Miracle-dz/UniFAR-FTUs huggingface dataset:
Large-Scale Approximate Kernel Canonical Correlation Analysis

Kernel canonical correlation analysis (KCCA) is a nonlinear multi-view representation learning technique with broad applicability in statistics and machine learning. Although there is a closed-form solution for the KCCA objective, it involves solving an $N\times N$ eigenvalue system where $N$ is the training set size, making its computational requirements in both memory and time prohibitive for large-scale problems. Various approximation techniques have been developed for KCCA. A commonly used approach is to first transform the original inputs to an $M$-dimensional random feature space so that inner products in the feature space approximate kernel evaluations, and then apply linear CCA to the transformed inputs. In many applications, however, the dimensionality $M$ of the random feature space may need to be very large in order to obtain a sufficiently good approximation; it then becomes challenging to perform the linear CCA step on the resulting very high-dimensional data matrices. We show how to use a stochastic optimization algorithm, recently proposed for linear CCA and its neural-network extension, to further alleviate the computation requirements of approximate KCCA. This approach allows us to run approximate KCCA on a speech dataset with $1.4$ million training samples and a random feature space of dimensionality $M=100000$ on a typical workstation.
Climate, not Aboriginal landscape burning, controlled the historical demography and distribution of fire-sensitive conifer populations across Australia

Climate and fire are the key environmental factors that shape the distribution and demography of plant populations in Australia. Because of limited palaeoecological records in this arid continent, however, it is unclear as to which factor impacted vegetation more strongly, and what were the roles of fire regime changes owing to human activity and megafaunal extinction (since ca 50 kya). To address these questions, we analysed historical genetic, demographic and distributional changes in a widespread conifer species complex that paradoxically grows in fire-prone regions, yet is very sensitive to fire. Genetic demographic analysis showed that the arid populations experienced strong bottlenecks, consistent with range contractions during the Last Glacial Maximum (ca 20 kya) predicted by species distribution models. In southern temperate regions, the population sizes were estimated to have been mostly stable, followed by some expansion coinciding with climate amelioration at the end of the last glacial period. By contrast, in the flammable tropical savannahs, where fire risk is the highest, demographic analysis failed to detect significant population bottlenecks. Collectively, these results suggest that the impact of climate change overwhelmed any modifications to fire regimes by Aboriginal landscape burning and megafaunal extinction, a finding that probably also applies to other fire-prone vegetation across Australia.
Fluorescence in situ hybridization ( FISH ) of Microcystis strains producing microcystin using specific mRNA probes

Cyanobacteria are ubiquitous microorganisms that can produce toxic compounds, the cyanotoxins. The monitoring of such producers in the environment is of prime importance for human health. An attractive technology for such monitoring is fluorescence in situ hybridization (FISH), which allows the detection and enumeration of environmental microorganisms. We present here the application of tyramide signal amplification A cc ep te d A rt ic le This article is protected by copyright. All rights reserved. fluorescence in situ hybridization (TSA-FISH) to the detection of microcystin producing Microcystis strains. We used a 16S rRNA specific probe, MICR3, to specifically label and observe by epifluorescence microscopy M. aeruginosa strains. Using confocal laser scanning microscopy and a specific probe, MCYA, targeting the mcyA mRNA we have labeled M. aeruginosa PCC 7806, which produces microcystins. M. aeruginosa PCC 7005 which does not produce microcystins is not labeled by this probe. Furthermore, we show here that this specific mRNA labeling in M. aeruginosa PCC 7806 is enhanced in cells illuminated for one hour just after a dark period of cultivation of 24 hours, conditions in which the mcyA gene is up regulated. The data presented here might be applicable to the monitoring of toxic Microcystis strains in the environment.
A non-stop S-antigen gene mutation is associated with late onset hereditary retinal degeneration in dogs

Purpose To identify the causative mutation of canine progressive retinal atrophy (PRA) segregating as an adult onset autosomal recessive disorder in the Basenji breed of dog. Methods Basenji dogs were ascertained for the PRA phenotype by clinical ophthalmoscopic examination. Blood samples from six affected cases and three nonaffected controls were collected, and DNA extraction was used for a genome-wide association study using the canine HD Illumina single nucleotide polymorphism (SNP) array and PLINK. Positional candidate genes identified within the peak association signal region were evaluated. Results The highest -Log10(P) value of 4.65 was obtained for 12 single nucleotide polymorphisms on three chromosomes. Homozygosity and linkage disequilibrium analyses favored one chromosome, CFA25, and screening of the S-antigen (SAG) gene identified a non-stop mutation (c.1216T>C), which would result in the addition of 25 amino acids (p.*405Rext*25). Conclusions Identification of this non-stop SAG mutation in dogs affected with retinal degeneration establishes this canine disease as orthologous to Oguchi disease and SAG-associated retinitis pigmentosa in humans, and offers opportunities for genetic therapeutic intervention.
Efficient Secondary Attribute Lookup in NoSQL Databases

