Miracle-dz/UniFAR-FTUs huggingface dataset:
An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding

Riboswitches are RNA genetic control elements that were originally discovered in bacteria and provide a unique mechanism of gene regulation. They work without the participation of proteins and are believed to represent ancient regulatory systems in the evolutionary timescale. One of the biggest challenges in riboswitch research is to find additional eukaryotic riboswitches since more than 20 riboswitch classes have been found in prokaryotes but only one class has been found in eukaryotes. Moreover, this single known class of eukaryotic riboswitch, namely the TPP riboswitch class, has been found in bacteria, archaea, fungi and plants but not in animals. The few examples of eukaryotic riboswitches were identified using sequence-based bioinformatics search methods such as a combination of BLAST and pattern matching techniques that incorporate base-pairing considerations. None of these approaches perform energy minimization structure predictions. There is a clear motivation to develop new bioinformatics methods, aside of the ongoing advances in covariance models, that will sample the sequence search space more flexibly using structural guidance while retaining the computational efficiency of sequence-based methods. We present a new energy minimization approach that transforms structure-based search into a sequence-based search, thereby enabling the utilization of well established sequence-based search utilities such as BLAST and FASTA. The transformation to sequence space is obtained by using an extended inverse RNA folding problem solver with sequence and structure constraints, available within RNAfbinv. Examples in applying the new method are presented for the purine and preQ1 riboswitches. The method is described in detail along with its findings in prokaryotes. Potential uses in finding novel eukaryotic riboswitches and optimizing pre-designed synthetic riboswitches based on ligand simulations are discussed. The method components are freely available for use.
From Imitation to Conversation: The First Dialogues with Human Neonates.

The functional maturity of the newborn infant's brain, the resemblances between neonatal imitation and imitation in adults and the possibly lateralized neonatal imitation suggest that the mirror neuron system may contribute to neonatal imitation. Newborn infants not only imitate but also initiate previously imitated gestures, and are able to participate in overlapping imitation–initiation communicative cycles. Additionally, these social responses in neonates are faster than previously thought, and may enable them to have long-lasting intimate interactions much before language develops. Infants are equipped with a powerful, innate, reciprocal communicative ability already at birth. The earliest communication originates from imitation and this communicative ability presumably later evolves to language. Copyright © 2006 John Wiley & Sons, Ltd.
Intermittent Theta-Burst Transcranial Magnetic Stimulation Alters Electrical Properties of Fast-Spiking Neocortical Interneurons in an Age-Dependent Fashion

Modulation of human cortical excitability by repetitive transcranial magnetic stimulation (rTMS) appears to be in part related to changed activity of inhibitory systems. Our own studies showed that intermittent theta-burst stimulation (iTBS) applied via rTMS to rat cortex primarily affects the parvalbumin-expressing (PV) fast-spiking interneurons (FSIs), evident via a strongly reduced PV expression. We further found the iTBS effect on PV to be age-dependent since no reduction in PV could be induced before the perineuronal nets (PNNs) of FSIs start to grow around postnatal day (PD) 30. To elucidate possible iTBS-induced changes in the electrical properties of FSIs and cortical network activity during cortical critical period, we performed ex vivo—in vitro whole-cell patch clamp recordings from pre-labeled FSIs in the current study. FSIs of verum iTBS-treated rats displayed a higher excitability than sham-treated controls at PD29–38, evident as higher rates of induced action potential firing at low current injections (100–200 pA) and a more depolarized resting membrane potential. This effect was absent in younger (PD26–28) and older animals (PD40–62). Slices of verum iTBS-treated rats further showed higher rates of spontaneous excitatory postsynaptic currents (sEPSCs). Based on these and previous findings we conclude that FSIs are particularly sensitive to TBS during early cortical development, when FSIs show an activity-driven step of maturation which is paralleled by intense growth of the PNNs and subsequent closure of the cortical critical period. Although to be proven further, rTMS may be a possible early intervention to compensate for hypo-activity related mal-development of cortical neuronal circuits.
Factors Affecting Small and Medium-Sized Enterprise's Information Technology Absorptive Capability: An Empirical Study of Jilin Province in China

