Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissecting protein-induced DNA looping dynamics in real time

Many proteins that interact with DNA perform or enhance their specific functions by binding simultaneously to multiple target sites, thereby inducing a loop in the DNA. The dynamics and energies involved in this loop formation influence the reaction mechanism. Tethered particle motion has proven a powerful technique to study in real time protein-induced DNA looping dynamics while minimally perturbing the DNA–protein interactions. In addition, it permits many single-molecule experiments to be performed in parallel. Using as a model system the tetrameric Type II restriction enzyme SfiI, that binds two copies of its recognition site, we show here that we can determine the DNA–protein association and dissociation steps as well as the actual process of protein-induced loop capture and release on a single DNA molecule. The result of these experiments is a quantitative reaction scheme for DNA looping by SfiI that is rigorously compared to detailed biochemical studies of SfiI looping dynamics. We also present novel methods for data analysis and compare and discuss these with existing methods. The general applicability of the introduced techniques will further enhance tethered particle motion as a tool to follow DNA–protein dynamics in real time.
On the long time behavior of second order differential equations with asymptotically small dissipation

We investigate the asymptotic properties as $ t\to \infty$ of the following differential equation in the Hilbert space $ H$: $$(\mathcal{S})\qquad\qquad\qquad\ddot{x}(t)+a(t)\dot{x}(t)+ \nabla G(x(t))=0, \quad t\geq 0$$ where the map $ a:\mathbb{R}_+\to \mathbb{R}_+$ is nonincreasing and the potential $ G:H\to \mathbb{R}$ is of class $ \mathcal{C}^1$. If the coefficient $ a(t)$ is constant and positive, we recover the so-called ``Heavy Ball with Friction'' system. On the other hand, when $ a(t)=1/(t+1)$ we obtain the trajectories associated to some averaged gradient system. Our analysis is mainly based on the existence of some suitable energy function. When the function $ G$ is convex, the condition $ \int_0^\infty a(t) dt =\infty$ guarantees that the energy function converges toward its minimum. The more stringent condition $ \int_0^{\infty} e^{-\int_0^t a(s) ds}dt<\infty$ is necessary to obtain the convergence of the trajectories of $ (\mathcal{S})$ toward some minimum point of $ G$. In the one-dimensional setting, a precise description of the convergence of solutions is given for a general nonconvex function $ G$. We show that in this case the set of initial conditions for which solutions converge to a local minimum is open and dense.
Integration of Carbon and Nitrogen Metabolism with Energy Production Is Crucial to Light Acclimation in the Cyanobacterium Synechocystis1[W][OA]

Light drives the production of chemical energy and reducing equivalents in photosynthetic organisms required for the assimilation of essential nutrients. This process also generates strong oxidants and reductants that can be damaging to the cellular processes, especially during absorption of excess excitation energy. Cyanobacteria, like other oxygenic photosynthetic organisms, respond to increases in the excitation energy, such as during exposure of cells to high light (HL) by the reduction of antenna size and photosystem content. However, the mechanism of how Synechocystis sp. PCC 6803, a cyanobacterium, maintains redox homeostasis and coordinates various metabolic processes under HL stress remains poorly understood. In this study, we have utilized time series transcriptome data to elucidate the global responses of Synechocystis to HL. Identification of differentially regulated genes involved in the regulation, protection, and maintenance of redox homeostasis has offered important insights into the optimized response of Synechocystis to HL. Our results indicate a comprehensive integrated homeostatic interaction between energy production (photosynthesis) and energy consumption (assimilation of carbon and nitrogen). In addition, measurements of physiological parameters under different growth conditions showed that integration between the two processes is not a consequence of limitations in the external carbon and nitrogen levels available to the cells. We have also discovered the existence of a novel glycosylation pathway, to date known as an important nutrient sensor only in eukaryotes. Up-regulation of a gene encoding the rate-limiting enzyme in the hexosamine pathway suggests a regulatory role for protein glycosylation in Synechocystis under HL.
Distribution of the cell substratum attachment (CSAT) antigen on myogenic and fibroblastic cells in culture

