Miracle-dz/UniFAR-FTUs huggingface dataset:
Splice Site Recognition in DNA Sequences Using K-mer Frequency Based Mapping for Support Vector Machine with Power Series Kernel

Recognition of specific functionally-important DNA sequence fragments is considered one of the most important problems in bioinformatics. One type of such fragments is splice-junction (intron-exon or exon-intron) sites. Detection of splice-junction sites in DNA sequences is important for successful gene prediction. In this paper, support vector machine (SVM) is used for classification of DNA sequences and splice-site recognition. For optimal classification, four position-independent k-mer frequency based methods for mapping DNA sequences into SVM feature space are analyzed. Classification is performed using SVM power series kernels. Kernel parameters are optimized using a modification of the Nelder-Mead (downhill simplex) optimization method. Precision of classification is evaluated using F-measure, which is a combination of precision and recall metrics. Best classification results are achieved using 4-mers for exon-intron dataset (78%) and 6-mers for intron-exon dataset (70%) using 4-nucleotide frequencies.
What is value—accumulated reward or evidence?

Why are you reading this abstract? In some sense, your answer will cast the exercise as valuable—but what is value? In what follows, we suggest that value is evidence or, more exactly, log Bayesian evidence. This implies that a sufficient explanation for valuable behavior is the accumulation of evidence for internal models of our world. This contrasts with normative models of optimal control and reinforcement learning, which assume the existence of a value function that explains behavior, where (somewhat tautologically) behavior maximizes value. In this paper, we consider an alternative formulation—active inference—that replaces policies in normative models with prior beliefs about the (future) states agents should occupy. This enables optimal behavior to be cast purely in terms of inference: where agents sample their sensorium to maximize the evidence for their generative model of hidden states in the world, and minimize their uncertainty about those states. Crucially, this formulation resolves the tautology inherent in normative models and allows one to consider how prior beliefs are themselves optimized in a hierarchical setting. We illustrate these points by showing that any optimal policy can be specified with prior beliefs in the context of Bayesian inference. We then show how these prior beliefs are themselves prescribed by an imperative to minimize uncertainty. This formulation explains the saccadic eye movements required to read this text and defines the value of the visual sensations you are soliciting.
Energy Minimization for Real-Time Data Gathering in Wireless Sensor Networks

This paper studies the challenging problem of energy minimization for data gathering over a multiple-sources single-sink communication substrate in wireless sensor networks by exploring the energy-latency tradeoffs using rate adaptation techniques. We consider a real-time scenario for mission-critical applications, where the data gathering must be performed within a specified latency constraint. We first propose an offline numerical optimization algorithm with performance analysis for a special case with a complete binary data gathering tree. Then, by discretizing the transmission time, we present a simple, distributed on-line protocol that relies only on the local information available at each sensor node. Extensive simulations were conducted for both long and short-range communication scenarios using two different source placement models. We used the baseline of transmitting all packets at the highest speed and shutting down the radios afterwards. Our simulation results show that compared with this baseline, up to 90% energy savings can be achieved by our techniques (both off-line and on-line), under different settings of several key system parameters
Toward the Implementation of Relevance and Reputation Indicators in Edu-AREA

This paper introduces the first implementation of relevance and reputation indicators in Edu-AREA. This Web 2.0 application promotes users creating, viewing, adopting, adapting, and curating elements in an open way, following the principles of the open educational resources movement. A main issue is the management and control of quality. Users can provide elements freely, so some mechanism that can estimate or rank their quality is needed. A solution based on usage by other users inspired in the hypertext-induced topic search algorithm is adopted. Taking into account the usages of the elements, a relevance measure for each element and a reputation measure for each user are calculated.
Genome-Wide Identification and Evolution of HECT Genes in Soybean

