Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosphorylation of Arabidopsis transketolase at Ser428 provides a potential paradigm for the metabolic control of chloroplast carbon metabolism

Calcium is an important second messenger in eukaryotic cells that regulates many different cellular processes. To elucidate calcium regulation in chloroplasts, we identified the targets of calcium-dependent phosphorylation within the stromal proteome. A 73 kDa protein was identified as one of the most dominant proteins undergoing phosphorylation in a calcium-dependent manner in the stromal extracts of both Arabidopsis and Pisum. It was identified as TKL (transketolase), an essential enzyme of both the Calvin–Benson–Bassham cycle and the oxidative pentose phosphate pathway. Calcium-dependent phosphorylation of both Arabidopsis isoforms (AtTKL1 and AtTKL2) could be confirmed in vitro using recombinant proteins. The phosphorylation is catalysed by a stroma-localized protein kinase, which cannot utilize GTP. Phosphorylation of AtTKL1, the dominant isoform in most tissues, occurs at a serine residue that is conserved in TKLs of vascular plants. By contrast, an aspartate residue is present in this position in cyanobacteria, algae and mosses. Characterization of a phosphomimetic mutant (S428D) indicated that Ser428 phosphorylation exerts significant effects on the enzyme's substrate saturation kinetics at specific physiological pH values. The results of the present study point to a role for TKL phosphorylation in the regulation of carbon allocation.
A Beacon System for the Localization of Distributed Robotic Teams

This paper presents the design of a localization system for a team of centimeter-scale robots that collaborate to map and explore unknown environments. The localization system uses ultrasound to measure the distance from each moving robot to three stationary robots that serve as beacons. From these distance measurements the position of the robots is derived using a trilateration algorithm. The robot team can move over large distances by using a leap-frogging approach in which different robots serve as beacons at different times. The localization system is able to obtain position estimates more accurate than can be achieved through dead reckoning, and yet, does not require any landmarks or previously deployed beacons.
Relative Placement in Child Protection Cases: A Judicial Perspective

Child welfare agencies and courts place thousands of children in out-of-home care every year. This paper examines whether the state should give relatives preference over non-relatives when placing children—and, if so, how to accomplish that goal. In the 1980s, state and federal government policies shifted toward favoring relatives (so-called “kinship care”), but significant problems arise when delays occur in implementing these policies. For example, relatives do not always know that child protection proceedings are pending, and delays in the child protection and court systems often exclude them from consideration for placement even when they have notice. When relatives request placement long after a child has entered foster care, child welfare agencies and courts struggle with the competing placement interests of relatives, foster parents, and the child. To implement relative preference policies effectively, child protection agencies and courts must modify their practices and procedures. The stakes are high because placement will have a lifelong impact on the families involved and, most significantly, on the child. Section II briefly describes child placement history in the United States. The third section addresses the emergence of relative preference as a goal within the child protection system. This discussion includes reasons why policy makers prefer relative placements to non-relative placements, and when and why states and the federal government began passing legislation reinforcing this preference. The fourth section examines the
Visualizing a Personal Timeline By Adding Multiple Social Contexts

We improve the readability of a personal timeline byweaving multiple social contexts of tweets into a visualization.Our social contexts consist of three dimensions:community membership, key persons, and interestingtweets within a personal timeline. A person is oftena member of several communities, such as a family,a class, or a team, simultaneously. We identify all communitiesthat a user participates in. Labeling a tweetwith a visual representation to indicate what communityit belongs to can help readers to understand why thetweet is written, since different communities are likelyto carry tweets in different contexts. We then discoverkey persons and interesting tweets within a personaltimeline. Our prototype design demonstrates how threesocial contexts work together for visualizing a personaltimeline.
New insights into the nuclear localization of retroviral gag proteins

