Miracle-dz/UniFAR-FTUs huggingface dataset:
The influence of early neutrophil-Leishmania interactions on the host immune response to infection

Neutrophils are the first cells recruited to the dermal site of Leishmania infection following injection by needle or sand fly bite. The role of neutrophils in either promoting or suppressing host immunity remains controversial. We discuss the events driving neutrophil recruitment, their interaction with the parasite and apoptotic fate, and the nature of their encounters with other innate cells. We suggest that the influence of the neutrophil response on infection outcome critically depends on the timing of their recruitment and the tissue environment in which it occurs.
Simvastatin Protects Against Long-Lasting Behavioral and Morphological Consequences of Neonatal Hypoxic/Ischemic Brain Injury

Background and Purpose— Recent studies suggest that statins (3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors) not only reduce the incidence of stroke by lowering cholesterol levels but may also exert neuroprotective effects via a mechanism not related to their lipid-lowering effect. Despite the growing body of evidence, however, the neuroprotective effect of statins in stroke is still controversial. Herein, we studied whether a prophylactic administration of simvastatin (Sim) provides significant protection against brain damage, and we sought to determine its long-lasting behavioral consequences in a neonatal model of hypoxia/ischemia. Methods— Newborn male rats were injected daily from postnatal days 1 to 7 with activated Sim (20 mg/kg) or an equivalent volume of vehicle. On postnatal day 7, the rats were subjected to ligation of the right common carotid artery, followed by 3 hours of hypoxia or by sham operation. The neuroprotective effect of Sim was evaluated after the rats had achieved adulthood by using a battery of behavioral tests and histological analysis. Results— Sim-treated ischemic rats performed the circular water maze, the radial arm maze, and the multiple-choice water maze significantly better than did vehicle-treated ischemic rats. Furthermore, in contrast to the ischemic rats, hypoxia/ischemia-injured rats pretreated with Sim were not hyperactive at weaning and showed less behavioral asymmetry. Consistently, it was found that brain damage was significantly attenuated. Conclusions— These findings indicate that prophylactic administration of statins may provide a potential neuroprotective strategy leading to an improvement in functional outcome in ischemic stroke. However, toxicity concern must be addressed before these agents can be directed to the asphyxiated fetus or newborn.
Human XPC-hHR23B interacts with XPA-RPA in the recognition of triplex-directed psoralen DNA interstrand crosslinks

DNA interstrand crosslinks (ICLs) represent a severe form of damage that blocks DNA metabolic processes and can lead to cell death or carcinogenesis. The repair of DNA ICLs in mammals is not well characterized. We have reported previously that a key protein complex of nucleotide excision repair (NER), XPA-RPA, recognizes DNA ICLs. We now report the use of triplex technology to direct a site-specific psoralen ICL to a target DNA substrate to determine whether the human global genome NER damage recognition complex, XPC-hHR23B, recognizes this lesion. Our results demonstrate that XPC-hHR23B recognizes psoralen ICLs, which have a structure fundamentally different from other lesions that XPC-hHR23B is known to bind, with high affinity and specificity. XPC-hHR23B and XPA-RPA protein complexes were also observed to bind psoralen ICLs simultaneously, demonstrating not only that psoralen ICLs are recognized by XPC-hHR23B alone, but also that XPA-RPA may interact cooperatively with XPC-hHR23B on damaged DNA, forming a multimeric complex. Since XPC-hHR23B and XPA-RPA participate in the recognition and verification of DNA damage, these results support the hypothesis that interplay between components of the global genome repair sub-pathway of NER is critical for the recognition of psoralen DNA ICLs in the mammalian genome.
Am I Overweight? A Longitudinal Study on Parental and Peers Weight-Related Perceptions on Dietary Behaviors and Weight Status Among Adolescents