Previous studies (Neff et al., 1982, J. Cell. Biol. 95:654-666; Decker et al., 1984. J. Cell. Biol. 99:1388-1404) have described a monoclonal antibody (CSAT Mab) directed against a complex of three integral membrane glycoproteins of 120,000-160,000 mol wt (CSAT antigen [ag]) involved in the cell matrix adhesion of myoblasts and fibroblasts. In localization studies on fibroblasts presented here, CSAT ag has a discrete, well-organized distribution pattern. It co-aligns with portions of stress fibers and is enriched at the periphery of, but not directly beneath vinculin-rich focal contacts. In this last location, it co-distributes with fibronectin, consistent with the suggestion that the CSAT ag participates in the mechanism by which fibroblasts attach to fibronectin. In prefusion myoblasts, which are rapidly detached by CSAT Mab, CSAT ag is distributed diffusely as are vinculin, laminin, and fibronectin. After fusion, myotubes become more difficult to detach with CSAT Mab. The CSAT ag and vinculin are organized in a much more discrete pattern on the myotube surface, becoming enriched at microfilament bundle termini and in lateral lamellae which appear to attach myotubes to the substratum. These results suggest that the organization of CSAT ag-adhesive complexes on the surface of myogenic cells can affect the stability of their adhesive contacts. We conclude from the sum of the studies presented that, in both myogenic and fibroblastic cells, the CSAT ag is localized in sites expected of a surface membrane mediator of cell adhesion to extracelluon of CSAT ag- adhesive complexes on the surface of myogenic cells can affect the stability of their adhesive contacts. We conclude from the sum of the studies presented that, in both myogenic and fibroblastic cells, the CSAT ag is localized in sites expected of a surface membrane mediator of cell adhesion to extracellular matrix. The results from studies that use fibroblasts in particular suggest the involvement of CSAT ag in the adhesion of these cells to fibronectin.
Knowledge Lean Word-Sense Disambiguation

We present a corpus-based approach to word-sense disambiguation that only requires information that can be automatically extracted from untagged text. We use unsupervised techniques to estimate the parameters of a model describing the conditional distribution of the sense group given the known contextual features. Both the EM algorithm and Gibbs Sampling are evaluated to determine which is most appropriate for our data. We compare their disambiguation accuracy in an experiment with thirteen different words and three feature sets. Gibbs Sampling results in small but consistent improvement in disambiguation accuracy over the EM algorithm.
Modeling and behavioral simulation of noise transfer characteristics of a 2 GHz phased-locked loop for frequency synthesizer

We present here an analytical phase noise model of phased-locked loop for frequency synthesizer and its simulation in GHz frequency range. The noise model has been derived and simulated considering two different filter sections in the loop of the phased-locked loop model, namely: (i) active lag-lead filter and (ii) standard feedback approach. The noise transfer functions of the phased-locked loop frequency synthesizer are derived in s-domain for analysis. The mathematical model and analysis for the five main noise transfer functions which are existed in the system have been derived for analysis. The simulation of the phase noise is performed by using MATLAB (Version: 7.1). Here we will discuss in details the procedure for mathematical derivation of the noise model for both active leg-lead filter and filter with standard feedback approach in the loop, its simulation and their results.
Computing Robust Counter-Strategies

Adaptation to other initially unknown agents often requires computing an effective counter-strategy. In the Bayesian paradigm, one must find a good counter-strategy to the inferred posterior of the other agents' behavior. In the experts paradigm, one may want to choose experts that are good counter-strategies to the other agents' expected behavior. In this paper we introduce a technique for computing robust counter-strategies for adaptation in multiagent scenarios under a variety of paradigms. The strategies can take advantage of a suspected tendency in the decisions of the other agents, while bounding the worst-case performance when the tendency is not observed. The technique involves solving a modified game, and therefore can make use of recently developed algorithms for solving very large extensive games. We demonstrate the effectiveness of the technique in two-player Texas Hold'em. We show that the computed poker strategies are substantially more robust than best response counter-strategies, while still exploiting a suspected tendency. We also compose the generated strategies in an experts algorithm showing a dramatic improvement in performance over using simple best responses.
Open-Domain Attribute-Value Acquisition from Semi-Structured Texts

