Miracle-dz/UniFAR-FTUs huggingface dataset:
Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data

Although two-color fluorescent DNA microarrays are now standard equipment in many molecular biology laboratories, methods for identifying differentially expressed genes in microarray data are still evolving. Here, we report a refined test for differentially expressed genes which does not rely on gene expression ratios but directly compares a series of repeated measurements of the two dye intensities for each gene. This test uses a statistical model to describe multiplicative and additive errors influencing an array experiment, where model parameters are estimated from observed intensities for all genes using the method of maximum likelihood. A generalized likelihood ratio test is performed for each gene to determine whether, under the model, these intensities are significantly different. We use this method to identify significant differences in gene expression among yeast cells growing in galactose-stimulating versus non-stimulating conditions and compare our results with current approaches for identifying differentially-expressed genes. The effect of sample size on parameter optimization is also explored, as is the use of the error model to compare the within- and between-slide intensity variation intrinsic to an array experiment.
2D DIGE proteomic analysis of early post mortem muscle exudate highlights the importance of the stress response for improved water‐holding capacity of fresh pork meat

Variation in water‐holding capacity (WHC), which presents a major economic burden to the swine industry, is considered to be underpinned by variation at a molecular and biochemical level. High‐resolution 2D DIGE followed by MS analysis and Western blot were used to unravel the proteome of muscle exudate, collected following centrifugation, in the pH 4–7 range. A first 2DE‐based protein map of this substrate was produced where 89 spots were successfully characterised. Two phenotypes divergent for WHC plus one intermediate were compared with a view to deciphering the biochemical processes impacting on variation in WHC. Twenty spots were observed to be altered across the phenotypes. Of these, 14 represented sixteen proteins including metabolic enzymes, stress response proteins and structural proteins. Triosephosphate isomerase and transferrin showed a major difference between the two extreme phenotypes, and may have potential as biological markers for WHC prediction. Several members of the HSPs family were highlighted. This proteomic study makes an important contribution towards a more detailed molecular view of the processes behind WHC and will provide a valuable resource for future investigations.
Toward building a robust and intelligent video surveillance system: a case study

With the proliferation of inexpensive cameras, availability of large-capacity disk storage, and the ubiquitous presence of high-speed, broad-band communication networks, it is now economically and technically feasible to construct and deploy multi-camera video surveillance systems. In line with this is the need of intelligent, robust, (semi-)automated video analysis paradigms to assist the operators in scene analysis and event classification. In this paper, we summarize our current research work toward realizing such a multi-camera video surveillance system. Interested readers can visit our web sites http://www.ece. ucsb.edu/~echang and http://www.cs. ucsb.edu/ ~yfwang for more information
Small Multifidus Muscle Size Predicts Football Injuries

Background In Australian Football, hip, groin and thigh (HGT) muscle injuries have had the highest incidence and prevalence. A previous study showed that football players with relatively more severe pre-season ‘HGT’ injuries had a significantly smaller size of the multifidus muscle. Objective This study was designed to examine the robustness of multifidus muscle measurements as a predictor of lower limb injuries incurred by Australian Football League players. Design This was a prospective quasi-experimental research design. Muscle measurements were conducted at the start of the pre-season to predict pre-season injuries, and at the start of the playing season to predict injuries in the playing season. Setting Players from 6 clubs of the Australian National football league were eligible for inclusion (n=275). Players were assessed on club premises. Participants Assessments were conducted on 259 elite football players for the pre-season (94.2% of eligible players), and 261 players at the start the playing season (94.9%). Risk factor assessment Morphology of the multifidus muscle was assessed using ultrasound imaging. Injury data were obtained from records collected by the AFL club staff during the pre-season and the playing season. Main outcome measurements The dependent variable in the binomial logistic regression was occurrence of lower limb injuries in the pre-season and the playing season. Results A lower limb injury was incurred by 38.2% of the players in the pre-season and 69.5% of the players in the playing season. A new model using cross-sectional area of the multifidus muscle reliably and consistently predicted lower limb injury in both the pre-season and playing season. In the season, ‘kicking leg’ was related to injury. Conclusions The results of this study have established the predictive power of multifidus muscle size to predict injury in elite football players. These results provide a strong direction for clinicians who screen and treat athletes.
Upper gastrointestinal bleeding among users of NSAIDs: a population-based cohort study in Denmark.

