Miracle-dz/UniFAR-FTUs huggingface dataset:
Design principles underlying circadian clocks

A fundamental problem for regulatory networks is to understand the relation between form and function: to uncover the underlying design principles of the network. Circadian clocks present a particularly interesting instance, as recent work has shown that they have complex structures involving multiple interconnected feedback loops with both positive and negative feedback. While several authors have speculated on the reasons for this, a convincing explanation is still lacking.We analyse both the flexibility of clock networks and the relationships between various desirable properties such as robust entrainment, temperature compensation, and stability to environmental variations and parameter fluctuations. We use this to argue that the complexity provides the flexibility necessary to simultaneously attain multiple key properties of circadian clocks. As part of our analysis we show how to quantify the key evolutionary aims using infinitesimal response curves, a tool that we believe will be of general utility in the analysis of regulatory networks. Our results suggest that regulatory and signalling networks might be much less flexible and of lower dimension than their apparent complexity would suggest.
Temporal Factors in Beer Ratings CSE 255 , Winter 2014 Project 1

Predicting a user’s rating of a product without taking how their preferences might change over time leaves out a lot of data that could be used to improve that prediction. Why not track that change in preferences and change the recommendations accordingly? As long as keeping track of that doesn’t add significantly to the model there should be no reason not to. In this paper, I aim to do precisely this for user preferences towards beers. For beer in particular, there are multiple different timescales that could affect a user’s preference and I add three different timescales into my prediction model. This model is then compared to a baseline collaborative filtering model based on the Pearson similarity ranking. The comparison is made using the commonly used Root Mean-Squared Error (RMSE) and precision@k metrics. The Temporal Factor model built in this work is demonstrated to perform better at both metrics.
Transcriptional activation of NFI/CTF1 depends on a sequence motif strongly related to the carboxyterminal domain of RNA polymerase II

Initiation of RNA polymerase II-directed transcription is mediated by DNA sequence specific activator proteins interacting with components of the basal transcription machinery. NFI/CTF is a family of such binding proteins which have been shown to stimulate transcription via proline-rich activation domains. In order to identify residues crucial for its activator function, a pool of CTF1 mutants was cloned and fused to the bacterial repressor LexA. Transcriptional activation of these constructs was monitored in a Saccharomyces cerevisiae reporter assay. Our studies reveal the existence of a core domain in CTF1 between residues 463 and 508 essential for transcriptional activation functions. It contains the sequence motif SPTSPSYSP, which is strongly related to the heptapeptide repeat YSPTSPS present in the carboxyterminal domain (CTD) of RNA polymerase II. Removal of the entire CTD related motif, as well as substitution of key amino acids therein, abolish CTF1 mediated transcriptional activation.
SNAPPING SHRIMP DOMINATED NATURAL SOUNDSCAPE IN SINGAPORE WATERS

Snapping shrimp dominate the high frequency soundscape in the warm shallow waters around Singapore. The noises produced by these small creatures are a result of the collapse of cavitation bubbles they produce. During the rapid collapse, the temperatures in the bubble can momentarily reach the surface temperature of the sun, and produce impulsive noise with source levels higher than 190 dB re 1 μPa @ 1m. With millions of snapping shrimp, the resulting cacophony is heard in the form of a background crackle familiar to many tropical divers. The resulting ambient noise has a heavy tailed pressure amplitude probability distribution. This has an adverse impact on the performance of acoustic sensing and communication systems that are developed using the commonly adopted Gaussian noise model. On the other hand, systems designed with a proper understanding of the snapping shrimp noise statistics are able to perform well in Singapore waters. Interestingly, snapping shrimp can also serve as sources of opportunity for acoustic sensing. For example, ROMANIS, an ambient noise-imaging camera developed at the Acoustic Research Laboratory, is able to image underwater objects using snapping shrimp noise as acoustic 'illumination'. To develop techniques for acoustic sensing in snapping shrimp dominated soundscapes, a good understanding of the spatio-temporal statistics of the noise made by these creatures is vital. We present statistical analysis of acoustic data from several experiments in Singapore waters. We discuss the spatial anisotropy that is observed and its implications on acoustic sensing. We also present point process models that accurately capture the observed temporal clustering of shrimp snaps. Contributions to Marine Science 2012: 127-134
Interprocedural slicing in the presence of global variables

