0.6, and 1.0 Å thresholds, respectively (5 σ). Our principal and most robust result is that the n(z) value of low-redshift Mg II systems determined for the CORALS survey is in excellent agreement with that of optically selected, magnitude-limited QSO samples. We use empirically determined Mg II equivalent width statistics to estimate the likely number of DLAs in this sample. The statistically inferred number density of DLAs, n(z) = 0.16, is consistent with other low-redshift samples, although the large 1 σ error bars permit up to a factor of 2.5 more DLAs in CORALS. However, confirmation of the DLA candidates, precise evaluation of their n(z) values, and measurement of their H I column densities awaits UV observations with the Hubble Space Telescope. Finally, we report an excess of intermediate-redshift Mg II systems observed toward bright QSOs, which could be due to a lensing amplification bias. However, there is also evidence that this excess could simply be due to more sensitive EW detection limits toward brighter QSOs. We also emphasize that absorber statistics determined from magnitude-limited surveys reach a steady value if the completeness limit is significantly fainter than the fiducial value of the quasar luminosity function.
Deviance Regulation: A Theory of Action and Identity

The authors propose a behavioral decision theory relevant to the maintenance of desirable identities. The theory, termed deviance regulation theory (DRT), predicts that actions translate into meaningful identities to the extent that they cause the individual to deviate from reference group norms. This straightforward proposition is used to predict the patterning of behavior across a wide array of social contexts. The authors present evidence that predictions generalize across Eastern and Western cultures and to both personal and collective identities. Finally, they show how DRT alters current theoretical assumptions about social motives and social and cultural influence, and they illustrate how it can help explain the structure of both informal and formal social forces.
Pose estimation using line-based dynamic vision and inertial sensors

An observer problem from a computer vision application is studied. Rigid body pose estimation using inertial sensors and a monocular camera is considered and it is shown how rotation estimation can be decoupled from position estimation. Orientation estimation is formulated as an observer problem with implicit output where the states evolve on SO(3). A careful observability study reveals interesting group theoretic structures tied to the underlying system structure. A locally convergent observer where the states evolve on SO (3) is proposed and numerical estimates of the domain of attraction is given. Further, it is shown that, given convergent orientation estimates, position estimation can be formulated as a linear implicit output problem. From an applications perspective, it is outlined how delayed low bandwidth visual observations and high bandwidth rate gyro measurements can provide high bandwidth estimates. This is consistent with real-time constraints due to the complementary characteristics of the sensors which are fused in a multirate way.
cDNA Microarrays as a Tool for Identification of Biomineralization Proteins in the Coccolithophorid Emiliania huxleyi (Haptophyta)

ABSTRACT Marine unicellular coccolithophore algae produce species-specific calcite scales otherwise known as coccoliths. While the coccoliths and their elaborate architecture have attracted the attention of investigators from various scientific disciplines, our knowledge of the underpinnings of the process of biomineralization in this alga is still in its infancy. The processes of calcification and coccolithogenesis are highly regulated and likely to be complex, requiring coordinated expression of many genes and pathways. In this study, we have employed cDNA microarrays to investigate changes in gene expression associated with biomineralization in the most abundant coccolithophorid, Emiliania huxleyi. Expression profiling of cultures grown under calcifying and noncalcifying conditions has been carried out using cDNA microarrays corresponding to approximately 2,300 expressed sequence tags. A total of 127 significantly up- or down-regulated transcripts were identified using a P value of 0.01 and a change of >2.0-fold. Real-time reverse transcriptase PCR was used to test the overall validity of the microarray data, as well as the relevance of many of the proteins predicted to be associated with biomineralization, including a novel gamma-class carbonic anhydrase (A. R. Soto, H. Zheng, D. Shoemaker, J. Rodriguez, B. A. Read, and T. M. Wahlund, Appl. Environ. Microbiol. 72:5500-5511, 2006). Differentially regulated genes include those related to cellular metabolism, ion channels, transport proteins, vesicular trafficking, and cell signaling. The putative function of the vast majority of candidate transcripts could not be defined. Nonetheless, the data described herein represent profiles of the transcription changes associated with biomineralization-related pathways in E. huxleyi and have identified novel and potentially useful targets for more detailed analysis.
EXAMINATION OF COLLEGE STUDENTS’ ATTITUDES, BELIEFS, OR INTENTIONS TO BECOMING AN ORGAN DONOR