NoSQL databases achieve fast write throughput and fast lookups on the primary key. However, many applications also require queries on non-primary attributes. For that, several NoSQL databases have added support for secondary indexes. However, these works are fragmented as each system generally supports one type of secondary index, and may be using different names or no name at all to refer to such indexes. Also there exists no experimental head to head comparison or performance analysis of the various secondary indexing techniques in terms of throughput and space, as there is no single system that supports all of them. In this paper, we present a taxonomy of NoSQL secondary indexes, and also propose a natural new space-efficient secondary index, called embedded index, based on Bloom filters. Further, we built a system, LevelDB++, on top of Google’s popular open-source LevelDB key-value store where we implemented all these indexing schemes to make a fair comparison between them. Our comprehensive experimental and theoretical evaluation show that stand-alone secondary indexes achieve faster query times, but embedded indexes offer superior write throughput.
A protein that binds to the P1 origin core and the oriC 13mer region in a methylation‐specific fashion is the product of the host seqA gene.

The P1 plasmid replication origin P1oriR is controlled by methylation of four GATC adenine methylation sites within heptamer repeats. A comparable (13mer) region is present in the host origin, oriC. The two origins show comparable responses to methylation; negative control by recognition of hemimethylated DNA (sequestration) and a positive requirement for methylation for efficient function. We have isolated a host protein that recognizes the P1 origin region only when it is isolated from a strain proficient for adenine methylation. The substantially purified 22 kDa protein also binds to the 13mer region of oriC in a methylation‐specific fashion. It proved to be the product of the seqA gene that acts in the negative control of oriC by sequestration. We conclude that the role of the SeqA protein in sequestration is to recognize the methylation state of P1oriR and oriC by direct DNA binding. Using synthetic substrates we show that SeqA binds exclusively to the hemimethylated forms of these origins forms that are the immediate products of replication in a methylation‐proficient strain. We also show that the protein can recognize sequences with multiple GATC sites, irrespective of the surrounding sequence. The basis for origin specificity is primarily the persistence of hemimethylated forms that are over‐represented in the natural. DNA preparations relative to controls.
MEDIATOR25 Acts as an Integrative Hub for the Regulation of Jasmonate-Responsive Gene Expression in Arabidopsis1[C][W]

The PHYTOCHROME AND FLOWERING TIME1 gene encoding the MEDIATOR25 (MED25) subunit of the eukaryotic Mediator complex is a positive regulator of jasmonate (JA)-responsive gene expression in Arabidopsis (Arabidopsis thaliana). Based on the function of the Mediator complex as a bridge between DNA-bound transcriptional activators and the RNA polymerase II complex, MED25 has been hypothesized to function in association with transcriptional regulators of the JA pathway. However, it is currently not known mechanistically how MED25 functions to regulate JA-responsive gene expression. In this study, we show that MED25 physically interacts with several key transcriptional regulators of the JA signaling pathway, including the APETALA2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) transcription factors OCTADECANOID-RESPONSIVE ARABIDOPSIS AP2/ERF59 and ERF1 as well as the master regulator MYC2. Physical interaction detected between MED25 and four group IX AP2/ERF transcription factors was shown to require the activator interaction domain of MED25 as well as the recently discovered Conserved Motif IX-1/EDLL transcription activation motif of MED25-interacting AP2/ERFs. Using transcriptional activation experiments, we also show that OCTADECANOID-RESPONSIVE ARABIDOPSIS AP2/ERF59- and ERF1-dependent activation of PLANT DEFENSIN1.2 as well as MYC2-dependent activation of VEGETATIVE STORAGE PROTEIN1 requires a functional MED25. In addition, MED25 is required for MYC2-dependent repression of pathogen defense genes. These results suggest an important role for MED25 as an integrative hub within the Mediator complex during the regulation of JA-associated gene expression.
Expression profiling of DNA repair genes in human oocytes and blastocysts using microarrays.

BACKGROUND The early preimplantation embryo relies on mRNA and protein from the oocyte to detect DNA damage and activate DNA repair, cell cycle arrest or apoptosis. Expression of some repair genes has been detected in mammalian oocytes and embryos; however, little is known about DNA repair gene expression in human blastocysts. In this study, DNA repair gene expression was investigated in human oocytes and blastocysts to identify the pathways involved at these stages and detect potential differences in repair mechanisms pre- and post-embryonic genome activation. METHODS Triplicate sets of pooled metaphase II oocytes or blastocysts were processed for analysis using the Human Genome Survey Microarrays V2.0 (Applied Biosystems). RESULTS Of 154 DNA repair genes investigated, 109 were detected in blastocysts and 107 in oocytes. Among differentially expressed DNA repair genes, 40/55 (73%) had lower expression levels in blastocysts compared with oocytes (P < 0.05, fold change >3). CONCLUSION Despite experimental limitations due to culture or freezing and thawing of samples, large numbers of repair genes were detected indicating that all DNA repair pathways are potentially functional in human oocytes and blastocysts. The higher mRNA level for most repair genes in oocytes compared with blastocysts ensures sufficient availability of template until embryonic genome activation.
Crew resource management: improving team work in high reliability industries

