Miracle-dz/UniFAR-FTUs huggingface dataset:
Self Containment, a Property of Modular RNA Structures, Distinguishes microRNAs

RNA molecules will tend to adopt a folded conformation through the pairing of bases on a single strand; the resulting so-called secondary structure is critical to the function of many types of RNA. The secondary structure of a particular substring of functional RNA may depend on its surrounding sequence. Yet, some RNAs such as microRNAs retain their specific structures during biogenesis, which involves extraction of the substructure from a larger structural context, while other functional RNAs may be composed of a fusion of independent substructures. Such observations raise the question of whether particular functional RNA substructures may be selected for invariance of secondary structure to their surrounding nucleotide context. We define the property of self containment to be the tendency for an RNA sequence to robustly adopt the same optimal secondary structure regardless of whether it exists in isolation or is a substring of a longer sequence of arbitrary nucleotide content. We measured degree of self containment using a scoring method we call the self-containment index and found that miRNA stem loops exhibit high self containment, consistent with the requirement for structural invariance imposed by the miRNA biogenesis pathway, while most other structured RNAs do not. Further analysis revealed a trend toward higher self containment among clustered and conserved miRNAs, suggesting that high self containment may be a characteristic of novel miRNAs acquiring new genomic contexts. We found that miRNAs display significantly enhanced self containment compared to other functional RNAs, but we also found a trend toward natural selection for self containment in most functional RNA classes. We suggest that self containment arises out of selection for robustness against perturbations, invariance during biogenesis, and modular composition of structural function. Analysis of self containment will be important for both annotation and design of functional RNAs. A Python implementation and Web interface to calculate the self-containment index are available at http://kim.bio. upenn.edu/software/.
Comparison of different Collection Fusion Models in Distributed Information Retrieval

Distributed information retrieval comes into play when a user wants to get information from di erent sources in parallel. One of the challenges of this topic is the Collection Fusion problem: The distinct result lists of the underlying information retrieval systems (IR) have to be fused to give a global relevance-ranked result list according to the user's information need. In this paper several Collection Fusion models were scrutinized which obey certain restrictions. They should not use more parameters than are given by common collections of distributed digital libraries so that they could be deployed in a real-life distributed retrieval environment. The selected models are evaluated in a test system with an interface to the IR systems of Managing Gigabytes (MG) and Oracle. The quantitative analysis of the models was performed using test queries, test documents and relevance evaluations from TREC. Two test runs were executed, one with all four collections stored in MG, another with three collections in MG and one in Oracle. The results of these test runs are discussed with respect to the test setup.
Making sense of teaching methods in computing education

The goal of this paper is to provide an initial guidepost for computer science (CS) educators seeking to make better use of educational theory research. The authors provide an overview of the latest and most prominent methods for science teaching, and discuss their application to CS education. They provide examples of current applications. For those methods which have not yet been applied to CS, they outline possible future applications.
How well do you know Tom Hanks?: using a game to learn about face recognition

Human face recognition abilities vastly outperform computer-vision algorithms working on comparable tasks, especially in the case of poor lighting, bad image quality, or partially hidden faces. In this paper, we describe a novel game with a purpose in which players must guess the name of a celebrity whose face appears blurred. The game combines a successful casual game paradigm with meaningful applications in both human- and computer-vision science. Preliminary user studies were conducted with 28 users and more than 7,000 game rounds. The results supported and extended pre-existing knowledge and hypotheses from controlled scientific experiments, which show that humans are remarkably good at recognizing famous faces, even with a significant degree of blurring. Our results will be further incorporated into research in human vision as well as machine-learning and computer-vision algorithms for face recognition.
Emotional movie: A new art form designed at the heart of human-technology interaction

Innovative art forms emerge along with the development of new materials for displaying multimedia content and the new possibilities for interaction with the spectator they offer. Interactive movie in one of them; It consists in providing a personalized content by interacting with the emotional state of the spectator. In this study, we define this new form of artwork and describe how it can be implemented by providing functional criteria that will determine how different parts of the movie will be connected to form a particular scenario. We measured neurophysiological and ocular activities of 60 subjects watching an experimental short-movie realized for the “emotional movie” project, composed of 12 different scenarios. We combined an electroencephalography headset which directly provides emotional data with an eye-tracker to investigate the simultaneous positions of gaze. From our results we propose that the emotional proximity between the scenario and the spectator could be a relevant selection criterion to customize the movie.
Achievement motivation and self-evaluative emotions in preschool children from low-income families.

