Miracle-dz/UniFAR-FTUs huggingface dataset:
Setaria viridis: A Model for C4 Photosynthesis[C][W]

C4 photosynthesis drives productivity in several major food crops and bioenergy grasses, including maize (Zea mays), sugarcane (Saccharum officinarum), sorghum (Sorghum bicolor), Miscanthus x giganteus, and switchgrass (Panicum virgatum). Gains in productivity associated with C4 photosynthesis include improved water and nitrogen use efficiencies. Thus, engineering C4 traits into C3 crops is an attractive target for crop improvement. However, the lack of a small, rapid cycling genetic model system to study C4 photosynthesis has limited progress in dissecting the regulatory networks underlying the C4 syndrome. Setaria viridis is a member of the Panicoideae clade and is a close relative of several major feed, fuel, and bioenergy grasses. It is a true diploid with a relatively small genome of ~510 Mb. Its short stature, simple growth requirements, and rapid life cycle will greatly facilitate genetic studies of the C4 grasses. Importantly, S. viridis uses an NADP-malic enzyme subtype C4 photosynthetic system to fix carbon and therefore is a potentially powerful model system for dissecting C4 photosynthesis. Here, we summarize some of the recent advances that promise greatly to accelerate the use of S. viridis as a genetic system. These include our recent successful efforts at regenerating plants from seed callus, establishing a transient transformation system, and developing stable transformation.
Causal judgements about two causal candidates: Accounting for occurrences, estimating strength, and the importance of interaction judgements

When two possible causes of an outcome are under consideration, contingency information concerns each possible combination of presence and absence of the two causes with occurrences and nonoccurrences of the outcome. White (2008) proposed that such judgements could be predicted by a weighted averaging model integrating these kinds of contingency information. The weights in the model are derived from the hypothesis that causal judgements seek to meet two main aims, accounting for occurrences of the outcome and estimating the strengths of the causes. Here it is shown that the model can explain many but not all relevant published findings. The remainder can be explained by reasoning about interactions between the two causes, by scenario-specific effects, and by variations in cell weight depending on quantity of available information. An experiment is reported that supports this argument. The review and experimental results support the case for a cognitive model of causal judgement in which different kinds of contingency information are utilised to satisfy particular aims of the judgement process.
Clinical and epidemiologic significance of coagulase-negative staphylococci bacteremia in a tertiary care university Israeli hospital.

OBJECTIVES To characterize the clinical significance of coagulase-negative staphylococci (CNS) bacteremia. DESIGN Prospective cohort study. SETTING A 900-bed hospital in Haifa, Israel, from November 1996 to March 1997. RESULTS Of 137 episodes of positive blood cultures for CNS, 41 (30%) were considered as true infection. Twenty-seven of 119 episodes associated with only 1 blood culture positive for CNS (23%) met the definition of infection as compared with 14 of 18 episodes (78%) associated with 2 or more blood cultures positive for CNS (P <.001). Methicillin resistance was significantly more frequent among Staphylococcus epidermidis isolates of episodes of true bacteremia than of episodes of contamination (15 of 22 [68%] vs. 11 of 33 [33%], respectively; P =.02). S hominis was isolated only in episodes considered as contamination (P =.01). It was estimated that CNS represents 24% of all nosocomial bloodstream pathogens. When CNS were isolated in the first 48 hours of hospitalization, an intravascular device was more frequently associated with episodes of true bacteremia than in those considered as contamination (7 of 7 [100%] vs. 10 of 57 [18%], respectively; P <.001). The mortality rate among patients with true CNS bacteremia was 16%. CONCLUSION Some laboratory parameters may help identify episodes of true CNS bacteremia, which appears to be more common than previously considered.
Kinetic characterization of a bacteriophage T4 antimutator DNA polymerase.

Fidelity of DNA replication by bacteriophage T4 DNA polymerase is achieved in a multiplicative process: base selection by its polymerase activity and removal of misincorporated nucleotides by its exonuclease activity. The wild-type polymerase is capable of maintaining a balance between the two activities so that DNA replication fidelity is maximized without excessive waste of nucleotides. Antimutator enzymes exhibit a higher DNA replication fidelity than the wild-type enzyme, at the cost of increased nucleotide turnover. The antimutator A737V polymerase has been characterized kinetically using pre-steady-state and steady-state methods to provide a kinetic sequence which defines the effect of the mutation on the discrete steps controlling DNA replication fidelity. Comparison of this sequence to that of the wild type [Capson, L. T. , Peliska, J. A. , Kaboord, B. F. , Frey, M. W. , Lively, C. , Dahlberg, M. , and Benkovic, S. J. (1992) Biochemistry 31, 10984-10994] revealed that A737V polymerase differs in two ways. The rates at which DNA is transferred between the exonuclease and polymerase sites are reduced approximately 7-fold for a duplex DNA containing a mismatched 3'-terminus, and the partitioning of the mismatched duplex between the polymerase and exonuclease sites is 1:2 versus 4:1 for the wild-type enzyme. The exonuclease activity of A737V relative to the wild-type enzyme is unchanged on single-stranded DNA. However, the difference in partitioning the duplex DNA between the exonuclease and polymerase active sites results in an enhanced exonuclease activity for the antimutator enzyme.
Real-time Human Detection based on Personness Estimation

