Miracle-dz/UniFAR-FTUs huggingface dataset:
A guide to Dynamic Transcriptome Analysis (DTA)

Total RNA levels in a cell are the consequence of two opposing mechanisms, namely RNA synthesis and RNA degradation. DTA allows monitoring these contributions in a non-perturbing manner. It is provided with a kinetic modeling approach capable of the precise determination of synthesisand decay rates, which is implemented in this package (see supplementary methods in [6]). DTA can be applied to reveal rate changes for all kinds of perturbations, e.g. in knock-out or point mutation strains, as responses to stress stimuli or in small molecule interfering assays like treatments through miRNA or siRNA inhibitors. The experimental setup for DTA requires culturing cells in the presence of a labeling substrate (e.g. 4 thiouridine (4sU) or 4 thiouracil (4tU)) for a certain amount of time. Until the extraction of the RNA samples, the analogous (labeling) substrate will be incorporated into newly transcribed RNA. This setup yields three types of RNA fractions: total cellular RNA, newly transcribed labeled RNA and pre-existing unlabeled RNA. All three fractions can subsequently be quantified through gene expression profiling on microarrays or next generation sequencing (RNAseq). The DTA package implements methods to process a given DTA experiment (total (T), labeled (L) and unlabeled (U) RNA measurements) and derive RNA synthesis and decay rate estimates. The package DTA is broadly applicable to virtually every organism. This manual is a hands-on tutorial and describes all functions and R commands that are required. The method is applied to real and synthetic data. Important quality control plots and error assessment to prove the reliability of the data and the estimation are discussed throughout this manual. For details on the theoretical background and a thorough description of the experimental design, we refer the reader to [6] (supplementary methods).
Shared data modeling with UML-G

Groupware is explicitly designed to support the cooperation among group members. The implementation of cooperation-aware groupware is supported by several object-oriented toolkits and frameworks, but there is no unified way to model applications built on top of these. We have proposed UML-G as an extensible UML profile for modeling groupware and are in the process of turning it into a community effort. In this article, we identify modeling needs specific to shared data modeling. Shared data is a prerequisite to supporting cooperating users. We present UML extensions to address the identified needs as a part of UML-G. Usage scenarios demonstrate how UML-G can be used to assist shared data modeling. UML-G provides explicit modeling of shared data related aspects. In addition, it supports a shared understanding between developers, which is independent of, and thus abstracts from, the latter implementation. CASE tool support for UML-G strengthens its practical relevance.
Is Oral Vitamin D Supplementation Safe and Effective for Adults as Therapy to Improve Symptoms Associated with Seasonal Affective Disorder (SAD) during Wintertime

Objective: The objective of this selective EBM review is to determine whether or not oral vitamin D supplementation is safe and effective for adults as therapy to improve symptoms associated with seasonal affective disorder (SAD) during wintertime. Study Design: This review is based on three randomized controlled trials (RCTs) which were published in 2006, 2012, 2014. Two of the studies were double blind and placebo controlled. The studies evaluated the efficacy of oral vitamin D supplementation for improvement of seasonal affective disorder (SAD) symptoms. One of the studies also evaluated safety. Data Sources: All articles used were published in English, in peer-reviewed journals and found in PubMed during the time period of November 2015 to February 2016. Outcomes Measured: The outcomes measured were symptoms associated with SAD. One study measured subjective psychological well-being qualities (energy and vitality, social functioning, role functioning, and mental health), which were measured by Mean Component Score (MCS). The other two studies evaluated symptoms associated with SAD and perceived change from normal in: length of sleep, social activities, mood, weight, appetite, energy level by using Structured Interview Guide for the Hamilton Depression Rating Scale – Seasonal Affective Disorders (SIGH-SAD) and Global Seasonality Score (GSS) tools. Results: None of the studies evaluated in this review had results to suggest that vitamin D supplementation is effective for improving symptoms associated with SAD. Dumville (2006) found no significant evidence (p = 0.262). Frandsen (2014) and Kjaergaard et al. (2012) both found no significant difference between placebo and vitamin D with p values of 0.7 and 0.734 respectively. Kjaergaard et al. (2012) also found there to be no significant difference in adverse events between the placebo and vitamin D groups. Conclusions: This review suggests that although oral vitamin D supplementation is safe, it is not effective for adults as therapy to improve symptoms associated with SAD during wintertime.
Activation of Toll-Like Receptor-9 Promotes Cellular Migration via Up-Regulating MMP-2 Expression in Oral Squamous Cell Carcinoma