In order to find out the key factors affecting the Information Technology (IT) absorptive capability of Small and Medium-sized Enterprises (SMEs), an empirical study is conducted in this paper. Based on the three-dimensional structure and the influence model of IT absorptive capability proposed by Cuiling Yu, and combined with the characteristics of SMEs, this paper proposes a new model of influence factors, and meanwhile makes an empirical study on the SMEs in Jilin province. Empirical results show that IT consulting, IT infrastructure and government support have significantly impacts on the three-dimension of SMEs' IT absorptive capability. On one hand, the paper reveals how the regions and industries as control variables influence the IT absorptive capacity of SMEs, on the other hand, the paper reveals that IT consulting has a special effect on IT absorptive capacity of SMEs.
Models of Cooperative Teaching and Learning

While most supervised machine learning models assume that training examples are sampled at random or adversarially, this article is concerned with models of learning from a cooperative teacher that selects "helpful" training examples. The number of training examples a learner needs for identifying a concept in a given class C of possible target concepts (sample complexity of C) is lower in models assuming such teachers, that is, "helpful" examples can speed up the learning process. The problem of how a teacher and a learner can cooperate in order to reduce the sample complexity, yet without using "coding tricks", has been widely addressed. Nevertheless, the resulting teaching and learning protocols do not seem to make the teacher select intuitively "helpful" examples. The two models introduced in this paper are built on what we call subset teaching sets and recursive teaching sets. They extend previous models of teaching by letting both the teacher and the learner exploit knowing that the partner is cooperative. For this purpose, we introduce a new notion of "coding trick"/"collusion". We show how both resulting sample complexity measures (the subset teaching dimension and the recursive teaching dimension) can be arbitrarily lower than the classic teaching dimension and known variants thereof, without using coding tricks. For instance, monomials can be taught with only two examples independent of the number of variables. The subset teaching dimension turns out to be nonmonotonic with respect to subclasses of concept classes. We discuss why this nonmonotonicity might be inherent in many interesting cooperative teaching and learning scenarios.
Modelling of primary aerosols in the chemical transport model MOCAGE: development and evaluation of aerosol physical parameterizations

Abstract. This paper deals with recent improvements to the global chemical transport model of Meteo-France MOCAGE (Modele de Chimie Atmospherique a Grande Echelle) that consists of updates to different aerosol parameterizations. MOCAGE only contains primary aerosol species: desert dust, sea salt, black carbon, organic carbon, and also volcanic ash in the case of large volcanic eruptions. We introduced important changes to the aerosol parameterization concerning emissions, wet deposition and sedimentation. For the emissions, size distribution and wind calculations are modified for desert dust aerosols, and a surface sea temperature dependant source function is introduced for sea salt aerosols. Wet deposition is modified toward a more physically realistic representation by introducing re-evaporation of falling rain and snowfall scavenging and by changing the in-cloud scavenging scheme along with calculations of precipitation cloud cover and rain properties. The sedimentation scheme update includes changes regarding the stability and viscosity calculations. Independent data from satellites (MODIS, SEVIRI), the ground (AERONET, EMEP), and a model inter-comparison project (AeroCom) are compared with MOCAGE simulations and show that the introduced changes brought a significant improvement on aerosol representation, properties and global distribution. Emitted quantities of desert dust and sea salt, as well their lifetimes, moved closer towards values of AeroCom estimates and the multi-model average. When comparing the model simulations with MODIS aerosol optical depth (AOD) observations over the oceans, the updated model configuration shows a decrease in the modified normalized mean bias (MNMB; from 0.42 to 0.10) and a better correlation (from 0.06 to 0.32) in terms of the geographical distribution and the temporal variability. The updates corrected a strong positive MNMB in the sea salt representation at high latitudes (from 0.65 to 0.16), and a negative MNMB in the desert dust representation in the African dust outflow region (from −1.01 to −0.22). The updates in sedimentation produced a modest difference; the MNMB with MODIS data from 0.10 in the updated configuration went to 0.11 in the updated configuration only without the sedimentation updates. Yet, the updates in the emissions and the wet deposition made a stronger impact on the results; the MNMB was 0.27 and 0.21 in updated configurations only without emission, and only without wet deposition updates, respectively. Also, the lifetime, the extent, and the strength of the episodic aerosol events are better reproduced in the updated configuration. The wet deposition processes and the differences between the various configurations that were tested greatly influence the representation of the episodic events. However, wet deposition is not a continuous process; it has a local and episodic signature and its representation depends strongly on the precipitation regime in the model.
Making explicit pre-service teachers’ implicit beliefs about inclusive education

