Miracle-dz/UniFAR-FTUs huggingface dataset:
A framework for interprocedural optimization in the presence of dynamic class loading

Dynamic class loading during program execution in the Java Programming Language is an impediment for generating code that is as efficient as code generated using static whole-program analysis and optimization. Whole-program analysis and optimization is possible for languages, such as C++, that do not allow new classes and/or methods to be loaded during program execution. One solution for performing whole-program analysis andavoiding incorrect execution after a new class is loaded is to invalidate and recompile affected methods. Runtime invalidation and recompilation mechanisms can be expensive in both space and time, and, therefore, generally restrict optimization. To address these drawbacks, we propose a new framework, called the extant analysis framework, for interprocedural optimization of programs that support dynamic class (or method)loading. Given a set of classes comprising the closed world, we perform an offline static analysis which partitions references into two categories:(1) unconditionally extant references which point only to objects whose runtime type is guaranteed to be in the closed world; and (2) conditionally extant references which point to objects whose runtime type is not guaranteed to be in the closed world. Optimizations solely dependent on the first categorycan be statically performed, and are guaranteed to be correct even with any future class/method loading. Optimizations dependent on the second category are guarded by dynamic tests, called extant safety tests, for correct execution behavior.We describe the properties for extant safety tests, and provide algorithms for their generation and placement.
Finding people in archive films through tracking

The goal of this work is to find all people in archive films. Challenges include low image quality, motion blur, partial occlusion, non-standard poses and crowded scenes. We base our approach on face detection and take a tracking/temporal approach to detection. Our tracker operates in two modes, following face detections whenever possible, switching to low-level tracking if face detection fails. With temporal correspondences established by tracking, we formulate detection as an inference problem in one-dimensional chains/tracks. We use a conditional random field model to integrate information across frames and to re-score tentative detections in tracks. Quantitative evaluations on full-length films show that the CRF-based temporal detector greatly improves face detection, increasing precision for about 30% (suppressing isolated false positives) and at the same time boosting recall for over 10% (recovering difficult cases where face detectors fail).
Ancient Polyploidy and Genome Evolution in Palms

Abstract Mechanisms of genome evolution are fundamental to our understanding of adaptation and the generation and maintenance of biodiversity, yet genome dynamics are still poorly characterized in many clades. Strong correlations between variation in genomic attributes and species diversity across the plant tree of life suggest that polyploidy or other mechanisms of genome size change confer selective advantages due to the introduction of genomic novelty. Palms (order Arecales, family Arecaceae) are diverse, widespread, and dominant in tropical ecosystems, yet little is known about genome evolution in this ecologically and economically important clade. Here, we take a phylogenetic comparative approach to investigate palm genome dynamics using genomic and transcriptomic data in combination with a recent, densely sampled, phylogenetic tree. We find conclusive evidence of a paleopolyploid event shared by the ancestor of palms but not with the sister clade, Dasypogonales. We find evidence of incremental chromosome number change in the palms as opposed to one of recurrent polyploidy. We find strong phylogenetic signal in chromosome number, but no signal in genome size, and further no correlation between the two when correcting for phylogenetic relationships. Palms thus add to a growing number of diverse, ecologically successful clades with evidence of whole-genome duplication, sister to a species-poor clade with no evidence of such an event. Disentangling the causes of genome size variation in palms moves us closer to understanding the genomic conditions facilitating adaptive radiation and ecological dominance in an evolutionarily successful, emblematic tropical clade.
desynaptic5 carries a spontaneous semi-dominant mutation affecting Disrupted Meiotic cDNA 1 in barley