ABSTRACT Background : Despite increased awareness and visible organ donation campaigns, it is estimated in the United States that every ten minutes someone is added to the national transplant list and, on average, twenty-two people die while waiting for an organ transplant. Design : This study, conducted in the United States, utilized an anonymous, online organ donor survey to gather preliminary qualitative and quantitative data about college students’ attitudes, beliefs, or intentions towards becoming an organ donor. Aim : To examine college students’ attitudes, beliefs, or intentions towards becoming an organ donor. Method : The study population included a convenience sample of undergraduate and graduate students enrolled during the Spring 2016 semester at a university in a southern state of the United States. Students completed an anonymous SurveyMonkey 22 item survey that included items on demographics, attitudes, beliefs, and intentions to become an organ donor. Results: Eighty-seven percent of 968 students surveyed stated they were willing to be an organ donor; however, only 83% of the students surveyed had placed the organ donor symbol on their driver's license. A large majority of students (92%) stated one factor positively affecting willingness to donate was knowing it could save someone's life. In contrast, 30% of students stated they did not trust the medical system when they were asked about particular beliefs that made them less likely to donate. Conclusion : Based on the survey results, there remains some misunderstanding about organ and tissue donation. Educational awareness remains a vital component of increasing public awareness.
Grid-based online road model estimation for advanced driver assistance systems

The information about the road course and individual lanes is an important requirement in driver assistance systems and for automated driving applications. It is often stored in a highly accurate offline map so that the road and the lanes are known in advance. However, there exist situations where an offline map can become unusable or invalid. This paper presents a novel approach for a road model estimation solely based on online measurements from sensors mounted on the ego vehicle. It combines perception data like detected lane markings, the movement history of dynamic objects in the vehicle's environment and detected road boundaries into a grid-based road model. This approach allows for an estimation of the road model even when one source of information is not available and offers a redundant source of information about the road, which is necessary in critical applications such as automated driving. The presented approach was tested and evaluated with a prototype vehicle and real sensor data from German highway scenarios.
Dynamic Virtual Bats Algorithm (DVBA) for Global Numerical Optimization

This paper presents a novel Dynamic Virtual Bats Algorithm (DVBA) for global optimization. This algorithm is inspired by bat's echolocation behavior, in particular, focusing on the way they change the wavelength and frequency of the emitted sound wave while looking for prey. The role based search is developed to improve global and local search capability of Yang's Bat Algorithm. In the DVBA, there are just two bats which are dynamically switching roles from the explorer bat to the exploiter bat according to their position. DVBA has been evaluated, in comparison with standard Particle Swarm Optimization (PSO) and standard Bat Algorithm (BA) on a number of mathematical benchmark functions. Experimental results show that the DVBA can provide superior performance than BA and PSO in optimizing these benchmark functions, mainly, in terms of its accuracy and robustness.
Nse2, a Component of the Smc5-6 Complex, Is a SUMO Ligase Required for the Response to DNA Damage

ABSTRACT The Schizosaccharomyces pombe SMC proteins Rad18 (Smc6) and Spr18 (Smc5) exist in a high-M r complex which also contains the non-SMC proteins Nse1, Nse2, Nse3, and Rad62. The Smc5-6 complex, which is essential for viability, is required for several aspects of DNA metabolism, including recombinational repair and maintenance of the DNA damage checkpoint. We have characterized Nse2 and show here that it is a SUMO ligase. Smc6 (Rad18) and Nse3, but not Smc5 (Spr18) or Nse1, are sumoylated in vitro in an Nse2-dependent manner, and Nse2 is itself autosumoylated, predominantly on the C-terminal part of the protein. Mutations of C195 and H197 in the Nse2 RING-finger-like motif abolish Nse2-dependent sumoylation. nse2.SA mutant cells, in which nse2.C195S-H197A is integrated as the sole copy of nse2, are viable, whereas the deletion of nse2 is lethal. Smc6 (Rad18) is sumoylated in vivo: the sumoylation level is increased upon exposure to DNA damage and is drastically reduced in the nse2.SA strain. Since nse2.SA cells are sensitive to DNA-damaging agents and to exposure to hydroxyurea, this implicates the Nse2-dependent sumoylation activity in DNA damage responses but not in the essential function of the Smc5-6 complex.
A Systematic Review of the Application and Empirical Investigation of Search-Based Test Case Generation

