Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

Determining how an organism responds to its environment by altering gene expression is key to understanding its ecology. Here, we used RNA-seq to comprehensively and quantitatively assess the transcriptional response of the bacterial opportunistic cystic fibrosis (CF) pathogen and endemic soil dweller, Burkholderia cenocepacia, in conditions mimicking these 2 environments. By sequencing 762 million bases of cDNA from 2 closely related B. cenocepacia strains (one isolated from a CF patient and one from soil), we identified a number of potential virulence factors expressed under CF-like conditions, whereas genes whose protein products are involved in nitrogen scavenging and 2-component sensing were among those induced under soil-like conditions. Interestingly, 13 new putative noncoding RNAs were discovered using this technique, 12 of which are preferentially induced in the soil environment, suggesting that ncRNAs play an important role in survival in the soil. In addition, we detected a surprisingly large number of regulatory differences between the 2 strains, which may represent specific adaptations to the niches from which each strain was isolated, despite their high degree of DNA sequence similarity. Compared with the CF strain, the soil strain shows a stronger global gene expression response to its environment, which is consistent with the need for a more dynamic reaction to the heterogeneous conditions of soil.
The Design and Implementation of a Programming Infrastructure for the Integration and Application of Implicit Surface Research

We describe a C++ class hierarchy to support the efficient implementation of implicit surface functions and algorithms. The structure of the hierarchy allows many methods to be defined automatically over a wide range of specific implicit surface types. This structure also provides the infrasture for integrating many various methods and models found in modern implicit surface research. This paper also contains helpful derivations for automatically maintaining derivates, interval extensions and Lipschitz bounds of functions as they are composed from simpler elements. An object specifically designed to support blending simplifies the implementation of new and existing blending techniques. Sample implementations of some members of the library are provided as examples to better understand the details of the implementation. We expect this work to result in a tool the implicit surface community finds valuable, and provide an effective way for this community to share the efficient implementation of its results.
The Microeconomics of Household Collection of Wild Coffee in Ethiopia : Some Policy Implications for In-situ Conservation of Coffea arabica Genetic Diversity 1

World-wide cultivated arabica coffee is a native plant to Ethiopian highlands. Its wild populations can still be found in the fragmented montane rainforests of the country. To halt degradation and loss of the forest coffee genetic resources, the Ethiopian Government has established in-situ conservation areas in the south and southwestern montane rain forest regions of the country. However, there are several thousands of people who have been and still are dependent on the wild coffee populations from these forests for direct consumption and/or market sales. Thus, policy makers need to consider the needs and economic options of the local people in the periphery, so as to create a win-win relationship between conservation and local agricultural development. This paper substantiates the interface between the forest coffee genetic resources and the local agriculture by exploring the economic importance to farm families of wild coffee from the Geba-Dogi forest coffee conservation area, Southwest Ethiopia. A random sample of 121 farm families was used in this empirical study. Descripitive results demonstrate the very different resource use behavior of the population and the diversity of the (local) people living in the periphery in terms of socioeconomic interests, skills, culture, demographic history, resource use behavior and wealth. Probit regression indicates that household collection of wild coffee from the protected site is positively and significantly associated with family size, ownership of adjacent farm plot, and maleheadship of the household. Number of economically active (adult) labor in the family, distances to the nearest market town and the edge of protected site are found to exert significant disincentives to wild coffee collection portfolio in the peasant household economy.
Disaster Survival Guide in Petascale Computing: An Algorithmic Approach

1 Disaster Survival Guide in Petascale Computing: An Algorithmic Approach 3 Jack J. Dongarra, Zizhong Chen, George Bosilca, and Julien Langou 1.1 FT-MPI: A fault tolerant MPI implementation . 6 1.1.1 FT-MPI Overview . 6 1.1.2 FT-MPI: A Fault Tolerant MPI Implementation . 6 1.1.3 FT-MPI Usage . 7 1.2 Application Level Diskless Checkpointing . 8 1.2. 1 Neighbor-Based Checkpointing . 10 1.2. 2 Checksum-Based Checkpointing . 11 1.2. 3 Weighted-Checksum-Based Checkpointing . 13 1.3 A Fault Survivable Iterative Equation Solver . 17 1.3. 1 Preconditioned Conjugate Gradient Algorithm . 17 1.3. 2 Incorporating Fault Tolerance into PCG . 18 1.4 Experimental Evaluation . 21 1.4. 1 Performance of PCG with Different MPI Implementations . 21 1.4. 2 Performance Overhead of Taking Checkpoint . 22 1.4. 3 Performance Overhead of Performing Recovery . 24 1.4. 4 Numerical Impact of Round-Off Errors in Recovery . 26 1.5 Discussion . 27 1.6 Conclusion and Future Work . 28
Towards Semantically Enhanced File-Sharing

