Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell signalling regulates dynamics of Nanog distribution in embryonic stem cell populations

A population of mouse embryonic stem (ES) cells is characterized by a distribution of Nanog, a gene whose expression is associated with the degree of pluripotency. Cells exhibiting high levels of Nanog maintain a state of pluripotency, while those with low levels are more likely to undergo differentiation. Using a cell line with a fluorescence tag for Nanog enables measurements of the distribution of Nanog in an ES cell culture in a stationary state or after a perturbation. In order to model the dynamics of the system, we assume that the distribution of Nanog-GFP for single cells shows distinct attractor steady states of Nanog levels, with individual cells moving between these states stochastically. The addition of synthetic inhibitors of signal transduction induces strong shifts in the distribution of Nanog. In particular, the addition of Chiron and PD03, inhibitors for the ERK and GSK3 signalling pathways, induces a high level of Nanog. In this study, we placed ES cells in different culture conditions, including the above inhibitors, and recorded the change in Nanog-GFP distribution over several days. In order to interpret the measurements of Nanog levels, we propose a new stochastic modelling strategy for the dynamics of the system not requiring detailed knowledge of regulatory or signalling mechanisms, while still capturing the stochastic and the deterministic components of the stochastic dynamical system. Despite its relative simplicity, the model provides an insight into key features of the cell population under various conditions, including the level of noise and occupancy and location of attractor steady states, without the need for strong assumptions about the underlying cellular mechanisms. By applying the model to our experimental data, we infer the existence of three stable steady states for Nanog levels, which are the same in all the different conditions of the cell-culture medium. Noise, on the other hand, and the proportion of cells in each steady state are subject to large shifts. Surprisingly, the isolated effects of PD03 and Chiron on noise and dynamics of the system are quite different from their combined effect. Our results show that signalling determines the occupancy of each state, with a particular role for GSK3 in the regulation of the noise across the population.
Dynamic Data Structures for Document Collections and Graphs

In the dynamic indexing problem, we must maintain a changing collection of text documents so that we can efficiently support insertions, deletions, and pattern matching queries. We are especially interested in developing efficient data structures that store and query the documents in compressed form. All previous compressed solutions to this problem rely on answering rank and select queries on a dynamic sequence of symbols. Because of the lower bound in [Fredman and Saks, 1989], answering rank queries presents a bottleneck in compressed dynamic indexing. In this paper we show how this lower bound can be circumvented using our new framework. We demonstrate that the gap between static and dynamic variants of the indexing problem can be almost closed. Our method is based on a novel framework for adding dynamism to static compressed data structures. Our framework also applies more generally to dynamizing other problems. We show, for example, how our framework can be applied to develop compressed representations of dynamic graphs and binary relations.
Round One — Placing the Child in the Right Reader

A method for placing children in appropriate readers was devised and implemented; it combines aspects of the Informal Reading Inventory with techniques developed by applied behavior analysts. Using this method, three different reading behaviors of pupils were measured directly and frequently: correct oral reading rate, incorrect oral reading rate, and correct comprehension percentage. Subjects were seven intermediate age boys with reading problems. Each pupil was placed in a reader based on his three performance scores. The effectiveness of the placement method was judged in terms of how well it predicted subsequent reading performance in the instructional readers. There were two major findings: First, although oral reading rates and comprehension scores generally worsened as the grade level of the material increased, the performance differences between adjacent books were minimal. Correct rate was more sensitive to changes in grade level than either incorrect rate or comprehension percentage. Second, after placement in the readers, all pupils progressed satisfactorily throughout the remainder of the year.
Orographic Primary and Secondary Gravity Waves in the Middle Atmosphere From 16‐Year SABER Observations

The seasonal and height dependencies of the orographic primary and larger‐scale secondary gravity waves (GWs) have been studied using the temperature profiles measured by Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) from 2002 to 2017. At ~40°S and during Southern Hemisphere winter, there is a strong GW peak over the Andes mountains that extend to z ~ 55 km. Using wind and topographic data, we show that orographic GWs break above the peak height of the stratospheric jet. At z ~ 55–65 km, GW breaking and momentum deposition create body forces that generate larger‐scale secondary GWs; we show that these latter GWs form a wide peak above 65 km with a westward tilt. At middle latitudes during summer in the respective hemisphere, orographic GW breaking also generates larger‐scale secondary GWs that propagate to higher altitudes. Both orographic primary and larger‐scale secondary GWs are likely responsible for most of the non‐equatorial peaks of the persistent global distribution of GWs in SABER.
A Performance Comparison between Efficiency and Pheromone Approaches in Dynamic Manufacturing Scheduling

