Miracle-dz/UniFAR-FTUs huggingface dataset:
Range-Expanding Populations of a Globally Introduced Weed Experience Negative Plant-Soil Feedbacks

Background Biological invasions are fundamentally biogeographic processes that occur over large spatial scales. Interactions with soil microbes can have strong impacts on plant invasions, but how these interactions vary among areas where introduced species are highly invasive vs. naturalized is still unknown. In this study, we examined biogeographic variation in plant-soil microbe interactions of a globally invasive weed, Centaurea solstitialis (yellow starthistle). We addressed the following questions (1) Is Centaurea released from natural enemy pressure from soil microbes in introduced regions? and (2) Is variation in plant-soil feedbacks associated with variation in Centaurea's invasive success? Methodology/Principal Findings We conducted greenhouse experiments using soils and seeds collected from native Eurasian populations and introduced populations spanning North and South America where Centaurea is highly invasive and noninvasive. Soil microbes had pervasive negative effects in all regions, although the magnitude of their effect varied among regions. These patterns were not unequivocally congruent with the enemy release hypothesis. Surprisingly, we also found that Centaurea generated strong negative feedbacks in regions where it is the most invasive, while it generated neutral plant-soil feedbacks where it is noninvasive. Conclusions/Significance Recent studies have found reduced below-ground enemy attack and more positive plant-soil feedbacks in range-expanding plant populations, but we found increased negative effects of soil microbes in range-expanding Centaurea populations. While such negative feedbacks may limit the long-term persistence of invasive plants, such feedbacks may also contribute to the success of invasions, either by having disproportionately negative impacts on competing species, or by yielding relatively better growth in uncolonized areas that would encourage lateral spread. Enemy release from soil-borne pathogens is not sufficient to explain the success of this weed in such different regions. The biogeographic variation in soil-microbe effects indicates that different mechanisms may operate on this species in different regions, thus establishing geographic mosaics of species interactions that contribute to variation in invasion success.
Evaluation of text document clustering approach based on particle swarm optimization

Clustering, an extremely important technique in Data Mining is an automatic learning technique aimed at grouping a set of objects into subsets or clusters. The goal is to create clusters that are coherent internally, but substantially different from each other. Text Document Clustering refers to the clustering of related text documents into groups based upon their content. It is a fundamental operation used in unsupervised document organization, text data mining, automatic topic extraction, and information retrieval. Fast and high-quality document clustering algorithms play an important role in effectively navigating, summarizing, and organizing information. The documents to be clustered can be web news articles, abstracts of research papers etc. This paper proposes two techniques for efficient document clustering involving the application of soft computing approach as an intelligent hybrid approach PSO algorithm. The proposed approach involves partitioning Fuzzy C-Means algorithm and K-Means algorithm each hybridized with Particle Swarm Optimization (PSO). The performance of these hybrid algorithms has been evaluated against traditional partitioning techniques (K-Means and Fuzzy C Means).
Role of thioredoxin reductase in the Yap1p‐dependent response to oxidative stress in Saccharomyces cerevisiae

The Saccharomyces cerevisiae Yap1p transcription factor is required for the H2O2‐dependent activation of many antioxidant genes including the TRX2 gene encoding thioredoxin 2. To identify factors that regulate Yap1p activity, we carried out a genetic screen for mutants that show elevated expression of a TRX2–HIS3 fusion in the absence of H2O2. Two independent mutants isolated in this screen carried mutations in the TRR1 gene encoding thioredoxin reductase. Northern blot and whole‐genome expression analysis revealed that the basal expression of most Yap1p targets and many other H2O2‐inducible genes is elevated in Δtrr1 mutants in the absence of external stress. In Δtrr1 mutants treated with H2O2, the Yap1p targets, as well as genes comprising a general environmental stress response and genes encoding protein‐folding chaperones, are hyperinduced. However, despite the elevated expression of genes encoding antioxidant enzymes, Δtrr1 mutants are extremely sensitive to H2O2. The results suggest that cells lacking thioredoxin reductase have diminished capacity to detoxify oxidants and/or to repair oxidative stress‐induced damage and that the thioredoxin system is involved in the redox regulation of Yap1p transcriptional activity.
Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils

ABSTRACT The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N2 fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.
Research on Numerical Simulation Metadata

