bluuebunny/crossref_metadata_2025_split huggingface dataset:
A decoupled non-SSA global register allocation using bipartite liveness graphs
Authors: Barik Rajkishore , Zhao Jisheng , Sarkar Vivek 
Published: January 2014

Register allocation is an essential optimization for all compilers. A number of sophisticated register allocation algorithms have been developed over the years. The two fundamental classes of register allocation algorithms used in modern compilers are based on Graph Coloring (GC) and Linear Scan (LS). However, these two algorithms have fundamental limitations in terms of precision. For example, the key data structure used in GC-based algorithms, the interference graph, lacks information on the program points at which two variables may interfere. The LS-based algorithms make local decisions regarding spilling, and thereby trade off global optimization for reduced compile-time and space overheads. Recently, researchers have proposed Static Single Assignment (SSA)-based decoupled register allocation algorithms that exploit the live-range split points of the SSA representation to optimally solve the spilling problem. However, SSA-based register allocation often requires extra complexity in repairing register assignments during SSA elimination and in addressing architectural constraints such as aliasing and ABI encoding; this extra overhead can be prohibitively expensive in dynamic compilation contexts.
This article proposes a decoupled non-SSA--based global register allocation algorithm for dynamic compilation. It addresses the limitations in current algorithms by introducing a Bipartite Liveness Graph (BLG)-based register allocation algorithm that models the spilling phase as an optimization problem on the BLG itself and the assignment phase as a separate optimization problem. Advanced register allocation optimizations such as move coalescing, live-range splitting, and register class handling are also performed along with the spilling and assignment phases. In the presence of register classes, we propose a bucket-based greedy heuristic for assignment that strikes a balance between spill-cost and register class constraints. We present experimental evaluation of our BLG-based register allocation algorithm and compare it with production-quality register allocators in Jikes RVM and LLVM.
Neural Substrates of Social Status Inference: Roles of Medial Prefrontal Cortex and Superior Temporal Sulcus
Authors: Mason Malia , Magee Joe C. , Fiske Susan T. 
Published: January 2014

Abstract
The negotiation of social order is intimately connected to the capacity to infer and track status relationships. Despite the foundational role of status in social cognition, we know little about how the brain constructs status from social interactions that display it. Although emerging cognitive neuroscience reveals that status judgments depend on the intraparietal sulcus, a brain region that supports the comparison of targets along a quantitative continuum, we present evidence that status judgments do not necessarily reduce to ranking targets along a quantitative continuum. The process of judging status also fits a social interdependence analysis. Consistent with third-party perceivers judging status by inferring whose goals are dictating the terms of the interaction and who is subordinating their desires to whom, status judgments were associated with increased recruitment of medial pFC and STS, brain regions implicated in mental state inference.
Quantitative Characterization of Functional Anatomical Contributions to Cognitive Control under Uncertainty
Authors: Fan Jin , Van Dam Nicholas T. , Gu Xiaosi , Liu Xun , Wang Hongbin , Tang Cheuk Y. , Hof Patrick R. 
Published: January 2014

Abstract
Although much evidence indicates that RT increases as a function of computational load in many cognitive tasks, quantification of changes in neural activity related to increasing demand of cognitive control has rarely been attempted. In this fMRI study, we used a majority function task to quantify the effect of computational load on brain activation, reflecting the mental processes instantiated by cognitive control under conditions of uncertainty. We found that the activation of the frontoparieto-cingulate system as well as the deactivation of the anticorrelated default mode network varied parametrically as a function of information uncertainty, estimated as entropy with an information theoretic model. The current findings suggest that activity changes in the dynamic networks of the brain (especially the frontoparieto-cingulate system) track with information uncertainty, rather than only conflict or other commonly proposed targets of cognitive control.
Distributed and Dynamic Storage of Working Memory Stimulus Information in Extrastriate Cortex
Authors: Sreenivasan Kartik K. , Vytlacil Jason , D'Esposito Mark 
Published: January 2014