In this work, we study a real-time human detection method for mobile devices using window proposals. We find that the normed gradients, designed for generic objectness estimation, are also able to rapidly generate high quality object windows for a singlecategory object. We also notice that fusing the normed gradients with additional color feature improves the performance of objectness estimation for the single-category object. Based on these observations, we propose an efficient method, which we call personness estimation, to produce candidate windows that are highly likely to contain a person. The produced candidate windows are used to search over feature maps of an image so that a human detection method can achieve high detection performance within a short period of time. We further present how personness estimation can be efficiently combined into part-based human detection. Our experiments indicate that the proposed method is directly applicable to mobile devices, and allows real-time human detection.
Understanding the relationship between crime victimisation and mental health: A longitudinal analysis of population data

Aim: To determine whether a change in crime victimisation status (from non-victim to victim) affects mental health. Method: Fixed effects models were used to examine the effect of physical violence and property crime victimisation in the past year on future mental health. The sample pooled 110,671 records from 16,187 persons aged 15 years or older who participated in at least two waves of the Australian Household, Income and Labour Dynamics (HILDA) survey between 2002 and 2011. The analysis controlled for all time-stable factors as well as a wide range of dynamic variables known to be associated with mental health (i.e., partner status, area of residence, labour force status, financial prosperity, ability to raise funds in an emergency, alcohol consumption, smoking status, physical activity, general health, social networks and number of life events). Results: The analysis revealed that becoming a victim of violent crime results in a decrease in mental health. Females had a more pronounced decline in mental health after becoming a victim of violence compared with males. By contrast, there was no evidence that becoming a victim of property crime has a detectable impact on mental health for either females or males. Conclusion: Being a victim of violent crime has an adverse effect on mental health. This effect is apparent for both male and female victims, however there is a greater effect of violent crime on women's mental health.
Forward-Looking Bistatic SAR Range Migration Alogrithm

Forward-looking bistatic synthetic aperture radar (FL-BSAR) owns smart space-variant geometry feature, so it is difficult to use precise monostatic SAR frequency domain imaging algorithms, such as range migration algorithm (RMA). In this paper, according to the geometry configuration of FL-BSAR, in each pulse repetition interval, the slant range was compensated precisely, then through the coordinate rotation, the FL-BSAR is transformed into the equivalent squinted SAR. Using the principal of stationary phase (PSP), the data is transformed into the frequency domain and range migration imaging algorithm (RMA) can be used. Meanwhile the simulation results demonstrated the phase error after compensation can be ignored
MopEye: Opportunistic Monitoring of Per-app Mobile Network Performance

Crowdsourcing mobile user's network performance has become an effective way of understanding and improving mobile network performance and user quality-of-experience. However, the current measurement method is still based on the landline measurement paradigm in which a measurement app measures the path to fixed (measurement or web) servers. In this work, we introduce a new paradigm of measuring per-app mobile network performance. We design and implement Mop-Eye, an Android app to measure network round-trip delay for each app whenever there is app traffic. This opportunistic measurement can be conducted automatically without user intervention. Therefore, it can facilitate a large-scale and long-term crowdsourcing of mobile network performance. In the course of implementing Mop-Eye, we have overcome a suite of challenges to make the continuous latency monitoring lightweight and accurate. We have deployed MopEye to Google Play for an IRB-approved crowdsourcing study in a period of ten months, which obtains over five million measurements from 6,266 Android apps on 2,351 smartphones. The analysis reveals a number of new findings on the per-app network performance and mobile DNS performance.
Changing media representations of youth in the news – a content analysis of Danish newspapers 1953–2003

Media plays an important role in shaping public perceptions of youth. Previous studies have shown consistently negative images of youth in news media through a heavy focus on crime, accidents, and moral decay. Most research in this area has only collected data over short timeframes, which makes it difficult to register possible changes in modes of representation. The present study has sought to overcome this short come by emphasizing long-term data collection, by focusing on how newspapers have portrayed youth in the period 1953–2003. On the basis of quantitative content analyses of Danish newspapers, we find a strong emphasis on crime and accidents; however, culture takes up almost as much space. Furthermore, we cannot confirm a tendency toward increasingly negative media representations regarding young people. Our data show more neutral portrayals and an increase in news items quoting young people.
Word-of-Mouth Processes within a Services Purchase Decision Context

