Miracle-dz/UniFAR-FTUs huggingface dataset:
Analyzing the Performance of an Externally Journaled Filesystem

Journaling is a common technique used by current filesystems to ensure data consistency in face of a crash. Because the journal is often stored as a file within the filesystem, journal and fixed-position writes are likely to compete for disk bandwidth, posing a considerable overhead to the storage system. In order to isolate journal and fixed-position traffic, some filesytems allow the journal to be stored in an external device, thereby allowing the exploitation of parallelism and increasing the spatial locality. In this paper we analyze the performance of an externally journaled filesystem under different scenarios and journaling modes and compare it to a traditional journaled filesystem. We found that ordered and writeback journaling modes in an external device can obtain about 40% of performance improvement in a mail server workload if compared to a traditional journaled filesystem; in addition, we also observed that data journaling mode can provide substantial performance gains under very specific workloads.
An Analytical Model of Packet Collisions in IEEE 802.15.4 Wireless Networks

Numerous studies have shown that concurrent transmissions can help to boost wireless network performance despite the possibility of packet collisions. However, while these works provide empirical evidence that concurrent transmissions may be received reliably, existing signal capture models only partially explain the root causes of this phenomenon. We present a comprehensive mathematical model for MSK-modulated signals that makes the reasons explicit and thus provides fundamental insights on the key parameters governing the successful reception of colliding transmissions. A major contribution is the closed-form derivation of the receiver bit decision variable for an arbitrary number of colliding signals and constellations of power ratios, time offsets, and carrier phase offsets. We systematically explore the factors for successful packet delivery under concurrent transmissions across the whole parameter space of the model. We confirm the capture threshold behavior observed in previous studies but also reveal new insights relevant to the design of optimal protocols: We identify capture zones depending not only on the signal power ratio but also on time and phase offsets.
An eMERGE Clinical Center at Partners Personalized Medicine

The integration of electronic medical records (EMRs) and genomic research has become a major component of efforts to advance personalized and precision medicine. The Electronic Medical Records and Genomics (eMERGE) network, initiated in 2007, is an NIH-funded consortium devoted to genomic discovery and implementation research by leveraging biorepositories linked to EMRs. In its most recent phase, eMERGE III, the network is focused on facilitating implementation of genomic medicine by detecting and disclosing rare pathogenic variants in clinically relevant genes. Partners Personalized Medicine (PPM) is a center dedicated to translating personalized medicine into clinical practice within Partners HealthCare. One component of the PPM is the Partners Healthcare Biobank, a biorepository comprising broadly consented DNA samples linked to the Partners longitudinal EMR. In 2015, PPM joined the eMERGE Phase III network. Here we describe the elements of the eMERGE clinical center at PPM, including plans for genomic discovery using EMR phenotypes, evaluation of rare variant penetrance and pleiotropy, and a novel randomized trial of the impact of returning genetic results to patients and clinicians.
Trade-offs for video-providers in LTE networks: Smartphone energy consumption vs wasted traffic

Long Term Evolution (LTE) networks provide broadband Internet access to mobile users. One of the main use cases for LTE is a mobile video. When selecting a video transmission mechanism, a video provider has to consider different and orthogonal metrics. The consumer expects a high video Quality of Experience (QoE) and a low energy consumption during download and playback. The video provider is interested in minimizing its resources and corresponding costs, like bandwidth and wasted traffic. Wasted traffic occurs if a user aborts and additional video data is already downloaded but not played out, consuming resources unnecessarily. This raises the questions 1) how a video provider delivers the video contents while reducing the operational costs and satisfying the customers demands 2) what is the influence of the customer abort behaviour. To answer these questions, we first study the influence of mechanism selection on energy consumption and wasted traffic. Second, we show that the different user models do not influence the wasted traffic significantly. Finally, we provide parameter selection guidelines for the Streaming mechanism, which are shown to satisfy better both the requirements of the video provider as well as those of the customer, to achieve Pareto optimal results with regard to the smartphone energy consumption and wasted traffic.
Synthesis of Symmetrical and Non-symmetrical Diimines from Dimedone