—In many research fields of numerical simulations, programs of scientific computing often produce a large amount of simulation simulation data with complex structure and lacking for explaining information. It is a fatal bottleneck for scientists to organize and manage such large-scale simulation data. This paper takes typical numerical simulation procedure and its result data as the application backgrounds, provides the definition and classification of metadata which faces to the numerical simulation, puts forward the method to distinguish the characteristics of various of data documents. The functions of collecting metadata online and storage them automatically are realized by imbedding thread task module in the interface of access data. I.e. the metadata are stored into the database while the calculation results in each step of outputting time are sent to the file system. In addition, a scientific calculating metadata management prototype system was designed, the users can browse and inquire about the metadata through webs, and further obtain and analyze the distributed numerical simulations data, carry on the inquiries about space scope and physical quantity ranges and its visualization in which they are interested, thus offers the users the services which are top-graded, simple to use and with data as its core. Simultion results can be look over and trace conveniently and real-timely by the researchers in this field, and the analysis and assessment ability to the calculation result can be improved efficiently.
A Service-Based Selfish Routing for Mobile Social Networks

Routing in mobile social networks is a challenging task due to the characteristic of intermittent connectivity, especially when the nodes behave selfishly in real world. Selfish behaviors of node always influence its altruism to provide forwarding service for others and degrade network performance strongly. In this paper, to address the selfishness problem in MSNs, we propose a service-based selfish routing protocol, SSR. When making forwarding decision, SSR employ user altruism and the amount of service that the relay nodes provide. User altruism is determined by the social selfishness and the individual selfishness. The services include pairwise services and social services, which is also considered as the incentives to stimulate node to be more cooperative. The more services the node provides, the more chance the node has to be served. The node with higher altruism and fewer services is the preferred relay node. Simulation results show SSR achieves better performance when the user altruism is low and demonstrate the effectiveness of the service-based scheme.
Partially Informed Depth-First Search for the Job Shop Problem

We propose a partially informed depth-first search algorithm to cope with the Job Shop Scheduling Problem with makespan minimization. The algorithm is built from the well-known P. Brucker's branch and bound algorithm. We improved the heuristic estimation of Brucker's algorithm by means of constraint propagation rules and so devised a more informed heuristic which is proved to be monotonic. We conducted an experimental study across medium and large instances. The results show that the proposed algorithm reaches optimal solutions for medium instances taking less time than branch and bound and that for large instances it reaches much better lower and upper bounds when both algorithms are given the same amount of time.
Global and local statistical regularities control visual attention to object sequences

Many previous studies have shown that both infants and adults are skilled statistical learners. Because statistical learning is affected by attention, learners' ability to manage their attention can play a large role in what they learn. However, it is still unclear how learners allocate their attention in order to gain information in a visual environment containing multiple objects, especially how prior visual experience (i.e., familiarly of objects) influences where people look. To answer these questions, we collected eye movement data from adults exploring multiple novel objects while manipulating object familiarity with global (frequencies) and local (repetitions) regularities. We found that participants are sensitive to both global and local statistics embedded in their visual environment and they dynamically shift their attention to prioritize some objects over others as they gain knowledge of the objects and their distributions within the task.
A β AMYLOID & GLUCOSE METABOLISM IN THREE VARIANTS OF PRIMARY PROGRESSIVE APHASIA

