Miracle-dz/UniFAR-FTUs huggingface dataset:
Coalescent experiments II: Markov bases of classical population genetic statistics

Evaluating the likelihood function of parameters in complex population genetic models from extant deoxyribonucleic acid (DNA) se- quences is computationally prohibitive. In such cases, one may approxi- mately infer the parameters from various summary statistics of the data. Such method are known as approximate likelihood/Bayesian computa- tions. We employ computational commutative algebraic methods to ob- tain the exact likelihood of a large class of summary statistics that are linear combinations of the site frequency spectrum.
Transferable XCS

Traditional accuracy-based XCS classifier system generally learns and evolves classifiers from scratch when facing each particular problem. Inspired by humans with the ability to learn new skills by inducing knowledge from related problems, transfer learning (TL) focuses on leveraging the knowledge of source domains to help the problem solving of another different but related domain. This paper attempts to combine XCS and TL to propose a novel extension transferable XCS (tXCS). tXCS utilizes the inherent characteristics of XCS, that naturally discovers expressive classifiers as the generalized knowledge of domains, to realize the classifier transfer from source domains to a target domain that makes it learn faster, which is conceptually different from the previous integrations between XCS and TL. The systematic study is presented to verify the ability of knowledge transfer between domains with different degrees of similarity, which has been pointed out to be the challenge of TL. We demonstrate that tXCS can significantly speed up the learning efficiency of canonical XCS in both of single-step and multi-step benchmark problems.
Lecture notes on Knowledge-Based and Learning Systems by Maciej Lískiewicz Lecture 3 : Learning in the Limit II 1 The Pattern Languages

Patterns are a very natural way to define formal languages. Suppose you are interested in the language of all strings over the alphabet A = {0, 1} starting with 11 , ending with 010 , and containing the substring 01011 somewhere, but may be otherwise arbitrary. Thus, all strings in your language follow the pattern π1 = 11x001011x1010 , provided you are willing to allow the variables x0, x1 to be substituted by any string over {0, 1} including the empty one. As for another example, consider the set of all strings having even length 2n such that the prefix of length n is identical to the suffix starting at position n + 1 . In that case, the wanted language follows the pattern π2 = x0x0 . Before continuing with learning of pattern languages, we provide another example showing how the languages may be applied to learn data structures. Quite often, one has huge bibliographies, i.e., list of references. For example, let us look at the following ones. Gold, M.E. (1967), Language identification in the limit, Information and Control 10, 447 – 474. Lange, S. and Wiehagen, R. (1991), Polynomial-time inference of arbitrary pattern languages, New Generation Computing 8, 361 – 370. Thus, the underlying structure might have the following pattern: Authors, Initials. (Year), Title, Journal Volume, number – number. or more formally: x0, x2. (x3), x4, x5x6, x7 − x8 . where A consists of the Latin alphabet, the punctuation symbols, the digits {0, 1, . , 9} , and “ as well as ”. Note, however, that more ‘descriptive’ pattern (in the sense that it describes the sample in less general way) for the above sample is
Notice of RetractionOrganization-level stress interventions: EAP perspective

The occupational health area is developing models with a variety of methods to address and prevent job stress at the organization-level. A review of literature on employee assistance program (EAP) was conducted to explore relevant methods from its perspective. Result reveals that EAP is a potential good partner in the efforts to prevent Job stress at organization-level.
The Potato Aphid Salivary Effector Me47 Is a Glutathione-S-Transferase Involved in Modifying Plant Responses to Aphid Infestation

