Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative Trait Loci for the Circadian Clock in Neurospora crassa

Neurospora crassa has been a model organism for the study of circadian clocks for the past four decades. Among natural accessions of Neurospora crassa, there is significant variation in clock phenotypes. In an attempt to investigate natural allelic variants contributing to quantitative variation, we used a quantitative trait loci mapping approach to analyze three independent mapping populations whose progenitors were collected from geographically isolated locations. Two circadian clock phenotypes, free-running period and entrained phase, were evaluated in the 188 F1 progeny of each mapping population. To identify the clock QTL, we applied two QTL mapping analyses: composite interval mapping (CIM) and Bayesian multiple QTL analysis (BMQ). When controlling false positive rates ≤0.05, BMQ appears to be the more sensitive of the two approaches. BMQ confirmed most of the QTL from CIM (18 QTL) and identified 23 additional QTL. While 13 QTL colocalize with previously identified clock genes, we identified 30 QTL that were not linked with any previously characterized clock genes. These are candidate regions where clock genes may be located and are expected to lead to new insights in clock regulation.
Automatically Assessing Machine Summary Content Without a Gold Standard

The most widely adopted approaches for evaluation of summary content follow some protocol for comparing a summary with gold-standard human summaries, which are traditionally called model summaries. This evaluation paradigm falls short when human summaries are not available and becomes less accurate when only a single model is available. We propose three novel evaluation techniques. Two of them are model-free and do not rely on a gold standard for the assessment. The third technique improves standard automatic evaluations by expanding the set of available model summaries with chosen system summaries.We show that quantifying the similarity between the source text and its summary with appropriately chosen measures produces summary scores which replicate human assessments accurately. We also explore ways of increasing evaluation quality when only one human model summary is available as a gold standard. We introduce pseudomodels, which are system summaries deemed to contain good content according to automatic evaluation. Combining the pseudomodels with the single human model to form the gold-standard leads to higher correlations with human judgments compared to using only the one available model. Finally, we explore the feasibility of another measure—similarity between a system summary and the pool of all other system summaries for the same input. This method of comparison with the consensus of systems produces impressively accurate rankings of system summaries, achieving correlation with human rankings above 0.9.
Post-seismic motion following the 1997 Manyi (Tibet) earthquake: InSAR observations and modelling

SUMMARY On November 8 1997 a Mw 7.6 earthquake occurred in the Manyi region of northern Tibet, near the western end of the Kunlun Fault. Over 7 m of left-lateral slip occurred on a 200-kmlong fault. Here we use InSAR observations of post-seismic surface deformation following the Manyi earthquake to investigate possible causal mechanisms. Time-series of deformation are constructed from 26 interferograms, covering the entire length of the fault for nearly 4 yr after the earthquake. Three different modelling approaches are used to try and understand the observed variations in surface displacement. First order poroelastic models predict displacement fields which do not match those observed. Modelling of viscoelastic stress relaxation in a half-space with standard linear solid rheology beneath an elastic lid provides a reasonable fit to the observations, and demonstrates that two relaxation times are needed to characterize the post-seismic transient. The best-fitting viscosity is 4 £ 10 18 Pa s, and the fully-relaxed shear modulus is 32 per cent of the purely elastic value. A model with a Maxwell viscoelastic halfspace underlying the lid cannot explain the observations: at later times, larger viscosities are required than at earlier times. This increase in effective viscosity with time may be consistent with stress relaxation occurring in a power-law rheology. The time-series are also inverted for distributed afterslip on an extension of the coseismic rupture. Along-strike correlation of coseismic and post-seismic slip maxima suggests that afterslip is a plausible mechanism. The maximum slip in the afterslip model is 0.72 m after 3 yr, and the equivalent moment release is approximately 20 per cent of the coseismic moment. This study shows that it is possible to rule out certain mechanisms as the dominant post-seismic process, but with the current InSAR data set it is difficult to distinguish between other plausible options.
Force control on antagonistic Twist-drive Actuator robot