Objective: An investigation of the interplay between various types of adolescents’ perceptions of weight status in predicting adolescents’ nutrition behavior and their body mass was conducted. In particular, it was hypothesized that the relationship between parental and peers’ perceptions of their own weight status (reported by adolescents) and objectively measured weight status of adolescents would be mediated by three types of adolescents’ weight status perceptions (adolescents’ own weight perceptions, parental perceptions of adolescents’ weight status perceived by participants, and peers’ perceptions of adolescents’ weight status perceived by participants) and by adolescents’ nutrition behaviors. Design: Data were collected twice, with a 13-month follow-up. Participants (N = 1096) were aged 14–20, with BMI ranging from 16.20 to 41.21. Multiple mediation analysis with two sequential mediators was applied. Main outcome measures: At the baseline adolescents completed the questionnaire assessing their nutrition behaviors and weight status perceptions. Weight and height were measured objectively at baseline and follow-up. Results: Two types of weight perceptions (adolescents’ own weight status perceptions, peers’ perceptions of adolescents’ weight status reported by participants), and adolescents’ nutrition behaviors mediated the relationship between the others’ own weight perceptions and adolescents’ weight status. No indirect effects of others’ own weight perceptions on adolescents’ weight status through parental perceptions were found. Conclusion: Adolescents’ nutrition behaviors and body weight status depend on what they think about their own weight status and what they think of their peers’ perceptions, but do not depend on what adolescents think of their parents’ perceptions.
Study of Ensemble Pruning Algorithms Based on the Idea of Pattern Mining

At first the thesis introduces a new concept: coverage-based pattern mining. Then based on this concept, two ensemble pruning algorithms, CPM-EP and PMEP are put forward. By the algorithms we get candidate sub-patterns,and applies coverage pattern mining and a greedy strategy to acquire candidate target ensemble. Experiments show that pat- tern mining is an efficient selective integration strategy, able to obtain predictive ability, small-scale target integrated clas- sifier, the paper presents that the CPM-EP and PMEP algorithm is able to meet the demand for online learning.
A theory of high-frequency distortion in bipolar transistors

High-frequency distortion in bipolar transistors is examined by using the charge-control approach of Poon and Narayanan (H.C. Poon, IEEE Trans. Electron Dev., vol. ED-19, pp. 719-731, 1972; S. Narayanan and H.C. Poon, IEEE Trans. Circuit Theory, vol. CT-20, pp. 341-351, 1973; H.C. Poon, IEEE Trans. Electron Dev., vol. ED-21, pp. 110-112, 1974) to connect the device's distortion behavior to its "loaded" unity-current-gain frequency (/spl omega//spl circ//sub T/). The resulting expressions for the distortion reveal considerable information on its frequency and bias dependence. Points on the /spl omega//spl circ//sub T/ versus collector current curve yielding optimum distortion performance are identified and interpreted in terms of current cancellation. Both second- and third-order distortion are considered, and the results are validated by both simulation and experiment.
A motion control scheme for animating expressive arm movements

Current methods for figure animation involve a tradeoff between the level of realism captured in the movements and the ease of generating the animations. We introduce a motion control paradigm that circumvents this tradeoff—it provides the ability to generate a wide range of natural-looking movements with minimal user labor. Effort, which is one part of Rudolf Laban's system for observing and analyzing movement, describes the qualitative aspects of movement. Our motion control paradigm simplifies the generation of expressive movements by proceduralizing these qualitative aspects to hide the non-intuitive, quantitative aspects of movement. We build a model of Effort using a set of kinematic movement parameters that defines how a figure moves between goal keypoints. Our motion control scheme provides control through Effort's four-dimensional system of textual descriptors, providing a level of control thus far missing from behavioral animation systems and offering novel specification and editing capabilities on top of traditional keyframing and inverse kinematics methods. Since our Effort model is inexpensive computationally, Effort-based motion control systems can work in real-time. We demonstrate our motion control scheme by implementing EMOTE (Expressive MOTion Engine), a character animation module for expressive arm movements. EMOTE works with inverse kinematics to control the qualitative aspects of end-effector specified movements. The user specifies general movements by entering a sequence of goal positions for each hand. The user then expresses the essence of the movement by adjusting sliders for the Effort motion factors: Space, Weight, Time, and Flow. EMOTE produces a wide range of expressive movements, provides an easy-to-use interface (that is more intuitive than joint angle interpolation curves or physical parameters), features interactive editing, and real-time motion generation.
Pathfinder/MonetDB: A High-Performance Relational Runtime for XQuery