Polyphagous aphid pests cause considerable economic damage to crop plants, primarily through the depletion of photoassimilates and transfer of viruses. The potato aphid (Macrosiphum euphorbiae) is a notable pest of solanaceous crops, however, the molecular mechanisms that underpin the ability to colonize these hosts are unknown. It has recently been demonstrated that like other aphid species, M. euphorbiae injects a battery of salivary proteins into host plants during feeding. It is speculated that these proteins function in a manner analagous to secreted effectors from phytopathogenic bacteria, fungi and oomycetes. Here, we describe a novel aphid effector (Me47) which was identified from the potato aphid salivary secretome as a putative glutathione-S-transferase (GST). Expression of Me47 in Nicotiana benthamiana enhanced reproductive performance of green peach aphid (Myzus persicae). Similarly, delivery of Me47 into leaves of tomato (Solanum lycopersicum) by Pseudomonas spp. enhanced potato aphid fecundity. In contrast, delivery of Me47 into Arabidopsis thaliana reduced GPA reproductive performance, indicating that Me47 impacts the outcome of plant–aphid interactions differently depending on the host species. Delivery of Me47 by the non-pathogenic Pseudomonas fluorescens revealed that Me47 protein or activity triggers defense gene transcriptional upregulation in tomato but not Arabidopsis. Recombinant Me47 was purified and demonstrated to have GST activity against two specific isothiocyanates (ITCs), compounds implicated in herbivore defense. Whilst GSTs have previously been associated with development of aphid resistance to synthetic insecticides, the findings described here highlight a novel function as both an elicitor and suppressor of plant defense when delivered into host tissues.
Cell-Wide Responses to Low-Oxygen Exposure in Desulfovibrio vulgaris Hildenborough

ABSTRACT The responses of the anaerobic, sulfate-reducing organism Desulfovibrio vulgaris Hildenborough to low-oxygen exposure (0.1% O2) were monitored via transcriptomics and proteomics. Exposure to 0.1% O2 caused a decrease in the growth rate without affecting viability. Concerted upregulation of the predicted peroxide stress response regulon (PerR) genes was observed in response to the 0.1% O2 exposure. Several of the candidates also showed increases in protein abundance. Among the remaining small number of transcript changes was the upregulation of the predicted transmembrane tetraheme cytochrome c 3 complex. Other known oxidative stress response candidates remained unchanged during the low-O2 exposure. To fully understand the results of the 0.1% O2 exposure, transcriptomics and proteomics data were collected for exposure to air using a similar experimental protocol. In contrast to the 0.1% O2 exposure, air exposure was detrimental to both the growth rate and viability and caused dramatic changes at both the transcriptome and proteome levels. Interestingly, the transcripts of the predicted PerR regulon genes were downregulated during air exposure. Our results highlight the differences in the cell-wide responses to low and high O2 levels in D. vulgaris and suggest that while exposure to air is highly detrimental to D. vulgaris, this bacterium can successfully cope with periodic exposure to low O2 levels in its environment.
Time-constrained sequential pattern discovery for music genre classification

Music consists of both local and long-term temporal information. However, for a genre classification task, most of the text categorization based approaches only capture local temporal dependences (e.g. statistics of unigrams and bigrams). In our previous work, we use sequential patterns to capture long-term temporal information from the tokenized sequences of music pieces. In this paper, we propose the use of time-constrained sequential patterns (TSPs) to enhance the mined long-term temporal structures so that these TSPs can fit more closely to the human perception. Experimental results show that the proposed method can discover more temporal structures than statistical language modeling approaches and achieves better recognition accuracy.
Absolute Radiometric In-Flight Validation of Mid Infrared and Thermal Infrared Data From ASTER and MODIS on the Terra Spacecraft Using the Lake Tahoe, CA/NV, USA, Automated Validation Site