Retroviruses assemble new virus particles that are released by budding from the plasma membranes of infected cells. Gag proteins, encoded by retroviruses, orchestrate the assembly of virus particles in close collaboration with host cell machinery. The earliest steps in retrovirus assembly—those immediately following synthesis of Gag on cytosolic ribosomes—are poorly understood. Rous sarcoma virus (RSV) offers a unique model system for dissecting these early steps because the RSV Gag protein undergoes transient nuclear trafficking prior to plasma membrane transport. Other Gag proteins, including those of human immunodeficiency virus (HIV), murine leukemia virus (MLV), foamy virus, and retrotransposons in Schizosaccharomyces pombe and Drosophila, have also been detected in the nucleus, suggesting that nuclear trafficking of Gag proteins is a common property of retroviruses and retrotransposons. In addition to retroviruses, many structural proteins of unrelated viruses, including influenza M1, NEP and NP proteins, Borna disease virus N and P proteins and coronavirus N protein, undergo nuclear localization and bind viral RNAs to form viral ribonuclear protein (RNP) complexes that are exported from the nucleus for packaging into virus particles. Similarly, nuclear trafficking of the RSV Gag protein is required for efficient encapsidation of the viral genomic RNA (gRNA) into assembling virus particles. Recently, we reported that the viral RNA itself appears to be a key factor in controlling the nucleus/cytosol distribution of RSV Gag. Our data demonstrate that binding of RSV RNA to the Gag protein promotes Gag-CRM1-RanGTP binding, resulting in export of the retroviral RNP from the nucleus. We propose that association of the viral RNA induces a conformational change in Gag that reveals its nuclear export signal (NES) and prepares that complex for its journey to the plasma membrane for budding. This work challenges existing dogmas regarding the molecular basis of Gag-mediated selection of gRNA for packaging and may lead to novel paradigms for the mechanism of retroviral genome encapsidation.
Differentiation mechanisms for IEEE 802.11

The IETF is currently working on service differentiation in the Internet. However, in wireless environments where bandwidth is scarce and channel conditions are variable, IP differentiated services are sub-optimal without lower layers' support. We present three service differentiation schemes for IEEE 802.11. The first one is based on scaling the contention window according to the priority of each flow or user. The second one assigns different inter-frame spacings to different users. Finally, the last one uses different maximum frame lengths for different users. We simulate and analyze the performance of each scheme with TCP and UDP flows.
Encoding Featherweight Java with assignment and immutability using the Coq proof assistant

We develop a mechanized proof of Featherweight Java with Assignment and Immutability in the Coq proof assistant. This is a step towards more machine-checked proofs of a non-trivial type system. We used object immutability close to that of IGJ [9]. We describe the challenges of the mechanisation and the encoding we used inside of Coq.
Structural basis for the reversible activation of a Rho protein by the bacterial toxin SopE

The bacterial enteropathogen Salmonella typhimurium employs a type III secretion system to inject bacterial toxins into the host cell cytosol. These toxins transiently activate Rho family GTP‐binding protein‐dependent signaling cascades to induce cytoskeletal rearrangements. One of these translocated Salmonella toxins, SopE, can activate Cdc42 in a Dbl‐like fashion despite its lack of sequence similarity to Dbl‐like proteins, the Rho‐specific eukaryotic guanine nucleotide exchange factors. To elucidate the mechanism of SopE‐mediated guanine nucleotide exchange, we have analyzed the structure of the complex between a catalytic fragment of SopE and Cdc42. SopE binds to and locks the switch I and switch II regions of Cdc42 in a conformation that promotes guanine nucleotide release. This conformation is strikingly similar to that of Rac1 in complex with the eukaryotic Dbl‐like exchange factor Tiam1. However, the catalytic domain of SopE has an entirely different architecture from that of Tiam1 and interacts with the switch regions via different amino acids. Therefore, SopE represents the first example of a non‐Dbl‐like protein capable of inducing guanine nucleotide exchange in Rho family proteins.
On the role of informed search in veristic computing