We characterize publication and retrieval of structured documents in peer-to-peer (P2P) file-sharing systems, based on the abstract notion of community, emcompassing a shared document schema, a network protocol and data presentation tools. We present an extension of this model to manage multiple communities, and to describe relations between documents or communities. Our approach is based on the idea of reifying complex concepts to structured documents, then sharing these documents in the P2P network. The design of our prototype P2P client involves components interacting asynchronously using the blackboard model. This decoupled architecture allows the system to dynamically extend its query processing functionality by creating new components that implement the processing described in downloaded documents.
Non-Surgical Management of Cord Compression in Tuberculosis: A Series of Surprises

Study Design Prospective study. Purpose We present a series of 50 patients with tuberculous cord compression who were offered systematic non-surgical treatment, and thereby, the author proposes that clinico-radiological soft tissue cord compression is not an emergency indication for surgery. Overview of Literature Spinal cord compression whether clinical or radiological has usually been believed to be an indication for emergency surgery in spinal tuberculosis. Methods Fifty adults were prospectively studied at our clinic for spinal cord compression due to tuberculous spondylitis, between May 1993 and July 2002. The inclusion criteria were cases with clinical and/or radiological evidence of cord compression (documented soft tissue effacement of the cord with complete obliteration of the thecal sac at that level on magnetic resonance imaging scan). Exclusion criteria were lesions below the conus level, presence of bony compression, severe or progressive neurological deficit (<than Frankel grade C) and children below the age of maturity. All patients were treated with a fixed, methodically applied non-surgical protocol including hospital admission, antitubercular medications, baseline somatosensory evoked potentials and a regular clinico-radiological follow-up. Results At the time of presentation, 10 patients had a motor deficit, 18 had clinically detectable hyper-reflexia and 22 had normal neurology. Forty-seven of the 50 patients responded completely to non-operative treatment and healed with no residual neurological deficit. Three patients with progressive neurological deficit while on treatment were operated on with eventual excellent recovery. Conclusions Radiological evidence of cord compression and early neurological signs need not be an emergency surgical indication in the management of spinal tuberculosis.
Singularities of the closed RW metric in Regge Calculus: a generalized evolution of the 600-cell

An evolution scheme is developed, based on Sorkin algorithm, to evolve the most complex regular tridimensional polytope, the 600-cell. The solution of 600-cell, already studied before, is generalized by allowing a larger number of free variables. The singularities of Robertson-Walker (RW) metric are studied and a reason is given why the evolution of the 600-cell stops when its volume is still far from zero. A fit of 600-cell's evolution with a continuos metric is studied by writing a metric generalizing Friedmann's and including the 600-cell evolution too. The result is that the 600-cell meets a causality-breaking point of space-time. We also shortly discuss the way matter is introduced in Regge calculus.
A Web Service Architecture for Bidirectional XML Updating

We propose a Web service architecture for achieving bidirectional XML updating. The update mechanism exploits the power of bidirectioanl transformations so that users can update XML data by editing a view that is generated by some transformation of the XML data. This architecture consists of three tiers: data viewer clients, a bidirectional transformation engine, and some content servers accessible through the Internet. Due to the use of standard Web service technologies, data viewer clients and contents servers can be easily replaced by the ones chosen by users. Users can use this architecture to implement their own applications that exploit the power of bidirectional transformations without the burden of installing and maintaining the bidirectional
Interaction of fish oil and a glucocorticoid on metabolic responses to an oral glucose load in healthy human subjects