AIMS It is well-known that use of nonsteroidal anti-inflammatory drugs (NSAIDs) increases the risk of upper gastrointestinal bleeding (UGIB), but characteristics of the association and quantification of excess risk at the population level require clarification. METHODS All users of nonaspirin prescription NSAIDs in North Jutland County, Denmark during 1991-95 were identified in the regional Pharmaco-Epidemiologic Database. Using the Hospital Discharge Register, all hospitalizations for UGIBs were identified among the 156,138 users of NSAIDs and compared with the number of expected based on the North Jutland population who did not receive NSAID prescriptions. RESULTS During periods of NSAID use without use of other drugs associated with UGIB, we observed 365 UGIBs, a number 3.6 times higher than expected (95% CI = 3.3, 4.0). The excess risk varied by sex, type of NSAID and form and route of administration of the NSAID, but not by age at first NSAID prescription or number of prior prescriptions. Risk declined sharply following cessation of use. For ibuprofen and naproxen, there was a clear trend in rising risk by increasing dose, although the lowest doses were also associated with an excess of UGIB. Concurrent use of corticosteroids, anticoagulants and aspirin further increased the risk of UGIB. CONCLUSIONS All types and formulations of NSAIDs appear to increase the risk of UGIBs, but the effect appear not to be cumulative and diminish rapidly with discontinue of use. Up to 15% of the UGIBs in the entire population of the North Jutland County may be explained by use of this drug.
A Case Report of Familial Sudden Cardiac Death

The annual incidence of sudden cardiac death (SCD) in the general population is 0.1%. SCDs in the young are mainly caused by genetic heart disorders which can lead to inherited arrhythmia syndromes, such as long QT, short QT and Brugada syndromes. One of the most effective therapies for this disease is implantable cardioverter defibrillators (ICD). In this article, we reported a case of 46 years old patient with repeated syncope. Investigation of the family history we found a familial SCDs and the members died in 28.5 years old on average and all of them were male.
Spatial and temporal expression of the I factor during oogenesis in Drosophila melanogaster.

The I factor is a functional non-viral retrotransposon, or LINE, from Drosophila melanogaster. Its mobility is associated with the I-R hybrid dysgenesis. In order to study the expression pattern of this LINE in vivo, a translational fusion between the first ORF of the I factor and the lacZ gene of Escherichia coli has been carried out and introduced in the genome of reactive (R) flies. Homozygous transgenic Drosophila lines have been established and analysed. ORF1 expression is limited to germ-line cells (nurse cells and oocyte) between stage 2 and 10 of oogenesis. No somatic expression is found. Position effects may limit the level of expression of a given transgene but do not modify its basic pattern of expression during the development of the fly. This reproducible control demonstrates both that I factor is driven by its own promoter, probably the internal one suggested by Mizrokhi et al. (Mizrokhi, L.J., Georgevia, S.G. and Ilying, Y.V. (1988). Cell 54, 685-691), and that tissue-specific regulatory sequences are present in the 5' untranslated part of the I factor. The nuclear localization of the fusion protein reveals the presence of nuclear localization signals (NLS) in the ORF1-encoded protein correlating with the possible structural and/or regulatory role of this protein. This expression is restricted to dysgenic and reactive females, and is similar in the two conditions. All the results obtained in this work suggest that I factor transposition occurs as a meiotic event, between stage 2 and 10 of the oogenesis and is regulated at the transcriptional level. It also appears that our transgene is an efficient marker to follow I factor expression.
On the Path Processing under Energy Constraints

In wireless sensor networks and pervasive environments situations occur where only one path between a source of raw data and a target requiring processed data is available by topology and/or by the network layer. All nodes - source, target, and relay nodes between them - underly energy constraints. The depletion of the energy of any involved node would disable the network. In consequence, a scheme for the distribution of data processing that minimizes local peaks in energy consumption isneeded. This paper introduces solutions for the given problem, where no information about the battery status is available. Furthermore, model modifications to meet more practical situations and the problem of total energy consumption are discussed.
Roles of the Kinase TAK1 in TRAF6-Dependent Signaling by CD40 and Its Oncogenic Viral Mimic, LMP1

The Epstein-Barr virus (EBV)-encoded protein latent membrane protein 1 (LMP1) is essential for EBV-mediated B cell transformation and plays a critical role in the development of post-transplant B cell lymphomas. LMP1 also contributes to the exacerbation of autoimmune diseases such as systemic lupus erythematosus (SLE). LMP1 is a functional mimic of the tumor necrosis factor receptor (TNFR) superfamily member CD40, and relies on TNFR-associated factor (TRAF) adaptor proteins to mediate signaling. However, LMP1 activation signals to the B cell are amplified and sustained compared to CD40 signals. We previously demonstrated that LMP1 and CD40 use TRAF molecules differently. Although associating with CD40 and LMP1 via separate mechanisms, TRAF6 plays a significant role in signal transduction by both. It is unknown whether TRAF6 mediates CD40 versus LMP1 functions via distinct or shared pathways. In this study, we tested the hypothesis that TRAF6 uses the kinase TAK1 to trigger important signaling pathways following both CD40 and LMP1 stimulation. We determined that TAK1 was required for JNK activation and interleukin-6 (IL-6) production mediated by CD40 and LMP1, in both mouse and human B cells. Additionally, TRAF3 negatively regulated TRAF6-dependent, CD40-mediated TAK1 activation by limiting TRAF6 recruitment. This mode of regulation was not observed for LMP1 and may contribute to the dysregulation of LMP1 compared to CD40 signals.
Field trials of two 802.11 residual bandwidth estimation methods