Abstract Despite conservation of the process of meiosis, recombination landscapes vary between species, with large genome grasses such as barley (Hordeum vulgare L.) exhibiting a pattern of recombination that is very heavily skewed to the ends of chromosomes. We have been using a collection of semi-sterile desynaptic meiotic mutant lines to help elucidate how recombination is controlled in barley and the role of the corresponding wild-type (WT) meiotic genes within this process. Here we applied a combination of genetic segregation analysis, cytogenetics, and immunocytology to genetically map and characterize the meiotic mutant desynaptic5 (des5). We identified an exonic insertion in the positional candidate ortholog of Disrupted Meiotic cDNA 1 (HvDMC1) on chromosome 5H of des5. des5 exhibits a severe meiotic phenotype with disturbed synapsis, reduced crossovers, and chromosome mis-segregation. The meiotic phenotype and reduced fertility of des5 is similarly observed in Hvdmc1RNAi transgenic plants and HvDMC1p:GusPlus reporter lines show DMC1 expression specifically in the developing inflorescence. The des5 mutation maintains the reading frame of the gene and exhibits semi-dominance with respect to recombination in the heterozygote indicating the value of non-knockout mutations for dissection of the control of recombination in the early stages of meiosis.
Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

We introduce a novel computational approach, CoReCo, for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species. Leveraging on the exponential growth in sequenced genome availability, our method reconstructs genome-scale gapless metabolic networks simultaneously for a large number of species by integrating sequence data in a probabilistic framework. High reconstruction accuracy is demonstrated by comparisons to the well-curated Saccharomyces cerevisiae consensus model and large-scale knock-out experiments. Our comparative approach is particularly useful in scenarios where the quality of available sequence data is lacking, and when reconstructing evolutionary distant species. Moreover, the reconstructed networks are fully carbon mapped, allowing their use in 13C flux analysis. We demonstrate the functionality and usability of the reconstructed fungal models with computational steady-state biomass production experiment, as these fungi include some of the most important production organisms in industrial biotechnology. In contrast to many existing reconstruction techniques, only minimal manual effort is required before the reconstructed models are usable in flux balance experiments. CoReCo is available at http://esaskar.github. io/CoReCo/.
A comparison of parallel Gaussian elimination solvers for the computation of electrochemical battery models on the cell processor

The rising cost of fossil fuels, together with a push for more eco-friendly methods of transportation, has increased interest in and demand for electrically powered or assisted vehicles. The majority of these electric or hybrid electric vehicles will be, for the foreseeable future, powered by batteries. One of the major problems with batteries is their aging. For batteries, aging means that the maximum charge they can store decreases as number of charge/discharge cycles increases. Aging also means that after a certain number of charge/discharge cycles, the battery will fail. In lead-acid batteries, one of the major phenomenon that promotes battery failure is the development of a non-uniform concentration gradient of electrolyte along the electrodes' height. This phenomenon is known as electrolyte stratification. This thesis develops a simple two-level circuit model that can be used to model electrolyte stratification. The two-level circuit model is justified experimentally using digital Mach-Zehnder interferometry and is explained theoretically by means of two different electrochemical battery models. The experiments show how the usage of the electrode varies along its height while the simulations indicate that the high resistivity of the lead dioxide electrode plays a major role in the development of a stratified electrolyte. Finally, computational issues associated with the computation of a sophisticated two dimensional electrochemical battery model on the multicore Cell Broadband Engine processor are addressed in detail. In particular, three different banded parallel Gaussian elimination solvers are developed and compared. These three solvers vividly illustrate how performance achieved on the new multicore processors is strongly dependent on the algorithm used. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Genomic Plasticity Mediated by Transposable Elements in the Plant Pathogenic Fungus Colletotrichum higginsianum

Abstract Phytopathogen genomes are under constant pressure to change, as pathogens are locked in an evolutionary arms race with their hosts, where pathogens evolve effector genes to manipulate their hosts, whereas the hosts evolve immune components to recognize the products of these genes. Colletotrichum higginsianum (Ch), a fungal pathogen with no known sexual morph, infects Brassicaceae plants including Arabidopsis thaliana. Previous studies revealed that Ch differs in its virulence toward various Arabidopsis thaliana ecotypes, indicating the existence of coevolutionary selective pressures. However, between-strain genomic variations in Ch have not been studied. Here, we sequenced and assembled the genome of a Ch strain, resulting in a highly contiguous genome assembly, which was compared with the chromosome-level genome assembly of another strain to identify genomic variations between strains. We found that the two closely related strains vary in terms of large-scale rearrangements, the existence of strain-specific regions, and effector candidate gene sets and that these variations are frequently associated with transposable elements (TEs). Ch has a compartmentalized genome consisting of gene-sparse, TE-dense regions with more effector candidate genes and gene-dense, TE-sparse regions harboring conserved genes. Additionally, analysis of the conservation patterns and syntenic regions of effector candidate genes indicated that the two strains vary in their effector candidate gene sets because of de novo evolution, horizontal gene transfer, or gene loss after divergence. Our results reveal mechanisms for generating genomic diversity in this asexual pathogen, which are important for understanding its adaption to hosts.
GENCODE: The reference human genome annotation for The ENCODE Project