This article investigates the processes of word of mouth (WOM) within a services purchase decision context. The authors argue that to understand these processes, researchers must examine the role of interpersonal influences in the traditional WOM models based within the noninterpersonal paradigm. As a result of the current investigation, three distinct relations emerge: first, the effect of the noninterpersonal forces (receiver’s expertise, receiver’s perceived risk, and sender’s expertise) on the influence of WOM on service purchase decisions; second, the effect of the interpersonal forces (ties strength and how actively WOM is sought) on the influence of WOM on service purchase decisions; and third, the effects of noninterpersonal forces on interpersonal forces. Managerial implications and avenues for future research are addressed.
Platform Envelopment

Due to network effects and switching costs in platform markets, entrants generally must offer revolutionary functionality. We explore a second entry path that does not rely upon Schumpeterian innovation: platform envelopment. Through envelopment, a provider in one platform market can enter another platform market, combining its own functionality with the target’s in a multi-platform bundle that leverages shared user relationships. We build upon the traditional view of bundling for economies of scope and price discrimination and extend this view to include the strategic management of a firm's user network. Envelopers capture share by foreclosing an incumbent’s access to users; in doing so, they harness the network effects that previously had protected the incumbent. We present a typology of envelopment attacks based on whether platform pairs are complements, weak substitutes or functionally unrelated, and we analyze conditions under which these attack types are likely to succeed.
The Effects of Liminality on Individual and Organizational Learning

This article uses an examination of the changing nature of organization in the UK television industry to reflect on the impact of liminality on learning. We take as our starting point Garsten’s (1999) use of the term ‘liminality’ (being situated ‘betwixt and between’) to examine individual and organizational learning in the context of organizational recomposition, where learning increasingly occurs at the limits of organizations within networks and teams that cross organizational divides. Garsten argues that the contractualization of work can be seen to challenge the old boundaries of organization and that it suggests new ways of organizing and experiencing work. By extending liminality to the concept of learning, we suggest that as more industries adopt temporary project teams as a way of organizing work, this not only challenges the concept of organization as an enduring social artefact, but also raises issues about how learning and knowledge development takes place. We examine the effects of liminal episodes on learning, both for organizations and individuals, in a context where the old limits of organization are being redefined while new ways of organizing are throwing up their own learning challenges. We suggest that it is crucial to explore how, in a more transient organizational context arising from the greater use of temporary teams, individualized careers, fashioned out of liminality, impact upon organizational learning.
sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes

Background Bacterial non-coding small RNAs (sRNAs) have attracted considerable attention due to their ubiquitous nature and contribution to numerous cellular processes including survival, adaptation and pathogenesis. Existing computational approaches for identifying bacterial sRNAs demonstrate varying levels of success and there remains considerable room for improvement. Methodology/Principal Findings Here we have proposed a transcriptional signal-based computational method to identify intergenic sRNA transcriptional units (TUs) in completely sequenced bacterial genomes. Our sRNAscanner tool uses position weight matrices derived from experimentally defined E. coli K-12 MG1655 sRNA promoter and rho-independent terminator signals to identify intergenic sRNA TUs through sliding window based genome scans. Analysis of genomes representative of twelve species suggested that sRNAscanner demonstrated equivalent sensitivity to sRNAPredict2, the best performing bioinformatics tool available presently. However, each algorithm yielded substantial numbers of known and uncharacterized hits that were unique to one or the other tool only. sRNAscanner identified 118 novel putative intergenic sRNA genes in Salmonella enterica Typhimurium LT2, none of which were flagged by sRNAPredict2. Candidate sRNA locations were compared with available deep sequencing libraries derived from Hfq-co-immunoprecipitated RNA purified from a second Typhimurium strain (Sittka et al. (2008) PLoS Genetics 4: e1000163). Sixteen potential novel sRNAs computationally predicted and detected in deep sequencing libraries were selected for experimental validation by Northern analysis using total RNA isolated from bacteria grown under eleven different growth conditions. RNA bands of expected sizes were detected in Northern blots for six of the examined candidates. Furthermore, the 5′-ends of these six Northern-supported sRNA candidates were successfully mapped using 5′-RACE analysis. Conclusions/Significance We have developed, computationally examined and experimentally validated the sRNAscanner algorithm. Data derived from this study has successfully identified six novel S. Typhimurium sRNA genes. In addition, the computational specificity analysis we have undertaken suggests that ∼40% of sRNAscanner hits with high cumulative sum of scores represent genuine, undiscovered sRNA genes. Collectively, these data strongly support the utility of sRNAscanner and offer a glimpse of its potential to reveal large numbers of sRNA genes that have to date defied identification. sRNAscanner is available from: http://bicmku.in:8081/sRNAscanner or http://cluster.physics. iisc.ernet. in/sRNAscanner/.
What's in a name? Lexical knowledge drives infants' visual preferences in the absence of referential input