OBJECTIVE—Alzheimer’s disease (AD) is found at autopsy in up to one-third of patients with primary progressive aphasia (PPA), but clinical features that predict AD pathology in PPA are not well defined. We studied the relationships between language presentation, Aβ amyloidosis and glucose metabolism in three variants of PPA using [11C]PIB and [18F]FDG-PET. METHODS—Patients meeting PPA criteria (N=15) were classified as logopenic aphasia (LPA), progressive non-fluent aphasia (PNFA) or semantic dementia (SD) based on language testing. [11C] PIB distribution volume ratios were calculated using Logan graphical analysis (cerebellar reference). [18F]FDG images were normalized to pons. Partial volume correction was applied. RESULTS—Elevated cortical PIB (by visual inspection) was more common in LPA (4/4 patients) than in PNFA (1/6) and SD (1/5) (p<0.02). In all PIB-positive cases, PIB uptake was diffuse and indistinguishable from the pattern in matched AD patients (N=10). FDG patterns were focal and varied by PPA subtype, with left temporoparietal hypometabolism in LPA, left frontal hypometabolism in PNFA, and left anterior temporal hypometabolism in SD. FDG patterns in PIBpositive PNFA and SD were similar to PIB-negative cases. Language regions showed asymmetric left hypometabolism in PPA (p<0.005) but not in AD. INTERPRETATION—LPA is associated with Aβ amyloidosis, suggesting that sub-classification of PPA based on language features can help predict the likelihood of underlying AD pathology. Language phenotype in PPA is closely related to metabolic changes that are focal and anatomically distinct between subtypes, but not to amyloid deposition patterns that are diffuse and similar to AD. Corresponding Author: Gil D. Rabinovici, MD, UCSF Memory & Aging Center, 350 Parnassus Ave., Suite 706, San Francisco, CA 94143, Tel. : (415) 514-9320, Fax: (415) 476-4800, Email: grabinovici@memory.ucsf. edu. Disclosures: Dr. Jagust has received consulting fees from GE Healthcare, which holds a license agreement with the University of Pittsburgh based on the PIB compound described in this manuscript. The other authors do not report potential conflicts of interest. NIH Public Access Author Manuscript Ann Neurol. Author manuscript; available in PMC 2009 February 26. Published in final edited form as: Ann Neurol. 2008 October ; 64(4): 388–401. doi:10.1002/ana.21451. N IH PA Athor M anscript N IH PA Athor M anscript N IH PA Athor M anscript
Influence of Features Extraction Methods in Performance of Continuous Speech Recognition for Romanian

This paper describes continuous speech recognition experiments for Romanian language, based on statistical modelling by using hidden Markov models. These experiments are made in order to select the most appropriate features extraction method. The compared methods are cepstral and LPC analysis, in standard and perceptual versions. In our tests the cepstral coefficients perform in the most situations better versus the linear prediction ones, and the perceptual coefficients better than the standard ones.
On cost-informed pricing and customer value: a resource-advantage perspective on industrial innovation pricing practices

By empirically testing a framework of pricing strategies and their determinants in an industrial setting, Noble and Gruca (1999a) help to overcome the lack of empirical validation of pricing theory. In a commentary to the article, Cressman (1999) (1) expresses worries about the high percentage of firms that engages in cost-based pricing; (2) raises a definition question on value-based pricing; and (3) stresses that empirical pricing literature does not provide ideas on successful pricing practices in relation to customer value created. The aim of this study is to respond to calls for research on successful pricing practices. A perspective from resource-advantage theory (Hunt and Morgan 1995) is used to formulate expectations on the degree to which the use of information on customer value, competition, and costs contributes to the success of a price decision. It is argued that the success of these practices is contingent on the relative customer value the firm has created and the degree to which this position of relative value is sustainable in the competitive market place.These expectations are empirically tested on pricing decisions with respect to the introduction of new industrial capital goods. It is concluded that Noble and Gruca’s (1999a) findings on cost-based pricing can be complemented, since our results show that under most circumstances cost-informed
Facial expressiveness in patients with schizophrenia compared to depressed patients and nonpatient comparison subjects.

OBJECTIVE Blunted affect is a major symptom in schizophrenia, and affective deficits clinically encompass deficits in expressiveness. Emotion research and ethological studies have shown that patients with schizophrenia are impaired in various modalities of expressiveness (posed and spontaneous emotion expressions, coverbal gestures, and smiles). Similar deficits have been described in depression, but comparative studies have brought mixed results. Our aim was to study and compare facial expressive behaviors related to affective deficits in patients with schizophrenia, depressed patients, and nonpatient comparison subjects. METHOD Fifty-eight nondepressed inpatients with schizophrenia, 25 nonpsychotic inpatients with unipolar depression, and 25 nonpatient comparison subjects were asked to reproduce facial emotional expressions. Then the subjects were asked to speak about a specific emotion for 2 minutes. Each time, six cross-cultural emotions were tested. Facial emotional expressions were rated with the Facial Action Coding System. The number of facial coverbal gestures (facial expressions that are tied to speech) and the number of words were calculated. RESULTS In relation to nonpatient comparison subjects, both patient groups were impaired for all expressive variables. Few differences were found between schizophrenia and depression: depressed subjects had less spontaneous expressions of other-than-happiness emotions, but overall, they appeared more expressive. Fifteen patients with schizophrenia were tested without and with typical or atypical antipsychotic medications: no differences could be found in study performance. CONCLUSIONS The patients with schizophrenia and the patients with depression presented similar deficits in various expressive modalities: posed and spontaneous emotional expression, smiling, coverbal gestures, and verbal output.
The human side of hypoxia-inducible factor