Abstract
The predominant neurobiological model of working memory (WM) posits that stimulus information is stored via stable, elevated activity within highly selective neurons. On the basis of this model, which we refer to as the canonical model, the storage of stimulus information is largely associated with lateral PFC (lPFC). A growing number of studies describe results that cannot be fully explained by the canonical model, suggesting that it is in need of revision. In this study, we directly tested key elements of the canonical model. We analyzed fMRI data collected as participants performed a task requiring WM for faces and scenes. Multivariate decoding procedures identified patterns of activity containing information about the items maintained in WM (faces, scenes, or both). Although information about WM items was identified in extrastriate visual cortex (EC) and lPFC, only EC exhibited a pattern of results consistent with a sensory representation. Information in both regions persisted even in the absence of elevated activity, suggesting that elevated population activity may not represent the storage of information in WM. Additionally, we observed that WM information was distributed across EC neural populations that exhibited a broad range of selectivity for the WM items rather than restricted to highly selective EC populations. Finally, we determined that activity patterns coding for WM information were not stable, but instead varied over the course of a trial, indicating that the neural code for WM information is dynamic rather than static. Together, these findings challenge the canonical model of WM.
The Timing and Neuroanatomy of Conscious Vision as Revealed by TMS-induced Blindsight
Authors: Allen Christopher P. G. , Sumner Petroc , Chambers Christopher D. 
Published: January 2014

Abstract
Following damage to the primary visual cortex, some patients exhibit “blindsight,” where they report a loss of awareness while retaining the ability to discriminate visual stimuli above chance. Transient disruption of occipital regions with TMS can produce a similar dissociation, known as TMS-induced blindsight. The neural basis of this residual vision is controversial, with some studies attributing it to the retinotectal pathway via the superior colliculus whereas others implicate spared projections that originate predominantly from the LGN. Here we contrasted these accounts by combining TMS with visual stimuli that either activate or bypass the retinotectal and magnocellular (R/M) pathways. We found that the residual capacity of TMS-induced blindsight occurs for stimuli that bypass the R/M pathways, indicating that such pathways, which include those to the superior colliculus, are not critical. We also found that the modulation of conscious vision was time and pathway dependent. TMS applied either early (0–40 msec) or late (280–320 msec) after stimulus onset modulated detection of stimuli that did not bypass R/M pathways, whereas during an intermediate period (90–130 msec) the effect was pathway independent. Our findings thus suggest a prominent role for the R/M pathways in supporting both the preparatory and later stages of conscious vision. This may help resolve apparent conflict in previous literature by demonstrating that the roles of the retinotectal and geniculate pathways are likely to be more nuanced than simply corresponding to the unconscious/conscious dichotomy.
Producing Speech with a Newly Learned Morphosyntax and Vocabulary: An Magnetoencephalography Study
Authors: Hultén Annika , Karvonen Leena , Laine Matti , Salmelin Riitta 
Published: January 2014

Abstract
Ten participants learned a miniature language (Anigram), which they later employed to verbally describe a pictured event. Using magnetoencephalography, the cortical dynamics of sentence production in Anigram was compared with that in the native tongue from the preparation phase up to the production of the final word. At the preparation phase, a cartoon image with two animals prompted the participants to plan either the corresponding simple sentence (e.g., “the bear hits the lion”) or a grammar-free list of the two nouns (“the bear, the lion”). For the newly learned language, this stage induced stronger left angular and adjacent inferior parietal activations than for the native language, likely reflecting a higher load on lexical retrieval and STM storage. The preparation phase was followed by a cloze task where the participants were prompted to produce the last word of the sentence or word sequence. Production of the sentence-final word required retrieval of rule-based inflectional morphology and was accompanied by increased activation of the left middle superior temporal cortex that did not differ between the two languages. Activation of the right temporal cortex during the cloze task suggested that this area plays a role in integrating word meanings into the sentence frame. The present results indicate that, after just a few days of exposure, the newly learned language harnesses the neural resources for multiword production much the same way as the native tongue and that the left and right temporal cortices seem to have functionally different roles in this processing.
Action Sentences Activate Sensory Motor Regions in the Brain Independently of Their Status of Reality
Authors: de Vega Manuel , León Inmaculada , Hernández Juan A. , Valdés Mitchell , Padrón Iván , Ferstl Evelyn C. 
Published: January 2014

