Miracle-dz/UniFAR-FTUs huggingface dataset:
Biochemical Characterization of the C4-Dicarboxylate Transporter DctA from Bacillus subtilis

ABSTRACT Bacterial secondary transporters of the DctA family mediate ion-coupled uptake of C4-dicarboxylates. Here, we have expressed the DctA homologue from Bacillus subtilis in the Gram-positive bacterium Lactococcus lactis. Transport of dicarboxylates in vitro in isolated membrane vesicles was assayed. We determined the substrate specificity, the type of cotransported ions, the electrogenic nature of transport, and the pH and temperature dependence patterns. DctA was found to catalyze proton-coupled symport of the four C4-dicarboxylates from the Krebs cycle (succinate, fumurate, malate, and oxaloacetate) but not of other mono- and dicarboxylates. Because (i) succinate-proton symport was electrogenic (stimulated by an internal negative membrane potential) and (ii) the divalent anionic form of succinate was recognized by DctA, at least three protons must be cotransported with succinate. The results were interpreted in the light of the crystal structure of the homologous aspartate transporter GltPh from Pyrococcus horikoshii.
Evaluation and development of payment methods , using the Agency theory

In cooperation between two parties, the parties are seldom equal to size, strength of negotiation or information. In many cases the relationship consists of one party delegating work to the other party who performs the work, for example a subcontractor and its customer. This, to nature unbalanced, cooperation increases the demands on the relationship that connects the parties, enabling success for both sides. A theory that deals with the situation mentioned is the Agency theory. In order to reach a successful relationship, the agency theory explains how to organise and use contracts in a two-part relationship, in which one part (the agent) acts on the behalf of the other part (the principle). [1]
Identification and Asymptotic Localization of Rumor Sources Using the Method of Types

We are interested in identifying a rumor source on a tree network. We begin with extended star networks under the SI infection model with exponential waiting times. We present and analyze the <italic>types center</italic>, a highly tractable approximation of the ML source estimate, obtained using the method of types. We empirically show that this approximate ML estimator is exact for some small test cases. We prove that the approximation error is at most logarithmic in infection size on large networks, providing highly efficient source identification (especially compared to the accuracy in similar problems, such as the <inline-formula><tex-math notation="LaTeX">$\mathcal {O}(\sqrt{n})$</tex-math></inline-formula> best possible accuracy estimate in a line network). We also show that the qualitative properties of the types and rumor centers are different on extended star networks. We further propose a heuristic-based generalization of this approach to trees: the <italic>relative-leaf counting algorithm</italic>. In simulations on regular and nonregular trees, types center's performance is competitive with rumor centrality (which is optimal for <inline-formula><tex-math notation="LaTeX">$d$</tex-math></inline-formula>-regular trees), while requiring less computation time. In addition to providing a faster (and sometimes more accurate) alternative on its own, our approach could potentially be used with rumor centrality to improve results with less than twice the total computation time.
Dynamic joint sentiment-topic model

Social media data are produced continuously by a large and uncontrolled number of users. The dynamic nature of such data requires the sentiment and topic analysis model to be also dynamically updated, capturing the most recent language use of sentiments and topics in text. We propose a dynamic Joint Sentiment-Topic model (dJST) which allows the detection and tracking of views of current and recurrent interests and shifts in topic and sentiment. Both topic and sentiment dynamics are captured by assuming that the current sentiment-topic-specific word distributions are generated according to the word distributions at previous epochs. We study three different ways of accounting for such dependency information: (1) sliding window where the current sentiment-topic word distributions are dependent on the previous sentiment-topic-specific word distributions in the last S epochs; (2) skip model where history sentiment topic word distributions are considered by skipping some epochs in between; and (3) multiscale model where previous long- and short- timescale distributions are taken into consideration. We derive efficient online inference procedures to sequentially update the model with newly arrived data and show the effectiveness of our proposed model on the Mozilla add-on reviews crawled between 2007 and 2011.
Stress resilience and the risk of inflammatory bowel disease: a cohort study of men living in Sweden