In recent researches relating to robotic fingers, a novel power transmission mechanism had been designed, and developed as Twist-drive Actuators or Twisted String Actuator systems (TSA). These actuation structures, state of the art, include compact designs, light-weight mechanical structures, inherent compliance, and variable gearing, resulting in the fabrication of anthropomorphic robotic hands. However, those studies mentioned position control of the joint, and focused on the control performance of the pulling forces of a twisted string. This paper, therefore, introduces a novel joint mechanism composed of an Antagonistically-twisted Round-belt Actuator (ARA), which is able to make rotating motion by means of contraction forces induced by twisting small-diameter elastic round-belts. A noteworthy point in this paper is that the ARA robot is extremely well-suited for contact force control, which is exerted on the tip of the single joint robot. First, we demonstrate the existence of hysteresis characteristics of static contraction forces induced by the round-belt twisting, in which three belts are simultaneously twisted at constant low-speed. In addition, there exists a stress relaxation phenomenon when strongly twisting the elastic round-belts. We reveal that such sorts of discontinuous and nonlinear properties do not influence control performance in either the contraction force on the belts or contact force on the tip of the robot. Finally, this paper clearly shows stable and accurate tracking performance of the contact force of the ARA robot. In these experiments, we newly develop a twin/triple-twisted round-belt structure for the agonist side actuator, thus enhancing the contact forces effectively.
Contrasting Patterns of Transposable Element and Satellite Distribution on Sex Chromosomes (XY1Y2) in the Dioecious Plant Rumex acetosa

Rumex acetosa is a dioecious plant with the XY1Y2 sex chromosome system. Both Y chromosomes are heterochromatic and are thought to be degenerated. We performed low-pass 454 sequencing and similarity-based clustering of male and female genomic 454 reads to identify and characterize major groups of R. acetosa repetitive DNA. We found that Copia and Gypsy retrotransposons dominated, followed by DNA transposons and nonlong terminal repeat retrotransposons. CRM and Tat/Ogre retrotransposons dominated the Gypsy superfamily, whereas Maximus/Sireviruses were most abundant among Copia retrotransposons. Only one Gypsy subfamily had accumulated on Y1 and Y2 chromosomes, whereas many retrotransposons were ubiquitous on autosomes and the X chromosome, but absent on Y1 and Y2 chromosomes, and others were depleted from the X chromosome. One group of CRM Gypsy was specifically localized to centromeres. We also found that majority of previously described satellites (RAYSI, RAYSII, RAYSIII, and RAE180) are accumulated on the Y chromosomes where we identified Y chromosome-specific variant of RAE180. We discovered two novel satellites—RA160 satellite dominating on the X chromosome and RA690 localized mostly on the Y1 chromosome. The expression pattern obtained from Illumina RNA sequencing showed that the expression of transposable elements is similar in leaves of both sexes and that satellites are also expressed. Contrasting patterns of transposable elements (TEs) and satellite localization on sex chromosomes in R. acetosa, where not only accumulation but also depletion of repetitive DNA was observed, suggest that a plethora of evolutionary processes can shape sex chromosomes.
User-oriented document summarization through vision-based eye-tracking

We propose a new document summarization algorithm which is personalized. The key idea is to rely on the attention (reading) time of individual users spent on single words in a document as the essential clue. The prediction of user attention over every word in a document is based on the user's attention during his previous reads, which is acquired via a vision-based commodity eye-tracking mechanism. Once the user's attentions over a small collection of words are known, our algorithm can predict the user's attention over every word in the document through word semantics analysis. Our algorithm then summarizes the document according to user attention on every individual word in the document. With our algorithm, we have developed a document summarization prototype system. Experiment results produced by our algorithm are compared with the ones manually summarized by users as well as by commercial summarization software, which clearly demonstrates the advantages of our new algorithm for user-oriented document summarization.
Social but safe? Quality and safety of diabetes-related online social networks