In December 1999, the first Moderate Resolution Imaging Spectroradiometer (MODIS) instrument and an Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) instrument were launched into polar orbit on the Terra spacecraft. Both instruments measure surface radiance, which requires that they are calibrated and validated in flight. In-flight validation is essential to independently verify that instrument calibration correctly compensates for any changes in instrument response over time. In order to meet this requirement, an automated validation site was established at Lake Tahoe on the California/Nevada border in 1999 to validate the ASTER and MODIS thermal infrared (TIR, 7-13 mum) and MODIS mid infrared (MIR, 3-5 mum) land-monitoring channels. Daytime and nighttime data were used to validate the TIR channels, and only nighttime data were used to validate the MIR channels to avoid any reflected solar contribution. Sixty-nine ASTER scenes and 155 MODIS-Terra scenes acquired between years 2000 and 2005 with near-nadir views were validated. The percent differences between the predicted and instrument at-sensor radiances for ASTER channels 10-14 were 0.165plusmn0. 776, 0.103plusmn0. 613, -0.305plusmn0. 613, -0.252plusmn0. 464, and -0.118plusmn0. 489, respectively. The percent differences for MODIS-Terra channels 20, 22, 23, 29, 31, and 32 were -1.375plusmn0. 973, -1.743plusmn1. 027, -0.898plusmn0. 970, 0.082plusmn0. 631, 0.044plusmn0. 541, and 0.151plusmn0. 563, respectively. The results indicate that the TIR at-sensor radiances from ASTER and MODIS-Terra have met the preflight radiometric calibration accuracy specification and provide well-calibrated data sets that are suitable for measuring absolute change. The results also show that the at-sensor radiances from the MODIS-Terra MIR channels have greater bias than expected based on the preflight radiometric calibration accuracy specification
Classifiers for educational technology

The idea of classification is to place an object into one class or category, based on its other characteristics. In education, teachers and instructors are all the time classifying their students for their knowledge, motivation, and behaviour. Assessing exam answers is also a classification task, where a mark is determined according to certain evaluation criteria. Automatic classification is an inevitable part of intelligent tutoring systems and adaptive learning environments. Before the system can select any adaptation action like selecting tasks, learning material, or advice, it should first classify the learner’s current situation. For this purpose, we need a classifier – a model, which predicts the class value from other explanatory attributes. For example, one can derive the student’s motivation level from her/his actions in the tutoring system or predict the students who are likely to fail or drop out from their task scores. Such predictions are equally useful in the traditional teaching, but computerized learning systems often serve larger classes and collect more data for deriving classifiers. Classifiers can be designed manually, based on expert’s knowledge, but nowadays it is more common to learn them from real data. The basic idea is the following: First, we have to choose the classification method, like decision
Soft Real-Time Hadoop Scheduler for Big Data Processing in Smart Cities

We live in a world where every electronic device generates data, and does so in a variety of ways that respect a multitude of patterns particular to every device and user. Some users user their phone to browse the Internet on their daily commute, some check it for updates every hour, and some may use it constantly throughout the day to accomplish different tasks. Even the same device can be used in variety of ways, let alone different devices. Besides the user generated data, there is also machine generated data, which can have a more foreseeable pattern, like nightly backups or scheduled tasks, but usually imply more CPU or I/O intensive tasks than the sporadic ones generated by human users. In a context where the analyzed data size is constantly increasing and we start to talk about Big Data in more and more daily tasks, we need a way to handle all these diverse tasks that serve a variety of purposes. Some of this data must be sometimes analyzed as fast as possible, or, in some cases the analysis can be done at the end of the day, as part of a batch process. In order to handle all this diversity we design a real-time and job scheduler in Hadoop for Big Data processing that addresses both the problem of small tasks that need to be executed in real time, and in the same time, adjust for long-running jobs where time of completion is not that strictly defined. The case study is applied as support for Smart City applications that are gathered / routed / stored via mobile devices and processed / diffused via a more standard Clouds.
Identification of FHL1 as a regulator of skeletal muscle mass: implications for human myopathy

Regulators of skeletal muscle mass are of interest, given the morbidity and mortality of muscle atrophy and myopathy. Four-and-a-half LIM protein 1 (FHL1) is mutated in several human myopathies, including reducing-body myopathy (RBM). The normal function of FHL1 in muscle and how it causes myopathy remains unknown. We find that FHL1 transgenic expression in mouse skeletal muscle promotes hypertrophy and an oxidative fiber-type switch, leading to increased whole-body strength and fatigue resistance. Additionally, FHL1 overexpression enhances myoblast fusion, resulting in hypertrophic myotubes in C2C12 cells, (a phenotype rescued by calcineurin inhibition). In FHL1-RBM C2C12 cells, there are no hypertrophic myotubes. FHL1 binds with the calcineurin-regulated transcription factor NFATc1 (nuclear factor of activated T cells, cytoplasmic, calcineurin-dependent 1), enhancing NFATc1 transcriptional activity. Mutant RBM-FHL1 forms aggregate bodies in C2C12 cells, sequestering NFATc1 and resulting in reduced NFAT nuclear translocation and transcriptional activity. NFATc1 also colocalizes with mutant FHL1 to reducing bodies in RBM-afflicted skeletal muscle. Therefore, via NFATc1 signaling regulation, FHL1 appears to modulate muscle mass and strength enhancement.
A process variation tolerant, high-speed and low-power current mode signaling scheme for on-chip interconnects