The aviation industry recognised the significance of human error in accidents in the 1970s, and has been instrumental in the development of special training, designed to reduce error and increase the effectiveness of flight crews. These crew resource management (CRM) programmes focus on “non‐technical skills” critical for enhanced operational performance, such as leadership, situation awareness, decision making, team work and communication. More recently CRM has been adopted by other “high reliability” team environments including anaesthesiology, air traffic control, the Merchant Navy, the nuclear power industry, aviation maintenance, and the offshore oil industry. This review paper describes the basic principles of crew resource management, then outlines recent developments in aviation and other high reliability work environments.
Investigation of the Relationship of Attention Deficit Hyperactivity Disorder to the EKN1 Gene on Chromosome 15q21

Recently a gene, termed EKN1, has been identified because of a chromosomal breakpoint that occurred in this gene. This chromosomal breakpoint was found in 4 family members that had specific reading disabilities (RDs), indicating that disruption of this gene may be contributing to the risk of developing RDs. This gene was further supported as contributing to RD by association studies. Because of the evidence from twin studies for shared genetic factors contributing to RD and attention deficit hyperactivity disorder (ADHD), particularly inattention symptoms, we investigated the relationship of DNA markers in this gene to ADHD and ADHD symptoms in a sample of 186 nuclear families (probands, their parents, and affected siblings) collected through a proband with ADHD. We used 6 polymorphic DNA markers located across the gene, including the 2 markers previously reported to be associated with RD in a Finnish sample and a marker associated with RD in a sample of families collected in Toronto. We found a trend for association for several markers to the ADHD phenotype analyzed as a categorical trait using the transmission disequilibrium test and significant evidence for biased transmission of the haplotypes containing these markers, χ2(3) = 9.312, p =. 025. Using quantitative analysis, we observed evidence for association of one of the haplotypes to the inattention and hyperactive/impulsive symptom dimensions as reported by parents and to the inattention symptoms as reported by teachers, as well as a trend for association with the reading phenotypes of word identification and decoding. The results provide preliminary support for the role of the EKN1 chromosomal region in ADHD, suggesting that this region may contribute to ADHD symptoms in addition to RD.
Cloning, Characterization, and Transcriptional Analysis of a Gene Encoding an α-Crystallin-Related, Small Heat Shock Protein from the Thermophilic Cyanobacterium Synechococcus vulcanus

ABSTRACT hspA, a gene encoding a 16-kDa heat-induced protein from the thermophilic cyanobacterium Synechococcus vulcanus, has been cloned and sequenced. The deduced amino acid sequence of the gene product showed significant homology to sequences of the family of α-crystallin-related, small heat shock proteins. A monocistronic mRNA of hspA increased transiently in response to heat shock. The heat shock induction occurred at a vegetative promoter but without the CIRCE (controlling inverted repeat of chaperone expression) element.
Tense and agreement morphemes in the speech of children with specific language impairment during intervention: phase 2.

PURPOSE The goals of this investigation were to determine whether treatment assists children with specific language impairment (SLI) in the use of grammatical morphemes that mark tense and agreement and whether treatment gains influence the children's use of other, untreated morphemes. METHOD Twenty-five children with SLI participated in 96 intervention sessions designed to facilitate the children's use of third-person singular -s or auxiliary is/are/was. RESULTS The children showed significantly larger gains on the target forms than on control forms (e.g., past tense -ed) that were monitored but not included in intervention. Along with possible treatment-related generalization across morpheme types, there was also evidence of one morpheme type influencing another when neither was the target of intervention. CONCLUSIONS Although the results provide clear evidence for intervention effects, it appeared as if maturational factors also played a role. The findings are discussed in terms of their implications for treatment and for characterizing development in SLI.
On phase noise in quadrature cross-coupled oscillators

A cross-coupled relaxation oscillator has two outputs of the same frequency, which are in quadrature. In this paper a comparative study of the phase noise in a cross-coupled relaxation oscillator is given. We present a high level (system) study of the oscillator and analyse the oscillator stability. The derivation proves analytically that cross-coupling reduces the influence of a perturbation (noise) on the oscillator output. Both high-level and circuit simulations at 5GHz are presented to confirm the theoretical results. Close to 10dB improvement in phase noise performance due to coupling was found, and the phase noise performance compared with that of a coupled LC oscillator was achieved.
Brief Report on Socially Desirable Responses Given in Self-Reports of Everyday Hassles and Life Events