Compared with saturated fat, n-3 long-chain PUFA-rich fish oil improves insulin sensitivity in rats. We studied whether n-3 long-chain PUFA could prevent insulin resistance induced by dexamethasone (a glucocorticoid) in healthy human volunteers. A group of eight subjects was studied twice after a 2d dexamethasone treatment, before and after a 3-week supplementation with fish oil (providing daily doses of 1·1g 20:5n-3 and 0·7g 22:6n-3). The subjects were studied during the basal state and over the 6h following an oral glucose load (1g/kg). Plasma glucose fluxes were traced with [6,6-2H2]glucose and [13C]glucose (naturally 13C-enriched corn glucose). Substrate oxidation was obtained from indirect calorimetry. Following fish oil supplementation, plasma glucose fluxes and substrate oxidation were maintained despite a 17% reduction (P<0·05) in the area under the curve of plasma insulin response, suggesting an insulin-sensitizing effect.
ConAnnotator: Ontology-Aided Collaborative Annotation System

The paper focuses on ConAnnotator, a domain ontology-based collaborative annotation system, which is a main component of cooperative ontology development environment and repository system (CODERS), a domain oriented semantic Web testbed for enhancing the collaboration in designs and in applications. SVM classifications and NLP approaches are used to facilitate the automated generation of annotations with the support of the domain ontology. We discuss the design and evaluation of ConAnnotator to illustrate our proposed approach
Models and methods for knowledge formalisation in a PLM context

Knowledge management is one of the critical issues for the improvement of enterprise performances. Different methods exist for extracting and formalizing knowledge in order to create knowledge-based applications. Most of integrated design and manufacturing technological processes are more or less based on knowledge that has been translated into models and then into Knowledge-Based Computer-Aided Applications. This paper presents some examples of bases and applications concerning the issues of knowledge-based engineering for integrated design and manufacturing
Controlled Transactional Consistency for Web Caching

In-memory read-only caches are widely used in cloud infrastructure to reduce access latency and to reduce load on backend databases. Operators view coherent caches as impractical at genuinely large scale and many clientfacing caches are updated in an asynchronous manner with best-effort pipelines. Existing incoherent cache technologies do not support transactional data access, even if the backend database supports transactions. We propose T-Cache, a cache that supports read-only transactions despite asynchronous and unreliable communication with the database. We also define cache-serializability, a variant of serializability that is suitable for incoherent caches, and prove that with unbounded resources T-Cache implements it. With limited resources, T-Cache allows the system manager to choose a trade-off between performance and consistency. Our evaluation shows that T-Cache detects many inconsistencies with only nominal overhead. We use synthetic workloads to demonstrate the efficacy of T-Cache when data accesses are clustered and its adaptive reaction to workload changes. With workloads based on the real-world topologies, T-Cache detects 43− 70% of the inconsistencies and increases the rate of consistent transactions by 33−58%.
Recent Advances in Fetal Electrocardiography

Since the first observations of Cremer in 1906, fetal electrocardiogram (ECG) measurements via the maternal abdominal wall have remained a formidable challenge for clinical technicians and engineers in the cutting-edge field of information theory. Previous obstacles in extracting fetal ECG still complicate their acquisition at the present. These include three main difficulties for non-invasive measurement of fetal ECG: first, the low signal to noise ratio; second, the lack of a standard lead system for fetal ECG on the maternal abdomen; and third, the factor of fetal movement or non-stationarity during recording. A new extraction system based on blind source separation with reference signals (BSSR) was utilized and our detection rates, both off-line (91%) and on-line (60%), in pregnancies of 20 to 41 weeks of gestation have shown a marked improvement from earlier attempts. With this development, we discuss the potentials and limitations of this new system.
Using linear classifiers in the integration of user modeling and text content analysis in the person