Pathfinder/MonetDB is a collaborative effort of the University of Konstanz, the University of Twente, and the Centrum voor Wiskunde en Informatica (CWI) in Amsterdam to develop an XQuery compiler that targets an RDBMS back-end. The author of this abstract is student at the University of Konstanz and spent six months as an intern at the CWI, designing and implementing a translation of XQuery Core to (a variant of) relational algebra. His work continues in the research group at the University of Konstanz.
Affective content based music video paring system using real coded GA

As the high quality cameras, video editing software and music composition software are more available, making videos becomes popular. However, processing home videos is time-consuming. Some popular commercial software such as iMovie and Adobe Premiere provide user-friendly interface to help people make films on their own, but adding adequate music to a clip is still a non-trivial work that highly depends on human feelings and emotions. This paper proposes an emotion-based evolutionary music video pairing system by utilizing affective information of videos and musics to remedy this problem. Empirical results show that our system is capable of pairing videos with adequate musics and self-adapting to human preferences.
DESES : Middleware for Dynamic End-to-end Session-Enhancing Services for Java-enabled Mobile Phones

Networking middleware approaches that offer endto-end (e2e) TCP/IP session enhancements are gaining importance in the Internet research community. Examples of such session enhancements include protection from disconnections, mobility support, congestion management, encryption and compression. These session-enhancing frameworks require only middleware support at the end-nodes, thus making them ideal for dynamic environments where there is little or no infrastructure support. Mobile devices would benefit the most from such frameworks, especially if they were dynamic, extensible and platformindependent. In this paper we describe such a framework optimized for mobile devices called DESES: Dynamic End-toend Session-Enhancing Services for Java-enabled mobile devices. DESES enhances networked J2ME applications by allowing the dynamic addition and removal of e2e session-enhancing services during the lifetime of an active TCP/IP session. We describe the DESES architecture and how DESES services can be deployed transparently, if desired, on existing J2ME applications using a technique called byte-code engineering. Finally, we describe our experience implementing DESES on actual J2ME-enabled smartphones.
Conversion of lowland tropical forests to tree cash crop plantations loses up to one-half of stored soil organic carbon

Significance Deforestation for tree cash crop plantations such as oil palm, rubber, and cacao agroforest in the tropics results in strong decreases in soil organic carbon (SOC) stocks, with much of this carbon lost through carbon dioxide (CO2) emissions and leaching. We found that SOC stock losses in oil palm, rubber, and cacao agroforestry plantations in Indonesia, Cameroon, and Peru could be predicted by the amount of SOC in the original forests: the more SOC present initially, the more SOC lost after conversion. When natural forests were replaced by tree cash crop plantations, SOC losses of up to 50% were found. We recommend that these SOC losses be incorporated in the Intergovernmental Panel on Climate Change tier 1 method for carbon accounting. Tropical deforestation for the establishment of tree cash crop plantations causes significant alterations to soil organic carbon (SOC) dynamics. Despite this recognition, the current Intergovernmental Panel on Climate Change (IPCC) tier 1 method has a SOC change factor of 1 (no SOC loss) for conversion of forests to perennial tree crops, because of scarcity of SOC data. In this pantropic study, conducted in active deforestation regions of Indonesia, Cameroon, and Peru, we quantified the impact of forest conversion to oil palm (Elaeis guineensis), rubber (Hevea brasiliensis), and cacao (Theobroma cacao) agroforestry plantations on SOC stocks within 3-m depth in deeply weathered mineral soils. We also investigated the underlying biophysical controls regulating SOC stock changes. Using a space-for-time substitution approach, we compared SOC stocks from paired forests (n = 32) and adjacent plantations (n = 54). Our study showed that deforestation for tree plantations decreased SOC stocks by up to 50%. The key variable that predicted SOC changes across plantations was the amount of SOC present in the forest before conversion—the higher the initial SOC, the higher the loss. Decreases in SOC stocks were most pronounced in the topsoil, although older plantations showed considerable SOC losses below 1-m depth. Our results suggest that (i) the IPCC tier 1 method should be revised from its current SOC change factor of 1 to 0.6 ± 0.1 for oil palm and cacao agroforestry plantations and 0.8 ± 0.3 for rubber plantations in the humid tropics; and (ii) land use management policies should protect natural forests on carbon-rich mineral soils to minimize SOC losses.
Sequence Evolution and Expression Regulation of Stress-Responsive Genes in Natural Populations of Wild Tomato