Objective To determine if low psychosocial stress resilience in adolescence (increasing chronic stress arousal throughout life) is associated with an increased inflammatory bowel disease (IBD) risk in adulthood. Subclinical Crohn's disease (CD) and ulcerative colitis (UC) can exist over many years and we hypothesise that psychosocial stress may result in conversion to symptomatic disease through its proinflammatory or barrier function effects. Design National register-based cohort study of men followed from late adolescence to middle age. Setting A general population cohort of men in Sweden. Participants Swedish population-based registers provided information on all men born between 1952 and 1956 who underwent mandatory Swedish military conscription assessment (n=239 591). Men with any gastrointestinal diagnoses (except appendicitis) prior to follow-up were excluded. Primary outcome measures An inpatient or outpatient diagnosis of CD or UC recorded in the Swedish Patient Register (1970–2009). Results A total of 938 men received a diagnosis of CD and 1799 UC. Lower stress resilience in adolescence was associated with increased IBD risk, with unadjusted HRs (95% CIs) of 1.54 (1.26 to 1.88) and 1.24 (1.08 to 1.42), for CD and UC, respectively. After adjustment for potential confounding factors, including markers of subclinical disease activity in adolescence, they are 1.39 (1.13 to 1.71) and 1.19 (1.03 to 1.37). Conclusions Lower stress resilience may increase the risk of diagnosis of IBD in adulthood, possibly through an influence on inflammation or barrier function.
EPB41L3, TSP-1 and RASSF2 as new clinically relevant prognostic biomarkers in diffuse gliomas

Hypermethylation of tumor suppressor genes is one of the hallmarks in the progression of brain tumors. Our objectives were to analyze the presence of the hypermethylation of EPB41L3, RASSF2 and TSP-1 genes in 132 diffuse gliomas (astrocytic and oligodendroglial tumors) and in 10 cases of normal brain, and to establish their association with the patients’ clinicopathological characteristics. Gene hypermethylation was analyzed by methylation-specific-PCR and confirmed by pyrosequencing (for EPB41L3 and TSP-1) and bisulfite-sequencing (for RASSF2). EPB41L3, RASSF2 and TSP-1 genes were hypermethylated only in tumors (29%, 10.6%, and 50%, respectively), confirming their cancer-specific role. Treatment of cells with the DNA-demethylating-agent 5-aza-2′-deoxycytidine restores their transcription, as confirmed by quantitative-reverse-transcription-PCR and immunofluorescence. Immunohistochemistry for EPB41L3, RASSF2 and TSP-1 was performed to analyze protein expression; p53, ki-67, and CD31 expression and 1p/19q co-deletion were considered to better characterize the tumors. EPB41L3 and TSP-1 hypermethylation was associated with worse (p = 0.047) and better (p = 0.037) prognosis, respectively. This observation was confirmed after adjusting the results for age and tumor grade, the role of TSP-1 being most pronounced in oligodendrogliomas (p = 0.001). We conclude that EPB41L3, RASSF2 and TSP-1 genes are involved in the pathogenesis of diffuse gliomas, and that EPB41L3 and TSP-1 hypermethylation are of prognostic significance.
Hes1 Desynchronizes Differentiation of Pluripotent Cells by Modulating STAT3 Activity

Robust development of the early embryo may benefit from mechanisms that ensure that not all pluripotent cells differentiate at exactly the same time: such mechanisms would build flexibility into the process of lineage allocation. This idea is supported by the observation that pluripotent stem cells differentiate at different rates in vitro. We use a clonal commitment assay to confirm that pluripotent cells commit to differentiate asynchronously even under uniform differentiation conditions. Stochastic variability in expression of the Notch target gene Hes1 has previously been reported to influence neural versus mesodermal differentiation through modulation of Notch activity. Here we report that Hes1 also has an earlier role to delay exit from the pluripotent state into all lineages. The early function of Hes1 to delay differentiation can be explained by an ability of Hes1 to amplify STAT3 responsiveness in a cell‐autonomous manner. Variability in Hes1 expression therefore helps to explain why STAT3 responsiveness varies between individual ES cells, and this in turn helps to explain why pluripotent cells commit to differentiate asynchronously. STEM Cells 2013;31:1511–1522
Searching and skimming: An exploratory study

