Miracle-dz/UniFAR-FTUs huggingface dataset:
Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession

Significance Across ecology, and particularly within microbial ecology, there is limited understanding of the mechanisms governing the relative influences of stochastic and deterministic processes. Filling this knowledge gap is a major challenge that requires the development of novel conceptual paradigms, experiments, and ecological models. Here we (i) present a conceptual model that couples the stochastic/deterministic balance to primary and secondary ecological succession, thereby integrating previously isolated conceptual domains; (ii) evaluate this model over 105 years of ecosystem development, revealing a systematic shift in the type and strength of ecological selection; and (iii) couple empirical data with a new simulation model to elucidate underlying mechanisms and characterize their scale dependency. The insights and conceptual framework provided here represent a nexus for cross-system integration. Ecological succession and the balance between stochastic and deterministic processes are two major themes within microbial ecology, but these conceptual domains have mostly developed independent of each other. Here we provide a framework that integrates shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. Synthesizing previous work, we devised a conceptual model that links ecosystem development to alternative hypotheses related to shifts in ecological assembly processes. Conceptual model hypotheses were tested by coupling spatiotemporal data on soil bacterial communities with environmental conditions in a salt marsh chronosequence spanning 105 years of succession. Analyses within successional stages showed community composition to be initially governed by stochasticity, but as succession proceeded, there was a progressive increase in deterministic selection correlated with increasing sodium concentration. Analyses of community turnover among successional stages—which provide a larger spatiotemporal scale relative to within stage analyses—revealed that changes in the concentration of soil organic matter were the main predictor of the type and relative influence of determinism. Taken together, these results suggest scale-dependency in the mechanisms underlying selection. To better understand mechanisms governing these patterns, we developed an ecological simulation model that revealed how changes in selective environments cause shifts in the stochastic/deterministic balance. Finally, we propose an extended—and experimentally testable—conceptual model integrating ecological assembly processes with primary and secondary succession. This framework provides a priori hypotheses for future experiments, thereby facilitating a systematic approach to understand assembly and succession in microbial communities across ecosystems.
Evaluating adaptive user profiles for news classification

Never before have so many information sources been available. Most are accessible on-line and some exist on the Internet alone. However, this large information quantity makes interesting articles hard to find. Modern Personal Digital Assistants (PDAs), mobile phones, and the advent of ubiquitous computing will further complicate matters. Away from the desktop, the time to select important articles might be even harder to find. Strategies to select relevant information are sorely needed.One such strategy is content-based filtering, coupled with User Profiles. Our prototype uses a Bayesian classifier to select articles of interest to a specific user, according to his profile. The articles are extracted from web pages and displayed in a zoomable interface-based browser on a PDA. Interests may change over time, making it important to keep the profile up to date. The system monitors the users' reading behaviors, from which it infers their interest in particular articles and updates the profile accordingly. Results show that, from the start, most articles are correctly classified. An initial profile opposite to the user's actual interests can be reversed in less than ten days, showing the robustness of our approach. A user's interest in an article is inferred with a high degree of accuracy (over 90%).
ANALISIS FAKTOR-FAKTOR YANG MEMPENGARUHI INTENSI AUDITOR UNTUK MELAKUKAN TINDAKAN WHISTLEBLOWING (Studi Empiris pada Kantor Akuntan Publik di Semarang)

This study aims to obtain empirical evidence of factors that affect auditor to make whistleblowing intention. This study refers to Curtis and Taylor (2010) by using the concept of the Theory of Planned Behavior (TPB) as a theoritical basis. This study uses primary data to obtained important information from the respondents by using convinience sampling method. Respondents in this study were 55 auditors who worked in public accounting firm in Semarang City, Indonesia. Statistical analysis method used is multiple linear regression. Hypothesis testing is done with the help of software IBM SPSS Statistics 19. The result of this study indicates: (1) Professional Identity positively significant influence whistleblowing intention; (2) Auditor who have higher organizational commitment that auditors who have a commitment to co-workers has not significant influence whistleblowing intention; (3) Moral intensity positively significant influence whistleblowing intention; (4) Auditor's personal characteristics is consisted of Gender, Age, Education, Experience (based on years experience) and Level Position at firm has not significant influence whistleblowing intention.
Tree-structured Data Regeneration in Distributed Storage Systems with Regenerating Codes