These days competition is played in an environment characterized by high market shifting, rapid development as well as introduction of new technologies, global competition and customer needs focalization. Therefore, manufacturing environments are becoming more dynamic and turbulent than ever before. Traditional manufacturing facilities, however, are not able to cope with such environments, as no single aBsTracT
A Systematic Review and Meta-analysis of Yoga for Low Back Pain

Objectives:To systematically review and meta-analyze the effectiveness of yoga for low back pain. Methods:MEDLINE, the Cochrane Library, EMBASE, CAMBASE, and PsycINFO, were screened through January 2012. Randomized controlled trials comparing yoga to control conditions in patients with low back pain were included. Two authors independently assessed risk of bias using the risk of bias tool recommended by the Cochrane Back Review Group. Main outcome measures were pain, back-specific disability, generic disability, health-related quality of life, and global improvement. For each outcome, standardized mean differences (SMD) and 95% confidence intervals (CI) were calculated. Results:Ten randomized controlled trials with a total of 967 chronic low back pain patients were included. Eight studies had low risk of bias. There was strong evidence for short-term effects on pain (SMD=−0.48; 95% CI, −0.65 to −0.31; P<0.01), back-specific disability (SMD=−0.59; 95% CI, −0.87 to −0.30; P<0.01), and global improvement (risk ratio=3.27; 95% CI, 1.89-5.66; P<0.01). There was strong evidence for a long-term effect on pain (SMD=−0.33; 95% CI, −0.59 to −0.07; P=0.01) and moderate evidence for a long-term effect on back-specific disability (SMD=−0.35; 95% CI, −0.55 to −0.15; P<0.01). There was no evidence for either short-term or long-term effects on health-related quality of life. Yoga was not associated with serious adverse events. Discussion:This systematic review found strong evidence for short-term effectiveness and moderate evidence for long-term effectiveness of yoga for chronic low back pain in the most important patient-centered outcomes. Yoga can be recommended as an additional therapy to chronic low back pain patients.
Minimum Variance Estimation of a Sparse Vector Within the Linear Gaussian Model: An RKHS Approach

We consider minimum variance estimation within the sparse linear Gaussian model (SLGM). A sparse vector is to be estimated from a linearly transformed version embedded in Gaussian noise. Our analysis is based on the theory of reproducing kernel Hilbert spaces (RKHS). After a characterization of the RKHS associated with the SLGM, we derive a lower bound on the minimum variance achievable by estimators with a prescribed bias function, including the important special case of unbiased estimation. This bound is obtained via an orthogonal projection of the prescribed mean function onto a subspace of the RKHS associated with the SLGM. It provides an approximation to the minimum achievable variance (Barankin bound) that is tighter than any known bound. Our bound holds for an arbitrary system matrix, including the overdetermined and underdetermined cases. We specialize it to compressed sensing measurement matrices and express it in terms of the restricted isometry constant. For the special case of the SLGM given by the sparse signal in noise model, we derive closed-form expressions of the Barankin bound and of the corresponding locally minimum variance estimator. Finally, we compare our bound with the variance of several well-known estimators, namely, the maximum-likelihood estimator, the hard-thresholding estimator, and compressive reconstruction using orthogonal matching pursuit and approximate message passing.
Data-Driven Processing in Sensor Networks

Wireless sensor networks are poised to enable continuous data collection on unprecedented scales, in terms of area location and size, and frequency. This is a great boon to elds such as ecological modeling. We are collaborating with researchers to build sophisticated temporal and spatial models of forest growth, utilizing a variety of measurements. There exists a crucial challenge in supporting this activity: network nodes have limited battery life, and radio communication is the dominant energy consumer. The straightforward solution of instructing all nodes to report their measurements as they are taken to a base station will quickly consume the network’s energy. On the other hand, the solution of building models for node behavior and substituting these in place of the actual measurements is in conict with the end goal of constructing models. To address this dilemma, we propose data-driven processing, the goal of which is to provide continuous data without continuous reporting, but with checks against the actual data. Our primary strategy for this is suppression, which uses in-network monitoring to limit the amount of communication to the base station. Suppression employs models for optimization of data collection, but not at the risk of correctness. We discuss techniques for designing data-driven collection, such as building suppression schemes and incorporating models into them. We then present and address some of the major challenges to making this approach practical, such as handling failure and avoiding the need to co-design the network application and communication layers.
The Music Retrieval Method Based on The Audio Feature Analysis Technique with The Real World Polyphonic Music