Source code search is an important activity for programmers working on a change task to a software system. As part of a larger project to improve tool support for finding information in source code, we conducted a formative study in which programmers were asked to perform corrective tasks to a system they were initially unfamiliar with. Our analysis focused specifically on how programmers decide what to search for, and how they decide which results are relevant to their task. Based on our analysis, we present five observations about our participant's approach to finding information and some of the challenges they faced. We also discuss the implications these observations have for the design of source code search tools.
Vibrotactile score: A score metaphor for designing vibrotactile patterns

Despite the plethora of vibrotactile applications that already have begun to impact our everyday life, how to design vibrotactile patterns easily and efficiently remains to be a challenge. In this paper, we introduce a vibrotactile score, an effective means for composing vibrotactile patterns. The vibrotactile score is a metaphor of the musical score to vibrotaction, and its design is adapted from two common musical scores (the piano score and the guitar tablature). Moreover, we developed an authoring tool, Vibrotactile Score Editor (VibScoreEditor), that fully supports the vibrotactile score with intuitive graphical user interface. Another metaphorical feature, vibrotactile clef (analogous to the musical clef), is incorporated in the editor to make the process of composing vibrotactile patterns decoupled from the process of considering the signal-level characteristics of vibration. A few examples of vibrotactile patterns designed using the VibScoreEditor are also presented.
A case study of process-variation effect to SoC analog circuits

Recent submicron process technology scaling leads the urgency to build an efficient methodology of characterizing and modeling the process variation effect, for example, the threshold voltage, Vt. This is one of the key process parameters that must be extensively modeled and validated for accurate circuit performance. Furthermore, this requirement is even much more critical for analog applications which demand an ability to match devices precisely. Analog circuits use larger device dimensions as compared to digital circuits in order to minimize the process variation implication. This has led Negative Bias Temperature Instability (NBTI) to be the most performance limiter compared to the rest of reliability mechanisms. This reliability sensitivity is even more challenging as most of the circuit blocks (digital and analog) are fabricated on the same chip for system-on-chip (SoC) applications. This paper will describe in detail the actions taken to minimize impact to customers and will show how important proper aging simulations to be conducted with the right combination of process, voltage, temperature (PVT) and coupling/timing to occur due to process variation effect beyond specifications on analog differential amplifier (diffamp) circuits in SoC products.
Implementing Stack E6 via OS Linux Sockets

New software implementation of Ukrainian national stack of networking protocols E6 was presented. Within operating system Linux kernel, families of E6 protocols and addresses were created as well as functions of their processing, in the form of a loadable module. Application of socket technology gives a series of considerable advantages among which unified with other stacks application interface, reuse of the kernel resources facilitating the further development and enterprise implementation of stack E6, engineering corresponding networking devices.
Work-Family Enrichment and Job-Family Satisfaction among Hotel Employees

The aim of the study is to advance understanding of bi-directions of positive side of work-family interaction with job and family satisfaction. Using structural equation modelling (SEM), the researcher tested the data from 306 employees from selected hotels in Sarawak on the relationship between work-family enrichment (WFE) and family-work enrichment (FWE) with job satisfaction (JS) and family satisfaction (FS). The results indicated that both WFE and FWE have a positive relationship with JS. The result from SEM also provided empirical support for a significant positive relationship between FWE with FS. The results support a bi-directional approach towards positive side of work-family interaction and provide a better understanding of any domain-specific effects.
First Validation of a Generic Method for Emotional Body Posture Generation for Social Robots