Current mode signaling(CMS) scheme is one of the promising alternatives to voltage mode buffer insertion scheme for high-speed low-power data transmission over long on-chip interconnects. In this paper we present a CMS scheme with dynamic overdriving driver (DOD) whose performance is robust against intra-die and inter-die process variations. We show that throughput of the CMS scheme proposed in [1] degrades by 33% in the presence of intra-die process variations whereas that of the scheme in [2] degrades by 36% in the worst case process corner. Simulation results show that throughput of the proposed CMS scheme degrades by only 9.5% in presence of intra-die process variations and 22% in the worst case process corner. In this process corner, logic speed itself degrades by 23% and hence 22% of throughput degradation of the proposed signaling scheme is not a major concern. In the typical process corner, the proposed CMS scheme shows 14% and 19% improvement in delay and power, respectively over CMS scheme proposed in [1].
Direct lookup and hash-based metadata placement for local file systems

New challenges to file systems' metadata performance are imposed by the continuously growing number of files existing in file systems. The total amount of metadata can become too big to be cached, potentially leading to multiple storage device accesses for a single metadata lookup operation. This paper takes a look at the limitations of traditional file system designs and discusses an alternative metadata handling approach, using hash-based concepts already established for metadata and data placement in distributed storage systems. Furthermore, a POSIX compliant prototype implementation based on these concepts is introduced and benchmarked. A variety of file system metadata and data operations as well as the influence of different storage technologies are taken into account and performance is compared with traditional file systems.
A Sequence-Independent Strategy for Amplification and Characterisation of Episomal Badnavirus Sequences Reveals Three Previously Uncharacterised Yam Badnaviruses

Yam (Dioscorea spp.) plants are potentially hosts to a diverse range of badnavirus species (genus Badnavirus, family Caulimoviridae), but their detection is complicated by the existence of integrated badnavirus sequences in some yam genomes. To date, only two badnavirus genomes have been characterised, namely, Dioscorea bacilliform AL virus (DBALV) and Dioscorea bacilliform SN virus (DBSNV). A further 10 tentative species in yam have been described based on their partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences, generically referred to here as Dioscorea bacilliform viruses (DBVs). Further characterisation of DBV species is necessary to determine which represent episomal viruses and which are only present as integrated badnavirus sequences in some yam genomes. In this study, a sequence-independent multiply-primed rolling circle amplification (RCA) method was evaluated for selective amplification of episomal DBV genomes. This resulted in the identification and characterisation of nine complete genomic sequences (7.4–7.7 kbp) of existing and previously undescribed DBV phylogenetic groups from Dioscorea alata and Dioscorea rotundata accessions. These new yam badnavirus genomes expand our understanding of the diversity and genomic organisation of DBVs, and assist the development of improved diagnostic tools. Our findings also suggest that mixed badnavirus infections occur relatively often in West African yam germplasm.
Spatiotemporal Dynamics of Early DNA Damage Response Proteins on Complex DNA Lesions