ACHIEVEMENT MOTIVATION AND SELF-EVALUATIVE EMOTIONS IN PRESCHOOL CHILDREN FROM LOW-INCOME FAMILIES Crystal A. Day March 28, 2011 The current study was designed to better understand the early behavioral and emotional factors influencing young children's responses to challenge, which have important implications for learning. Understanding why children respond to challenge as they do is particularly important for young children from poverty, who face many contextual factors that place them at-risk for experiencing negative academic outcomes (Brooks-Gunn, Linver, & Fauth, 2005). Previous research suggests that children adopt distinct behavioral and emotional reactions to challenge. Such reactions have been studied in terms of either achievement motivation or self-evaluative emotion research (Dweck & Leggett, 1988; Lewis & Sullivan, 2005), with achievement motivation researchers explaining behavioral responses and self-evaluative emotion researchers explaining emotional responses. The present study integrated the research on achievement motivation and selfevaluative emotions and tested a new model that described the early developmental relationship between these variables in preschool-aged children from poverty. The goals of this research were to: (1) replicate and extend upon research examining children's
The Role of Nitric Oxide in Mouse Cerulein‐Induced Pancreatitis With and Without Lipopolysaccharide Pretreatment

Nitric oxide (NO) has been shown to play a significant role in inflammation. To clarify the role of NO in acute pancreatitis, we investigated the serum concentrations of NOx (NO2− plus NO3−) and tumor necrosis factor-α (TNF-α) and the grade of pancreatitis in cerulein-induced pancreatitis in mice pretreated with lipopolysac-charide (LPS) or not. LPS pretreatment aggravated the cerulein pancreatitis in association with a transient increase in serum TNF-α, which was followed by a gradual elevation of serum NOx. This elevation of serum NOx concentration was inhibited by the NO synthase inhibitor NG-nitro-L-arginine (L-NNA). In addition, the activity of NADPH-diaphorase (NADPH-d), a marker for NO synthase, appeared in the peritoneal macrophages of LPS-pretreated mice after the induction of pancreatitis. No elevation of serum NOx or appearance of NADPH-d activity in peritoneal cells was found in mice without LPS pretreatment. Administration of L-NNA enhanced the elevation of pancreatitis-induced serum amylase in mice untreated with LPS, while L-NNA inhibited the elevation in LPS-pretreated mice. The effects of L-NNA were reversed by the administration of L-arginine but were not affected by D-arginine. These results suggested that (a) inflammatory cells may not be fully activated to produce excessive NO in uncomplicated edematous pancreatitis, and (b) edematous pancreatitis may be aggravated by excessively produced NO if bacterial infection is complicated and inflammatory cells are activated to express in-ducible NO synthase.
ASSESSING THE INFLUENCE OF THE SOLAR ORBIT ON TERRESTRIAL BIODIVERSITY

The terrestrial fossil record shows a significant variation in the extinction and origination rates of species during the past half-billion years. Numerous studies have claimed an association between this variation and the motion of the Sun around the Galaxy, invoking the modulation of cosmic rays, gamma rays, and comet impact frequency as a cause of this biodiversity variation. However, some of these studies exhibit methodological problems, or were based on coarse assumptions (such as a strict periodicity of the solar orbit). Here we investigate this link in more detail, using a model of the Galaxy to reconstruct the solar orbit and thus a predictive model of the temporal variation of the extinction rate due to astronomical mechanisms. We compare these predictions as well as those of various reference models with paleontological data. Our approach involves Bayesian model comparison, which takes into account the uncertainties in the paleontological data as well as the distribution of solar orbits consistent with the uncertainties in the astronomical data. We find that various versions of the orbital model are not favored beyond simpler reference models. In particular, the distribution of mass extinction events can be explained just as well by a uniform random distribution as by any other model tested. Although our negative results on the orbital model are robust to changes in the Galaxy model, the Sun's coordinates, and the errors in the data, we also find that it would be very difficult to positively identify the orbital model even if it were the true one. (In contrast, we do find evidence against simpler periodic models.) Thus, while we cannot rule out there being some connection between solar motion and biodiversity variations on the Earth, we conclude that it is difficult to give convincing positive conclusions of such a connection using current data.
Brain cancer immunoediting: novel examples provided by immunotherapy of malignant gliomas