Gestures for social robots are often preprogrammed off-line or generated by mapping motion capture data to the robot. Since these gestures are dependent on the robot’s joint configuration, new joint trajectories to reach the desired postures need to be implemented when using a new robot platform with a different morphology. The method proposed here aims to minimize the workload when implementing gestures on a new robot platform and facilitate the sharing of gestures between different robots. The innovative aspect of this method is that it is constructed independently of any robot configuration, and therefore it can be used to generate gestures for different robot platforms. To calculate a posture for a certain configuration, the developed method uses a set of target gestures listed in a database and maps them to that specific configuration. The method was validated on a series of configurations, including those of existing robots.Categories and Subject DescriptorsJ.4 [Computer Applications]: Social and behavioral sciences; I.2. 9 [Artificial Intelligence]: Robotics
Targeted Disruption of the Plasmodium berghei Ctrp Gene Reveals Its Essential Role in Malaria Infection of the Vector Mosquito

CTRP (circumsporozoite protein and thrombospondin-related adhesive protein [TRAP]-related protein) of the rodent malaria parasite Plasmodium berghei (PbCTRP) makes up a protein family together with other apicomplexan proteins that are specifically expressed in the host-invasive stage 1. PbCTRP is produced in the mosquito-invasive, or ookinete, stage and is a protein candidate for a role in ookinete adhesion and invasion of the mosquito midgut epithelium. To demonstrate involvement of PbCTRP in the infection of the vector, we performed targeting disruption experiments with this gene. PbCTRP disruptants showed normal exflagellation rates and development into ookinetes. However, no oocyst formation was observed in the midgut after ingestion of these parasites, suggesting complete loss of their invasion ability. On the other hand, when ingested together with wild-type parasites, disruptants were able to infect mosquitoes, indicating that the PbCTRP gene of the wild-type parasite rescued infectivity of disruptants when they heterologously mated in the mosquito midgut lumen. Our results show that PbCTRP plays a crucial role in malaria infection of the mosquito midgut and suggest that similar molecular mechanisms are used by malaria parasites to invade cells in the insect vector and the mammalian host.
Query Performance Prediction and Topic Shift in Microblog Retrieval

In Microblog retrieval, a system’s ability to know when to ”shut up” and how many results to return for a given query can have huge impact on its performance [1]. In addition, since relevant but redundant tweets will be deemed as irrelevant, it is also important to detect whether a tweet contain novel information or not. Therefore, in this year’s Real-Time Summarization Track, we focus on estimating result cut-oﬀ thresholds and redundancy thresholds. Query performance prediction techniques [2, 3] can be used to predict the performance of a query and therefore would be helpful in deciding both thresholds. Moreover, we deﬁne topic shift of a query as the change of subtopics or aspects discussed or mentioned on Twitter over time. We suggests that using it could help us further reﬁne the thresholds since it reﬂects how much new information emerges on Twitter.
High-Order Central ENO Finite-Volume Scheme for MHD on Three-Dimensional Cubed-Sphere Grids