Abstract
Some studies have reported that understanding concrete action-related words and sentences elicits activations of motor areas in the brain. The present fMRI study goes one step further by testing whether this is also the case for comprehension of nonfactual statements. Three linguistic structures were used (factuals, counterfactuals, and negations), referring either to actions or, as a control condition, to visual events. The results showed that action sentences elicited stronger activations than visual sentences in the SMA, extending to the primary motor area, as well as in regions generally associated with the planning and understanding of actions (left superior temporal gyrus, left and right supramarginal gyri). Also, we found stronger activations for action sentences than for visual sentences in the extrastriate body area, a region involved in the visual processing of human body movements. These action-related effects occurred not only in factuals but also in negations and counterfactuals, suggesting that brain regions involved in action understanding and planning are activated by default even when the actions are described as hypothetical or as not happening. Moreover, some of these regions overlapped with those activated during the observation of action videos, indicating that the act of understanding action language and that of observing real actions share neural networks. These results support the claim that embodied representations of linguistic meaning are important even in abstract linguistic contexts.
Neural Systems Underlying the Reappraisal of Personally Craved Foods
Authors: Giuliani Nicole R. , Mann Traci , Tomiyama A. Janet , Berkman Elliot T. 
Published: January 2014

Abstract
Craving of unhealthy food is a common target of self-regulation, but the neural systems underlying this process are understudied. In this study, participants used cognitive reappraisal to regulate their desire to consume idiosyncratically craved or not craved energy-dense foods, and neural activity during regulation was compared with each other and with the activity during passive viewing of energy-dense foods. Regulation of both food types elicited activation in classic top–down self-regulation regions including the dorsolateral prefrontal, inferior frontal, and dorsal anterior cingulate cortices. This main effect of regulation was qualified by an interaction, such that activation in these regions was significantly greater during reappraisal of craved (versus not craved) foods and several regions, including the dorsolateral prefrontal, inferior frontal, medial frontal, and dorsal anterior cingulate cortices, were uniquely active during regulation of personally craved foods. Body mass index significantly negatively correlated with regulation-related activation in the right dorsolateral PFC, thalamus, and bilateral dorsal ACC and with activity in nucleus accumbens during passive viewing of craved (vs. neutral, low-energy density) foods. These results suggest that several of the brain regions involved in the self-regulation of food craving are similar to other kinds of affective self-regulation and that others are sensitive to the self-relevance of the regulation target.
Genomic, regulatory and epigenetic mechanisms underlying duplicated gene evolution in the natural allotetraploid Oryza minuta
Authors: Sui Yi , Li Bo , Shi Jinfeng , Chen Mingsheng 
Published: January 2014

Abstract

Background
Polyploid species contribute to Oryza diversity. However, the mechanisms underlying gene and genome evolution in Oryza polyploids remain largely unknown. The allotetraploid Oryza minuta, which is estimated to have formed less than one million years ago, along with its putative diploid progenitors (O. punctata and O. officinalis), are quite suitable for the study of polyploid genome evolution using a comparative genomics approach.