Distributed storage systems provide large-scale reliable data storage by storing a certain degree of redundancy in a decentralized fashion on a group of storage nodes. To recover from data losses due to the instability of these nodes, whenever a node leaves the system, additional redundancy should be regenerated to compensate such losses. In this context, the general objective is to minimize the volume of actual network traffic caused by such regenerations. A class of codes, called regenerating codes, has been proposed to achieve an optimal trade-off curve between the amount of storage space required for storing redundancy and the network traffic during the regeneration. In this paper, we jointly consider the choices of regenerating codes and network topologies. We propose a new design, referred to as RCTREE, that combines the advantage of regenerating codes with a tree-structured regeneration topology. Our focus is the efficient utilization of network links, in addition to the reduction of the regeneration traffic. With the extensive analysis and quantitative evaluations, we show that RCTREE is able to achieve a both fast and stable regeneration, even with departures of storage nodes during the regeneration.
The Broadcast Storm Problem in a Mobile Ad Hoc Network

Broadcasting is a common operation in a network to resolve many issues. In a mobile ad hoc network (MANET) in particular, due to host mobility, such operations are expected to be executed more frequently (such as finding a route to a particular host, paging a particular host, and sending an alarm signal). Because radio signals are likely to overlap with others in a geographical area, a straightforward broadcasting by flooding is usually very costly and will result in serious redundancy, contention, and collision, to which we call the broadcast storm problem. In this paper, we identify this problem by showing how serious it is through analyses and simulations. We propose several schemes to reduce redundant rebroadcasts and differentiate timing of rebroadcasts to alleviate this problem. Simulation results are presented, which show different levels of improvement over the basic flooding approach.
Information seeking and mediated searching study. Part 3. Successive searching

Our project has investigated the processes of mediated information retrieval (IR) searching during human information-seeking processes to characterize aspects of this process, including information seekers' changing situational contexts; information problems; uncertainty reduction; successive searching, cognitive styles; and cognitive and affective states. The research has involved observational, longitudinal data collection in the United States and the United Kingdom. Three questionnaires were used for pre- and postsearch interviews: reference interview, information-seeker postsearch, and search intermediary postsearch questionnaires. In addition, the Sheffield team employed a fourth set of instruments in a follow-up interview some 2 months after the search. A total of 198 information seekers participated in a mediated on-line search with a professional intermediary using the Dialog Information Service. Each mediated search process was audiotaped and search transaction logs recorded. The findings are presented in four parts. Part I presents the background, theoretical framework, models, and research design used during the research. Part II is devoted to exploring changes in information seekers' uncertainty during the mediated process. Part III provides results related to successive searching. Part IV reports findings related to cognitive styles, individual differences, age and gender. Additional articles that discuss further findings from this complex research project, including: (1) an integrated model of information seeking and searching, (2) assessment of mediated searching, and (3) intermediary information-seeker communication, are in preparation and will be published separately.
Sentinel Surveillance of Sexually Transmitted Infections/HIV and Risk Behaviors in Vulnerable Populations in 5 Central American Countries

In El Salvador, Guatemala, Honduras, Nicaragua, and Panama, we recruited 2466 female sex workers (FSWs) by probabilistic or comprehensive sampling and 1418 men who have sex with men (MSM) by convenience sampling to measure sociobehavioral risk and sexually transmitted infections. For MSM, HIV seroprevalence ranged from 7.6% in Nicaragua to 15.3% in El Salvador, and estimated HIV seroincidence per 100 person-years ranged from 2.7 in Panama to 14.4 in Nicaragua; 61% reported using condoms consistently with casual male partners, 29% reported exposure to behavioral interventions, and 22% reported recent sex with male and female partners. For FSWs, HIV seroprevalence ranged from 0.2% in Nicaragua and Panama to 9.6% in Honduras, where estimated HIV seroincidence was also highest (3.2 per 100 person-years); 77% and 72% of FSWs reported using condoms consistently with new and regular clients. Herpes simplex virus (HSV)-2 seroprevalence averaged 85.3% in FSWs and 48.2% in MSM, and syphilis seropositivity averaged 9.6% in FSWs and 8.3% in MSM. Chlamydia trachomatis and Neisseria gonorrhoeae prevalences in FSWs averaged 20.1% and 8.1%, and Trichomonas vaginalis and bacterial vaginosis prevalences averaged 11.0% and 54.8%. An ongoing HIV epidemic involves Central American MSM with potential bridging to women. In FSWs, HSV-2 infection was associated with HIV infection (odds ratio = 11.0, 95% confidence interval: 2.9 to 7.9). For these vulnerable populations, prevention must incorporate acceptable and effective sexual health services, including improved condom access and promotion.
Revolutionaries, barbarians or war machines?; gangs in Nicaragua and South Africa