This paper proposes an unsupervised method that acquires a set of attribute-value pairs (avps, e.g., ⟨director, W. Wyler⟩) for a given object (e.g., “Ben-Hur”) from semi-structured HTML documents. The objects’ avps are one of the principal components of domain ontologies. We first acquire class attributes that are used by many web authors to describe the objects’ avps. Then, we exploit the acquired class attributes to induce patterns for extracting avps from web pages. Experimental results show that, with our method, at least one set of correct avps are acquired for 67.7% of objects among open-domain class-object pairs whose source documents (web pages) include the objects’ avps in layouts.
Long-term follow-up of the West of Scotland Coronary Prevention Study.

To the Editor: Ford et al. (Oct. 11 issue)1 report long-term follow-up data from the West of Scotland Coronary Prevention Study (WOSCOPS), which showed that statin treatment for 5 years provided an ongoing reduction in cardiovascular events for an additional 10 years. Stabilization of existing plaque, slowing of the progression of coronary artery disease, and possibly regression of atherosclerosis are suggested as potential mechanisms for this benefit. This follow-up study adjusted for the presence or absence of a history of diabetes at entry. Previous data from WOSCOPS have shown that randomized assignment to pravastatin therapy resulted in a 30% reduction in the risk of the development of diabetes.2 Could this reduction in the incidence of diabetes during the 5-year trial period account, in part, for the observed reduction in future cardiovascular events in the 10 years after completion of the trial?
Visual navigation in an open environment without map

We describe how a mobile robot controlled only by visual information can retrieve a particular goal location in an open environment. Our model does not need a precise map nor to learn all the possible positions in the environment. The system is a neural architecture inspired from neurobiological studies using the recognition of visual patterns called landmarks. The robot merges this visual information and its azimuth to build a plastic representation of its location. This representation is used to learn the best movement to reach the goal. A simple and fast online learning of a few places located near the goal allows the robot to reach the goal from anywhere in its neighborhood. The system uses only an egocentric representation of the robot environment and presents very high generalization capabilities. We describe an efficient implementation tested on our robot in two real indoor environments. We show the limitations of the model and its possible extensions to create autonomous robots only guided by visual information.
GENERATION AND WEIGHTING OF 3D POINT CORRESPONDENCES FOR IMPROVED REGISTRATION OF RGB-D DATA

Registration of RGB-D data using visual features is often influenced by errors in the transformation of visual features to 3D space as well as the random error of individual 3D points. In a long sequence, these errors accumulate and lead to inaccurate and deformed point clouds, particularly in situations where loop closing is not feasible. We present an epipolar search method for accurate transformation of the keypoints from 2D to 3D space, and define weights for the 3D points based on the theoretical random error of depth measurements. Our results show that the epipolar search method results in more accurate 3D correspondences. We also demonstrate that weighting the 3D points improves the accuracy of sensor pose estimates along the trajectory.
Relation Between Cognitive Testing Performance and Pattern of Substance Use in Males at Treatment Entry

This study examined the frequency and pattern of cognitive impairment in individuals entering substance use disorder treatment and additionally examined the relation between pattern of cognitive impairment and type of substance(s) used: alcohol (n = 116), cocaine (n = 49), alcohol/cocaine (n = 76), and alcohol/multiple substance (n = 54). The Cognistat, a screening measure of cognitive functioning, and the Addiction Severity Index were given to male veterans at the time of entering 3- to 4-week residential/day drug treatment. The most prominent areas of impairment were memory (37% of the total sample) and similarities or abstract concept formation (21% of the total sample). Moderate or greater severity of impairment was noted on at least one Cognistat scale in 35% of the participants. Results indicated no significant differences in the patterns of cognitive domain impairment between groups based on type(s) of substances used at the time of entering treatment. Multiple substance use was significantly related to greater levels of psychiatric problems as identified by the Alcohol Severity Index. Given the rate of impairment in memory and verbal abstract reasoning noted, it is suggested that cognitive screening be a standard consideration in residential substance use disorder treatment to assist in treatment selection and delivery that is optimized to provide maximal benefit to patients.
Smoothed Body Composition Percentiles Curves for Mexican Children Aged 6 to 12 Years