Results
Here, we performed a comparative study of a large genomic region surrounding the Shattering4 locus in O. minuta, as well as in O. punctata and O. officinalis. Duplicated genomes in O. minuta have maintained the diploid genome organization, except for several structural variations mediated by transposon movement. Tandem duplicated gene clusters are prevalent in the Sh4 region, and segmental duplication followed by random deletion is illustrated to explain the gene gain-and-loss process. Both copies of most duplicated genes still persist in O. minuta. Molecular evolution analysis suggested that these duplicated genes are equally evolved and mostly manipulated by purifying selection. However, cDNA-SSCP analysis revealed that the expression patterns were dramatically altered between duplicated genes: nine of 29 duplicated genes exhibited expression divergence in O. minuta. We further detected one gene silencing event that was attributed to gene structural variation, but most gene silencing could not be related to sequence changes. We identified one case in which DNA methylation differences within promoter regions that were associated with the insertion of one hAT element were probably responsible for gene silencing, suggesting a potential epigenetic gene silencing pathway triggered by TE movement.

Conclusions
Our study revealed both genetic and epigenetic mechanisms involved in duplicated gene silencing in the allotetraploid O. minuta.
Polyploidy and the petal transcriptome of Gossypium
Authors: Rambani Aditi , Page Justin T , Udall Joshua A 
Published: January 2014

Abstract

Background
Genes duplicated by polyploidy (homoeologs) may be differentially expressed in plant tissues. Recent research using DNA microarrays and RNAseq data have described a cacophony of complex expression patterns during development of cotton fibers, petals, and leaves. Because of its highly canalized development, petal tissue has been used as a model tissue for gene expression in cotton. Recent advances in cotton genome annotation and assembly now permit an enhanced analysis of duplicate gene deployment in petals from allopolyploid cotton.

Results
Homoeologous gene expression levels were quantified in diploid and tetraploid flower petals of Gossypium using the Gossypium raimondii genome sequence as a reference. In the polyploid, most homoeologous genes were expressed at equal levels, though a subset had an expression bias of AT and DT copies. The direction of gene expression bias was conserved in natural and recent polyploids of cotton. Conservation of direction of bias and additional comparisons between the diploids and tetraploids suggested different regulation mechanisms of gene expression. We described three phases in the evolution of cotton genomes that contribute to gene expression in the polyploid nucleus.

Conclusions
Compared to previous studies, a surprising level of expression homeostasis was observed in the expression patterns of polyploid genomes. Conserved expression bias in polyploid petals may have resulted from cis-acting modifications that occurred prior to polyploidization. Some duplicated genes were intriguing exceptions to general trends. Mechanisms of gene regulation for these and other genes in the cotton genome warrants further investigation.
Factors affecting quantity of pollen dispersal of spray cut chrysanthemum (Chrysanthemum morifolium)
Authors: Wang Xiao-Guang , Wang Hai-Bin , Chen Fa-Di , Jiang Jia-Fu , Fang Wei-Min , Liao Yuan , Teng Nian-Jun 
Published: January 2014

Abstract

Background
Spray cut chrysanthemum is a vital flower with high ornamental value and popularity in the world. However, the excessive quantity of pollen dispersal of most spray cut chrysanthemum is an adverse factor during its flowering stage, and can significantly reduce its ornamental value and quickly shorten its vase life. More seriously, excessive pollen grains in the air are usually harmful to people, especially for those with pollen allergies. Therefore, in order to obtain some valuable information for developing spray cut chrysanthemum with less-dispersed or non-dispersed pollen in the future breeding programs, we here investigated the factors affecting quantity of pollen dispersal of spray cut chrysanthemum with four cultivars, i.e. ‘Qx-097’, ‘Noa’, ‘Qx-115’, and ‘Kingfisher’, that have different quantity of pollen dispersal.

Results
‘Qx-097’ with high quantity of pollen dispersal has 819 pollen grains per anther, 196.4 disk florets per inflorescence and over 800,000 pollen grains per inflorescence. The corresponding data for ‘Noa’ with low quantity of pollen dispersal are 406, 175.4 and over 350,000, respectively; and 219, 144.2 and nearly 160,000 for ‘Qx-115’ without pollen dispersal, respectively. ‘Kingfisher’ without pollen dispersal has 202.8 disk florets per inflorescence, but its anther has no pollen grains. In addition, ‘Qx-097’ has a very high degree of anther cracking that nearly causes a complete dispersal of pollen grains from its anthers. ‘Noa’ has a moderate degree of anther cracking, and pollen grains in its anthers are not completely dispersed. However, the anthers of ‘Qx-115’ and ‘Kingfisher’ do not crack at all. Furthermore, microsporogenesis and pollen development are normal in ‘Qx-097’, whereas many microspores or pollen degenerate in ‘Noa’, most of them abort in ‘Qx-115’, and all of them degrade in ‘Kingfisher’.

