Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial potentials for uptake, solubilization and mineralization of extracellular phosphorus in agricultural soils are highly stable under different fertilization regimes

Phosphorus is one of the most important macronutrient for plants. In agriculture, amending fertilizer with phosphorus (P) is common practice. However, natural phosphorus sources are finite, making research for more sustainable management practices necessary. We postulated that the addition of carbon (C) and nitrogen (N) would stimulate phosphorus mobilization by bacteria because of their desire to maintain a stable intracellular C:N:P stoichiometry. Therefore, we chose a metagenomic approach to investigate two agricultural soils, which only received mineral N fertilizer or mineral N and organic fertilizer for more than 20 years. The most abundant genes involved in the acquisition of external P sources in our study were those involved in solubilization and subsequent uptake of inorganic phosphorus. Independent of site and season, the relative abundance of genes involved in P turnover was not significantly affected by the addition of fertilizers. However, the type of fertilization had a significant impact on the diversity pattern of bacterial families harbouring genes coding for the different P transformation processes. This gives rise to the possibility that fertilizers can substantially change phosphorus turnover efficiency by favouring different families. Additionally, none of the families involved in phosphorus turnover covered all investigated processes. Therefore, promoting bacteria which play an essential role specifically in mobilization of hardly accessible phosphorus could help to secure the phosphorus supply of plants in soils with low P input.
Mineral resource management: Evaluating mineral resource throughput management

Mining operations are increasingly challenged to sustain and improve its profitability. Mineral Resource Throughput Management (MRTM) is showing immense promise to become a fit for use mining management and improvement methodology. Research indicated that the three dimensions of MRTM, namely physical and non-physical constraint management, product payability improvement and optimised decision-making are largely based on the theory of mechanistic and organic systems, the theory of constraints and chaos theory. It also enhances best practices in quality and mining operations management. Managing the impact of variable geology (variable ore and ore body morphology), mining (variable and changing process flow chains) and beneficiation (material compatibility) conditions as well as external variables on production within the MRTM context, mainly centres around understanding and predicting the correct flow behaviour of ore (physical and quality) in downstream processes and synchronisation of the total mining value chain.
Stumbling onto New Ideas: Technical Structure and Interactional Norms on Online Social Media

In its early stages, the Internet was viewed as an open forum for sharing and learning. Now, with a few dominant social media sites mediating most web access and the popular conception of these sites as polarizing filter bubbles, the promise of the open web appears to have been compromised. However, users of the microblogging website Tumblr do not experience this effect, instead encountering new ideas and topics alongside the content with which they intend to engage. Through a survey of over 250 Tumblr users, computational analysis of blogs, and interviews with users, my thesis seeks to uncover why Tumblr has become fertile ground for exposure to new content, expanding users’ information networks rather than reinforcing their preconceptions. I identify the key technical features of the site and social norms that work in combination to create this effect. The technical affordances include Tumblr’s disconnect from users’ offline networks, the site’s less socially focused user experience, reblogs and tags, and the customizability and control given to blog owners. The social understandings that have developed within these affordances include perceived anonymity, low-risk participation, and self-centered blogging. Within the limitations and allowances imposed by these technical constraints and social rules, many users curate personal blogs where they post a diversity of content that reflects their own interests and thoughts. Because of the unsorted nature of the Tumblr dashboard, users that follow personal blogs will encounter all of the content posted on those blogs, and in this way, be exposed to topics and ideas they were not looking for originally.
Defining Requirements for Heterodimerization between the Retinoid X Receptor and the Orphan Nuclear Receptor Nurr1*

Nurr1, an orphan nuclear receptor mainly expressed in the central nervous system, is essential for the development of the midbrain dopaminergic neurons. Nurr1 binds DNA as a monomer and exhibits constitutive transcriptional activity. Nurr1 can also regulate transcription as a heterodimer with the retinoid X receptor (RXR) and activate transcription in response to RXR ligands. However, the specific physiological roles of Nurr1 monomers and RXR-Nurr1 heterodimers remain to be elucidated. The aim of this study was to define structural requirements for RXR-Nurr1 heterodimerization. Several amino acid substitutions were introduced in both Nurr1 and RXR in the I-box, a region previously shown to be important for nuclear receptor dimerization. Single amino acid substitutions introduced in either Nurr1 or RXR abolished heterodimerization. Importantly, heterodimerization-deficient Nurr1 mutants exhibited normal activities as monomers. Thus, by introducing specific amino acid substitutions in Nurr1, monomeric and heterodimeric properties of Nurr1 can be distinguished. Interestingly, substitutions in the RXR I-box differentially affected heterodimerization with Nurr1, retinoic acid receptor, thyroid hormone receptor, and constitutive androstane receptor demonstrating that the dimerization interfaces in these different heterodimers are functionally unique. Furthermore, heterodimerization between RXR and Nurr1 had a profound influence on the constitutive activity of Nurr1, which was diminished as a result of RXR interaction. In conclusion, our data show unique structural and functional properties of RXR-Nurr1 heterodimers and also demonstrate that specific mutations in Nurr1 can abolish heterodimerization without affecting other essential functions.
Protective Effect of SnCl2 on K2Cr2O7-Induced Toxicity in LLC-PK1 Cells