The response of cells to ionizing radiation-induced DNA double-strand breaks (DSB) is determined by the activation of multiple pathways aimed at repairing the injury and maintaining genomic integrity. Densely ionizing radiation induces complex damage consisting of different types of DNA lesions in close proximity that are difficult to repair and may promote carcinogenesis. Little is known about the dynamic behavior of repair proteins on complex lesions. In this study we use live-cell imaging for the spatio-temporal characterization of early protein interactions at damage sites of increasing complexity. Beamline microscopy was used to image living cells expressing fluorescently-tagged proteins during and immediately after charged particle irradiation to reveal protein accumulation at damaged sites in real time. Information on the mobility and binding rates of the recruited proteins was obtained from fluorescence recovery after photobleaching (FRAP). Recruitment of the DNA damage sensor protein NBS1 accelerates with increasing lesion density and saturates at very high damage levels. FRAP measurements revealed two different binding modalities of NBS1 to damage sites and a direct impact of lesion complexity on the binding. Faster recruitment with increasing lesion complexity was also observed for the mediator MDC1, but mobility was limited at very high damage densities due to nuclear-wide binding. We constructed a minimal computer model of the initial response to DSB based on known protein interactions only. By fitting all measured data using the same set of parameters, we can reproduce the experimentally characterized steps of the DNA damage response over a wide range of damage densities. The model suggests that the influence of increasing lesion density accelerating NBS1 recruitment is only dependent on the different binding modes of NBS1, directly to DSB and to the surrounding chromatin via MDC1. This elucidates an impact of damage clustering on repair without the need of invoking extra processing steps.
Medical image reconstruction based on Bayesian compressed sensing

A medical image reconstruction method based on sparse Bayesian compressed sensing is presented, and the method employs a hierarchical model of the Laplace prior to model the sparse wavelet coefficients and unknown images. The experiments are designed to compare the Bayesian Compressed Sensing (BCS) method with the Basis Pursuit (BP) algorithm and the Orthogonal Matching Pursuit (OMP) algorithm. The results imply that the presented algorithm exceeds the greedy algorithm and the linear programming such as BP and OMP etc.
A 15-b 40-MS/s CMOS pipelined analog-to-digital converter with digital background calibration

This study presents a 15-b 40-MS/s switched-capacitor CMOS pipelined analog-to-digital converter (ADC). High resolution is achieved by using a correlation-based background calibration technique that can continuously monitor the transfer characteristics of the critical pipeline stages and correct the digital output codes accordingly. The calibration can correct errors associated with capacitor mismatches and finite opamp gains. The ADC was fabricated using a 0.25-/spl mu/m 1P5M CMOS technology. Operating at a 40-MS/s sampling rate, the ADC attains a maximum signal-to-noise-plus-distortion ratio of 73.5 dB and a maximum spurious-free-dynamic-range of 93.3 dB. The chip occupies an area of 3.8/spl times/3.6 mm/sup 2/, and the power consumption is 370 mW with a single 2.5-V supply.
Self-Esteem’s Moderation of Self-Congruity Effects on Brand Loyalty

This research set out to find how consumer self-esteem moderates the relative importance of actual self-congruity vs. ideal self-congruity on women’s brand loyalty to fitness brands. College-aged women were the primary focus for this research because this demography represents an emerging consumer group and because the literature suggests women score significantly lower than men on self-esteem scales in physical appearance, athletic self, personal self, and self-satisfaction self-esteem. A survey of 151 women of 18 - 24 ages was conducted supporting prior research findings that actual and ideal self-congruity are both positively correlated with brand loyalty.
Tip tap tones: mobile microtraining of mandarin sounds

Learning a second language is hard, especially when the learner's brain must be retrained to identify sounds not present in his or her native language. It also requires regular practice, but many learners struggle to find the time and motivation. Our solution is to break down the challenge of mastering a foreign sound system into minute-long episodes of "microtraining" delivered through mobile gaming. We present the example of Tip Tap Tones - a mobile game with the purpose of helping learners acquire the tonal sound system of Mandarin Chinese. In a 3-week, 12-user study of this system, we found that an average of 71 minutes' gameplay significantly improved tone identification by around 25%, regardless of whether the underlying sounds had been used to train tone perception. Overall, results suggest that mobile microtraining is an efficient, effective, and enjoyable way to master the sounds of Mandarin Chinese, with applications to other languages and domains.