Symmetrical and non-symmetrical diimines derived from dimedone were synthesized by the reaction of their corresponding enaminothiones with primary amines. The synthesized compounds were characterized using micro analytical data and NMR spectroscopy. Theoretical calculations by B3LYP/6-31G(d,p) level of theory show that the enolic form is the most stable within the possible tautomeric forms of the compounds.
Six3 functions in anterior neural plate specification by promoting cell proliferation and inhibiting Bmp4 expression

Although it is well established that Six3 is a crucial regulator of vertebrate eye and forebrain development, it is unknown whether this homeodomain protein has a role in the initial specification of the anterior neural plate. In this study, we show that exogenous Six3 can expand the anterior neural plate in both Xenopus and zebrafish, and that this occurs in part through Six3-dependent transcriptional regulation of the cell cycle regulators cyclinD1 and p27Xic1, as well as the anti-neurogenic genes Zic2 and Xhairy2. However, Six3 can still expand the neural plate in the presence of cell cycle inhibitors and we show that this is likely to be due to its ability to repress the expression of Bmp4 in ectoderm adjacent to the anterior neural plate. Furthermore, exogenous Six3 is able to restore the size of the anterior neural plate in chordino mutant zebrafish, indicating that it has the ability to promote anterior neural development by antagonising the activity of the BMP pathway. On its own, Six3 is unable to induce neural tissue in animal caps, but it can do so in combination with Otx2. These results suggest a very early role for Six3 in specification of the anterior neural plate, through the regulation of cell proliferation and the inhibition of BMP signalling.
An Empirical Analysis of the Impact of Comment Statements on Fault-Proneness of Small-Size Module

Code size metrics are commonly useful in predicting fault-prone modules, and the larger module tends to be more faulty. In other words, small-size modules are considered to have lower risks of fault. However, since the majority of modules in a software are often small-size, many ``small but faulty'' modules have been found in the real world. Hence, another fault-prone module prediction method, intended for small-size module, is also required. Such a new method for small-size module should use metrics other than code size since all modules are small size. This paper focuses on ``comments'' written in the source code from a novel perspective of size-independent metrics, comments have not been drawn much attention in the field of fault-prone module prediction. The empirical study collects 11,512 small-size modules, whose LOC are less than the median, from three major open source software, and analyzes the relationship between the lines of comments and the fault-proneness in the set of small-size modules. The empirical results show the followings: 1) A module in which some comments are written is more likely to be faulty than non-commented ones, the fault rate of commented modules is about 1.8-3.5 times higher than that of non-commented ones. 2) Writing one to four lines of comments would be thresholds of the above tendency.
Parallel One-Shot Lagrange-Newton-Krylov-Schwarz Algorithms for Shape Optimization of Steady Incompressible Flows

We propose and study a new parallel one-shot Lagrange--Newton--Krylov--Schwarz (LNKSz) algorithm for shape optimization problems constrained by steady incompressible Navier--Stokes equations discretized by finite element methods on unstructured moving meshes. Most existing algorithms for shape optimization problems iteratively solve the three components of the optimality system: the state equations for the constraints, the adjoint equations for the Lagrange multipliers, and the design equations for the shape parameters. Such approaches are relatively easy to implement, but generally are not easy to converge as they are basically nonlinear Gauss--Seidel algorithms with three large blocks. In this paper, we introduce a fully coupled, or the so-called one-shot, approach which solves the three components simultaneously. First, we introduce a moving mesh finite element method for the shape optimization problems in which the mesh equations are implicitly coupled with the optimization problems. Second, we introd.
1 DIFFERENT ROLES OF EVALUATION IN INFORMATION SYSTEMS RESEARCH