Veristic computing is defined as computing with words. It necessarily entails the use of informed search in the solution of qualitatively constrained equations. Its use does not preclude computing with numbers. Veristic computing allows for the specification of higher-level programming languages, which can evolve domain-specific knowledge bases. The knowledge is evolved on a high-end computer for subsequent porting to a PC. The application of that knowledge to the translation of a higher-level program is termed expert compilation. This paper serves to clarify the ubiquitous role assumed by randomization in all aspects of software engineering-from programming language design to program design to program testing to knowledge transference.
Full-Chip Veri cation Methods for DSM Power Distribution Systems

Power distribution veri cation is rapidly becoming a necessary step in deep submicron (DSM) design of high performance integrated circuits. With the increased load and reduced tolerances of DSM circuits, more failures are being seen due to poorly designed power distribution systems. This paper describes an e cient approach for the veri cation of power distribution at the full-chip transistor level based on a combination of hierarchical static and dynamic techniques. Application of the methodology on practical design examples will be provided. We will also demonstrate the necessity of an analysis at the full-chip transistor level to verify the complex interactions between di erent design blocks based on static and dynamic e ects.
Representation of cognitive processes using the minimum spanning tree of local meshes

A new graphical model called Cognitive Process Graph (CPG) is proposed, for classifying cognitive processes based on neural activation patterns which are acquired via functional Magnetic Resonance Imaging (fMRI) in brain. In the CPG, first local meshes are formed around each voxel. Second, the relationships between a voxel and its neighbors in a local mesh, which are estimated by using a linear regression model, are used to form the edges among the voxels (graph nodes) in the CPG. Then, a minimum spanning tree (MST) of the CPG which spans all the voxels in the region of interest is computed. The arc weights of the MST are used to represent the underlying cognitive processes. The proposed method reduces the curse of dimensionality problem that is caused by very large dimension of the feature space of the fMRI measurements, compared to number of instances. Finally, the arc weights computed over the path of the MST called MST-Features (MST-F) are used to train a statistical learning machine. The proposed method is tested on a recognition memory experiment, including data pertaining to encoding and retrieval of words belonging to ten different semantic categories. Two popular classifiers, namely k-Nearest Neighbor (k-NN) and Support Vector Machine (SVM), are trained in order to predict the semantic category of the item being retrieved, based on activation patterns during encoding. The classification performance of the proposed learning model is superior to the classical multi-voxel pattern analysis (MVPA) methods for the underlying cognitive process.
A Survey of Query Expansion until June 2012

Here we present a survey of important work done on Query Expansion (QE) between the period 1970 to 2012. Queries formed by search engine users, are generally short and vague. It is very dicult to estimate the exact user need. Sometimes, the queries are well formed and clear, but the document collection does not contain the information in the same form as that of the query. Synonymous terms or related terms are present in the collection. Query expansion adds terms to the original query, which provides more information about the user need. There are various approaches to query expansion. Some of them use lexical resources or dictionaries for query expansion. Lexical methods cause more damage through topic drift. Relevance feedback approaches perform better than lexical approaches, but they depend on the performance of initial retrieval. In recent years Wikipedia is being used as an external knowledge source for QE. In this survey we cover important work done using all these approaches.
Moving Object Detection in Spatial Domain using Background Removal Techniques - State-of-Art

Identifying moving objects is a critical task for many computer vision applications; it provides a classification of the pixels into either foreground or background. A common approach used to achieve such classification is background removal. Even though there exist numerous of background removal algorithms in the literature, most of them follow a simple flow diagram, passing through four major steps, which are pre-processing, background modelling, foreground de- tection and data validation. In this paper, we survey many existing schemes in the literature of background removal, sur- veying the common pre-processing algorithms used in different situations, presenting different background models, and the most commonly used ways to update such models and how they can be initialized. We also survey how to measure the performance of any moving object detection algorithm, whether the ground truth data is available or not, presenting per- formance metrics commonly used in both cases.
FMRI studies of effects of hearing status on audio-visual speech perception