The exposure to hexavalent chromium is often known to cause acute renal failure. It has been found that nonenzymatic antioxidants and the induction of heme oxygenase 1 have protective effects against nephrotoxicity induced by potassium dichromate in vivo. In this work, the effect of stannous chloride, an inducer of heme oxygenase 1, on potassium dichromate-induced toxicity in proximal tubular epithelial cells was studied. Hexavalent chromium levels, peroxynitrite content, reduced thiol content, heme oxygenase activity, reactive oxygen species production, and stannous chloride scavenging capacity were measured. It was found that stannous chloride protects proximal tubular epithelial cells from potassium dichromate-induced cell death. The decrease in extracellular and intracellular hexavalent chromium concentration, the induction of heme oxygenase 1, and the ability to scavenge reactive oxygen species and peroxynitrite are involved in the mechanism by which stannous chloride protects proximal tubular epithelial cells from potassium dichromate-induced toxicity.
A clinical profile of memory impairment in humans due to endogenous glucocorticoid excess

Objective Glucocorticoid excess is commonly related to neuropsychiatric and neurological disorders, with memory impairment typically found among these disorders. The objective of this study is to offer a clinical profile of memory deficits resulting from exposure to chronic stress‐level elevations of endogenous glucocorticoids in patients with Cushing's Syndrome (CS).
The Effect of Path-Dependence and Uncertainty on the Value of Mature Technologies

This paper examines whether technological advances benefit more from path-dependent or path-creating capabilities. Consistently with recent advances in the literature, we argue that multiple technological trajectories can coexist in a field; therefore, firms may contribute to technological development by recombining in novel ways the capabilities that are widespread in the field, or by building novel and rare capabilities. The paper also conceptualises how technological uncertainty affects the value of such capabilities. Using patent data from 1977 to 2007 for firms developing the hydrocracking technology, the paper finds that both rare and widespread capabilities are valuable to the invention process, thereby suggesting that both path-dependent and path-creating strategies are beneficial for technological development. The paper shows that uncertainty has an inverted U-shaped effect on invention value. In particular, under conditions of low uncertainty, path-dependent capabilities tend to be more valuable.
Knowledge Representation and Inference in Context-Aware Computing Environments

The present document provides a comparison of different knowledge representations and their inference models that can be used for context aware computing. In order to execute inference, any ubiquitous computing environment has to maintain the existing knowledge. The way of representing this information in the knowledge representation has a great influence on the performance that the inference system would carry out. An example scenario whose purpose is to avoid rearend collision in a vehicular environment serves as basis to derive requirements for the knowledge representation and inference. We try to apply each approach to the example scenario (or parts of it) to obtain the benefits and limitations. Like that we come to the conclusion that Bayesian networks are the way that fits best for a ubiquitous computing scenario.
Exploring Arbitrage Opportunity toward Natural Disaster Based on Indonesia Capital Market Observation

Revisiting the EMH that the market price should reflect the true state efficiently, we have found some delay effect that can represent arbitrage opportunity to in Indonesia capital market during period 2009 – 2014. We believe to filter this effect from some popular effect which are January Effect and Holiday Effect in sampling process and we obtain the pattern that can give direction for future investment purpose in the future. The exciting classification stocks to be probed are the ones which give direct impact to the natural disaster emergency handling. They are: consumer goods (food & beverage), medicine which are for first aid in natural disaster, and cement for first temporary construction aftermath. We also interest to see the effect on media sector since they have active role in proliferating the news about. Most of the observation gives non normality data. Hence, instead utilize usual standard of classical statistical analysis, we employ non parametric approach. Aus. Aca. Acc & Fin. Rev Vol 1(2), Oct 2015, P 119-131
Sociodemographic, behavioural and environmental correlates of sweetened beverage consumption among pre-school children