The problemof computing slices of a program has received considerableattention over the last two decades because of its applicabil-ity in system generation, debugging, verifying requirements[23], program integration [10], restructuring [14, 16, 17],testing [6], program comprehension [4, 7], and reuse [3]. The interest and signiﬁcance of program slicing is furtheroutlined by the existence of three survey papers [2, 13, 22]on the subject and a recent special issue [8]. The currently prominent algorithm for interproceduralslicing is due to Horwitz, Reps, and Binkley [11]. Thisalgorithm uses a System Dependence Graph (SDG) repre-sentation of program. In a SDG, each actual parameter isrepresented by a pair of nodes representing the values be-fore and after the procedure call statement. Similarly, eachformal parameter too is represented by a pair of nodes rep-resenting the values at the entry and the exit of a procedure.The dependence between actual parameters due to a proce-dure call is represented using summary edges. A summaryedge starts from an actual-in node and terminates on anactual-out node. Its computation requires interproceduraldependence analysis, a fast algorithm for which was givenby Reps et al.[20]. In a SDG a global variable is represented by treating itas a reference parameter to every procedure. This leads toonly a linear expansion in the number of nodes. However,the expansion in the number of edges becomes quadratic,
Modeling locomotor control: The advantages of mobile gaze

In 1958, JJ Gibson put forward proposals on the visual control of locomotion. Research in the last 50 years has served to clarify the sources of visual and nonvisual information that contribute to successful steering, but has yet to determine how this information is optimally combined under conditions of uncertainty. Here, we test the conditions under which a locomotor robot with a mobile camera can steer effectively using simple visual and extra-retinal parameters to examine how such models cope with the noisy real-world visual and motor estimates that are available to humans. This applied modeling gives us an insight into both the advantages and limitations of using active gaze to sample information when steering.
Generation of Lung Adenocarcinoma DNA Aptamers for Cancer Studies

Lung cancer is the most lethal malignancy in the world, and each year thousands of people die from this disease. Early detection has proven to increase the 5-year survival for this cancer in general, independent of the origination site in the lung. To address this challenge, we have used cell-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment) to select a panel of aptamers capable of distinguishing lung adenocarcinoma cells from normal lung epithelial cells. These aptamers bind at physiological and formalin-fixed conditions and display affinity for their targets with apparent Kd's in the nanomolar range. Our findings suggest that the selected aptamers have the potential to be used in clinical settings, as well as to improve classification of nonsurgical specimens, another current challenge in lung cancer.
Algorithm for the identification of resting state independent networks in fMRI

Studies have shown that the brain is constituted by anatomically segregated and functionally specific regions working in synergy as a complex network. In this context, the brain at rest does not passively retrieve environmental information and respond but instead it maintains an active representation modulated by sensory information. Using independent component analysis (ICA) over resting state recordings a discrete set of resting state networks (RSNs) has been found, which proven to be systematically present across individuals and to be modified by the state of consciousness and also in disease. ICA's main drawback is that its output consists of a series of 3D z-score maps where noise and physiological components are randomly mixed. In this work we present a computational method composed by an ICA-based noise filtering preprocessing pipeline and a template-based identification algorithm that combines spatial comparison metrics through a voting system developed to find RSNs in a subject-by-subject basis. To validate it, we use a publicly available dataset consisting of 75 resting state fMRI sessions from 25 participants scanned three different times each one. For most common RSNs the correct candidate won the voting 93% of the times and it was voted at least once in 99%. Then we probe within-subject consistency in detected RSNs by showing augmented correlation in networks from the same subject. Finally, by comparing obtained mean RSNs with the ones from nearly 30,000 participants we show that our method constitutes a personalized-medicine oriented approach to shorten the gap between RSN research and clinical applications.
Combining Rewriting-Logic, Architecture Generation, and Simulation to Exploit Coarse-Grained Reconfigurable Architectures

This paper presents a simulator and an architecture generator to exploit coarse-grained reconfigurable arrays (CGRAs). The simulator is able to execute and dynamically schedule to the 1-D array the instructions in the static single assignment (SSA) intermediate representation output by the compiler or after the TRS step. This tool accepts a textual description of a CGRA and generates the VHDL code ready for logic synthesis.
Mapping Environmental Behaviour in the Spanish Context

In the present study we set out to examine an audience segmentation system that can be used to inform global warming public engagement campaigns and to test survey-based identification tools designed by the Yale Project on Climate Change Communication. A national poll was conducted in Spain with a representative sample of the population online (n = 602). The survey included measures concerning pro-environmental behavior and intentions, issue involvement, individuals’ beliefs, and preferred societal response. The population was classified with reference to their level of concern. Our results show four distinct interpretive communities, ranging from alarmist to dismissive. Overall, the largest audience segment was the concerned, who are convinced that global warming is happening but not engaged personally. The sample was classified using two-step cluster analysis, as we have a really large data set, which does clustering algorithms based on a distance measure. The relationships between the items were also examined in order to identify the possible correlations and recognize how behavior is affected by intentions, beliefs, preferred societal response, and issue involvement.
Language processing in both sexes: evidence from brain studies.