The overall goal of this research is to acquire a more complete picture of the neurological processes of visual influences on speech perception and to investigate effects of hearing status on AV speech perception. More specifically, functional magnetic resonance imaging (fMRI) was used to investigate the brain activity underlying audio-visual speech perception in three groups of subjects: (1) normally hearing, (2) congenitally deafened signers (American Sign Language) who do not use hearing aids, and (3) congenitally hearing impaired individuals with hearing aids. FMRI data were collected while subjects experienced three different types of speech stimuli: video of a speaking face with audio input, audio speech without visual input, and video of a speaking face without audio input. The cortical areas found to be active for speechreading included: visual cortex, auditory cortex (but not primary auditory cortex), speech motor network areas, supramarginal gyrus, thalamus, superior parietal cortex and fusiform gyrus. For hearing impaired subjects, in addition to the areas listed above, Heschl's gyrus, right angular gyrus (AG), cerebellum and regions around right inferior frontal sulcus (IFS) in the frontal lobe were also found to be active. Results from our study added to existing evidence of the engagement of motor-articulatory strategies in visual speech perception. We also found that an individual's speechreading ability is related to the amount of activity in superior temporal cortical areas, including primary auditory cortex, preSMA, IFS and right AG during visual speech perception. Results from effective connectivity analyses suggest that posterior superior temporal sulcus may be a potential AV speech integration site; and that AG serves a critical role in visual speech perception when auditory information is absent for hearing subjects, and when auditory information is available for hearing impaired subjects. Also, strong excitatory projections from STS to inferior frontal gyrus (IFG) and premotor/motor areas, and a strong inhibitory projection from IFG to STS seem to play an important role in visual speech perception in all subject groups. Finally, correlation analyses revealed that in hearing aid users, the amount of acoustic and speech signal gained by using hearing aids were significantly correlated with activity in IFG. Thesis Supervisor: Frank H. Guenther Title: Associate Professor
Environmental enhancement of loose groups around rich clusters of galaxies

We have studied the properties of Las Campanas Loose Groups (Tucker et al. 2000) in the neighbourhood of rich (Abell, APM and X-ray) clusters of galaxies. These loose groups show strong evidence of segregation measured in terms of the group richness and the group velocity dispersion: loose groups in the neighbourhood of a rich cluster are typically 2.5 times more massive and 1.6 times more luminous than groups on average, and these loose groups have velocity dispersions 1.3 times larger than groups on average. This is evidence that the large-scale gravitational field causing the formation of rich clusters enhances the evolution of neighbouring poor systems, a phenomenon recently established in numerical simulations of group and cluster formation.
Does return to work occur earlier after work-related sick leave episodes than after non-work-related sick leave episodes? A retrospective cohort study in Spain

Objective: In Spain, sick pay benefits for work-related sick leave episodes are higher than for non-work-related episodes. Our aim is to assess whether time to return to work is longer for higher paid sick leave episodes than for lower paid episodes. Methods: We used data from 62 376 work-related and 76 932 non-work-related sick leave episodes occurring among 338 226 workers from 56 099 companies in Spain in 2002. All episodes were followed for up to 18 months. Episodes were classified by a physician as being work- or non-work-related according to medico-legal judgments. The median episode duration and the 25th and 75th percentiles were calculated. The probability of remaining absent from work was estimated by a non-parametric estimator of the marginal survival function. The time ratio between both types of sick leave was estimated by a log-logistic regression model, using non-work-related episodes as the reference. Results: Median episode duration (25th–75th percentiles) was 11 (6–21) days for work-related episodes and 9 (4–29) days for non-work-related episodes. Time to return to work was longer for work-related episodes than for non-work-related episodes of less than 16 days (time ratio: 1.19 in men and 1.08 in women), while the opposite was observed for episodes of more than 15 days (0.58 in men and 0.40 in women). Conclusions: Sick pay benefits have a limited effect on time to return to work after a sick leave episode.
An Evaluation of Individually Delivered Secret Agent Society Social Skills Program for Children with High-Functioning Autism Spectrum Disorders: A Pilot Study