The view of gangs as proto-revolutionary vanguards has continued to inform the analyses of many gang researchers over the past few decades. During the course of our own research on gangs in respectively a poor neighbourhood in Managua, the capital city of Nicaragua, and a coloured township in Cape Town, South Africa, we have found considerable empirical resonance between Fanon's vision and the real-life discourses of many of the gangsters that we have interviewed and spent time with. Although narratives of fighting with the authorities, only stealing from the rich (or the racially dominant), and protecting local communities and neighbourhoods have long been features uncovered by research on gangs, we found these to often be actively framed in explicitly revolutionary terms. Nicaraguan gang members, for example, frequently compared their behaviour with the actions of the Sandinista revolutionary regime, while gangs in post-Apartheid South Africa explicitly justified themselves as ANC-inspired forms of resistance against institutionalised racism. We wish to propose that gangs are a phenomenon that can be understood using Deleuze and Guattari's concept of the 'war machine'. This captures not only the ambiguities of gangs, but also the underlying similarities between gangs that have emerged in very different contexts, each with their own localised histories of accumulation and marginalisation. In doing so it allows us to better understand what it is that gangs and their violent practices really represent, and what relation they have, if any, to revolution.
Overcoming organizational inertia to strengthen business model innovation

Purpose – This study aims to examine how open innovation can be effective in changing organizational inertia to create business model innovation and improve firm performance. It also seeks to explore whether the existence of open innovation has a mediating effect and influence. Design/methodology/approach – This study constructs a theoretical model to explore the relationship between latent variables and uses a questionnaire to collect research data. In the conceptual framework, organizational inertia is a second-order latent variable and comprises three first-order latent variables: insight inertia, action inertia, and psychological inertia. Open innovation is also a second-order latent variable, and consists of two first-order latent variables: outbound and inbound open innovation. To clarify the relationship between these latent variables, structural equation modeling (SEM) is used to test the goodness of fit of the theoretical model and research hypotheses. This study uses 141 small to medium-sized ma.
Characterization of Pseudomonas aeruginosa Chitinase, a Gradually Secreted Protein

ABSTRACT The gram-negative bacterium Pseudomonas aeruginosasecretes many proteins into its extracellular environment via the type I, II, and III secretion systems. In this study, a gene,chiC, coding for an extracellular chitinolytic enzyme, was identified. The chiC gene encodes a polypeptide of 483 amino acid residues, without a typical N-terminal signal sequence. Nevertheless, an N-terminal segment of 11 residues was found to be cleaved off in the secreted protein. The protein shows sequence similarity to the secreted chitinases ChiC of Serratia marcescens, ChiA of Vibrio harveyi, and ChiD ofBacillus circulans and consists of an activity domain and a chitin-binding domain, which are separated by a fibronectin type III domain. ChiC was able to bind and degrade colloidal chitin and was active on the artificial substrates carboxymethyl-chitin-Remazol Brilliant Violet andp-nitrophenyl-β-d-N,N′,N"-triacetylchitotriose, but not onp-nitrophenyl-β-d-N-acetylglucosamine, indicating that it is an endochitinase. Expression of thechiC gene appears to be regulated by the quorum-sensing system of P. aeruginosa, since this gene was not expressed in a lasIR vsmI mutant. After overnight growth, the majority of the ChiC produced was found intracellularly, whereas only small amounts were detected in the culture medium. However, after several days, the cellular pool of ChiC was largely depleted, and the protein was found in the culture medium. This release could not be ascribed to cell lysis. Since ChiC did not appear to be secreted via any of the known secretion systems, a novel secretion pathway seems to be involved.
Illegal use of natural resources in federal protected areas of the Brazilian Amazon

Background The Brazilian Amazon is the world’s largest rainforest regions and plays a key role in biodiversity conservation as well as climate adaptation and mitigation. The government has created a network of protected areas (PAs) to ensure long-term conservation of the region. However, despite the importance of and positive advances in the establishment of PAs, natural resource depletion in the Brazilian Amazon is pervasive. Methods We evaluated a total of 4,243 official law enforcement records generated between 2010 and 2015 to understand the geographical distribution of the illegal use of resources in federal PAs in the Brazilian Amazon. We classified illegal activities into ten categories and used generalized additive models (GAMs) to evaluate the relationship between illegal use of natural resources inside PAs with management type, age of PAs, population density, and accessibility. Results We found 27 types of illegal use of natural resources that were grouped into 10 categories of illegal activities. Most infractions were related to suppression and degradation of vegetation (37.40%), followed by illegal fishing (27.30%) and hunting activities (18.20%). The explanatory power of the GAMs was low for all categories of illegal activity, with a maximum explained variation of 41.2% for illegal activities as a whole, and a minimum of 14.6% for hunting activities. Discussion These findings demonstrate that even though PAs are fundamental for nature conservation in the Brazilian Amazon, the pressures and threats posed by human activities include a broad range of illegal uses of natural resources. Population density up to 50 km from a PA is a key variable, influencing illegal activities. These threats endanger long-term conservation and many efforts are still needed to maintain PAs that are large enough and sufficiently intact to maintain ecosystem functions and protect biodiversity.
Recoil and threshold corrections in short-distance cross sections