Purpose Activation of Toll like receptors (TLRs) signaling has been implicated in promoting malignant cell invasion and metastatic potential. Previously we demonstrated that increased TLR-9 expression predicted poor survival in oral cancer patients. The objective of this study is to further investigate the roles and potential molecular mechanisms of TLR-9 signaling in human oral cancer cell invasion. Methods Cell migration, invasion and protein expression were detected by wound healing assay, Transwell chambers model and western blot. The secretion and activity levels of metalloproteinases-2/9 were quantified by ELISA and Gelatin zymography. EMSA and ChIP assays were employed to detect the activity of AP-1signal pathway. TLR-9 siRNA transfection was used to regulate the expression and activity of TLR-9 in oral cancer cell line HB cells. Result The results of both wound healing assay and in vitro Transwell assay revealed that activation of TLR-9 induced dose- and time- dependent migration and invasion of HB cells. An increased expression, secretion and activity of MMP-2 were observed upon the treatment of CpG-ODN. The TLR-9 signaling-mediated MMP-2 expression appeared to be a consequence of AP-1 activation, because that their DNA binding activity was enhanced by CpG-ODN treatment. All these influences were efficiently repressed by the knockdown of TLR-9 through siRNA or pretreatment of an AP-1 inhibitor. Conclusion Activation of TLR-9 signaling could promote human oral cancer HB cells invasion with the induction of MMP-2 presentation by attenuating AP-1 binding activity, suggesting a novel anti-metastatic application for TLR-9 targeted therapy in oral cancer in the future.
Simulating the assembly of galaxies at redshifts z = 6–12

We use state-of-the-art simulations to explore the physical evolution of galaxies in the first billion years of cosmic time. First, we demonstrate that our model reproduces the basic statistical properties of the observed Lyman-break galaxy (LBG) population at z = 6 − 8, including the evolving ultra-violet (UV) luminosity function (LF), the stellar-mass density (SMD), and the average specific star-formation rates (sSFR) of LBGs with MUV −18 were in fact brighter at z ≃ 7 (and even at z ≃ 8) despite obviously being less massive at earlier times. At this end, the evolution of the UV LF involves a mix of positive and negative luminosity evolution (as low-mass galaxies temporarily brighten then fade) coupled with both positive and negative density evolution (as new low-mass galaxies form, and other low-mass galaxies are consumed by merging). We also predict the average sSFR of LBGs should rise from sSFR ≃ 4.5Gyr 1 at z ≃ 6 to sSFR ≃ 11Gyr 1 by
A Meta-level Architecture for Ambient-aware Objects

Programs written to be deployed in pervasive wireless ad hoc networks are notoriously difficult to program. We focus on programming languages specially tailored to writing such programs, in order to mitigate the technical constraints imposed by the ambient hardware. We describe the ramifications of the hardware properties on the software and argue in favour of a language distribution model that is aware of these effects. We conjecture that an ope implementation of the language is necessary: a proper meta-level architecture that allows for customisation of the language to adapt it to changes in the hardware environment.
Valence-bond crystal phase of a frustrated spin-1/2 square-lattice antiferromagnet.