Nowadays many newspapers and news agencies offer personalized information access services and, moreover, there is a growing interest in the improvement of these services. In this paper we present a methodology useful to improve the intelligent personalization of news services and the way it has been applied to a Spanish relevant newspaper: ABC. Our methodology integrates textual content analysis tasks and machine learning techniques to achieve an elaborated user model, which represents separately short-term needs and long-term multi-topic interests. The characterization of a user’s interests includes his preferences about structure (newspaper sections), content and information delivery. A wide coverage and non-specific-domain classification of topics and a personal set of keywords allow the user to define his preferences about content. Machine learning techniques are used to obtain an initial representation of each category of the topic classification. Finally, we introduce some details about the Mercurio system, which is being used to implement this methodology for ABC. We describe our experience and an evaluation of the system in comparison with other commercial systems.
Ultra-low voltage CMOS logic circuits

The operation of digital circuits from power supply voltages of the order of 200 mV or less imposes that, in general, MOSFETs are biased in the subthreshold regime, characterized by the exponential relation between the control voltages and the current. In this tutorial paper we analyze some of the basic building blocks of digital circuits operating in the subthreshold region. We analyze the basic CMOS inverter as regards the voltage transfer characteristic, dynamic behavior, and power dissipation. To reduce the dependence of the drain current on the process parameters we show some compensation circuits that adjust the body voltage, with a small silicon area penalty. Some properties of the static random access memory (SRAM) are reviewed. Finally, the Schmitt Trigger inverter, which is well suited to replace the standard inverter as a basic building block for ultra-low-voltage operation, is briefly analyzed.
NRAMP1 Polymorphisms like Susceptibility Marker in Mexican Focus of Cutaneous Leishmaniasis

Cutaneous leishmaniasis (CL) is endemic in Campeche state, Mexico. Host and parasite factors are involved in the establishment and development of CL. Host factors include immune response and genetic background. NRAMP1 (Natural Resistance Associated Macrophage Protein 1) is important in innate immunity. Polymorphisms in NRAMP1 have been associated with susceptibility or resistance to infectious and autoimmune diseases. To study the association of NRAMP1 mutations with CL in patients from Calakmul, Campeche, samples from 115 CL patients and 69 samples of healthy people from the same area were evaluated. Five regions in NRAMP1 were amplified and digested, looking for mutations in the promoter region (−524G/C), exon 3 (274C/T), exon 8 (823 C7T), and exon 15 (G/A) and deletion of 4 bp in the 3′UTR region. We found a statistical association between polymorphisms in 3′UTR region and exon 8 and CL [χ 2 = 13.26; p < 0.05; OR = 17.00; IC of 95% (2.24–128.99)]. Some patients who needed more than 40 doses of Glucantime® to heal injuries presented mutations in exons 3, 8, and 15. Multiple or ear lesions were not associated with NRAMP1 polymorphism.
Intravenous Administration of Lycopene, a Tomato Extract, Protects against Myocardial Ischemia-Reperfusion Injury

Background: Oral uptake of lycopene has been shown to be beneficial for preventing myocardial ischemia-reperfusion (I/R) injury. However, the strong first-pass metabolism of lycopene influences its bioavailability and impedes its clinic application. In this study, we determined an intravenous (IV) administration dose of lycopene protects against myocardial infarction (MI) in a mouse model, and investigated the effects of acute lycopene administration on reactive oxygen species (ROS) production and related signaling pathways during myocardial I/R. Methods: In this study, we established both in vitro hypoxia/reoxygenation (H/R) cell model and in vivo regional myocardial I/R mouse model by ligating left anterior artery descending. TTC dual staining was used to assess I/R induced MI in the absence and presence of acute lycopene administration via tail vein injection. Results: Lycopene treatment (1 μM) before reoxygenation significantly reduced cardiomyocyte death induced by H/R. Intravenous administration of lycopene to achieve 1 μM concentration in circulating blood significantly suppressed MI, ROS production, and JNK phosphorylation in the cardiac tissue of mice during in vivo regional I/R. Conclusion: Elevating circulating lycopene to 1 μM via IV injection protects against myocardial I/R injury through inhibition of ROS accumulation and consequent inflammation in mice.
The 3′ Untranslated Regions of Influenza Genomic Sequences Are 5′PPP-Independent Ligands for RIG-I