OBJECTIVE To foster informed decision-making about health social networking (SN) by patients and clinicians, the authors evaluated the quality/safety of SN sites' policies and practices. DESIGN Multisite structured observation of diabetes-focused SN sites. Measurements 28 indicators of quality and safety covering: (1) alignment of content with diabetes science and clinical practice recommendations; (2) safety practices for auditing content, supporting transparency and moderation; (3) accessibility of privacy policies and the communication and control of privacy risks; and (4) centralized sharing of member data and member control over sharing. RESULTS Quality was variable across n=10 sites: 50% were aligned with diabetes science/clinical practice recommendations with gaps in medical disclaimer use (30% have) and specification of relevant glycosylated hemoglobin levels (0% have). Safety was mixed with gaps in external review approaches (20% used audits and association links) and internal review approaches (70% use moderation). Internal safety review offers limited protection: misinformation about a diabetes 'cure' was found on four moderated sites. Of nine sites with advertising, transparency was missing on five; ads for unfounded 'cures' were present on three. Technological safety was poor with almost no use of procedures for secure data storage and transmission; only three sites support member controls over personal information. Privacy policies' poor readability impedes risk communication. Only three sites (30%) demonstrated better practice. Limitations English-language diabetes sites only. CONCLUSION The quality/safety of diabetes SN is variable. Observed better practice suggests improvement is feasible. Mechanisms for improvement are recommended that engage key stakeholders to balance autonomy, community ownership, conditions for innovation, and consumer protection.
Towards Multicast Delay Analysis for Ad hoc Wireless Networks

Delay performance of packet transmission in wireless ad hoc networks is highly dependent on the underlying medium access control (MAC) protocol. Since most delay-sensitive applications are transmitted in a multicast fashion, a dedicated access model for multicast is, therefore, needed to represent the actual characteristics of multicast packet access mechanisms. In this paper, a multicast station model is developed in order to provide an anticipated next-hop delay performance prediction, which can be used in a network layer for providing guarantee quality of service (QoS) in an ad hoc multicast network. Based on the assumption of unsaturated traffic, the multicast model is able to provide accurate estimation of access delay values when compared with simulations of access delay.
Determinan Kebahagiaan Di Indonesia

The research objective is to analyse the determinants of happiness in Indonesia. Using cross-section data from Indonesia Family Life Survey (IFLS) wave 4, 2007, this study takes 17.650 observations which estimated using Oprobit model. The Oprobit model was chosen because of ordinaled response variable and the normal assumption in error distribution. The result shows that happiness in Indonesia positively affected by income, education level, perceived health status and social capital. But social capital that connected with religion and ethnic don’t have significant effect on happiness. All predictors are robust. Demographic characteristics inform that married people, non household head, live in urban area, outside of Jawa-Bali islands and Javanese were happier than others. There is no difference in happiness level between man and woman. Happiness-age relationship indicated U-shaped curve. Marginal effect shows different effect for every happiness level due to a unit change in independent variable. Abstrak Tujuan penelitian ini adalah untuk menganalisis faktor-faktor penentu kebahagiaan di Indonesia. Dengan menggunakan data antar ruang/silang tempat dari Indonesia Family Life Survey (IFLS) wave 4, 2007, studi ini mengambil 17,650 pengamatan yang diestimasi menggunakan model Oprobit. Model Oprobit dipilih karena adanya variabel respon ordinal dan asumsi normal dalam distribusi kesalahan. Hasil penelitian menunjukkan bahwa kebahagiaan di Indonesia secara positif dipengaruhi oleh pendapatan, tingkat pendidikan, status kesehatan yang dirasakan dan modal sosial. Namun demikian, modal sosial yang berkaitan dengan agama dan etnis tidak memiliki pengaruh yang signifikan terhadap kebahagiaan. Semua prediktor bersifat robust. Karakteristik demografi menginformasikan bahwa orang yang menikah, bukan kepala rumah tangga, tinggal di daerah perkotaan, berada di luar pulau Jawa-Bali dan dari suku Jawa lebih bahagia daripada yang lain. Riset ini juga menemukan bahwa tidak terdapat perbedaan dalam tingkat kebahagiaan antara pria dan wanita. Kemudian, hubungan antara kebahagiaan dan usia menunjukkan kurva yang berbentuk U. Terakhir, efek marjinal menunjukkan efek yang berbeda untuk setiap tingkat kebahagiaan karena perubahan unit variabel independen.
Altered Ionic Selectivity of the Sodium Channel Revealed by Cysteine Mutations within the Pore