The wild tomato species Solanum chilense and S. peruvianum are a valuable non-model system for studying plant adaptation since they grow in diverse environments facing many abiotic constraints. Here we investigate the sequence evolution of regulatory regions of drought and cold responsive genes and their expression regulation. The coding regions of these genes were previously shown to exhibit signatures of positive selection. Expression profiles and sequence evolution of regulatory regions of members of the Asr (ABA/water stress/ripening induced) gene family and the dehydrin gene pLC30-15 were analyzed in wild tomato populations from contrasting environments. For S. chilense, we found that Asr4 and pLC30-15 appear to respond much faster to drought conditions in accessions from very dry environments than accessions from more mesic locations. Sequence analysis suggests that the promoter of Asr2 and the downstream region of pLC30-15 are under positive selection in some local populations of S. chilense. By investigating gene expression differences at the population level we provide further support of our previous conclusions that Asr2, Asr4, and pLC30-15 are promising candidates for functional studies of adaptation. Our analysis also demonstrates the power of the candidate gene approach in evolutionary biology research and highlights the importance of wild Solanum species as a genetic resource for their cultivated relatives.
Patch-based bilateral filter: Algorithms and performance

The bilateral filter has a weakness in its denoising ability, because the intensity similarity is evaluated by comparing just the intensity values of a given pixel and another pixel. To alleviate this problem, this paper proposes a patch-based bilateral (PBL) filter in which the intensity similarity is evaluated by comparing a whole patch around each pixel. Experimental results for real images show that this method outperforms the bilateral filter in all cases, is comparable to the nonlocal-(NL-)means filter, and outperforms the more elaborate variants of the NL-means filter in some cases.
Prognostic Significance of Volume-Based PET Parameters in Cancer Patients

Accurate prediction of cancer prognosis before the start of treatment is important since these predictions often affect the choice of treatment. Prognosis is usually based on anatomical staging and other clinical factors. However, the conventional system is not sufficient to accurately and reliably determine prognosis. Metabolic parameters measured by 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET) have the potential to provide valuable information regarding prognosis and treatment response evaluation in cancer patients. Among these parameters, volume-based PET parameters such as metabolic tumor volume and total lesion glycolysis are especially promising. However, the measurement of these parameters is significantly affected by the imaging methodology and specific image characteristics, and a standard method for these parameters has not been established. This review introduces volume-based PET parameters as potential prognostic indicators, and highlights methodological considerations for measurement, potential implications, and prospects for further studies.
Shadow theatre

Shadow theatre is a genre of performance art in which the actors are only visible as shadows projected on the screen. The goal of this study is to generate animated characters, the shadows of which match a sequence of target silhouettes. This poses several challenges. The motion of multiple characters are carefully coordinated to form a target silhouette on the screen, and each character's pose should be stable, balanced, and plausible. The resulting character animation should be smooth and coherent spatially and temporally. We formulate the problem as nonlinear constrained optimization with objectives, which were designed to generate plausible human motions. Our optimization algorithm was primarily inspired by the heuristic strategies of professional shadow theatre actors. Their know-how was studied and then incorporated into our optimization formulation. We demonstrate the effectiveness of our approach with a variety of target silhouettes and 3D fabrication of the results.
Automated Analysis of Cryptographic Protocols Using Mur '