ABSTRACT The present study investigated the development of pre-service teachers’ skills, beliefs and knowledge about inclusive education. At Time 1, pre-service teachers completed questionnaires on their beliefs and wrote a Teaching Philosophy. At Time 2, they identified differences in their responses from Time 1 to Time 2. Overall, teacher candidates reported an increased sense of self-efficacy in inclusive practice. Their beliefs about learning and teacher responsibility remained largely unchanged. Teacher candidates advocated strongly for student-centred learning and inclusive practices. However, they became significantly more self-assured about their initial position and felt that they had more resources to teach their inclusive beliefs in the classroom.
Metastatic sarcomatoid renal cell carcinoma treated with immune checkpoint inhibitors

ABSTRACT Introduction: Renal cell carcinoma (RCC) with sarcomatoid component carries a poor prognosis. Immune checkpoint inhibitors (CPIs) have been approved for the treatment of metastatic RCC, but their efficacy in patients with sarcomatoid component is not known. Materials and Methods: We conducted a retrospective chart review of 30 consecutive patients at our center who were treated for metastatic RCC with sarcomatoid component. Results: Ten patients were treated with CPI group while 20 patients were in No-CPI group. There were no significant differences in age, sex, race, and stage at diagnosis between the two groups. After a median follow-up of 35 months, 3 of 10 patients in CPI arm and 5 of 20 patients in No-CPI group were alive. The median overall survival was 33.8 m in immunotherapy group compared to 8.8 m in nonimmunotherapy group (p = .001). Discussion: In our experience, CPI therapy resulted in better outcomes compared to traditional therapy with molecular-targeted agents or chemotherapy in these patients.
Analytical Models for the Energetics of Cosmic Accretion Shocks, Their Cosmological Evolution, and the Effect of Environment

We present an analytical description of the energetics of the population of cosmic accretion shocks, for a concordance cosmology (Ωm + ΩΛ = 1). We calculate how the shock-processed accretion power and mass current are distributed among different shock Mach numbers and how they evolve with cosmic time. We calculate the cumulative energy input of cosmic accretion shocks of any Mach number to the intergalactic medium as a function of redshift and compare it with the energy output of supernova explosions, as well as with the energy input required to reionize the universe. In addition, we investigate and quantify the effect of environmental factors, such as local clustering properties and filament preheating, on the statistical properties of these shocks. We find that the energy processed by accretion shocks is higher than the supernova energy output for all z < 3 and that it becomes more than an order of magnitude higher in the local universe. The energy processed by accretion shocks alone becomes comparable to the energy required to reionize the universe by z ~ 3.5. Finally, we establish both qualitatively and quantitatively that local clustering, as well as filament compression and preheating, are important factors in determining the statistical properties of the cosmic accretion shock population.
LANGUAGE ASSESSMENT LITERACY DEVELOPMENT: A STUDENT-TEACHER�S EXPERIENCES IN TEACHING PRACTICE PROGRAM