Thank you for the interesting paper by Frost et al. (Frost et al ., 1999). As they suggest, understanding sex differences in the human brain is not trivial. Many studies of disease groups are conducted on one sex only and extrapolated across genders. Indeed, the basis of the Talairach atlas is one example of this approach. Therefore, determining whether clear sex differences exist in language-associated brain is important for future work. The work by Frost et al. adds important data to this confusing field. They report no differences between men and women on a semantic monitoring task (identify if an animal is \`found in the United States' and \`used by human') and then report no differences in functional MRI brain activation. The authors should be commended for their tight statistical design with a large number of subjects, an aspect of the work which should be used in future studies. However, it is important to note that such a semantic monitoring task would not be expected to show sex differences. These differences have been identified and replicated clearly in many studies in which females excel in tasks of verbal fluency and verbal memory types of language skills (Bradshaw, 1989; Mann et al ., 1990; Halpern, 1992; Kimura, 1996). In defence of the expectation of Frost et al. that their semantic–lexical task would show sex differences, the authors argue that their task is an auditory equivalent of Pugh's task on sex differences in aspects of reading. However, the task of Pugh et al . …
The Visibility of Galactic Bars and Spiral Structure at High Redshifts

We investigate the visibility of galactic bars and spiral structure in the distant universe by artificially redshifting 101 B-band CCD images of local spiral galaxies from the Ohio State University Bright Spiral Galaxy Survey. These local galaxy images represent a much fairer statistical baseline than the galaxy atlas images presented by Frei et al. in 1995, the most commonly used calibration sample for morphological work at high redshifts. Our artificially redshifted images correspond to Hubble Space Telescope I814-band observations of the local galaxy sample seen at z = 0.7, with integration times matching those of both the very deep northern Hubble Deep Field (HDF) data and the much shallower HDF flanking field observations. The expected visibility of galactic bars is probed in two ways: (1) using traditional visual classification and (2) by charting the changing shape of the galaxy distribution in "Hubble space," a quantitative two-parameter description of galactic structure that maps closely onto Hubble's original tuning fork. Both analyses suggest that over two-thirds of strongly barred luminous local spirals (i.e., objects classified as SB in the Third Reference Catalogue) would still be classified as strongly barred at z = 0.7 in the HDF data. Under the same conditions, most weakly barred spirals (classified SAB in the Third Reference Catalogue) would be classified as regular spirals. The corresponding visibility of spiral structure is assessed visually, by comparing luminosity classifications for the artificially redshifted sample with the corresponding luminosity classifications from the Revised Shapley-Ames Catalog. We find that for exposure times similar to that of the HDF, spiral structure should be detectable in most luminous (MB ∼ M*) low-inclination spiral galaxies at z = 0.7 in which it is present. However, obvious spiral structure is only detectable in ∼30% of comparable galaxies in the HDF flanking field data using the Wide Field Planetary Camera 2. Our study of artificially redshifted local galaxy images suggests that, when viewed at similar resolution, noise level, and redshift-corrected wavelength, barred spirals are less common at z ∼ 0.7 than they are at z = 0.0, although more data are needed to definitively rule out the possibility that cosmic variance is responsible for much of this effect.
A case of musical preference for Johnny Cash following deep brain stimulation of the nucleus accumbens

Music is among all cultures an important part of the live of most people. Music has psychological benefits and may generate strong emotional and physiological responses. Recently, neuroscientists have discovered that music influences the reward circuit of the nucleus accumbens (NAcc), even when no explicit reward is present. In this clinical case study, we describe a 60-year old patient who developed a sudden and distinct musical preference for Johnny Cash following deep brain stimulation (DBS) targeted at the NAcc. This case report substantiates the assumption that the NAcc is involved in musical preference, based on the observation of direct stimulation of the accumbens with DBS. It also shows that accumbens DBS can change musical preference without habituation of its rewarding properties.
Using Microsoft Powerpoint© to conduct a Paired Stimulus Preference Assessment

iv Introduction to Preference Assessment . 1 Evaluating Preference Assessments . 6 The Use of Technology in Preference Assessments . 10 The Purpose of the Present Study . 13 Method . 14 Participants and Setting . 14 Teacher Interviews and Tangible PS Assessment . 15 Paired Stimulus PowerPoint© Presentation . 16 Discrimination Assessment . 17 Interobserver Agreement and Procedural Fidelity . 17 Results . 18 Discrimination Assessment, IOA, and Procedural Fidelity . 19 Discussion . 20
The Identified Model of the Strength of Competition-Cooperation Relationship between Enterprises