Proteins containing domains homologous to the E6-associated protein (E6-AP) carboxyl terminus (HECT) are an important class of E3 ubiquitin ligases involved in the ubiquitin proteasome pathway. HECT-type E3s play crucial roles in plant growth and development. However, current understanding of plant HECT genes and their evolution is very limited. In this study, we performed a genome-wide analysis of the HECT domain-containing genes in soybean. Using high-quality genome sequences, we identified 19 soybean HECT genes. The predicted HECT genes were distributed unevenly across 15 of 20 chromosomes. Nineteen of these genes were inferred to be segmentally duplicated gene pairs, suggesting that in soybean, segmental duplications have made a significant contribution to the expansion of the HECT gene family. Phylogenetic analysis showed that these HECT genes can be divided into seven groups, among which gene structure and domain architecture was relatively well-conserved. The Ka/Ks ratios show that after the duplication events, duplicated HECT genes underwent purifying selection. Moreover, expression analysis reveals that 15 of the HECT genes in soybean are differentially expressed in 14 tissues, and are often highly expressed in the flowers and roots. In summary, this work provides useful information on which further functional studies of soybean HECT genes can be based.
Interleukin‐10 is associated with resistance to febrile seizures: Genetic association and experimental animal studies

Purpose: Febrile seizures (FS) are the most common form of childhood convulsions. Many reports have shown that a proinflammatory cytokine, interleukin‐1 (IL‐1) β, may have a facilitatory effect on the development of FS. We have previously shown that the IL1B ‐511C/T single nucleotide polymorphism (SNP) is associated with simple FS of sporadic occurrence. The balance between pro‐ and antiinflammatory cytokines influences the regulation of infections and could, therefore, play a role in the pathogenesis of FS. Here, to determine whether pro‐ and antiinflammatory cytokine genes are responsible for the susceptibility to FS, we have performed an association study on functional SNPs of cytokine genes in FS patients and controls.
Abusing Phone Numbers and Cross-Application Features for Crafting Targeted Attacks

With the convergence of Internet and telephony, new applications (e.g., WhatsApp) have emerged as an important means of communication for billions of users. These applications are becoming an attractive medium for attackers to deliver spam and carry out more targeted attacks. Since such applications rely on phone numbers, we explore the feasibility, automation, and scalability of phishing attacks that can be carried out by abusing a phone number. We demonstrate a novel system that takes a potential victim's phone number as an input, leverages information from applications like Truecaller and Facebook about the victim and his / her social network, checks the presence of phone number's owner (victim) on the attack channels (over-the-top or OTT messaging applications, voice, e-mail, or SMS), and finally targets the victim on the chosen channel. As a proof of concept, we enumerate through a random pool of 1.16 million phone numbers. By using information provided by popular applications, we show that social and spear phishing attacks can be launched against 51,409 and 180,000 users respectively. Furthermore, voice phishing or vishing attacks can be launched against 722,696 users. We also found 91,487 highly attractive targets who can be attacked by crafting whaling attacks. We show the effectiveness of one of these attacks, phishing, by conducting an online roleplay user study. We found that social (69.2%) and spear (54.3%) phishing attacks are more successful than non-targeted phishing attacks (35.5%) on OTT messaging applications. Although similar results were found for other mediums like e-mail, we demonstrate that due to the significantly increased user engagement via new communication applications and the ease with which phone numbers allow collection of information necessary for these attacks, there is a clear need for better protection of OTT messaging applications.
Psychology and Neuroscience of Person Perception