Metaheuristic search techniques have been extensively used to automate the process of generating test cases, and thus providing solutions for a more cost-effective testing process. This approach to test automation, often coined “Search-based Software Testing” (SBST), has been used for a wide variety of test case generation purposes. Since SBST techniques are heuristic by nature, they must be empirically investigated in terms of how costly and effective they are at reaching their test objectives and whether they scale up to realistic development artifacts. However, approaches to empirically study SBST techniques have shown wide variation in the literature. This paper presents the results of a systematic, comprehensive review that aims at characterizing how empirical studies have been designed to investigate SBST cost-effectiveness and what empirical evidence is available in the literature regarding SBST cost-effectiveness and scalability. We also provide a framework that drives the data collection process of this systematic review and can be the starting point of guidelines on how SBST techniques can be empirically assessed. The intent is to aid future researchers doing empirical studies in SBST by providing an unbiased view of the body of empirical evidence and by guiding them in performing well-designed and executed empirical studies.
Research Note - Knowledge Exploration and Exploitation: The Impacts of Psychological Climate and Knowledge Management System Access

Firms need to balance efficiency gains obtained through exploiting existing knowledge assets with long-term Fcompetitive viability achieved through exploring new knowledge resources. Because the use of knowledge management systems (KMSs) continues to expand, understanding how these systems affect exploration and exploitation practices at the individual level is important to advance both knowledge management theory and practice. This study reports the results of a multi-industry survey investigating how psychological climate and KMS access influence solution reuse (exploitation) and solution innovation (exploration) in the context of technical support work. Our results show that KMS access does not directly determine solution innovation or solution reuse. Instead, KMS access strengthens the positive relationship between a climate for innovation and solution innovation and reverses the positive relationship between a climate for autonomy and solution innovation. The implications for knowledge management research and practice are discussed. © 2011 INFORMS.
Flow optimization in Delay Tolerant Networks using dual decomposition

We study flow optimization in Delay Tolerant Networks (DTNs), which we model using Capacity Region Evolving Graphs (CREGs). CREGs consist of different instances (called replicas) of the network graph in cascade; each replica is associated with a distinct time period (called epoch) and its own Capacity Region. Although CREGs can model any DTN, they are particularly well suited for the study of wireless ones. We define a single-commodity utility maximization problem in a CREG of T replicas that contains as special cases various interesting flow maximization problems. Using dual decomposition, we cast the maximization as a dual problem that can be solved iteratively and where in each iteration a set of T problems, T times smaller than the original, are solved, potentially (if multiple processors are available) in parallel. In addition, we propose two suboptimal utility maximization heuristics that operate on an epoch-by-epoch basis and we discuss a multi-commodity extension to the problem.
Family language policy between the bilingual advantage and the monolingual mindset

ABSTRACT In contemporary Western societies, parenting has become the subject of a substantial body of advice and self-help literature. Within this literature, questions of bilingual parenting have begun to add yet another dimension to parental anxieties. Against this background, we examine how parents in a general Australian online parenting forum discuss the desires they have for their children's bilingualism and the challenges they experience to their bilingual parenting. We first demonstrate that individual bilingualism in the abstract is discussed in highly favourable terms and is widely conceptualised as a ‘gift’ from parents to children. However, posters’ belief in the bilingual advantage does not easily translate into effective bilingual parenting practices. First, many posters are concerned that bilingualism in the early years might be jeopardising their child's English language proficiency and hence school success. Second, a very narrow definition of ‘true’ bilingualism is connected with a relatively dogmatic belief in the ‘one parent, one language’ parenting strategy. As a result, consecutive bilinguals, particularly migrant fathers, come to be perceived as both problematic bilinguals and problematic parents. We close with implications for family language policy and advocacy in the face of entrenched institutional English monolingualism.
Invariant measures for general induced maps and towers

Absolutely continuous invariant measures (acims) for general induced transformations are shown to be related, in a natural way, to popular tower constructions regardless of any particulars of the latter. When combined with (an appropriate generalization of) the known integrability criterion for the existence of such acims, this leads to necessary and sufficient conditions under which acims can be lifted to, or projected from, nonsingular extensions.