Evaluation of information systems (IS) has come to be an important topic for study as well as practice. IS scholars perform studies of how to evaluate IS and different IS related phenomena, like e.g. methods and strategies. Evaluation is also used as a research approach in many IS research studies. However, the use and interest of evaluation seem to be rather fragmented and diversified in the IS field. The purpose of this paper is to bring more structure to evaluation in IS research. Based on a review of literature on evaluation in IS research and on evaluation research in general a conceptualisation of evaluation in IS is presented. This consists of 1) a conceptual practice model of evaluation (including generic questions for the design of evaluation) and 2) a classification of different roles of IS evaluation research. This classification consists of three main research types: 1) research about evaluation, 2) research through evaluation and 3) research about evaluation research. The second research type has been divided into three sub-classes: 2a) research through evaluation as main strategy, 2b) research through evaluation as companion strategy and 2c) research through evaluation as re-use strategy. The different research types have been characterized and exemplified.
Quantitative Trait Loci for Light Sensitivity, Body Weight, Body Size, and Morphological Eye Parameters in the Bumblebee, Bombus terrestris

Bumblebees such as Bombus terrestris are essential pollinators in natural and managed ecosystems. In addition, this species is intensively used in agriculture for its pollination services, for instance in tomato and pepper greenhouses. Here we performed a quantitative trait loci (QTL) analysis on B. terrestris using 136 microsatellite DNA markers to identify genes linked with 20 traits including light sensitivity, body size and mass, and eye and hind leg measures. By composite interval mapping (IM), we found 83 and 34 suggestive QTLs for 19 of the 20 traits at the linkage group wide significance levels of p = 0.05 and 0.01, respectively. Furthermore, we also found five significant QTLs at the genome wide significant level of p = 0.05. Individual QTLs accounted for 7.5-53.3% of the phenotypic variation. For 15 traits, at least one QTL was confirmed with multiple QTL model mapping. Multivariate principal components analysis confirmed 11 univariate suggestive QTLs but revealed three suggestive QTLs not identified by the individual traits. We also identified several candidate genes linked with light sensitivity, in particular the Phosrestin-1-like gene is a primary candidate for its phototransduction function. In conclusion, we believe that the suggestive and significant QTLs, and markers identified here, can be of use in marker-assisted breeding to improve selection towards light sensitive bumblebees, and thus also the pollination service of bumblebees.
Scalable Image Indexing and Retrieval using

With the development of world wide web and fast computer technology, the use of visual information has become a routine in scientiic and commercial applications. Images and videos are being captured and archived in large databases and it is extremely important to develop eecient technologies to process, manipulate, and search large visual information archives. In this context, retrieving images by content has gained increasing interest. The existing image indexing systems deliver poor performance for large image archives. In this paper, we present an eecient content based indexing and retrieval mechanism based on energy properties of wavelet coeecients. The system is scalable and provides fast retrievals. We show that in a database of 1000 images, query search takes less than 50 msec, compared to several seconds of retrieval time in the earlier systems. Given a query image, the ratio of the similar images over the number of images retrieved for a maximum quality search is 0:9, yielding eeciency close to 1.
Nash Bargaining Game Based Subcarrier Allocation for Physical Layer Security in Orthogonal Frequency Division Multiplexing System

Most orthogonal frequency division multiplexing (OFDM) wireless communication system cooperative schemes are poor in secure transmission. Based on Nash bargaining game (NBG), this paper presents a method of OFDM system cooperative scheme restricted in physical layer security. In the model, each wireless node can act as not only a source, but also a potential relay. The sub-carrier allocation problem among selfish nodes is formulated as a two-person bargaining game to guarantee fairness. It is proved that the Nash bargaining solution (NBS) of subcarrier allocation is existence of unique Nash equilibrium. Based on evolutionary game algorithm (EGA), the subcarrier allocation scheme can reach to an optimal value and achieve an extra system secrecy rate, compared with the direct transmission secrecy rate. Simulation results indicate that the subcarrier allocation fairness is dependent on how much rate increase its partner can make to.
Viruses transfer the antiviral second messenger cGAMP between cells