Seventeen-month-old infants were presented with pairs of images, in silence or with the non-directive auditory stimulus ‘look! ’. The images had been chosen so that one image depicted an item whose name was known to the infant, and the other image depicted an image whose name was not known to the infant. Infants looked longer at images for which they had names than at images for which they did not have names, despite the absence of any referential input. The experiment controlled for the familiarity of the objects depicted: in each trial, image pairs presented to infants had previously been judged by caregivers to be of roughly equal familiarity. From a theoretical perspective, the results indicate that objects with names are of intrinsic interest to the infant. The possible causal direction for this linkage is discussed and it is concluded that the results are consistent with Whorfian linguistic determinism, although other construals are possible. From a methodological perspective, the results have implications for the use of preferential looking as an index of early word comprehension.
Gradient domain editing of deforming mesh sequences

Many graphics applications, including computer games and 3D animated films, make heavy use of deforming mesh sequences. In this paper, we generalize gradient domain editing to deforming mesh sequences. Our framework is keyframe based. Given sparse and irregularly distributed constraints at unevenly spaced keyframes, our solution first adjusts the meshes at the keyframes to satisfy these constraints, and then smoothly propagate the constraints and deformations at keyframes to the whole sequence to generate new deforming mesh sequence. To achieve convenient keyframe editing, we have developed an efficient alternating least-squares method. It harnesses the power of subspace deformation and two-pass linear methods to achieve high-quality deformations. We have also developed an effective algorithm to define boundary conditions for all frames using handle trajectory editing. Our deforming mesh editing framework has been successfully applied to a number of editing scenarios with increasing complexity, including footprint editing, path editing, temporal filtering, handle-based deformation mixing, and spacetime morphing.
“When I have a Bad Dream, Mommy Holds Me”: Preschoolers’ Conceptions of Emotions, Parental Socialisation, and Emotional Competence

Described preschoolers’ conceptions of the consequences of their own emotions within the family demonstrated the linkage between this aspect of social cognition and emotional competence with peers, and examined contributions of parental emotion to both child variables. A total of 77 4- and 5-year-olds enacted dollhouse vignettes depicting consequences of their emotions. Parents completed questionnaires on negative emotion and sharing of positive affect, and teachers rated children’s emotional competence with peers. Children attributed plausible parental reactions to their own emotions; affective sharing/distress relief conceptions of parents’ reactions were most strongly associated with emotional competence in the preschool classroom. Socialisation of emotion indices exerted both direct and indirect influences on emotional competence, and conceptions of parents’ positive reactions also exerted a direct effect, as expected.
Comparing Five Sets of Five–Factor Model Personality Disorder Counts in a Heterogeneous Sample of Psychiatric Patients

The research agenda for DSM–5 emphasizes the implementation of dimensional trait models into the classification of personality disorders (PDs). However, because assessment psychologists may still want to recover the traditional DSM–IV categories, researchers developed a count technique that uses sums of selected Five–Factor Model facets to assess the DSM–IV PDs. The presented study examined the convergent and divergent validity of different linear combinations of trait facets to describe specific DSM–IV PDs in a heterogeneous clinical sample (N = 155) with sufficient prevalence of all PDs, using semi–structured interviews to obtain all diagnostic information, and comparing alternative counts from five different sources for each PD. The results show that none of the schizotypal, antisocial, and dependent counts succeeded in combining good convergent with adequate divergent validity. However, the original counts could be optimized for five of the seven remaining PDs by using alternative Five–Factor Model prototypes. The diagnostic and taxonomic implications of these findings are discussed. Copyright © 2012 John Wiley & Sons, Ltd.
Munc13-Independent Vesicle Priming at Mouse Photoreceptor Ribbon Synapses

Munc13 proteins are essential regulators of exocytosis. In hippocampal glutamatergic neurons, the genetic deletion of Munc13s results in the complete loss of primed synaptic vesicles (SVs) in direct contact with the presynaptic active zone membrane, and in a total block of neurotransmitter release. Similarly drastic consequences of Munc13 loss are detectable in hippocampal and striatal GABAergic neurons. We show here that, in the adult mouse retina, the two Munc13-2 splice variants bMunc13-2 and ubMunc13-2 are selectively localized to conventional and ribbon synapses, respectively, and that ubMunc13-2 is the only Munc13 isoform in mature photoreceptor ribbon synapses. Strikingly, the genetic deletion of ubMunc13-2 has little effect on synaptic signaling by photoreceptor ribbon synapses and does not prevent membrane attachment of synaptic vesicles at the photoreceptor ribbon synaptic site. Thus, photoreceptor ribbon synapses and conventional synapses differ fundamentally with regard to their dependence on SV priming proteins of the Munc13 family. Their function is only moderately affected by Munc13 loss, which leads to slight perturbations of signal integration in the retina.