The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.
The Officer Is Taller Than You, Who Race Yourself! Using Document Specific Word Associations in Poetry Generation

We propose a method for automatic poetry composition with a given document as inspiration. The poems generated are not limited to the topic of the document. They expand the topic or even put it in a new light. This capability is enabled by first detecting significant word associations that are unique to the document and then using them as the key lexicon for poetry composition.
Equity in access to healthcare among the urban elderly in China: does health insurance matter?

OBJECTIVE The aim of this study was to examine if inequity in healthcare among the urban elderly in China has been improved through the implementation of Urban Resident Basic Medical Insurance (URBMI). METHODS AND DATA SOURCE: We used the data from a nationwide household health survey conducted between December 2011 and February 2012 to compare the needs, uses, and non-uses of health services of the 7618 urban Chinese elderly 60 years and older covered by two different health insurance schemes. Frequency and percentages were used to examine the data. RESULTS Significant inequity in health service uses existed among different socioeconomic groups and the people covered by two different health insurance schemes. Compared with the elderly covered by Urban Employee Basic Medical Insurance, the elderly covered by URBMI had much lower rates of service use and higher non-use rates of health services. CONCLUSIONS Universal health insurance coverage alone cannot mitigate the existing inequity in healthcare; the Chinese government must develop appropriate financial policies and measures to provide more financial support to URBMI in order to improve equitable and affordable access to healthcare.
Cohort profile: the cardiovascular risk in Young Finns Study.

In Finland, coronary heart disease (CHD) incidence was very high in the 1960s and 1970s. In line with this high incidence, the Seven Countries Study showed that the level of serum cholesterol in Finns was also the highest among the investigated countries in the 1960s. Because several studies indicated that the atherosclerotic process starts early in life, and in accord with the World Health Organization Recommendation of 1978 which stated that studies assessing atherosclerosis precursors in children should be initiated, a program was launched in Finland in the late 1970s to study cardiovascular risk in the youth. The Cardiovascular Risk in Young Finns Study was designed as a collaborative effort between five university departments of medical schools (i.e. in Helsinki, Kuopio, Oulu, Tampere and Turku) and several other institutions in Finland. The aim was to study the levels of CHD risk factors and their determinants in children and adolescents of various ages in different parts of the country. Two pilot studies were carried out in 1978 (N1⁄4 264, age 8 years) and in 1979 (N1⁄4 634, aged 3, 12 and 17 years). The first main cross-sectional (baseline) study was performed in 1980. The baseline study included 3596 children and adolescents aged 3, 6, 9, 12, 15 and 18 years. Between 1980 and 1992, these cohorts were followed up at 3-year intervals. The latest examination of the Cardiovascular Risk in Young Finns Study was performed in 2001, when the participants were young adults, aged 24–39 years. At the time of writing, the 27-year (i.e. 27 years since the start of the study when the participants are aged 30–45 years) follow-up field studies are being conducted, and will be completed in the beginning of 2008.
Spatial calibration and image processing requirements of an image fiber bundle based snapshot hyperspectral imaging probe: from raw data to datacube

Hyperspectral imaging was first used in remote sensing and since then, it has been used in many other applications such as cancer diagnosis, precision farming and assessment of the level of flaking in ancient murals. In order to make hyperspectral imaging available for a wide variety of applications, its imagers can be made to operate using different methods and developed into different configurations. This leads to each variant having a set of specifications suitable for certain applications. The many variants of hyperspectral imager produce a set of three-dimensional spatial-spatialspectral datacube, which is made up of hundreds of spectral images of one scene. A snapshot hyperspectral imaging probe has recently been developed by integrating a fiber bundle, which is made up of specially-arranged optical fibers, with a spectrograph-based hyperspectral imager. The snapshot method is able to produce a datacube using the information from each scan. The fiber bundle has 100 fiberlets which are arranged in a row in the one-dimensional proximal end, and are rearranged into a 10×10 hexagonal array in the two-dimensional distal end. The image captured by the two-dimensional end of the fiber bundle is reduced from two to one spatial dimension at the one-dimensional end. The raw data acquired from each scan has to be remapped into a datacube with the correct representation of the spectral and spatial features of the captured scene. This paper reports the spatial calibrations of both ends of the fiber bundle and image processing that have to be performed for such a remapping.
Wideband circularly polarized single patch antenna using broadband feed network