Viruses pack antiviral mediators Viruses often hijack host proteins for their own use, turning host cells into virion-spewing machines. However, Bridgeman et al. and Gentili et al. now report a sneaky way that the host can fight back (see the Perspective by Schoggins). Host cells that expressed the enzyme cGAS, an innate immune receptor that senses cytoplasmic DNA, packaged the cGAS-generated second messenger cGAMP into virions. Virions could then transfer cGAMP to neighboring cells, triggering an antiviral gene program in these newly infected cells. Such transfer of an antiviral mediator may help to speed up the immune response to put the brakes on viral spread. Science, this issue pp. 1228 and 1232; see also p. 1166 Viruses package an antiviral second messenger into virions, facilitating an immune response in newly infected cells. [Also see Perspective by Schoggins] Cyclic GMP–AMP synthase (cGAS) detects cytosolic DNA during virus infection and induces an antiviral state. cGAS signals by synthesis of a second messenger, cyclic GMP-AMP (cGAMP), which activates stimulator of interferon genes (STING). We show that cGAMP is incorporated into viral particles, including lentivirus and herpesvirus virions, when these are produced in cGAS-expressing cells. Virions transferred cGAMP to newly infected cells and triggered a STING-dependent antiviral program. These effects were independent of exosomes and viral nucleic acids. Our results reveal a way by which a signal for innate immunity is transferred between cells, potentially accelerating and broadening antiviral responses. Moreover, infection of dendritic cells with cGAMP-loaded lentiviruses enhanced their activation. Loading viral vectors with cGAMP therefore holds promise for vaccine development.
A functional MRI Exploration of Hamstring Activation During the Supine Bridge Exercise

Abstract The single leg supine bridge (SLB) is a commonly employed strengthening exercise and is used as a clinical test for hamstring function in sports, however, little is known about the patterns of muscle activation in this task. To explore these activation patterns, nine healthy, recreationally active males underwent functional magnetic resonance imaging (fMRI) of their thighs at rest and immediately after 5 sets of 10 repetitions of the SLB exercise. Exercise-induced increases in the transverse (T2) relaxation time of the biceps femoris long and short heads, semitendinosus and semimembranosus, were determined via signal intensity changes in pre- and post-exercise images and used as an index of muscle activation. The Bonferroni adjusted alpha was set at p<0.008. The semitendinosus exhibited a greater T2 increase than the biceps femoris short head (p<0.001, d=2.0) and semimembranosus (p=0.001, d=1.2), but not biceps femoris long head (p=0.029, d=0.9). Furthermore, the percentage change in T2 for biceps femoris long head was greater than its short head (p=0.003, d=1.4). During the SLB exercise, the semitendinosus is most selectively targeted and the biceps femoris long head is preferentially activated over its short head. These findings may have implications for the use of the SLB in hamstring injury prevention and rehabilitation programs.
Major submissions tool developments at the European nucleotide archive

The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena), Europe's primary nucleotide sequence resource, captures and presents globally comprehensive nucleic acid sequence and associated information. Covering the spectrum from raw data to assembled and functionally annotated genomes, the ENA has witnessed a dramatic growth resulting from advances in sequencing technology and ever broadening application of the methodology. During 2011, we have continued to operate and extend the broad range of ENA services. In particular, we have released major new functionality in our interactive web submission system, Webin, through developments in template-based submissions for annotated sequences and support for raw next-generation sequence read submissions.
Brain Endoplasmic Reticulum Stress Mechanistically Distinguishes the Saline-Intake and Hypertensive Response to Deoxycorticosterone Acetate–Salt