We propose a new type of magnetically disordered ground state for a frustrated quantum antiferromagnet. This disordered state is an array of spin singlets spontaneously formed on four spin plaquettes. Both perturbation results and bond-operator calculations show that this phase has lower energy than the columnar dimer state. Analysis of available numerical data on finite clusters also supports the conclusion that this state is realized at intermediate frustrations.
High School Teachers’ Sense of Efficacy: Traditional Teaching vs. Teaching With a Learning Management System

Teacher efficacy has an impact on how students achieve in the classroom. There is a variety of ways teachers help students learn. For example, the method of traditional instruction includes the use of a textbook and teacher lectures. However, a current trend in education is for schools to use a Learning Management System, like Schoology, to help teachers organize and distribute resources to students. This study will help administrators understand if teachers have a stronger or weaker sense of efficacy through the use of traditional instruction or instruction with the use of Schoology. The study is important because administrators need to understand how the programs they are implementing in schools impact teacher efficacy beliefs. The purpose of this causal comparative study was to employ Bandura’s theory of self-efficacy, to identify if there was a difference in high school teacher efficacy beliefs of those who teach with Schoology in their classrooms and those employ traditional methods. The researcher attained permission from the Superintendent of five school districts and high school teachers were asked to participate in the Teacher Sense of Efficacy Scale (TSES) via email. Participants completed the survey through a link in their email, and the researcher analyzed data using the MANOVA to test if each dependent variable of teacher efficacy differs significantly. The MANOVA determined that there was no significant difference among the groups in terms of their teacher efficacy. Although no significant differences were reported, the research adds to the body of literature since there are very few studies on the impact of an LMS in K-12 education.
Latent factor model for traffic signal control

The increased ownership of motor vehicles has brought many urban problems, such as traffic congestion, environmental pollution. Traffic signal control is recognized as one of effective ways to alleviate these problems. However, it is still hard to automatically choose appropriate traffic signal timing plans for different traffic conditions due to the dynamics and uncertainty of transportation systems. In this paper, we propose a latent factor model based traffic signal timing plan recommendation method to address this problem. In the proposed method, we model the abstract traffic states as the “users” in recommendation systems, and timing plans as the “items”. And there are many explicit or implicit factors in the interactions between “users” and “items”. The latent factor model is successfully used to deal with uncertain factors which cannot be modeled accurately in math. The novel method adopted the model-free adaptive idea to solve the problem of modeling from the perspective of data mining and machine learning framework. And, the proposed method is tested by using simulation data generated by a microscopic traffic simulator called Paramics. The results are compared to the baseline Webster method. The results indicate that the proposed latent factor model based recommendation method outperforms the Webster method on reducing the delay.
Markets and Growth t ĕ pán

This paper studies key markets (financial, labor, natural resource, and product) to assess how they are facilitating or constraining growth. First, we draw on the body of existing theoretical and empirical literature to discuss the links between markets and growth. Second, we present four stylized scenarios of the process of growth, which summarize differences across six regions of the developing world. Financial market infrastructure and efficient factor reallocation in response to shocks appear to be among the most important growth determinants. We highlight the relative lack of research on the relationship between labor markets and growth, as opposed to the relationship between human capital production and growth. Finally, we combine suggestions of Topel (1999) and Pritchett (2000) to argue that country-specific markets should be a principal focus of future research on growth. This paper provides a framework for such studies.
Mental Practice for Relearning Locomotor Skills

Over the past 2 decades, much work has been carried out on the use of mental practice through motor imagery for optimizing the retraining of motor function in people with physical disabilities. Although much of the clinical work with mental practice has focused on the retraining of upper-extremity tasks, this article reviews the evidence supporting the potential of motor imagery for retraining gait and tasks involving coordinated lower-limb and body movements. First, motor imagery and mental practice are defined, and evidence from physiological and behavioral studies in healthy individuals supporting the capacity to imagine walking activities through motor imagery is examined. Then the effects of stroke, spinal cord injury, lower-limb amputation, and immobilization on motor imagery ability are discussed. Evidence of brain reorganization in healthy individuals following motor imagery training of dancing and of a foot movement sequence is reviewed, and the effects of mental practice on gait and other tasks involving coordinated lower-limb and body movements in people with stroke and in people with Parkinson disease are examined. Lastly, questions pertaining to clinical assessment of motor imagery ability and training strategies are discussed.
Adaptive Reward Mechanism for Sustainable Online Learning Community