Ad hoc networks have attracted much attention due to their decentralized architecture and potential mobility. The latter promise has sparked research aimed towards routing and quality of service (QoS) admission schemes. The volatile links that are inherent to these networks have however spawned a need for a cross-layering service below IP for local route and QoS decision making, or information dissemination to participating hosts. We have conducted field trials of an active and a passive estimation method implemented in a real wireless driver to estimate the residual bandwidth. Through these tests we show how residual bandwidth estimates can be obtained in an 802.11 wireless network and identify the strengths and weaknesses of their underlying methods. The implemented wireless driver collects per link bandwidth data, local retransmission count and expected transmission time
An Algorithmic Game-Theory Approach for Coarse-Grain Prediction of RNA 3D Structure

We present a new approach for the prediction of the coarse-grain 3D structure of RNA molecules. We model a molecule as being made of helices and junctions. Those junctions are classified into topological families that determine their preferred 3D shapes. All the parts of the molecule are then allowed to establish long-distance contacts that induce a 3D folding of the molecule. An algorithm relying on game theory is proposed to discover such long-distance contacts that allow the molecule to reach a Nash equilibrium. As reported by our experiments, this approach allows one to predict the global shape of large molecules of several hundreds of nucleotides that are out of reach of the state-of-the-art methods.
Interest Drifts in User Profiling: A Relevance-Based Approach and Analysis of Scenarios

For personal information agents, user profiles have to represent user interests and preferences in order to satisfy long-term information needs. An implicit assumption in user-profiling is the existence of persistent interests which, however, might suffer some changes over time. Each time the interests of a user change, his profile becomes inaccurate and the predictive quality decreases. Adaptation of user profiles is, therefore, an essential requirement for personal agents that need to be capable of adjusting their behavior quickly in order to shorten the period of reduced predictive quality. In this paper, a user-profiling technique named WebProfiler, which learns a hierarchical representation of user interests using conceptual clustering, is augmented with an adaptation strategy based on relevance feedback and time-based forgetting in order to deal with drifting interests. We empirically evaluate the performance of this strategy by analyzing its behavior on multiple scenarios of interest drifts and shifts.
Mindfulness-based stress reduction: Facilitating work outcomes through experienced affect and high -quality relationships

Mindfulness is a quality of consciousness that consists of purposeful attention to and awareness of the present moment, approached with an attitude of openness, acceptance, and nonjudgment. Research evidence shows that mindfulness has positive effects on mental health and psychological well-being, physical health, and quality of intimate relationships. However, few researchers have studied the effects of mindfulness in a work setting. In this project, I expanded previous research by exploring how mindfulness, as developed in a mindfulness-based training program, affects the workplace outcomes of performance and citizenship behavior. I proposed that these effects are mediated through the positive effects of mindfulness on one’s experienced affect and one’s work relationships. I also examined interdependence as a moderator of the relationship quality-work outcomes relationship. The research study employed an experimental group of participants in a mindfulness-based program and a nonequivalent control group to test the specific hypotheses. Data were provided by multiple sources: mindfulness, affect, and role interdependence by study participants; relationship quality by coworkers; performance and citizenship behavior by supervisors. Analytic strategy was comprised of correlational analysis and regression as well as analytical procedures for moderated mediation. The mindfulness-based programs were effective in increasing mindfulness, particularly for those participants who were lower in mindfulness prior to program participation. Participants also experienced improved affect. However, the proposed model relating mindfulness to work outcomes was not supported. Mindfulness was significantly related to positive and negative affect as predicted; however, mindfulness was not significantly correlated with relationship quality or job performance. Its significant relationship with citizenship behavior was in the opposite direction as hypothesized. In the full model, coefficients for mindfulness, experienced affect, relationship quality, and role interdependence in the prediction of job performance and citizenship behavior were not significant. Additionally, interdependence did not interact
Hybrid Temperature Sensor Network for Area-Efficient On-Chip Thermal Map Sensing