The development of a student-teachers language assessment literacy was viewed through her experiences in conducting teaching practice in one of the senior high schools in Yogyakarta, Indonesia. An interview was conducted to explore the experiences taking place in the teaching-practice in relation to the language assessment literacy development. It was found out that the experiences were understood as mostly dealing with administrative tasks and there is a need of more knowledge in administrative matter in teaching and assessment. From the results of the study it was obvious that further studies need to be conducted to explore the role of teaching-practice in the development of student-teaching language assessment literacy. More participants and multiple data collection methods in a longitudinal study are needed to help student-teachers to be more assessment literate, which in turn helps them to be better teachers.DOI:doi.org/10.24071/llt.2018. 210209
Some Unusual Dimensional Reductions of Gravity: Geometric Potentials, Separation of Variables, and Static - Cosmological Duality

We discuss some problems related to dimensional reductions of gravity theories to two-dimensional and one-dimensional dilaton gravity models. We first consider the most general cylindrical reductions of the four-dimensional gravity and derive the corresponding (1+1)-dimensional dilaton gravity, paying a special attention to a possibility of producing nontrivial cosmological potentials from pure geometric variables (so to speak, from `nothing'). Then we discuss further reductions of two-dimensional theories to the dimension one by a general procedure of separating the space and time variables. We illustrate this by the example of the spherically reduced gravity coupled to scalar matter. This procedure is more general than the usual `naive' reduction and apparently more general than the reductions using group theoretical methods. We also explain in more detail the earlier proposed `static-cosmological' duality (SC-duality) and discuss some unusual cosmologies and static states which can be obtained by using the method of separating the space and time variables.
Extending the understanding of critical success factors for implementing business intelligence systems

Extant studies suggest implementing a business intelligence (BI) system is a costly, resource‐intensive and complex undertaking. Literature draws attention to the critical success factors (CSFs) for implementation of BI systems. Leveraging case studies of seven large organizations and blending them with Yeoh and Koronios's (2010) BI CSFs framework, our empirical study gives evidence to support this notion of CSFs and provides better contextual understanding of the CSFs in BI implementation domain. Cross‐case analysis suggests that organizational factors play the most crucial role in determining the success of a BI system implementation. Hence, BI stakeholders should prioritize on the organizational dimension ahead of other factors. Our findings allow BI stakeholders to holistically understand the CSFs and the associated contextual issues that impact on implementation of BI systems.
Reaction Times and Movement Times: Benefits of Practice to Younger and Older Adults

The purpose of this study was to examine the effect of practice on simple reaction time (RT), movement time (MT), and response consistency for two arm-reaching tasks of graded complexity in younger and older adults. Forty subjects, 20 younger adults (age range = 20–29 years) and 20 older adults (age range = 60–82 years), were randomly subdivided into practice and control groups. All subjects were pretested on each arm-reaching movement on Day 1. The practice groups practiced each task for 160 trials over 2 consecutive days while the control groups practiced a memory task and answered a health survey. All subjects were posttested on Day 3. The major finding was that practice reduced the simple RTs of older persons to the level of younger persons. MTs for both practice age groups were reduced, but the age differences in MT performance were maintained.
“What about diet?” A qualitative study of cancer survivors' views on diet and cancer and their sources of information

Given the abundance of misreporting about diet and cancer in the media and online, cancer survivors are at risk of misinformation. The aim of this study was to explore cancer survivors' beliefs about diet quality and cancer, the impact on their behaviour and sources of information. Semi‐structured interviews were conducted with adult cancer survivors in the United Kingdom who had been diagnosed with any cancer in adulthood and were not currently receiving treatment (n = 19). Interviews were analysed using Thematic Analysis. Emergent themes highlighted that participants were aware of diet affecting risk for the development of cancer, but were less clear about its role in recurrence. Nonetheless, their cancer diagnosis appeared to be a prompt for dietary change; predominantly to promote general health. Changes were generally consistent with healthy eating recommendations, although dietary supplements and other non‐evidence‐based actions were mentioned. Participants reported that they had not generally received professional advice about diet and were keen to know more, but were often unsure about information from other sources. The views of our participants suggest cancer survivors would welcome guidance from health professionals. Advice that provides clear recommendations, and which emphasises the benefits of healthy eating for overall well‐being, may be particularly well‐received.
Risk stratification of thyroid nodules with Bethesda category III results on fine-needle aspiration cytology: The additional value of acoustic radiation force impulse elastography