Overweight children and childhood obesity are a public health problem in Mexico. Obesity is traditionally assessed using body mass index (BMI), but an excess of adiposity does not necessarily reflect a high BMI. Thus, body composition indexes are a better alternative. Our objective was to generate body composition percentile curves in children from Mexico City. A total of 2026 boys and 1488 girls aged 6 to 12 years old were studied in Mexico City. Body weight, height, and BMI calculation were measured. Total body fat percentage (TBFP) was derived from the skinfold thicknesses, and fat mass (FMI) and free fat mass indexes (FFMI) were calculated. Finally, age- and gender-specifıc smoothed percentile curves were generated with Cole’s Lambda, Mu, and Sigma (LMS) method. In general, height, weight, waist circumference (WC), and TBFP were higher in boys, but FFM was higher in girls. TBFP appeared to increase significantly between ages 8 and 9 in boys (+2.9%) and between ages 10 and 11 in girls (+1.2%). In contrast, FFM% decreased noticeably between ages 8 and 9 until 12 years old in boys and girls. FMI values peaked in boys at age 12 (P97 = 14.1 kg/m2) and in girls at age 11 (P97 = 8.8 kg/m2). FFMI percentiles increase at a steady state reaching a peak at age 12 in boys and girls. Smoothed body composition percentiles showed a different pattern in boys and girls. The use of TBFP, FMI, and FFMI along with BMI provides valuable information in epidemiological, nutritional, and clinical research.
Differentiation-dependent telomeric long non-coding transcription in a model of skeletal myogenesis

Telomeres comprise the distal ends of eukaryotic chromosomes, serve to maintain genomic integrity and are extended by the ribonucleoprotein telomerase. Recent evidence indicates that telomeres are transcribed to generate long non-coding RNAs (lncRNAs) and that these transcripts (TERRA) may inhibit telomerase activity. In this study we assessed telomerase activity and telomeric lncRNA expression in a mouse model of skeletal myogenesis. Using the C2C12 cell line we demonstrated decreased telomerase activity during differentiation into terminally-differentiated skeletal myotubes. Despite existing in a post-mitotic state, residual telomerase activity remained in C2C12 myotubes, indicating a role independent of telomere extension. Telomeric transcripts were detected in both myoblasts and myotubes, with reduced expression during differentiation correlating with reduced telomerase expression. Our data indicate that in a mouse model of skeletal myogenesis TERRA expression does not reduce telomerase activity, suggesting that their relationship is more complex than originally perceived; the role of telomeric derived lncRNAs in relation to telomerase activity may be cell-type specific. These findings raise the possibility for novel non-telomerase regulatory function for TERRA-lncRNAs during skeletal myogenesis.
Learning part-based templates from large collections of 3D shapes

As large repositories of 3D shape collections continue to grow, understanding the data, especially encoding the inter-model similarity and their variations, is of central importance. For example, many data-driven approaches now rely on access to semantic segmentation information, accurate inter-model point-to-point correspondence, and deformation models that characterize the model collections. Existing approaches, however, are either supervised requiring manual labeling; or employ super-linear matching algorithms and thus are unsuited for analyzing large collections spanning many thousands of models. We propose an automatic algorithm that starts with an initial template model and then jointly optimizes for part segmentation, point-to-point surface correspondence, and a compact deformation model to best explain the input model collection. As output, the algorithm produces a set of probabilistic part-based templates that groups the original models into clusters of models capturing their styles and variations. We evaluate our algorithm on several standard datasets and demonstrate its scalability by analyzing much larger collections of up to thousands of shapes.
The Effect of Leptin on Luteinizing Hormone Release Is Exerted in the Zona Incerta and Mediated by Melanin‐Concentrating Hormone