A high-order central essentially non-oscillatory (CENO) finite-volume scheme is developed for the compressible ideal magnetohydrodynamics (MHD) equations solved on threedimensional (3D) cubed-sphere grids. The proposed formulation is an extension to 3D geometries of a recent high-order MHD CENO scheme developed on two-dimensional (2D) grids. The main technical challenge in extending the 2D method to 3D cubed-sphere grids is to properly handle the nonplanar cell faces that arise in cubed-sphere grids. This difficulty is solved by considering general hexahedral cells with trilinear faces, which allow us to compute fluxes, areas and volumes with high-order accuracy by transforming to a reference cubic cell. The 3D CENO scheme is implemented within a flexible multi-block cubed-sphere grid framework to fourth-order accuracy, resulting in a high-order solution method for cubed-sphere grids with unique capabilities in terms of adaptive refinement and parallel scalability. The high-order method is applicable to the solution of general hyperbolic conservation laws with, in principle, arbitrary order. The CENO scheme is based on a hybrid solution reconstruction procedure that provides high-order accuracy in smooth regions, even for smooth extrema, and non-oscillatory transitions at discontinuities. The scheme is applied herein to MHD in combination with a GLM divergence correction technique to control the solenoidal condition for the magnetic field while preserving the high-order accuracy of the numerical procedure. The cubed-sphere simulation framework features a flexible design based on a genuine multi-block implementation, leading to high-order accuracy, flux calculation, adaptivity and parallelism that are fully transparent to the boundaries between the six sectors of the cubedsphere grid. The proposed 3D MHD CENO scheme is shown to achieve uniform fourth-order accuracy on cubed-sphere grids. Parallel domain partitioning and grid adaptivity are achieved on the 3D cubed-sphere grids using a hierarchical block-based division strategy with blocks of equal size. Numerical results to demonstrate the high-order accuracy, robustness and capability of the proposed high-order framework are presented and discussed for several test problems.
RiTMO: A Method for Runtime Testability Measurement and Optimisation

Runtime testing is emerging as the solution for the integration and assessment of highly dynamic, high availability software systems where traditional development-time integration testing is too costly, or cannot be performed. However, in many situations, an extra effort will have to be invested in implementing appropriate measures to enable runtime tests to be performed without affecting the running system or its environment. This paper introduces a method for the improvement of the runtime testability of a system, which provides an optimal implementation plan for the application of measures to avoid the runtime tests' interferences. This plan is calculated considering the trade-off between testability and implementation cost. The computation of the implementation plan is driven by an estimation of runtime testability, and based on a model of the system. Runtime testability is estimated independently of the test cases and focused exclusively on the architecture of the system at runtime.
Low Frequency Music Slows Heart Rate and Decreases Sympathetic Activity

Objectives: Increasing blood pressure (BP) increases the risk of developing cardiovascular disease (CVD). Lower frequency music may lower BP and heart rate (HR), therefore, decreases the CVD risk. Methods: Participants were 16 high BP individuals aged 20 to 50 years. The protocol consisted of 2 visits (experimental & control). Music was tuned between 440 Hz and 432 Hz, and the frequencies changed every 10 minutes. HR variability, diastolic function, oxytocin, and amylase were recorded at each phase. An (ANOVA) was used to examine the effects of music. Results: Mental arithmetic significantly increased BP and HR (all ps<0.01). There were significant differences between the stress condition and all other conditions, all p’s < . 02. There was a significant main effect for Music Order, F (1, 6) = 6.23, p = . 047, ƞp2= . 51, β = . 55. Participants had lower HR listening to 432 Hz music (M = -7.20, se = 2.47) than 440 Hz music (M = -5.33, se = 2.71), t(7) = 2.53, p = . 04, d ‘ = . 41. Conclusion: Listening to low frequency music has cardiovascular benefits including slowing heart rate and promoting relaxation. Further study is needed to determine the underlying mechanisms of music induced beneficial effects.
Changing pre-grasp strategies with increasing object location uncertainty

Successful and robust grasping for humanoid robots is still an ongoing research topic in robotics. Applying human-inspired grasping strategies does not only correspond with more natural looking motions but can also yield good results regarding task success when having to deal with uncertainty. This study investigates human high-level grasping strategies and how they tend to change for different objects when the uncertainty of object location or orientation increases in between two grasps. We are especially interested in potential gains for humanoid robots in a common household setting. By analyzing collected data from human subject grasp experiments with a set of typical objects found in people's homes, we get better insight into how humans handle uncertainty, as well as when and how they change their applied pre-grasp strategy. By adapting the by far most often observed change from a direct grasp attempt to a tapping strategy when dealing with high uncertainty, we can demonstrate a substantial increase of grasp success rate for our robot system with a Shadow Dexterous Hand mounted on a Motoman SDA10 robot while using less than two hand correction steps on average.