To explore the role of pore-lining amino acids in Na+ channel ion-selectivity, pore residues were replaced serially with cysteine in cloned rat skeletal muscle Na+ channels. Ionic selectivity was determined by measuring permeability and ionic current ratios of whole-cell currents in Xenopus oocytes. The rSkM1 channels displayed an ionic selectivity sequence Na+>Li+>NH4 +>>K+>>Cs+ and were impermeable to divalent cations. Replacement of residues in domain IV showed significantly enhanced current and permeability ratios of NH4 + and K+, and negative shifts in the reversal potentials recorded in the presence of external Na+ solutions when compared to cysteine mutants in domains I, II, and III (except K1237C). Mutants in domain IV showed altered selectivity sequences: W1531C (NH4 +>K+>Na+≥Li+≈Cs+), D1532C, and G1533C (Na+>Li+≥NH4 +>K+>Cs+). Conservative replacement of the aromatic residue in domain IV (W1531) with phenylalanine or tyrosine retained Na+ selectivity of the channel while the alanine mutant (W1531A) reduced ion selectivity. A single mutation within the third pore forming region (K1237C) dramatically altered the selectivity sequence of the rSkM1 channel (NH4 +>K+>Na+≥Li+≈Cs+) and was permeable to divalent cations having the selectivity sequence Ca2+≥Sr2+>Mg2+>Ba2+. Sulfhydryl modification of K1237C, W1531C or D1532C with methanethiosulfonate derivatives that introduce a positively charged ammonium group, large trimethylammonium moiety, or a negatively charged sulfonate group within the pore was ineffective in restoring Na+ selectivity to these channels. Selectivity of D1532C mutants could be largely restored by increasing extracellular pH suggesting altering the ionized state at this position influences selectivity. These data suggest that K1237 in domain III and W1531, D1532, and G1533 in domain IV play a critical role in determining the ionic selectivity of the Na+ channel.
Effective Multi-step Temporal-Difference Learning for Non-Linear Function Approximation

Multi-step temporal-difference (TD) learning, where the update targets contain information from multiple time steps ahead, is one of the most popular forms of TD learning for linear function approximation. The reason is that multi-step methods often yield substantially better performance than their single-step counter-parts, due to a lower bias of the update targets. For non-linear function approximation, however, single-step methods appear to be the norm. Part of the reason could be that on many domains the popular multi-step methods TD($\lambda$) and Sarsa($\lambda$) do not perform well when combined with non-linear function approximation. In particular, they are very susceptible to divergence of value estimates. In this paper, we identify the reason behind this. Furthermore, based on our analysis, we propose a new multi-step TD method for non-linear function approximation that addresses this issue. We confirm the effectiveness of our method using two benchmark tasks with neural networks as function approximation.
Revision of the ostracode genus Fossocytheridea Swain and Brown 1964: Mesozoic ancestral root for the modern eurytopic Cyprideis Jones

Abstract The ostracode genus Fossocytheridea Swain and Brown 1964 is emended herein. A summary of the diagnostic characters include: (1) a median sulcus, (2) a tripartite antimerodont hinge with distinct heart-shaped terminal elements, (3) distinct sexual dimorphism; (4) a narrow inner margin that has 20–28 straight radial pore canals, and (5) variability in the external carapace (pore shape, pore density, and patterns of reticulation) that bears close resemblance to Cyprideis. Two new species are described from southwest Utah (U.S.A): Fossocytheridea mosbyense sp. nov. and Fossocytheridea kirklandi sp. nov. and 21 taxa previously assigned to Fabanella, Sarlatina, Ovocytheridea, Dolocytheridea, Antibythocypris, and Cytheridea are assigned to the emended genus. Fossocytheridea resembles Cyprideis with respect to both shell morphology and ecology since it occurs in association with euryhaline biota in coal-bearing strata. Expansion of marginal marine environments during the highest sea level of the Mesozoic saw Fossocytheridea successfully migrate and dominate restricted coastal environments. Since this expansion, the prominent characters of Fossocytheridea have been preserved in descendent genera belonging to the tribe Cyprideidini Kollmann 1960 that are preserved to this day in Cyprideis.
Does A Major Earthquake Change Job Preferences and Human Values?