Endoplasmic reticulum stress has become an important mechanism in hypertension. We examined the role of endoplasmic reticulum stress in mediating the increased saline-intake and hypertensive effects in response to deoxycorticosterone acetate (DOCA)–salt. Intracerebroventricular delivery of the endoplasmic reticulum stress–reducing chemical chaperone tauroursodeoxycholic acid did not affect the magnitude of hypertension, but markedly decreased saline-intake in response to DOCA-salt. Increased saline-intake returned after tauroursodeoxycholic acid was terminated. Decreased saline-intake was also observed after intracerebroventricular infusion of 4-phenylbutyrate, another chemical chaperone. Immunoreactivity to CCAAT homologous binding protein, a marker of irremediable endoplasmic reticulum stress, was increased in the subfornical organ and supraoptic nucleus of DOCA-salt mice, but the signal was absent in control and CCAAT homologous binding protein–deficient mice. Electron microscopy revealed abnormalities in endoplasmic reticulum structure (decrease in membrane length, swollen membranes, and decreased ribosome numbers) in the subfornical organ consistent with endoplasmic reticulum stress. Subfornical organ-targeted adenoviral delivery of GRP78, a resident endoplasmic reticulum chaperone, decreased DOCA-salt–induced saline-intake. The increase in saline-intake in response to DOCA-salt was blunted in CCAAT homologous binding protein–deficient mice, but these mice exhibited a normal hypertensive response. We conclude that (1) brain endoplasmic reticulum stress mediates the saline-intake, but not blood pressure response to DOCA-salt, (2) DOCA-salt causes endoplasmic reticulum stress in the subfornical organ, which when attenuated by GRP78 blunts saline-intake, and (3) CCAAT homologous binding protein may play a functional role in DOCA-salt–induced saline-intake. The results suggest a mechanistic distinction between the importance of endoplasmic reticulum stress in mediating effects of DOCA-salt on saline-intake and blood pressure.
Multiple Health Behavior Changes in a Cancer Prevention Intervention for Construction Workers, 2001-2003

Introduction Few multiple behavior change interventions have addressed tobacco use in conjunction with fruit and vegetable consumption, particularly among high-risk blue-collar workers. Tools for Health, a cancer prevention intervention for construction laborers, was effective in achieving behavior change for smoking cessation and fruit and vegetable consumption separately. This study examines whether addressing smoking and fruit and vegetable consumption was successful in achieving positive change for both behaviors. We also explored possible explanations for the relationship between behavior changes in these 2 behavioral domains. Methods We retrospectively analyzed data from a randomized controlled trial testing a smoking cessation and fruit and vegetable consumption intervention for construction workers. We used survey data from 300 intervention participants to answer our primary research question: Did participants who reported being smokers at baseline successfully quit smoking and increase their fruit and vegetable consumption by the end of the intervention? We used qualitative data from 16 small group discussions to help interpret these results. Results Tools for Health participants achieved substantial levels of smoking cessation and increased their fruit and vegetable consumption, concurrently, during the course of the intervention. Conclusion This study provides evidence that pairing smoking cessation with increasing fruit and vegetable consumption can be successful in a multiple behavior change intervention designed for high-risk blue-collar workers. Further, our findings provide potential directions for examining why this pairing might be complementary.
Evolutionary path planning and navigation of autonomous underwater vehicles

This paper presents a complete methodology for mission planning and navigation of autonomous underwater vehicles (AUVs) in ocean environment. Path planning near the ocean floor is accomplished via genetic algorithms and B-splines based on known data of the ocean floor. In addition, collision free navigation is achieved in unknown environments. Prior to vehicle's launch, a genetic algorithm based on ocean floor data and on mission restrictions calculates the optimal path. Once the path is calculated, the vehicle is navigated through the predefined path by a set of fuzzy controllers. A second evolutionary algorithm optimizes the membership functions of these controllers so as the vehicle has the minimum error through its course. Extensive simulations were performed in order to evaluate the methodology and the derived optimized controller.