A methodology is presented for using a general-purpose state enumeration tool, Mur', to analyze cryptographic and security-related protocols. We illustrate the feasibility of the approach by analyzing the Needham-Schroeder protocol, nding a known bug in a few seconds of computation time, and analyzing variants of Kerberos and the faulty TMN protocol used in another comparative study. The eeciency of Mur' allows us to examine multiple runs of relatively short protocols , giving us the ability to detect replay attacks, or errors resulting from confusion between independent execution of a protocol by independent parties.
A Versatile and User-Oriented Versioning File System

File versioning is a useful technique for recording a history of changes. Applications of versioning include backups and disaster recovery, as well as monitoring intruders' activities. Alas, modern systems do not include an automatic and easy-to-use file versioning system. Existing backup solutions are slow and inflexible for users. Even worse, they often lack backups for the most recent day's activities. Online disk snapshotting systems offer more fine-grained versioning, but still do not record the most recent changes to files. Moreover, existing systems also do not give individual users the flexibility to control versioning policies. We designed a lightweight user-oriented versioning file system called Versionfs. Versionfs works with any file system and provides a host of user-configurable policies: versioning by users, groups, processes, or file names and extensions; version retention policies and version storage policies. Versionfs creates file versions automatically, transparently, and in a file-system portable manner--while maintaining Unix semantics. A set of user-level utilities allow administrators to configure and enforce default policies: users can set policies within configured boundaries, as well as view, control, and recover files and their versions. We have implemented the system on Linux. Our performance evaluation demonstrates overheads that are not noticeable by users under normal workloads.
KFS: Exploring Flexibility in File System Design

This paper argues that file systems need to be customizable at the granularity of files and directories in order to meet the requirements and usage access patterns of various workloads. We present KFS, a file system designed to allow for fine-grained adaptability of services. In KFS, each file or directory may have its own tailored service implementation, and these implementations may be replaced on the fly. KFS runs under Linux and the K42 research operating system. We describe how KFS’s flexibility has been explored to achieve better schemes for meta-data management and consistency. Resumo. Este artigo discute a necessidade de sistemas de arquivos que sejam customizaveis no nivel de arquivos e diretorios, de forma a atender aos requisitos e padroes de acessos de varias cargas de execucao. Nos apresentamos o KFS, um sistema de arquivos projetado de forma a possibilitar adaptabilidade de servicos com granularidade fina. Em KFS, cada arquivo ou diretorio pode ter sua propria implementacao de servico, feita sob medida para suas necessidades. Estas implementacoes podem ser substituidas dinamicamente. KFS esta disponivel para o sistema operacional Linux e o sistema operacional de pesquisa K42. Nos descrevemos como a flexibilidade do KFS pode ser explorada de forma a obter esquemas melhores para gerenciamento de meta-dados e consistencia.
Coordinated Task Scheduling, Allocation and Synchronization on Multiprocessors

Chip-multiprocessors represent a dominant new shift in the field of processor design. Better utilization of such technology in the real-time context requires coordinated approaches to task allocation, scheduling, and synchronization. In this paper, we characterize various scheduling penalties arising from multiprocessor task synchronization, including (i) blocking delays on global critical sections, (ii) back-to-back execution due to jitter from blocking, and (iii) multiple priority inversions due to remote resource sharing. We analyze the impact of these scheduling penalties under different execution control policies (ECPs) which compensate for the scheduling penalties incurred by tasks due to remote blocking. Subsequently, we develop a synchronization-aware task allocation algorithm for explicitly accommodating these global task synchronization penalties. The key idea of our algorithm is to bundle tasks that access a common shared resource and co-locate them, thereby transforming global resource sharing into local sharing. This approach reduces the above-mentioned penalties associated with remote task synchronization. Experimental results indicate that such a coordinated approach to scheduling, allocation, and synchronization yields significant benefits (as much as 50% savings in terms of required number of processing cores). An implementation of this approach is available as a part of our RT-MAP library, which uses the pthreads implementation of Linux-2.6. 22.