This report describes the results of a portion of a larger health research project which obtained self-reports of illness and stress from 141 women and 38 men. These undergraduates under-reported everyday hassles and life events. Scores on everyday hassles correlated -. 47 and on life events -. 30 with social desirability. Researchers need to adjust their designs to control for possible socially desirable responses on these variables.
Neo-Institutional Economics and Planning Theory

In an institutional sense, planning theory is basically one dealing with the goals and form of and the procedure and justification for the regulation of the land market. Traditionally, welfare economics, a branch of mainstream economics fostered by Arthur C. Pigou, was the most persuasive ideological foundation for such regulation. The concepts of this branch of economics are often expressed in planning terms in the applied field of regional and urban economics, commonly taught in planning schools. However, what we may call ‘neo-institutional economics’ has begun to exert its impact on planning theory. This is evidenced by the appearance in the planning literature of a wave of works informed by a cluster of concepts in this branch of economics at the turn of the millennium by Alexander (1992, 2001a, 2001b, 2002), Benchetrit and Czamanski (2004), Booth (2002), Buitelaar (2003, 2004), Dawkins (2000), Gleeson and Low (2000), Lai (1994, 1996, 1997, 1998, 1999, 2000, 2002a, 2002b, 2004), Lai and Chan (2004), Lai and Ho (2003), Lai and Lorne (2003), Lai and Yu (2001), Micelli (2002), Pennington (1997, 1999, 2000a, 2000b, 2001, 2003a, 2003b, 2003c, 2003d, 2004), Poulton (1997), Sager (2001, 2002), Staley (2001), Webster (1998a, 1998b, 1998c, 2001a, 2001b, 2003), Webster and Wu (1999a, 1999b, 2001), and Webster and
Inverting flow durations from sampled traffic

The flow duration distribution is an important metric to the network operator for traffic prediction and accounting but also arguably from the viewpoint of the user. The inversion problem of recovering the flow duration distribution from sampled traffic is addressed here under several sampling methods. A theoretical framework for the inversion problem is developed using a probabilistic flow model. In this framework, direct equations for the distributions of sampled flow quantities are derived based on the distributions of original flow characteristics. The inversion of these equations provides estimators for the flow duration distribution. Finally, the inversion techniques under several sampling schemes are evaluated on two Internet traces.
Scaling of wingbeat frequency with body mass in bats and limits to maximum bat size

SUMMARY The ability to fly opens up ecological opportunities but flight mechanics and muscle energetics impose constraints, one of which is that the maximum body size must be kept below a rather low limit. The muscle power available for flight increases in proportion to flight muscle mass and wingbeat frequency. The maximum wingbeat frequency attainable among increasingly large animals decreases faster than the minimum frequency required, so eventually they coincide, thereby defining the maximum body mass at which the available power just matches up to the power required for sustained aerobic flight. Here, we report new wingbeat frequency data for 27 morphologically diverse bat species representing nine families, and additional data from the literature for another 38 species, together spanning a range from 2.0 to 870 g. For these species, wingbeat frequency decreases with increasing body mass as Mb–0.26. We filmed 25 of our 27 species in free flight outdoors, and for these the wingbeat frequency varies as Mb–0.30. These exponents are strikingly similar to the body mass dependency Mb–0.27 among birds, but the wingbeat frequency is higher in birds than in bats for any given body mass. The downstroke muscle mass is also a larger proportion of the body mass in birds. We applied these empirically based scaling functions for wingbeat frequency in bats to biomechanical theories about how the power required for flight and the power available converge as animal size increases. To this end we estimated the muscle mass-specific power required for the largest flying extant bird (12–16 kg) and assumed that the largest potential bat would exert similar muscle mass-specific power. Given the observed scaling of wingbeat frequency and the proportion of the body mass that is made up by flight muscles in birds and bats, we estimated the maximum potential body mass for bats to be 1.1–2.3 kg. The largest bats, extinct or extant, weigh 1.6 kg. This is within the range expected if it is the bat characteristic flight muscle mass and wingbeat frequency that limit the maximum body mass in bats. It is only a tenth the mass of the largest flying extant bird.
Neural mechanisms of saccade target selection: gated accumulator model of the visual–motor cascade

We review a new computational model developed to understand how evidence about stimulus salience in visual search is translated into a saccade command. The model uses the activity of visually responsive neurons in the frontal eye field as evidence for stimulus salience that is accumulated in a network of stochastic accumulators to produce accurate and timely saccades. We discovered that only when the input to the accumulation process was gated could the model account for the variability in search performance and predict the dynamics of movement neuron discharge rates. This union of cognitive modeling and neurophysiology indicates how the visual–motor transformation can occur, and provides a concrete mapping between neuron function and specific cognitive processes.