The adipose hormone, leptin, not only restrains appetite, but also influences energy expenditure. One such influence is to promote sexual maturation and fertility. The neuromodulatory circuits that mediate this effect are not well known but the present study suggests that one mediator could be melanin‐concentrating hormone (MCH). We show that the long‐form receptor (Ob‐Rb) is expressed in the zona incerta of the rat and that administration of leptin (both 0.5 µg and 1.0 µg/side) into this area of ovariectomized, oestrogen‐primed rats stimulated the release of luteinizing hormone (LH) within 1 h, the effect enduring for a further 1 h. Injections of leptin into the arcuate nucleus induced a smaller, transient rise in LH while injections into the paraventricular and ventromedial nuclei were without effect. MCH neurones are present in the zona incerta and administration of this hormone into the medial preoptic area (mPOA) stimulates LH release, therefore we investigated the possibility that MCH might mediate this effect of leptin. An injection of MCH antiserum into mPOA prevented the rise in LH normally induced by leptin injected into the zona incerta. In addition, melanocortin receptor antagonists ([D‐Arg8]ACTH(4‐10) and [Ala6]ACTH(4‐10)), previously shown to inhibit the stimulatory effect of MCH on LH release, also inhibited the effect of leptin. We propose that one route by which leptin may promote reproductive activity is by enhancing MCH release from fibres within the mPOA. Speculative mechanisms for the action of MCH include the following possibilities: MCH may be acting on the specific MCH receptor which in turn interacts with a melanocortin or melanocortin‐like receptor; MCH may bind directly to one of the melanocortin receptors; or melanocortin antagonists may interact with the MCH receptor.
How Can Skin Check Reminders be Personalised to Patient Conscientiousness?

This paper explores the potential of personalising health reminders to melanoma patients based on their personality (high vs low conscientiousness). We describe a study where we presented participants with a scenario with a fictional patient who has not performed a skin check for recurrent melanoma. The patient was described as either very conscientious, or very unconscientious. We asked participants to rate reminders inspired by Cialdini’s 6 principles of persuasion for their suitability for the patient. Participants then chose their favourite reminder and an alternative reminder to send if that one failed. We found that conscientiousness had an effect on both the ratings of reminder types and the most preferred reminders selected by participants.
Reasoning about mental states in sequential games : As simple as possible, as complex as necessary

Because of limited cognitive resources, humans use heuristics in problem solving and decision-making. We argue that reasoning about mental states also comprises the use of heuristics. This has been tested in sequential games, in which one player’s outcomes depend on another player’s decisions. Empirical findings show that participants apply simple strategies, or heuristics, for as long as these yield expected outcomes. However, participants were able to revise their strategies when presented with superficially similar but more difficult games. We have built a flexible and task-general computational cognitive model that can simulate these findings. The model uses a heuristic for as long as the heuristic yields expected outcomes. If the model’s decisions yield suboptimal outcomes, the model updates its strategy level. This updating can be considered a deliberate process, as it is based on an interaction between factual knowledge and problem solving skills.
Scaling law in signal recycled laser-interferometer gravitational-wave detectors

By mapping the signal-recycling (SR) optical configuration to a three-mirror cavity, and then to a single detuned cavity, we express the SR optomechanical dynamics, input-output relation, and noise spectral density in terms of only three characteristic parameters: the (free) optical resonant frequency and decay time of the entire interferometer, and the laser power circulating in the arm cavities. These parameters, and therefore the properties of the interferometer, are invariant under an appropriate scaling of SR-mirror reflectivity, SR detuning, arm-cavity storage time, and input power at the beam splitter. Moreover, so far the quantum-mechanical description of laser-interferometer gravitational-wave detectors, including radiation-pressure effects, has been obtained only at linear order in the transmissivity of arm-cavity internal mirrors. We relax this assumption and discuss how the noise spectral densities change.