Conclusions
These results suggest that quantity of pollen dispersal in spray cut chrysanthemum are mainly determined by pollen quantity per anther, and capacity of pollen dispersal. Abnormality during microsporogenesis and pollen development significantly affects pollen quantity per anther. Capacity of pollen dispersal is closely related to the degree of anther dehiscence. The entire degeneration of microspore or pollen, or the complete failure of anther dehiscence can cause the complete failure of pollen dispersal.
Laser in situ keratomileusis for astigmatism ≤ 0.75 Diopter combined with low myopia: a retrospective data analysis
Authors: Katz Toam , Frings Andreas , Linke Stephan J , Richard Gisbert , Druchkiv Vasyl , Steinberg Johannes 
Published: January 2014

Abstract

Background
This study examined the refractive and visual outcome of wavefront-optimized laser in situ keratomileusis (LASIK) in eyes with low myopia and compound myopic astigmatism ≤ 0.75 diopter (D).

Methods
153 eyes from 153 consecutive myopic patients (74 male, 79 female; mean age at surgery 40.4 ± 10.4 years) who had a preoperative refractive cylinder ≤ 0.75 D and a manifest sphere between -0.25 D and -2.75 D, and who had completed 4-month follow-up. Three subgroups defined by the magnitude of preoperative manifest refractive cylinder (0.25, 0.50, and 0.75 D) were formed. Manifest refraction, uncorrected and corrected visual acuity were assessed pre- and postoperatively. The astigmatic changes achieved were determined using the Alpins vector analysis.

Results
After 4 months (120.0 ± 27.6 days) of follow-up, a mean uncorrected distant visual acuity of 0.07 ± 0.11 logMAR and a mean manifest refraction spherical equivalent of -0.06 ± 0.56 D were found. There was no statistically significant difference in efficacy and safety between the preoperative cylinder groups. Astigmatic overcorrection for preoperative cylinder of ≤ 0.50 D was suggested by the correction index, the magnitude of error, the index of success, and the flattening index.

Conclusions
Low myopic eyes with a preoperative cylinder of ≤ 0.50 D were significantly overcorrected with regard to cylinder correction when combined with low myopic LASIK. Accordingly, we are cautious in recommending full astigmatic correction for eyes with low myopia and manifest cylinder of ≤ 0.50 D.
A rare thyroid hormone receptor beta (THRβ) gene mutation in a 15-year-old girl with thyroid hormone resistance syndrome: a case report
Authors: El Shafie Kawther , Ouhtit Allal , Al Farsi Yousuf , Al Sayegh Abeer , Al Shafaee Mohammed 
Published: January 2014

Abstract

Introduction
Resistance to thyroid hormone is a rare syndrome, where although the level of thyroid hormone is elevated, the level of thyroid stimulating hormone is not suppressed. The patient in our case report is, to the best of our knowledge, the first with this syndrome identified in Oman.

Case presentation
In one Omani family, a 15-year-old girl of Arabian origin was pre-diagnosed with resistance to thyroid hormone. Blood sample was collected and deoxyribonucleic acid was isolated for molecular genetic testing. The results revealed a rare mutation A268G in the gene for thyroid hormone receptor beta. We believe that this mutation is the cause of the pathology in our patient.

Conclusion
We report the presence of a rare mutation in the thyroid hormone receptor beta gene for the first time in the Omani population. Due to the rates of consanguinity being high among the Omani population, we are aiming to screen our patient’s family members and provide genetic counseling.