Abundance of user contributions does not necessarily indicate sustainability of an online community. On the contrary, excessive contributions in the systems may result in information overload and user withdrawal. We propose a user-and community-adaptive reward mechanism aiming to regulate the quantity of the contributions and encourage users to moderate the quality of contributions themselves. The mechanism has been applied and evaluated in an online community supporting undergraduate students to share course-related web-resources.
Daily life with early orphanhood from HIV/AIDS: An exploratory study

This study explored the everyday lived life by South African early adolescents orphaned by HIV/AIDS. Informants were ten early adolescents (age range 12 to 14 years; females = 6; males = 4) from a low socioeconomic status neighbourhood of Johannesburg. The adolescents completed autobiographical essays and in-depth individual interviews on their quality of life in the school, home, and community. Thematic analysis of the data revealed the early adolescents, orphaned due to HIV/AIDS, to experience extreme sadness, anxiety, and fear. Their sense of emotional distress was compounded by living in material and relational poverty, with frequent exposure to bullying at school, and crime in their neighbourhood. Integrated psycho-social interventions addressing both material and relational poverty might enhance the physical and psycho-social well-being of adolescents with orphanhood from HIV/AIDS.
Diffusive void bifurcation in stressed solid

Interconnects are susceptible to solid diffusion under residual stress, electric current, and elevated temperature. As atoms diffuse, voids nucleate, drift, and enlarge. At some point, the voids of rounded shape can collapse to narrow slits and sever the interconnects. The fatal slits are often found to be transgranular, i.e., each slit cuts across a single grain. They have raised many concerns, but the underlying mechanism has remained unclear. It is proposed that a void changes shape due to surface diffusion under the combined action of surface energy, elastic energy, and electric current. The void will be rounded if surface energy prevails, but will collapse to a slit if the elastic energy or the electric current prevails. A cylindrical void in an infinite crystal under biaxial stresses, but under no electric current, is analyzed. Four things are done, as follows: (1) A suitable thermodynamic potential is minimized and maximized to select, among a family of ellipses, equilibrium void shapes. The bifurc.
Rapid and Accurate Leakage Power Estimation for Nano-CMOS Circuits

This paper addresses the crucial problem of static power reduction for circuits implemented in nano-CMOS technologies. Its solution requires accurate and rapid power estimation, but the known power simulators are not accurate and quick at the same time. The paper proposes and discusses a new rapid and very accurate leakage power estimation method and related simulator. The maximum estimation error of the simulator is within 5%, with an average error of only 0.57%, and run-times in the range of seconds, while for the same circuits HSPICE runs for hours or days.
TESTING MODELS OF SOCIAL LEARNING ON NETWORKS : EVIDENCE FROM A FRAMED FIELD EXPERIMENT

Theory has focused on two leading models of social learning on networks: Bayesian and DeGroot rules of thumb learning. These models can yield greatly divergent behavior; individuals employing rules of thumb often double-count information and may not exhibit convergent behavior in the long run. By conducting a unique lab experiment in rural Karnataka, India, set up to exactly differentiate between these two models, we test which model best describes social learning processes on networks. We study experiments in which seven individuals are placed into a network, each with full knowledge of its structure. The participants attempt to learn the underlying (binary) state of the world. Individuals receive independent, identically distributed signals about the state in the first period only; thereafter, individuals make guesses about the underlying state of the world and these guesses are transmitted to their neighbors at the beginning of the following round. We consider various environments including incomplete information Bayesian models and provide evidence that individuals are best described by DeGroot models wherein they either take simple majority of opinions in their neighborhood.
Mechanisms Underlying a Decrease in KCl-Induced Contraction after Long-Term Serum-Free Organ Culture of Rat Isolated Mesenteric Artery