Abstract Objective To identify sociodemographic and environmental correlates of sweetened beverages (regular soft drinks, fruit juice) among children of pre-school age. Design Children's dietary intake, food behaviours and screen time were measured by parental report. A Geographic Informational System was used to assess the number of grocery stores and fast-food restaurants available within 1 km of the children's residence. Multivariate log-binomial regression models were constructed to determine correlates of drinking soft drinks during the previous week. Setting Edmonton region, Canada. Subjects Children aged 4 and 5 years (n 2114) attending a public health unit for immunization were recruited for a cohort study on determinants of childhood obesity, between 2005 and 2007. Results Children from neighbourhoods with low socio-economic status (relative risk (RR) = 1·17, 95 % CI 0·98, 1·40) or who participated in >2 h of screen time daily (RR = 1·28, 95 % CI 1·13, 1·45) were significantly more likely to have consumed regular soft drinks within the last week. Those who lived within 1 km of a grocery store were significantly less likely to consume regular soft drinks (RR = 0·84, 95 % CI 0·73, 0·96). Children who participated in >2 h of screen time daily (RR = 1·16, 95 % CI 1·06, 1·27) were more likely to exceed the recommended weekly number of servings of fruit juice. Conclusions Socio-economic and built environment factors are associated with soft drink consumption in children of pre-school age. These findings may help health professionals to advocate for policies that reduce soft drink consumption among children.
Understanding the divergence of manufacturing enterprisesʼ profitability in China

ABSTRACT The transition of the Chinese economy is placing increasing pressure on manufacturing enterprises to become more profitable. In this article, we first calculate and analyze the profitability of Chinese manufacturing enterprises based on data from the 2015 Chinese Enterprises–Employees Survey (CEES 2015), and find that there is an obvious profitability divergence tendency of manufacturing enterprises. We then analyze the different actions and strategies that may cause the profitability divergence and find that aggressive strategies in innovation, diversification, market development, and conservative strategies in production expansion tend to result in a good profitability, while the opposite strategies in each action lead a poor profitability. The different adoption of strategies in diverse actions may the possible causes of profitability divergence. Abbreviations: CEES: China Employer-Employee Survey, PGR: Profit growth rate, SME: Small and medium-sized enterprise
Walking on the slopes with tactile sensing system for humanoid robot

This paper presents a tactile sensing system for humanoid robot and an active tactile sensing technique to enable the humanoid robot to walk on the slopes autonomously. We introduce a novel method of walking pattern generation by applying the proposed technique to the biped humanoid robot. Our aim is to simplify the walking control by utilizing a real time tactile feedback instead of the complex ZMP calculations. We employ the minimum number of sensing elements with a specialized layout to the soles of robotic feet to enable the robot to walk on different uneven grounds. The effectiveness of the proposed method was confirmed by walking experiments with a 17 degree-of-freedoms, DOFs humanoid robot platform. The experiments show that the robot can perform balanced walking on the upward and downward slopes. In these experiments, information about ground floor or robot orientation is not required in advance.
Early unilateral cochlear implantation promotes mature cortical asymmetries in adolescents who are deaf

Unilateral cochlear implant (CI) stimulation establishes hearing to children who are deaf but compromises bilateral auditory development if a second implant is not provided within ∼1.5 years. In this study we asked: 1) What are the cortical consequences of missing this early sensitive period once children reach adolescence? 2) What are the effects of unilateral deprivation on the pathways from the opposite ear? Cortical responses were recorded from 64‐cephalic electrodes within the first week of bilateral CI activation in 34 adolescents who had over 10 years of unilateral right CI experience and in 16 normal hearing peers. Cortical activation underlying the evoked peaks was localized to areas of the brain using beamformer imaging. The first CI evoked activity which was more strongly lateralized to the contralateral left hemisphere than normal, with abnormal recruitment of the left prefrontal cortex (involved in cognition/attention), left temporo‐parietal‐occipital junction (multi‐modal integration), and right precuneus (visual processing) region. CI stimulation in the opposite deprived ear evoked atypical cortical responses with abnormally large and widespread dipole activity across the cortex. Thus, using a unilateral CI to hear beyond the period of cortical maturation causes lasting asymmetries in the auditory system, requires recruitment of additional cortical areas to support hearing, and does little to protect the unstimulated pathways from effects of auditory deprivation. The persistence of this reorganization into maturity could signal a closing of a sensitive period for promoting auditory development on the deprived side. Hum Brain Mapp 37:135–152, 2016. © 2015 Wiley Periodicals, Inc.
Comparison of the DiversiLab Repetitive Element PCR System with spa Typing and Pulsed-Field Gel Electrophoresis for Clonal Characterization of Methicillin-Resistant Staphylococcus aureus