Retinoic acid inducible gene-I (RIG-I) is a key regulator of antiviral immunity. RIG-I is generally thought to be activated by ssRNA species containing a 5′-triphosphate (PPP) group or by unphosphorylated dsRNA up to ∼300 bp in length. However, it is not yet clear how changes in the length, nucleotide sequence, secondary structure, and 5′ end modification affect the abilities of these ligands to bind and activate RIG-I. To further investigate these parameters in the context of naturally occurring ligands, we examined RNA sequences derived from the 5′ and 3′ untranslated regions (UTR) of the influenza virus NS1 gene segment. As expected, RIG-I-dependent interferon-β (IFN-β) induction by sequences from the 5′ UTR of the influenza cRNA or its complement (26 nt in length) required the presence of a 5′PPP group. In contrast, activation of RIG-I by the 3′ UTR cRNA sequence or its complement (172 nt) exhibited only a partial 5′PPP-dependence, as capping the 5′ end or treatment with CIP showed a modest reduction in RIG-I activation. Furthermore, induction of IFN-β by a smaller, U/A-rich region within the 3′ UTR was completely 5′PPP-independent. Our findings demonstrated that RNA sequence, length, and secondary structure all contributed to whether or not the 5′PPP moiety is needed for interferon induction by RIG-I.
Six-Port Reflectometer Based on Modified Hybrid Couplers

Six-port reflectometers have traditionally employed hybrid couplers as their building blocks, but the instruments reported thus far in the literature do not comply with the optimum design specifications. This paper describes a six-port reflectometer based on four-port coplanar-waveguide couplers that have been modified so as to meet such design requirements. Additional design parameters have been incorporated so that adjustments may be made to correct for residual hardware imperfections. Laboratory tests have confirmed an operating bandwidth of 90% (from 1.1 to 2.9 GHz) for the resulting reflectometer.
Inter-rater and intra-rater reliability of the Triple Joint Flexion Test (TJFT) scores in adolescent field and court athletes by novice raters

III ACKNOWLEDGEMENTS . IV TABLE OF CONTENTS . V SECTION 1: INTRODUCTION TO THESIS . 1 1.1 HEALTH BENEFITS AND POTENTIAL HARMS OF PHYSICAL ACTIVITY AND SPORT . 1 1.2 MITIGATING INJURIES AS A RESULT OF PHYSICAL ACTIVITY AND SPORT . 1 1.3 THE TRIPLE JOINT FLEXION TEXT . 3 2 LITERATURE REVIEW . 5 2.1 RISK AND BENEFITS OF PHYSICAL ACTIVITY AND SPORTS . 5 2.2 HOW ARE INJURIES MITIGATED IN SPORT AND PHYSICAL ACTIVITY? 6 2.2.1 Pre-participation evaluation . 6 2.2.2 The concept of movement screening . 7 2.2.3 A rationale for lower extremity movement screens . 7 2.2.4 What lower extremity movement screens exist and are they reliable? 8 2.2. 5 Example of movement screens originating within the literature . 9 2.2. 6 Example of movement screens originating from clinical practice . 10 2.2. 7 Why does reliability matter? 11 2.3 WHAT SOURCES OF VARIABILITY WITHIN A RATING ARE THERE? 12 2.3. 1 Sources of variability attributable to athlete performance . 12 2.3. 2 Sources of variability attributable to the rater . 13 2.3. 3 Summary of rater source of variability . 16 2.4 A METHODOLOGICAL CRITIQUE OF EXISTING RELIABILITY STUDIES. 18 2.4.
Measure and Model P2P Streaming System by Buffer Bitmap

The correct evaluation of P2P streaming system models needs the validation in real world system. However, there is lack of systematic and integrated measurement method for real world P2P streaming system. In this paper, we propose a P2P streaming network measurement method based on a peer's buffer occupancy probability. Our method is based on the fixed duration buffer property of commercial P2P streaming systems. We prove the measured buffer occupancy probability reflects the chunk propagation process in the P2P network. We then propose a P2P streaming chunk propagation model and verify it in the commercial P2P streaming network using our measurement method. Our measurement method is useful for measuring and analyzing miscellaneous P2P streaming systems. And our model and parameter estimation are useful for existing P2P simulators to choose correct parameters and are meaningful for researchers to understand the real meaning behind the parameters.