This paper describes a method of the Music Retrieval Method based on audio feature analysis techniques. This method contains three major algorithms with newly proposed advanced way and the implementation of the whole system including client and server side prototype to be applied on time to market. The first one of the major algorithms is to extract the feature from the polyphonic music, which is the advanced version using the harmonic structure of vocal and musical instruments. The second one is to extract the feature and suppress the noise of user humming signal recorded from input device. Noise suppression algorithm makes merge of MS for stationary noise and IMCRA for non-stationary noise, and the feature is estimated with temporal and spectral autocorrelation simultaneously to reduce the pitch having and doubling problem. The last one is the fusion matching engine improved with DTW (Dynamic Time Warp), LS (Linear Scaling) and QBCode (Quantized Binary Code). This system is extremely targeting on industrial services such as music portal service, fixed stand-alone devices, mobile devices, and so on. Especially, our very first focus is the Korean KARAOKE system which is the one of very popular music entertainment services in Asia and the music portal service like Bugs music, Mnet, zillernet, and so on. We have cooperated with TJ media co. to commercialize this system.
Are Poor Sleepers Afraid of the Dark? A Preliminary Investigation

No studies have investigated whether those with poor sleep are aware of being uncomfortable in the dark via subjective inquiry, and no study has evaluated whether poor sleepers have increased fear in the dark using objective indices (e.g., a validated startle paradigm). Good and poor sleepers (N = 108) completed questionnaires about their level of discomfort with the dark and were evaluated for an increased startle reflex by measuring eyeblink latency via electrooculogram in response to unexpected noise in the dark and the light. Participants listened to bursts of unexpected white noise, while in counterbalanced light/dark conditions. Relative to good sleepers, more poor sleepers reported increased discomfort in the dark. There was a significant lighting × time × sleeper status interaction for eyeblink latency. Relative to the first trial in the dark, eyeblink latency in good sleepers increased in the second dark exposure; suggesting habituation in the dark. Eyeblink latency in poor sleepers did not decrease. Thus, poor sleepers reported being uncomfortable in the dark and they remained more easily startled in the dark over the course of the study. It is unclear if the dark may predispose people to sleep problems, or if sleep problems sensitize poor sleepers to fear darkness.
Antimutagenic activity of two medicinal phytoextracts in somatic cells of Drosophila melanogaster

Context and Objective: We used the wing somatic assay in Drosophila melanogaster to test the hypothesis that two phytoextracts from Cecropia obtusifolia Bertol (Cecropiaceae) and Equisetum myriochaetum Schlecht. et Cham (Equisetaceae), which are used in folk medicine to treat type 2 diabetes mellitus, could detoxify the mutagen hydrogen peroxide. Materials and methods: Third instar larvae from standard (ST) and high-bioactivation (HB) crosses were chronically exposed to different concentrations of the phytoextracts. Hydrogen peroxide was used to induce oxidative stress and was chronically tested in both crosses. Catalase activity was measured in larvae of both strains 48 h after treatment with hydrogen peroxide. A pretreatment protocol was devised to test the antimutagenic potency of the medicinal extracts. Results: The present study showed that neither of the phytoextracts were genotoxic in Drosophila. Interestingly, the antioxidant enzyme activity levels were different between the larvae. Hydrogen peroxide resulted in a significant genotoxic effect in the ST cross, whereas a detoxification of hydrogen peroxide was found in the HB cross. Thus, catalase was stimulated in the HB cross, which was indicative of a cellular defense mechanism mounted against a xenobiotic hazard. We found that the percentage of inhibition of spots produced by E. myriochaetum was much higher than that induced by Cecropia obtusifolia. Discussion and conclusions: These results are in agreement with the uses of these phytoextracts in traditional medicine. Indeed, the lack of genotoxicity and the antimutagenic activity observed for both phytoextracts validates their use as a therapeutic modality to treat diabetic patients. Moreover, these extracts are suitable for consumption as teas and/or phytomedicines.
Management of maladaptive social behavior of a brain injured adult

This study examined the effectiveness of an individualized behavior point system for reducing the frequency of surplus maladaptive social behaviors of a severely brain injured adult. Treatment, given during meal periods, was applied in a multiple baseline design across three behaviors: loud verbal outburst, interruptions, and nonsensical talk. Generalization of treatment effects was assessed in informal community restaurants. The results revealed that each of the target behaviors declined with the introduction of the point system, although loud verbal outbursts and interruptions were more responsive to treatment than nonsensical talk. Some evidence was found for skill generalizations to untrained settings.
Frugal topology construction for stream aggregation in the cloud

Aggregation of streamed data is key to the expansion of the Internet of Things. This paper addresses the problem of designing a topology for reliably aggregating data flows from many devices arriving at a datacenter. Reliability here means ensuring operation without data loss. We seek a frugal solution that prevents wasteful resource consumption (over-provisioning). This problem is salient when building an aggregation service out of components (here aggregation nodes) that exhibit hard constraints on the amount of information they can handle per unit of time. We first formalize the problem and provide an analysis of the relation between monitored devices (plus information they send), and the operations performed at aggregation nodes, in terms of data rates. Building on this rate analysis, we devise a novel algorithm, which we call CSA, that basically outputs an aggregation topology capable of handling those incoming data rates, preventing thereby empirical trial-and-error design. We analyze the algorithm, before validating it on the Amazon Kinesis platform, using a device dataset from a European telco operator.
Tunable structural color in organisms and photonic materials for design of bioinspired materials