To assess the value of conventional ultrasound, conventional strain elastography (CSE) and acoustic radiation force impulse (ARFI) elastography in differentiating likelihood of malignancy for Bethesda category III thyroid nodules. 103 thyroid nodules with Bethesda category III results on fine-needle aspiration cytology (FNAC) in 103 patients were included and all were pathologically confirmed after surgery. Conventional ultrasound, CSE and ARFI elastography including ARFI imaging and point shear wave speed (SWS) measurement were performed. Univariate and multivariate analyses were performed to identify the independent factors associated with malignancy. Area under the receiver operating characteristic curve (Az) was calculated to assess the diagnostic performance. Pathologically, 65 nodules were benign and 38 were malignant. Significant differences were found between benign and malignant nodules in ARFI. The cut-off points were ARFI imaging grade ≥ 4, SWS > 2.94 m/s and SWS ratio > 1.09, respectively. ARFI imaging (Az: 0.861) had the highest diagnostic performance to differentiate malignant from benign nodules, following by conventional ultrasound (Az: 0.606 - 0.744), CSE (Az: 0.660) and point SWS measurement (Az: 0.725 - 0.735). Multivariate logistic regression analysis showed that ARFI imaging grade ≥ 4 was the most significant independent predictor. The combination of ARFI imaging with point SWS measurement significantly improved the specificity (100% vs. 80.0%) and positive predictive value (100 % vs. 72.9%) in comparison with ARFI imaging alone. ARFI elastography is a useful tool in differentiating malignant from benign thyroid nodules with Bethesda category III results on FNAC.
Pediatric skin care: what do nurses really know?

PURPOSE The purpose of this study was to explore pediatric nurses' knowledge of pressure ulcer prevention, investigate their beliefs and practices, and identify the barriers and facilitators to providing evidence-based pressure ulcer preventive practices. DESIGN AND METHODS An exploratory, descriptive, and cross-sectional survey was taken of registered nurses in a freestanding children's hospital. RESULTS Nurses have adequate knowledge of general pressure ulcer prevention; however, they struggle with individualization. Further, analysis revealed that nursing knowledge did not always correlate with nursing practice. PRACTICE IMPLICATIONS Nurses require education on individualized interventions and access to user-friendly, interactive, and comprehensive resources, including unit-based champions and order sets.
Integration of Arbitrary Lumped Multiport Circuit Networks Into the Discontinuous Galerkin Time-Domain Analysis

A hybrid electromagnetic (EM) circuit simulator is proposed for incorporating multiport lumped circuit networks through their admittance matrices into the discontinuous Galerkin time-domain (DGTD) method. The admittance matrix in the Laplace domain can be derived analytically or obtained from network parameters such as S-parameters in the frequency domain. To convert frequency-dependent S-parameters into the admittance matrix in the Laplace domain, the vector-fitting technique is employed to facilitate the mapping process. The computational domain of interest is split into two subdomains. One is the EM part solved by the DGTD, and another is the circuit part modeled by the basic I-V relationships in the time domain. The couplings between the EM and circuit parts happen at lumped ports where the port voltages and currents are solved via these coupled systems. Due to the local properties of DGTD operations, only small coupling matrix equation systems are involved. To further improve the efficiency, local time-stepping strategy is included. To show the validity of the proposed simulator, several numerical examples are presented and compared with results from other references.