The competition relationship between enterprises is not necessarily mutually exclusive with their cooperation one, but unified. Competition is the same as Cooperation in essence but different from each other in the expression of external form, which is the different relationship strength under different external constraints and internal force between enterprises. The Strength of Competition-Cooperation Relationship (SCCR) is a spectrum from the closest integration relationship to the most competitive hostile relationship; between the two extremes there are super-strong cooperation, strong cooperation, weak cooperation, weak correlation, weak competition, strong competition and super-strong competition in sequence. In this study, the authors construct the indicator system of SCCR judgment from the following five dimensions: Commitment validity, Strength of interaction, Strength of resource reliance (competition), Emotional depth Benefit degree, and build a SCCR identified model based on AHP (analytic hierarchy process ) and FCE (fuzzy comprehensive evaluation).
ADAMS Re-Trace: a traceability recovery tool

We present the traceability recovery tool developed in the ADAMS artefact management system. The tool is based on an information retrieval technique, namely latent semantic indexing and aims at supporting the software engineer in the identification of the traceability links between artefacts of different types. We also present a case study involving seven student projects, which represented an ideal workbench for the tool. The results emphasise the benefits provided by the tool in terms of new traceability links discovered, in addition to the links manually traced by the software engineer. Moreover, the tool was also helpful in identifying cases of lack of similarity between artefacts manually traced by the software engineer, thus revealing inconsistencies in the usage of domain terms in these artefacts. This information is valuable to assess the quality of the produced artefacts.
Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts

To attain native-like competence, second language (L2) learners must establish mappings between familiar speech sounds and new phoneme categories. For example, Spanish learners of English must learn that [d] and [ð], which are allophones of the same phoneme in Spanish, can distinguish meaning in English (i.e., /deɪ/ “day” and /ðeɪ/ “they”). Because adult listeners are less sensitive to allophonic than phonemic contrasts in their native language (L1), novel target language contrasts between L1 allophones may pose special difficulty for L2 learners. We investigate whether advanced Spanish late-learners of English overcome native language mappings to establish new phonological relations between familiar phones. We report behavioral and magnetoencepholographic (MEG) evidence from two experiments that measured the sensitivity and pre-attentive processing of three listener groups (L1 English, L1 Spanish, and advanced Spanish late-learners of English) to differences between three nonword stimulus pairs ([idi]-[iði], [idi]-[iɾi], and [iði]-[iɾi]) which differ in phones that play a different functional role in Spanish and English. Spanish and English listeners demonstrated greater sensitivity (larger d' scores) for nonword pairs distinguished by phonemic than by allophonic contrasts, mirroring previous findings. Spanish late-learners demonstrated sensitivity (large d' scores and MMN responses) to all three contrasts, suggesting that these L2 learners may have established a novel [d]-[ð] contrast despite the phonological relatedness of these sounds in the L1. Our results suggest that phonological relatedness influences perceived similarity, as evidenced by the results of the native speaker groups, but may not cause persistent difficulty for advanced L2 learners. Instead, L2 learners are able to use cues that are present in their input to establish new mappings between familiar phones.
THE EFFECT OF USING PICTURE WORD INDUCTIVE MODEL ON TEACHING DESCRIPTIVE TEXT WRITING

Abstract: The use of PWIM emphasized more on how students recognized the words by looking at the pictures teacher provided. The purpose of this research was to know the effect of using Picture Word Inductive Model on teaching descriptive text writing on the tenth - grade students of SMA Negeri 2 Sungai Raya, Kubu Raya. This research used quasi-experimental research pretest-posttest non-equivalent group design. The samples of this research were 20 students for experimental group and 20 students for control group. The use of Picture Word Inductive Model had an effect on teaching descriptive text writing. The effect size for the treatment was considered as strong, under the t-test the difference of the interval was significant. It is suggested that teacher uses PWIM as the alternative technique in teaching descriptive text. Keywords: Writing, Picture Word Inductive Model, quasi-experimental research Abstrak: Penggunaan teknik PWIM lebih menekankan bagaimana murid mangenali kata dengan melihat gambar yang telah guru sediakan. Penelitian ini bertujuan untuk mengetahui efek dari Picture Word Inductive Model terhadap pengajaran penulisan deskriptif teks di kelas X SMA Negeri 2 Sungai Raya Kubu Raya. Metode penelitian yang digunakan adalah quasi experiment dengan rancangan penelitian prete st-posttest non-equivalent group design. Sampel penelitian ini adalah 20 siswa untuk kelas experiment dan 20 siswa untuk kelas kontrol. Penggunaan PWIM berdampak pada pengajaran descriptive teks writing, efek dari perlakuan dianggap mempunyai efek yang kuat dan adanya perbedaan yang signifikan dari t-test . PWIM disarankan untuk digunakan oleh guru bahasa inggris untuk mendapatkan skor lebih baik dan sebagai teknik alternative untuk mangajar writing. Kata Kunci : Menulis, Picture Word Inductive Model, penelitian quasi- experimental