A number of studies in murine models have suggested that the immune system may edit different tumors by forcing their expression profiles so that they escape immune reactions and proliferate. Glioblastoma (GB), the most frequent and aggressive primary brain tumor, provides a good example of this, thanks to the production of numerous immunosuppressive molecules (with TGF-β being of paramount importance), downregulation of the MHC complex and deregulation of the potential for antigen presentation by the surrounding microglia. Given that surgery, radiotherapy and chemotherapy with available protocols have limited effects on the survival of GB patients, different immunotherapy strategies have been developed, based on the use of dendritic cells, antibodies and peptide vaccination. Presently, bevacizumab, a humanized anti-VEGF antibody, provides the most successful example for immune-based treatment of GB, however, its action is limited in time, as the often tumor relapses due to still undefined immunoediting mechanisms. Altered function of EGF receptor-driven pathways is common in GB and is most frequently due to the presence of a deleted form named EGFRvIII, providing a unique cancer epitope that has been targeted by immunotherapy. A recent trial of GB immunotherapy based on vaccination with the EGFRvIII peptide has shown clinical benefit: interestingly most GBs at relapse were negative for EGFRvIII expression, a relevant, direct example of cancer immunoediting. Investigations on the mechanisms of GB immunoediting will lead to an increased understanding of the biology of this malignancy and hopefully provide novel therapeutic targets.
Co-seismic displacements of the 1992 landers earthquake sequence

We present co-seismic displacement vectors derived from Global Positioning System (GPS) measurements of 92 stations in southern California. These GPS results are combined with five well-determined GPS displacement vectors from continuously tracking stations of the Permanent GPS Geodetic Array, as well as line-length changes from USGS Geodolite and two-color laser trilateration observations, to determine a self-consistent set of geodetic data for the earthquake. These combined displacements are modeled by an elastic dislocation representation of the primary fault rupture planes. On average, the model residuals are about twice the estimated measurement errors.
Blind source separation in a distributed microphone meeting environment for improved teleconferencing

From an audio perspective, the present state of teleconferencing technology leaves something to be desired; speaker overlap is one of the causes of this inadequate performance. To that end, this paper presents a frequency-domain implementation of convolutive BSS specifically designed for the nature of the teleconferencing environment. In addition to presenting a novel depermutation scheme, this paper presents a least-squares post-processing scheme, which exploits segments during which only a subset of all speakers are active. Experiments with simulated and real data demonstrate the ability of the proposed methods to provide SIRs at or near that of the adaptive noise cancellation (ANC) solution which is obtained under idealistic assumptions that the ANC filters are adapted with one source being on at a time.
Secure and Privacy-Aware Cloud-Assisted Video Reporting Service in 5G-Enabled Vehicular Networks

Vehicular networks are one of the main technologies that will be leveraged by the arrival of future fifth-generation (5G) mobile cellular networks. While scalability and latency are the major drawbacks of IEEE 802.11p and fourth-generation (4G) Long-Term Evolution (LTE)-enabled vehicular communications, respectively, the 5G technology is a promising solution to empower the real-time services offered by vehicular networks. However, the security and privacy of such services in 5G-enabled vehicular networks need to be addressed first. In this paper, we propose a novel system model for a 5G-enabled vehicular network that facilitates a reliable, secure, and privacy-aware real-time video reporting service. This service is designed for participating vehicles to instantly report the videos of traffic accidents to guarantee a timely response from official vehicles and/or ambulances toward accidents. While it provides strong security and privacy guarantees for the participating vehicle's identity and the video contents, the proposed service ensures traceability of misbehaving participants through a cooperation scheme among different authorities. We show the feasibility and the fulfillment of the proposed reporting service in 5G-enabled vehicular networks in terms of security, privacy, and efficiency.
A comparison of communication needs of charge nurses in two operating room suites

To achieve the potential inherent in the use of computer applications in distributed environments, we need to understand the information needs of users. Communication is the method by which information is transferred and is essential for all organizational interaction. The primary goal of operating room coordination is to insure the prompt, safe, and effective care of surgical patients. Nevertheless, larger organizational goals and characteristics can influence individual operating room information needs. The purpose of this paper is to describe the differing information needs in two operating suites by documenting the communication of OR charge nurses. A data collection tool was developed to record: 1) the purpose of the communication, 2) mode of communication, 3) the target individual, and 4) the length of time taken for each occurrence. The chosen data collection categories provided a functional structure for data collection and analysis involving communication. Study findings are discussed within the context of opportunities for application design
POSTER: Poor Man's URCU

RCU is, among other things, a well known mechanism for memory reclamation that is meant to be used in languages without an automatic Garbage Collector, unfortunately, it requires operating system support, which is currently provided only in Linux. An alternative is to use Userspace RCU (URCU) which has two variants that can be deployed on other operating systems, named \emph{Memory Barrier} and \emph{Bullet Proof}. We present a novel algorithm that implements the three core APIs of RCU: \texttt{rcu\_read\_lock()}, \texttt{rcu\_read\_unlock()}, and \texttt{synchronize\_rcu()}. Our algorithm uses one mutual exclusion lock and two reader-writer locks with \texttt{trylock()} capabilities, which means it does not need a language with a memory model or atomics API, and as such, it can be easily implemented in almost any language, regardless of the underlying CPU architecture, or operating system.
Physical activity status, but not age, influences inflammatory biomarkers and toll-like receptor 4.