ABSTRACT Organ culture of blood vessel is a better technique to investigate the long-term effects of drugs. However, some functional changes may occur from freshly isolated vessel (Fresh). Mammalian/mechanistic target of rapamycin (mTOR) regulates smooth muscle differentiation and Ca2+ mobilization. We thus investigated mechanisms of alteration in smooth muscle contractility after serum-free organ culture focusing on mTOR. Rat isolated mesenteric arteries were cultured for 5 days without (0% serum) or with rapamycin. In 0% serum, absolute contraction by KCl significantly decreased from Fresh, which was significantly rescued by rapamycin. In 0% serum, mTOR expression significantly increased from Fresh, which was significantly rescued by rapamycin. In 0% serum, expression of myocardin, a key regulator of smooth muscle differentiation markers, significantly decreased from Fresh, which was significantly rescued by rapamycin. However, the decrease in expression of contractile proteins, including SM22α and calponin, was not changed by rapamycin. Basal phosphorylation of calmodulin-dependent protein kinase II significantly increased in 0% serum, which was significantly rescued by rapamycin. In 0% serum, absolute contraction by caffeine significantly decreased from Fresh, which was significantly rescued by rapamycin. In conclusion, expression of mTOR increased during serum-free organ culture of rat isolated mesenteric artery for 5 days, which may be at least partly responsible for the decreased smooth muscle contractility perhaps due to the decrease in the stored Ca2+ in smooth muscle.
Theoretical Benchmarks of evaluation methodologies in XML Retrieval

According to INEX, the evaluation initiative for XML retrieval, the aim of XML retrieval is to retrieve not only relevant document components, but those at the right level of granularity, i.e. document components that specifically answer a query. This paper investigates the use of theoretical benchmarks to describe the INEX 2004 and 2005 evaluation methodology. Theoretical benchmarks concern the formal representation of qualitative properties of information retrieval models. To this end, a Situation Theory framework for the meta-evaluation of XML retrieval is introduced. This model is then used to exemplify theoretical models of user agents and assessment procedures in INEX 2004 and 2005.
Free Form Surface Design with A-Patches

We present a sufficient criterion for the Bernstein-Bezier (BB) form of a trivariate polynomial within a tetrahedron, such that the real zero contour of the polynomial defines a smooth and single sheeted algebraic surface patch. We call this an A-patch. We present algorithms to build a mesh of cubic A-patches to interpolate a given set of scattered point data in three dimensions, respecting the topology of any surface triangulation T of the gi ven point set. In these algorithms we first specify "normals" on the data points, then build a simplicial hull consisting of tetrahedra surrounding the surface triangulation T and finally construct cubic A-patches within each tetrahedron . The resulting surface constructed is C l (tangent plane) continuous and single sheeted in each of the tetrahedra. We al so show how to adjust the free parameters of the A-patches to achieve both local and global shape control.
Environmental Noise Classification and Cancellation using Fuzzy Classifier and Fuzzy Adaptive Filters

The background noise is one of the major factors, which adversely affects the perceived grade of service in audio communication systems. The main problem in most of the environmental noise reduction system is source of noise signal which is to be used as a reference signal. Once the noise source is known then the noise elimination process will become easier. In any environmental conditions, predominant noise signal which is corrupting the original speech signal can be identified using neural network classification. In conventional gradient-based learning algorithms, tuning methods need to be differentiable and it leads to slow in convergence and if the noise is nonlinear, it will not provide a good generalization performance. To overcome this, an automatic noise reduction system is proposed which is an integration of fuzzy classifier and fuzzy adaptive filter.