In this paper, a wideband circularly-polarized patch antenna is presented. The patch is fed by four probes arranged by sequential rotation arrays, the four probes are connected to a feed network comprising of a pair of broadband 90° phase shifter and Wilkinson power divider. The proposed antenna shows a compact low profile, wide axial-ratio (AR) bandwidth, wide reflection coefficient bandwidth, as well as easiness of integration. To verify the simulation performance of the design, the antenna has been fabricated and measured. The measured results show that the impedance bandwidth S11<; -10 dB of 70.2%, the 3-dB AR bandwidth of 63.1%, the gain is 6.65 dBi at 5.8 GHz, and the 3-dB gain bandwidth is 39.3% from 4.9 to 7.3 GHz. Good agreement is observed between simulation and measurement by comparison.
Epigenetics and Family-Centered Developmental Care for the Preterm Infant

Adverse experiences early in life have the potential to disrupt normal brain development and create stress response channels in preterm infants that are different from those observed in term infants. Animal models show that epigenetic modifications mediate the effects of maternal separation and environmental stress on susceptibility to disease and psychobehavioral problems later in life. Epigenetic research has the potential to lead to the identification of biological markers, gene expression profiles, and profile changes that occur overtime in response to early-life experiences. Combined with knowledge gained through the use of advanced technologies, epigenetic studies have the promise to refine our understanding about how the brain matures and functions from multiple perspectives including the effect of the environment on brain growth and maturation. Such an understanding will pave the way for care practices that will allow the premature brain to develop to its full capacity and will lead to the best possible outcomes. Neonatal epigenetic research is emerging and rapidly advancing. As scientists overcome biological, technical, and cost-related challenges, such research has a great potential in determining key environmental factors that affect the preterm genome, allowing for targeted interventions. The purpose of this article is to explore existing literature related to epigenetic mechanisms that potentially mediate the effects of the environment on preterm infant brain development.
Volumetric Bias in Segmentation and Reconstruction: Secrets and Solutions

Many standard optimization methods for segmentation and reconstruction compute ML model estimates for appearance or geometry of segments, e.g. Zhu-Yuille [23], Torr [20], Chan-Vese [6], GrabCut [18], Delong et al. [8]. We observe that the standard likelihood term in these formu-lations corresponds to a generalized probabilistic K-means energy. In learning it is well known that this energy has a strong bias to clusters of equal size [11], which we express as a penalty for KL divergence from a uniform distribution of cardinalities. However, this volumetric bias has been mostly ignored in computer vision. We demonstrate signif- icant artifacts in standard segmentation and reconstruction methods due to this bias. Moreover, we propose binary and multi-label optimization techniques that either (a) remove this bias or (b) replace it by a KL divergence term for any given target volume distribution. Our general ideas apply to continuous or discrete energy formulations in segmenta- tion, stereo, and other reconstruction problems.
Universal a posteriori metrics game

Over binary input channels, the uniform distribution is a universal prior, in the sense that it maximizes the worst case mutual information of all binary input channels and achieves at least 94.2% of the capacity. In this paper, we address a similar question. We look for the best collection of finitely many a posteriori metrics, to maximize the worst case mismatched mutual information achieved by decoding with these metrics (instead of an optimal decoder such as the Maximum Likelihood (ML) tuned to the true channel). It is shown that for binary input and output channels, two metrics suffice to actually achieve the same performance as an optimal decoder. In particular, this implies that there exist a decoder which is generalized linear and achieves at least 94.2% of the compound capacity on any compound set, without knowledge of the underlying set.