When humans are exposed to hypoxia, systemic and intracellular changes operate together to minimise hypoxic injury and restore adequate oxygenation. Emerging evidence indicates that the hypoxia‐inducible factor (HIF) family of transcription factors plays a central regulatory role in these homeostatic changes at both the systemic and cellular levels. HIF was discovered through its action as the transcriptional activator of erythropoietin, and has subsequently been found to control intracellular hypoxic responses throughout the body. HIF is primarily regulated by specific prolyl hydroxylase‐domain enzymes (PHDs) that initiate its degradation via the von Hippel‐Lindau tumour suppressor protein (VHL). The oxygen and iron dependency of PHD activity accounts for regulation of the pathway by both cellular oxygen and iron status. Recent studies conducted in patients with rare genetic diseases have begun to uncover the wider importance of the PHD‐VHL‐HIF axis in systems‐level human biology. These studies indicate that, in addition to regulating erythropoiesis, the system plays an important role in cardiopulmonary regulation. This article reviews our current understanding of the importance of HIF in human systems‐level physiology, and is modelled around the classic physiological response to high‐altitude hypoxia.
Characterization of Domains Admitting Strategy-Proof and Non-Dictatorial Social Choice Functions with Infinite Sets of Alternatives

We show, with an example, that the theorem on the characterization of the domains admitting strategy-proof and non-dictatorial social choice functions by Kalai and Muller (1977) does not hold when the set of alternatives is infinite. We consider two ways of overcoming this problem. The first identifies a set of domains admitting strategy-proof and non-dictatorial social choice functions when the set of alternatives is infinite. The second defines a class of social choice functions for which the theorem is true with both finite and infinite sets of alternatives. Journal of Economic Literature Classification Number: D71.
Evaluation of Pronunciation by means of Automatic Speech Recognition System for Computer Aided Indonesian Language Learning

Utilizing of speech recognizers as pronunciation evaluator is discussed in this work. The main reason is to put application of speech technology in assisting Indonesian learning as a part of on-going open learning environment. With the advanced technology of speech recognizers, the possibilities of applications become wider. Dealing with isolated word recognizer and medium-sized database, evaluation of pronunciation of learners based on prosody information is the objective. Two kinds of word set from non-native speakers are used to evaluate automatic pronunciation recognizer: mispronunciation by mistake and those by linguistical inheritance. The quality of evaluation is confirmed by human judgment. In addition, what kinds of mispronunciation they would do in Indonesian is also investigated. Herein it explores the possibility of using a hidden Markov model HTK tools recognizer and of obtaining correct prosody information in order to implement it in a system to aid in Indonesian language learning as L2.
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive, adult-onset neurodegenerative disease characterized by selective dysfunction and death of motor neurons in the brain and spinal cord.The disease

Amyotrophic lateral sclerosis (ALS) is a rapidly progressive, adult-onset neurodegenerative disease characterized by selective dysfunction and death of motor neurons in the brain and spinal cord.The disease is typically fatal within three to five years of symptom onset.There is no known cure and only riluzole, which was approved by the US Food and Drug Administration (FDA) in 1996 for the treatment of ALS, has shown some efficacy in humans. There remains a crucial unmet need for effective neuroprotective strategies in ALS. Recently, experimental data have highlighted the beneficial properties of the antibiotic minocycline in models of neurodegeneration. This article reviews the clinical potential of minocycline for the treatment of ALS.
Version models for software configuration management

After more than 20 years of research and practice in software configuration management (SCM), constructing consistent configurations of versioned software products still remains a challenge. This article focuses on the version models underlying both commercial systems and research prototypes. It provides an overview and classification of different versioning paradigms and defines and relates fundamental concepts such as revisions, variants, configurations, and changes. In particular, we focus on intensional versioning, that is, construction of versions based on configuration rules. Finally, we provide an overview of systems that have had significant impact on the development of the SCM discipline and classify them according to a detailed taxonomy.