Spatial thermal distribution of a chip is an essential information for dynamic thermal management. To get a rich thermal map, the sensor area is required to be reduced radically. However, squeezing the sensor size is about to face its physical limitation. In this background, we propose an area-efficient thermal sensing technique: hybrid temperature sensor network. The proposed sensor architecture fully exploits the spatial low-pass filtering effect of thermal systems, which implies that most of the thermal information resides in very low spatial frequency region. Our on-chip sensor network consists of a small number of accurate thermal sensors and a large number of tiny relative thermal sensors, responsible for low and high spatial frequency thermal information respectively. By combining these sensor readouts, a thermal map upsampler synthesizes a higher spatial resolution thermal map with a proposed guided upsampling algorithm.
Atelectasis and oxygenation in major surgery with either propofol with or without nitrous oxide or isoflurane anaesthesia

Forty‐two patients undergoing major colonic surgery were assigned at random to receive isoflurane‐fentanyl anaesthesia with nitrous oxide in oxygen, propofol‐fentanyl anaesthesia with air in oxygen or propofol‐fentanyl anaesthesia with nitrous oxide in oxygen. The groups were comparable in demographic data. Atelectases were identified, and the area measured by computerised tomography of the chest 203±69 min after extubation. and oxygenation was determined by arterial blood gas samples taken during operation at 30, 60, 90 and 120 min after extubation and on postoperative days 1, 2 and 3. Atelectases were seen in all three groups with no differences in the mean area between groups. After operation, the effect of 4 l.min−1 of oxygen by nasal catheter on Pao2 was similar in all groups. A significant decrease in PaO2 was found during the first 3 days after surgery, and was also the same in all groups. There was no correlation between area of atelectasis and postoperative PaO2. We conclude there is no difference in the incidence of postoperative atelectasis or oxygenation when using propofol, with or without nitrous oxide or isoflurane.
Finite-time Control Synthesis of Networked Control Systems with Time-varying Delays

Abstract This paper investigates the finite-time control problem for networked control systems (NCSs) with time-varying delays. The finite-time controller via state feedback is proposed to guarantee the finitetime boundedness and finite-time stabilization of the resulting closed loop system for all admissible disturbances and unknown time-delays. Based on Lyapunov stability theory, sufficient conditions that ensure finite-time performance of networked control systems are derived. The control criterion is formulated in the form of linear matrix inequalities and the designed finite-time stabilization controller is described as a feasibility one. The presented results are extended to networked control systems. with time-varying delay. Numerical example illustrates the feasibility of the developed approaches.
Student Achievement: Elementary Principal Catalysts— Instructional Leadership in Reading

role of the principal. Whereas traditional responsibilities for principals have included managerial duties, such as maintaining the school budget and ensuring safe school facilities (Whitaker, 1998), principals are currently charged with additional responsibilities associated with promoting school change, such as acting as school visionaries (Copland, 2001) and instructional leaders (Acheson & Gall, 1997; Bailey & Dyck, 1990; Blasé & Blasé, 1999, 2000; Boyd, 1996; Burnett & Pankake, 1990; Fink & Resnick, 2001; Ginsberg, 1988; Heck, 1992; Larsen & Malen, 1997; McAdams, 1998; Wanzare & Da Costa, 2001; Whale, 2000; Wildy & Dimmock, 1993) who set the tone for the achievement of all students in a school building. Studies have shown that successful schools utilize practices to promote student success, such as personalizing the school experience for students and establishing schoolwide responsibility for student achievement (Darling-Hammond, 1997). Furthermore, research suggests that principals’ behaviors can facilitate and influence student learning (Carter, 2000; Hallinger & Heck, 1998). In short, principals can shape schools into learning organizations (Senge, 1990).
Use of Inertial Sensors for Ambulatory Assessment of Center-of-Mass Displacements During Walking

Current methods for center-of-mass (CoM) estimation are restricted to gait laboratories. The aim of this study was to estimate CoM displacement under ambulatory conditions with inertial sensors. A sacral inertial sensor (SIS method) was used to estimate the CoM displacement by double integration of the acceleration. Overestimation of the displacement caused by pelvic rotations was compensated (CSIS method). The CoM displacement estimations using the (C)SIS method were compared to the conventional methods of the segmental analysis (SA) method and the sacral marker (SM) method by the intraclass correlations and the root-mean-square (RMS) differences between the CoM curves. Accurate ambulatory measurement of the CoM displacement using inertial sensors was possible. Estimations of the sacrum position using the SIS method and the SM method were similar with mean (SD) RMS differences of 3.23 (0.87), 2.96 (0.42), and 3.22 (0.78) mm for, respectively, the x-, y- and z-directions. The CoM estimation of the SIS method has RMS differences of 5.67 (1.20), 7.16 (3.28), and 3.49 (1.29) mm compared the SA method. The CSIS method shows a clear improvement in these estimations of the CoM with RMS differences of 5.52 (1.29), 4.44 (1.89), and 3.17 (1.41) mm and is generally applicable for healthy subjects.