Abstract In this paper, the key topics of tunable structural color in biology and material science are overviewed. Color in biology is considered for selected groups of tropical fish, octopus, squid and beetle. It is caused by nanoplates in iridophores and varies with their spacing, tilting angle and refractive index. These examples may provide valuable hints for the bioinspired design of photonic materials. 1D multilayer films and 3D colloidal crystals with tunable structural color are overviewed from the viewpoint of advanced materials. The tunability of structural color by swelling and strain is demonstrated on an example of opal composites.
Statins and Angiotensin‐Converting Enzyme Inhibitors are Associated with Reduced Mortality and Morbidity in Chronic Liver Disease

Liver fibrosis is a common response to many chronic liver diseases. The aim of our study was to explore whether pharmacotherapy for concurrent diseases affects overall mortality, liver‐related mortality and liver‐related morbidity in patients with chronic liver disease. We performed a register‐based cohort study of all patients with a first‐time diagnosis of chronic liver disease between 2005 and 2012 in Sweden (n = 70 546). Data from the Patient Register, the Prescribed Drug Register and the Death Certificate Register were linked. We studied whether the use of statins, angiotensin‐converting enzyme inhibitors, angiotensin receptor blockers and antibiotics affected the risk of total mortality, liver‐specific mortality and morbidity. We found a reduction in mortality risk for statin users (n = 11,245) with hazard ratios from 0.57 (95% CI: 0.32–0.99) for patients with autoimmune hepatitis to 0.84 (95% CI: 0.75–0.95) for patients with alcoholic liver disease. There was a significantly reduced liver‐related mortality for patients with alcoholic liver disease who used angiotensin‐converting enzyme inhibitors, 0.85 (95% CI: 0.65–0.96). There were increased overall mortality risks for antibiotic users (n = 44,572), with hazard ratios up to 1.67 (95% CI, 1.55–1.80) for viral hepatitis. Statin use was associated with decreased risks of liver‐specific mortality and morbidity, and reduced total mortality foremost among patients with alcoholic liver disease. Angiotensin ‐converting enzyme inhibitors was associated with reduced liver‐related mortality among patients with alcoholic liver disease.
Discovery of an expanded set of avian leukosis subroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline.

Transposable elements (TEs), such as endogenous retroviruses (ERVs), are common in the genomes of vertebrates. ERVs result from retroviral infections of germ-line cells, and once integrated into host DNA they become part of the host's heritable genetic material. ERVs have been ascribed positive effects on host physiology such as the generation of novel, adaptive genetic variation and resistance to infection, as well as negative effects as agents of tumorigenesis and disease. The avian leukosis virus subgroup E family (ALVE) of endogenous viruses of chickens has been used as a model system for studying the effects of ERVs on host physiology, and approximately 30 distinct ALVE proviruses have been described in the Gallus gallus genome. In this report we describe the development of a software tool, which we call Vermillion, and the use of this tool in combination with targeted next-generation sequencing (NGS) to increase the number of known proviruses belonging to the ALVE family of ERVs in the chicken genome by 4-fold, including expanding the number of known ALVE elements on chromosome 1 (Gga1) from the current 9 to a total of 40. Although we focused on the discovery of ALVE elements in chickens, with appropriate selection of target sequences Vermillion can be used to develop profiles of other families of ERVs and TEs in chickens as well as in species other than the chicken.
Enumeration of Rhombus Tilings of a Hexagon which Contain a Fixed Rhombus in the Centre

We compute the number of rhombus tilings of a hexagon with side lengths a, b, c, a, b, c which contain the central rhombus and the number of rhombus tilings of a hexagon with side lengths a, b, c, a, b, c which contain the “almost central” rhombus above the centre.
Bringing Respect to the Gymnasium: A Roadmap for Physical Educators

Tackling inactivity among young people of this country is more vital than ever. As a result, physical educators must generate increasing levels of respect within the education community for their role as competent professionals who guide children and adolescents toward physically active lifestyles. Fighting to destroy the image of those that simply “roll out the balls,” this decades-long battle for respect has never been more important. This article will not only illuminate a path one teacher takes to earn that respect, but it also will offer simple strategies for you to do the same in your gymnasium. You will read about the importance of developing your own quality program that engages colleagues in the building, impresses administrators down the hall, and involves parents and community leaders. We are in a critical window in this country that requires addressing the obesity issues plaguing our youth. This roadmap delivers skills necessary for physical educators to help fight, and eventually conquer, this nationwide problem.