BACKGROUND Chronic inflammation has been implicated in the development of cardiovascular disease, diabetes mellitus, cachexia, and osteoporosis. Regular physical activity has been purported to possess "anti-inflammatory" properties which may limit chronic inflammation. Recently, we hypothesized that toll-like receptor 4 (TLR4) may play a role in activity-induced modulation of inflammation. Therefore, the purpose of this study was to determine the association between age, physical activity status, biomarkers of inflammation, and TLR4. METHODS Male and female participants (n = 84) were recruited to fill one of the following groups: young (18-30 years), active; young, inactive; old (60-80 years), active; or old, inactive. To assess physical activity status, participants completed a Paffenbarger Physical Activity Questionnaire and a modified Balke submaximal treadmill test. After grouping and screening, participants were given a standard mixed diet to consume 24 hours prior to arriving at the laboratory. Participants were instructed to consume all food by 10 pm the night prior to blood sampling (8-hour fast). Following 30 minutes of seated rest in a quiet room, venous blood samples were collected. Lipopolysaccharide-stimulated inflammatory cytokine production and plasma high-sensitivity C-reactive protein (hsCRP) were determined by enzyme-linked immunosorbent assay, and TLR4 expression was determined by flow cytometry. RESULTS Lipopolysaccharide-stimulated interleukin-6, interleukin-1beta, and tumor necrosis factor-alpha production, TLR4 expression, and hsCRP were significantly lower in active compared to inactive participants (p <.05). Also, older participants had significantly higher hsCRP than young participants had (p <.05). CONCLUSIONS The findings of the present study support previous reports which infer that acute exercise or a physically active lifestyle may possess anti-inflammatory properties. Also this study, along with previous work from our laboratory, suggests that TLR4 may play a role in regulating the link between inflammatory cytokine production and a physically active lifestyle.
Self-made texture and clustering based road recognition for UGV

Three hierarchical algorithms are proposed to get the passable driving road detection for unmanned ground vehicle (UGV). The innovation of this paper is the self-made directional texture which will be produced if the inverse homography transform is exerted on the image. This self-made texture is firstly used to remove the image corresponding to the objects above road. In order to avoid the influence of other color object, the k-means clustering is used to get the seed for region growing. Finally, the directional texture is secondly used to judge whether the image holes after region growing are the road or not. The final experimental results show the proposed algorithm can remove the non-road objects, can and fill the stained color region and can get the rational driving road.
Respiratory Physiology and the Impact of Different Modes of Ventilation on the Photoplethysmographic Waveform

The photoplethysmographic waveform sits at the core of the most used, and arguably the most important, clinical monitor, the pulse oximeter. Interestingly, the pulse oximeter was discovered while examining an artifact during the development of a noninvasive cardiac output monitor. This article will explore the response of the pulse oximeter waveform to various modes of ventilation. Modern digital signal processing is allowing for a re-examination of this ubiquitous signal. The effect of ventilation on the photoplethysmographic waveform has long been thought of as a source of artifact. The primary goal of this article is to improve the understanding of the underlying physiology responsible for the observed phenomena, thereby encouraging the utilization of this understanding to develop new methods of patient monitoring. The reader will be presented with a review of respiratory physiology followed by numerous examples of the impact of ventilation on the photoplethysmographic waveform.
Charles Ogletree and Austin Sarat (eds), When Law Fails: Making Sense of Miscarriages of Justice

relies on secondary sources and bolsters her argument with victimization statistics. Although she notes in the Acknowledgements that she has had personal contact with women on whose cases she focuses, she does not present direct accounts of people like Mrs B as research respondents. However, because her contribution lies in identifying the consequences of the narrow mainstream idea of a victim of violence, her heavy use of secondary sources does not subtract from the argument. The book is a call for alarm and intervention on behalf of people who largely cannot self-advocate, but Richie cautions that – if we have learned nothing else from the consequences of anti-violence work – responses must be culturally appropriate. This book contributes to a growing body of research about the negative consequences of the cooptation of women’s movements by the State (other recent works have been published by Kristin Bumiller and Hester Eistenstein). While this kind of argument is not entirely new (Richie, 2000), together this body of work demands the reshaping of systems to respond to women who face victimization. Richie’s challenge to readers is to create better and more just interventions: ones that work to deconstruct the ‘prison nation’ while simultaneously addressing the conditions of women and the constructions of women that allow violence against marginalized Black women to continue.