ABSTRACT The emergence of methicillin-resistant Staphylococcus aureus (MRSA) has become an increasing problem worldwide in recent decades. Molecular typing methods have been developed to identify clonality of strains and monitor spread of MRSA. We compared a new commercially available DiversiLab (DL) repetitive element PCR system with spa typing, spa clonal cluster analysis, and pulsed-field gel electrophoresis (PFGE) in terms of discriminatory power and concordance. A collection of 106 well-defined MRSA strains from our hospital was analyzed, isolated between 1994 and 2006. In addition, we analyzed 6 USA300 strains collected in our institution. DL typing separated the 106 MRSA isolates in 10 distinct clusters and 8 singleton patterns. Clustering analysis into spa clonal complexes resulted in 3 clusters: spa-CC 067/548, spa-CC 008, and spa-CC 012. The discriminatory powers (Simpson's index of diversity) were 0.982, 0.950, 0.846, and 0.757 for PFGE, spa typing, DL typing, and spa clonal clustering, respectively. DL typing and spa clonal clustering showed the highest concordance, calculated by adjusted Rand's coefficients. The 6 USA300 isolates grouped homogeneously into distinct PFGE and DL clusters, and all belonged to spa type t008 and spa-CC 008. Among the three methods, DL proved to be rapid and easy to perform. DL typing qualifies for initial screening during outbreak investigation. However, compared to PFGE and spa typing, DL typing has limited discriminatory power and therefore should be complemented by more discriminative methods in isolates that share identical DL patterns.
Results from the ARTEMIS DISK Global Antifungal Surveillance Study, 1997 to 2007: 10.5-Year Analysis of Susceptibilities of Noncandidal Yeast Species to Fluconazole and Voriconazole Determined by CLSI Standardized Disk Diffusion Testing

ABSTRACT Fluconazole in vitro susceptibility test results determined by the CLSI M44-A disk diffusion method for 11,240 isolates of noncandidal yeasts were collected from 134 study sites in 40 countries from June 1997 through December 2007. Data were collected for 8,717 yeast isolates tested with voriconazole from 2001 through 2007. A total of 22 different species/organism groups were isolated, of which Cryptococcus neoformans was the most common (31.2% of all isolates). Overall, Cryptococcus (32.9%), Saccharomyces (11.7%), Trichosporon (10.6%), and Rhodotorula (4.1%) were the most commonly identified genera. The overall percentages of isolates in each category (susceptible, susceptible dose dependent, and resistant) were 78.0%, 9.5%, and 12.5% and 92.7%, 2.3%, and 5.0% for fluconazole and voriconazole, respectively. Less than 30% of fluconazole-resistant isolates of Cryptococcus spp. , Cryptococcus albidus, Cryptococcus laurentii, Trichosporon beigelii/Trichosporon cutaneum, Rhodotorula spp. , Rhodotorula rubra/Rhodotorula mucilaginosa, and Rhodotorula glutinis remained susceptible to voriconazole. Emerging resistance to fluconazole was documented among isolates of C. neoformans from the Asia-Pacific, Africa/Middle East, and Latin American regions but not among isolates from Europe or North America. This survey documents the continuing broad spectrum of activity of voriconazole against opportunistic yeast pathogens but identifies several of the less common species with decreased azole susceptibility. These organisms may pose a future threat to optimal antifungal therapy and emphasize the importance of prompt and accurate species identification.
X-Ray Structure of the Pestivirus NS3 Helicase and Its Conformation in Solution

ABSTRACT Pestiviruses form a genus in the Flaviviridae family of small enveloped viruses with a positive-sense single-stranded RNA genome. Viral replication in this family requires the activity of a superfamily 2 RNA helicase contained in the C-terminal domain of nonstructural protein 3 (NS3). NS3 features two conserved RecA-like domains (D1 and D2) with ATPase activity, plus a third domain (D3) that is important for unwinding nucleic acid duplexes. We report here the X-ray structure of the pestivirus NS3 helicase domain (pNS3h) at a 2.5-Å resolution. The structure deviates significantly from that of NS3 of other genera in the Flaviviridae family in D3, as it contains two important insertions that result in a narrower nucleic acid binding groove. We also show that mutations in pNS3h that rescue viruses from which the core protein is deleted map to D3, suggesting that this domain may be involved in interactions that facilitate particle assembly. Finally, structural comparisons of the enzyme in different crystalline environments, together with the findings of small-angle X-ray-scattering studies in solution, show that D2 is mobile with respect to the rest of the enzyme, oscillating between closed and open conformations. Binding of a nonhydrolyzable ATP analog locks pNS3h in a conformation that is more compact than the closest apo-form in our crystals. Together, our results provide new insight and bring up new questions about pNS3h function during pestivirus replication. IMPORTANCE Although pestivirus infections impose an important toll on the livestock industry worldwide, little information is available about the nonstructural proteins essential for viral replication, such as the NS3 helicase. We provide here a comparative structural and functional analysis of pNS3h with respect to its orthologs in other viruses of the same family, the flaviviruses and hepatitis C virus. Our studies reveal differences in the nucleic acid binding groove that could have implications for understanding the unwinding specificity of pNS3h, which is active only on RNA duplexes. We also show that pNS3h has a highly dynamic behavior—a characteristic probably shared with NS3 helicases from all Flaviviridae members—that could be targeted for drug design by using recent algorithms to specifically block molecular motion. Compounds that lock the enzyme in a single conformation or limit its dynamic range of conformations are indeed likely to block its helicase function.