High-functioning children with autism spectrum disorders display social skill deficits that can have a debilitating impact on their daily lives. The Secret Agent Society (SAS) program has been shown to be effective in improving the social skills of these children when delivered in a group setting. This pilot study evaluated whether individually delivered SAS would yield similar outcomes. Three participants were recruited for the 9-week intervention. Measures of social competence were administered at four points: pretest 1, pretest 2, post-intervention, and 6-week follow-up. Participants showed significant improvement in half of the measures assessing social competence. On a third of these measures, two participants demonstrated improvements to within the range of their typically developing peers. Follow-up results suggested that improvements were maintained at 6 weeks’ post-intervention. Limitations of this study and directions for future research are discussed.
Flanking sequences influence the presentation of an endogenously synthesized peptide to cytotoxic T lymphocytes

Cytotoxic T lymphocytes (CTL) recognize class I major histocompatibility complex molecules complexed to peptides of eight to nine residues generated from cytosolic proteins. We find that CTL recognize, in vitro and in vivo, cells synthesizing a 10-residue peptide consisting of an initiating methionine followed by nine residues corresponding to a naturally processed determinant from influenza virus nucleoprotein (NP) (residues 147-155). Addition of two COOH-terminal residues corresponding to NP residues 157 and 158 severely reduced presentation of the endogenously produced peptide to CTL in vitro and in vivo. Extension of NH2 and COOH terminal flanking residues to include residues corresponding to NP residues 137-146 and 159-168 failed to increase the antigenicity of this peptide. Its presentation was greatly enhanced, however, by further extending the NH2 and COOH termini to include all of the additional residues of NP. These findings indicate first, that a naturally processed viral ligand (with an NH2-terminal Met) of a class I molecule contains sufficient information to access intracellular class I molecules, and second, that flanking residues can influence the processing and presentation of antigens to CTL.
A 40-bp RNA Element That Mediates Stabilization of Vascular Endothelial Growth Factor mRNA by HuR*

VEGF is a critical mediator of hypoxia-induced angiogenesis in numerous physiological and pathophysiological conditions. The hypoxic induction of VEGF is due in large part to an increase in the stability of its mRNA. We recently demonstrated that the stabilization of VEGF mRNA by hypoxia is dependent upon the RNA-binding protein HuR. This report describes the identification of a 40-bp functional HuR binding site in the VEGF mRNA 3′-untranslated region. This element can confer HuR-mediated stabilization of a heterologous gene in vitroand in vivo. Furthermore, the element is sufficient to confer an increase in the hypoxic induction of a heterologous gene. Deletion of the HuR binding site within this 40-bp element as mapped by RNase T1 and lead footprinting uncouples a stabilizing sequence from a destabilizing sequence, thus providing a novel RNA-protein regulatory model that might be exploited to manipulate VEGF expression and hypoxia-induced angiogenesis.
To Resolve or Not to Resolve

Abstract Trauma workers may be at risk of secondary traumatic stress (STS) through indirect exposure to traumatic material, especially if they have experienced personal trauma. This is the first study to ask whether past trauma resolution influences STS and was examined in 64 volunteer crisis workers, a greatly ignored population. Those with non-resolved personal trauma had higher scores on an STS measure than volunteers whose trauma histories were resolved, while the latter showed less STS than the sample as a whole. STS was unrelated to volunteer experience, exposure to victims, or the type of cases found most distressing, indicating that accepted STS risk factors may not apply to volunteers. Findings have resounding implications for the popular view of trauma history as an STS risk factor: this may double as both a significant peril and a protection, depending on whether the past trauma is resolved.