We identify and resum corrections associated with the kinematic recoil of the hard scattering against soft-gluon emission in single-particle inclusive cross sections. The method avoids double counting and conserves the flow of partonic energy. It reproduces threshold resummation for high-pT single-particle cross sections, when recoil is neglected, and QTresummation at low QT, when higher-order threshold logarithms are suppressed. We exhibit explicit resummed cross sections, accurate to next-to-leading logarithm, for electroweak annihilation and prompt photon inclusive cross sections.
The clinicopathologic spectrum of focal cortical dysplasias: A consensus classification proposed by an ad hoc Task Force of the ILAE Diagnostic Methods Commission 1

Purpose: Focal cortical dysplasias (FCD) are localized regions of malformed cerebral cortex and are very frequently associated with epilepsy in both children and adults. A broad spectrum of histopathology has been included in the diagnosis of FCD. An ILAE task force proposes an international consensus classification system to better characterize specific clinicopathological FCD entities.
The evolution of adhesiveness as a social adaptation

Cellular adhesion is a key ingredient to sustain collective functions of microbial aggregates. Here, we investigate the evolutionary origins of adhesion and the emergence of groups of genealogically unrelated cells with a game-theoretical model. The considered adhesiveness trait is costly, continuous and affects both group formation and group-derived benefits. The formalism of adaptive dynamics reveals two evolutionary stable strategies, at each extreme on the axis of adhesiveness. We show that cohesive groups can evolve by small mutational steps, provided the population is already endowed with a minimum adhesiveness level. Assortment between more adhesive types, and in particular differential propensities to leave a fraction of individuals ungrouped at the end of the aggregation process, can compensate for the cost of increased adhesiveness. We also discuss the change in the social nature of more adhesive mutations along evolutionary trajectories, and find that altruism arises before directly beneficial behavior, despite being the most challenging form of cooperation. DOI: http://dx.doi. org/10.7554/eLife.08595. 001
Functional Analysis of Cyclin-Dependent Kinase Inhibitors of Arabidopsis

Cyclin-dependent kinase inhibitors, such as the mammalian p27Kip1 protein, regulate correct cell cycle progression and the integration of developmental signals with the core cell cycle machinery. These inhibitors have been described in plants, but their function remains unresolved. We have isolated seven genes from Arabidopsis that encode proteins with distant sequence homology with p27Kip1, designated Kip-related proteins (KRPs). The KRPs were characterized by their domain organization and transcript profiles. With the exception of KRP5, all presented the same cyclin-dependent kinase binding specificity. When overproduced, KRP2 dramatically inhibited cell cycle progression in leaf primordia cells without affecting the temporal pattern of cell division and differentiation. Mature transgenic leaves were serrated and consisted of enlarged cells. Although the ploidy levels in young leaves were unaffected, endoreduplication was suppressed in older leaves. We conclude that KRP2 exerts a plant growth inhibitory activity by reducing cell proliferation in leaves, but, in contrast to its mammalian counterparts, it may not control the timing of cell cycle exit and differentiation.
Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China

The long-term application of excessive chemical fertilizers has resulted in the degeneration of soil quality parameters such as soil microbial biomass, communities, and nutrient content, which in turn affects crop health, productivity, and soil sustainable productivity. The objective of this study was to develop a rapid and efficient solution for rehabilitating degraded cropland soils by precisely quantifying soil quality parameters through the application of manure compost and bacteria fertilizers or its combination during maize growth. We investigated dynamic impacts on soil microbial count, biomass, basal respiration, community structure diversity, and enzyme activity using six different treatments [no fertilizer (CK), N fertilizer (N), N fertilizer + bacterial fertilizer (NB), manure compost (M), manure compost + bacterial fertilizer (MB), and bacterial fertilizer (B)] in the plowed layer (0–20 cm) of potted soil during various maize growth stages in a temperate cropland of eastern China. Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. The Shannon index of bacterial and fungi communities displayed the highest value in the MB treatments and the lowest in the N treatment at the maize mature stage. Changes in soil microorganism community structure and diversity after different fertilizer treatments resulted in different microbial properties. Adding manure compost significantly increased the amount of cultivable microorganisms and microbial biomass, thus enhancing soil respiration and enzyme activities (p<0.01), whereas N treatment showed the opposite results (p<0.01). However, B and NB treatments minimally increased the amount of cultivable microorganisms and microbial biomass, with no obvious influence on community structure and soil enzymes. Our findings indicate that the application of manure compost plus bacterial fertilizers can immediately improve the microbial community structure and diversity of degraded cropland soils.