Does a major natural disaster change human values and job preferences? The present studies examined whether the experience of a natural disaster experience shifts people's values and job preferences toward pro–social directions. In Study 1 (cross–temporal analysis), we analysed job application data in nine cities in Japan over 12 years and found that the popularity of pro–social occupations (e.g. firefighter) increased after the Great Hanshin–Awaji Earthquake in 1995, in particular the area hit hardest by the quake. In Study 2 (a large national survey), we found that Japanese respondents who had experienced a major earthquake are more likely to hold a pro–social job than those who never experienced a major earthquake. Together, the current findings suggest that the experience of a major natural disaster shifts human values from the egocentric to the allocentric direction, which in turn could result in a social structure that values pro–social occupations. Copyright © 2017 European Association of Personality Psychology
Connectivity of random k-nearest-neighbour graphs

Let 𝓅 be a Poisson process of intensity one in a square S n of area n. We construct a random geometric graph G n,k by joining each point of 𝓅 to its k ≡ k(n) nearest neighbours. Recently, Xue and Kumar proved that if k ≤ 0.074 log n then the probability that G n, k is connected tends to 0 as n → ∞ while, if k ≥ 5.1774 log n, then the probability that G n, k is connected tends to 1 as n → ∞. They conjectured that the threshold for connectivity is k = (1 + o(1)) log n. In this paper we improve these lower and upper bounds to 0.3043 log n and 0.5139 log n, respectively, disproving this conjecture. We also establish lower and upper bounds of 0.7209 log n and 0.9967 log n for the directed version of this problem. A related question concerns coverage. With G n, k as above, we surround each vertex by the smallest (closed) disc containing its k nearest neighbours. We prove that if k ≤ 0.7209 log n then the probability that these discs cover S n tends to 0 as n → ∞ while, if k ≥ 0.9967 log n, then the probability that the discs cover S n tends to 1 as n → ∞.
Preconceptions and Individual Differences in Understanding Visual Metaphors

Understanding information visualization is more than a matter of reading a series of data values; it is also a matter of incorporating a visual structure into one's own thinking about a problem. We have proposed visual metaphors as a framework for understanding high‐level visual structure and its effect on visualization use. Although there is some evidence that visual metaphors can affect visualization use, the nature of this effect is still ambiguous. We propose that a user's preconceived metaphors for data and other individual differences play an important role in her ability to think in a variety of visual metaphors, and subsequently in her ability to use a visualization. We test this hypothesis by conducting a study in which a participant's preconceptions and thinking style were compared with the degree to which she is affected by conflicting metaphors in a visualization and its task questions. The results show that metaphor compatibility has a significant effect on accuracy, but that factors such as spatial ability and personality can lessen this effect. We also find a complex influence of self‐reported metaphor preference on performance. These findings shed light on how people use visual metaphors to understand a visualization.
Circumstellar and circumbinary discs in eccentric stellar binaries

We study the existence of stable trajectories, where gas could accumulate to form accretion discs, around stars that form binary systems in eccentric orbits. Since the potential is time dependent, no fixed, periodic, close orbits exist. Instead, we search for invariant loops: closed curves that change shape in synchronism with the binary orbital phase. Non-intersecting loops can provide the scaffolding for circumstellar and circumbinary discs in these systems. We investigate the range of regions in phase space where these non-intersecting loops can exist and find this to depend on both, the mass ratio of the stars and their orbital eccentricity, with a strong dependence on the latter. The recent discovery of planets within close binary systems makes this work very relevant.