Understanding other people amounts to one of the most important and complex challenges humans regularly encounter. And yet, despite the enormously variable and noisy nature of social stimuli (e.g., faces and bodies, both in static and in dynamic configurations), humans reliably extract information about one another in a process that appears automatic and obligatory. Among the information spontaneously extracted from viewing even a static image of another’s face are social categories, such as sex, race, and age; personality traits, such as trustworthiness and competence; emotion; identity; and intentions. The initial perceptual operations giving rise to such impressively efficient information processing are undoubtedly important and consequential for social interaction. However, most research on person perception carried out by social psychologists during the 20th century was not focused on people as perceptual targets. Instead of focusing on the role of external appearance and perceptual input (visual, auditory, etc.) that contributes to perceiving and understanding others, research typically focused on the internal states (intentions, beliefs, traits) that can be inferred about a person, the internal cognitive mechanisms responsible for processing such social knowledge, and the downstream consequences these inferences might have for interpersonal interaction (e.g., Brewer, 1988; Hassin, Bargh, & Uleman, 2002; Kunda & Thagard, 1996; for a review, see Gilbert, 1998). Indeed, early research typically investigated person perception by presenting research participants with written descriptions of a person’s behavior or personality characteristics or by directly presenting participants with social category labels and observing the kinds of assumptions and inferences made about a person based solely on category membership. Thus, within social psychology, early research focused on primarily postperceptual processes downstream of visually based perceptions, investigating the effects of placing someone in a social category on memory for and behaviors enacted toward that individual. Indeed, social categorization in particular has a long history in social psychology of being considered a precursor to the more consequential act of stereotyping (Allport, 1954; Bargh et al., 1996; Fiske & Taylor, 1991). Although social psychologists amassed an extensive literature on the downstream consequences of person perception and social categorization, a great deal of research in cognitive psychology and neuroscience began
A Puncturing Scheme for Low-Density Parity-Check Codes Based on 1-SR Nodes

A rate-compatible puncturing scheme for LDPC codes is proposed based on the fact that a one-step recoverable (1-SR) node is more reliable than a k-SR node (k>;1) and a 1-SR node with more survived check nodes can be recovered more reliably in a recovery tree, so the scheme tries to obtain 1-SR nodes which have multiple survived check nodes as many as possible. Simulation results show that the puncturing scheme has better performance than both the random puncturing scheme and the novel method in [5].
STROOP EFFECT WITH SYNONYMOUS HOMOGRAPHIC HETEROPHONEMIC WORDS IN JAPANESE KANJI

One of the three types of Japanese orthographic systems, kanji, consists of ideograms rather than phonograms. Most of the kanji originally introduced from China can be read in two ways: in on (Chinese old pronunciation; relatively lower reading proficiency) and in kun (Japanese inherent pronunciation; relatively higher reading proficiency). In the current experiment, the participants were asked to name the color of Stroop color words in kanji, which were accompanied by an alternation with either on or kun, their corresponding auditory words from one trial to the next. The accompanying auditory words in kun in higher proficiency had no impact on the Stroop interference, whereas those in on in lower proficiency had substantial effect on the Stroop interference.
Amplitudes in N = 4 SYM from the Quantum geometry of the Momentum Space

We discuss multiloop MHV amplitudes in the N = 4 SYM theory in terms of eﬀective gravity in the momentum space with IR regulator branes as degrees of freedom. Kinematical invariants of external particles yield the moduli spaces of complex or Kahler structures which are the playgrounds for the Kodaira-Spencer(KS) or Kahler type gravity. We suggest fermionic representation of the loop MHV amplitudes in the N = 4 SYM theory assuming the identiﬁcation of the IR regulator branes with KS fermions in the B model and Lagrangian branes in A model. The two-easy mass box diagram is related to the correlator of fermionic currents on the spectral curve in B model or hyperbolic volume in the A model and it plays the role of a building block in the whole picture. The BDS-like anzatz has the interpretation as the semiclassical limit of a fermionic correlator. It is argued that fermionic representation implies a kind of integrability on the moduli spaces. We conjecture the interpretation of the reggeon degrees of freedom in terms of the open strings stretched between the IR regulator branes.
Does eosinophilic COPD exacerbation have a better patient outcome than non-eosinophilic in the intensive care unit?

Background COPD exacerbations requiring intensive care unit (ICU) admission have a major impact on morbidity and mortality. Only 10%–25% of COPD exacerbations are eosinophilic. Aim To assess whether eosinophilic COPD exacerbations have better outcomes than non-eosinophilic COPD exacerbations in the ICU. Methods This retrospective observational cohort study was conducted in a thoracic, surgery-level III respiratory ICU of a tertiary teaching hospital for chest diseases from 2013 to 2014. Subjects previously diagnosed with COPD and who were admitted to the ICU with acute respiratory failure were included. Data were collected electronically from the hospital database. Subjects’ characteristics, complete blood count parameters, neutrophil to lymphocyte ratio (NLR), delta NLR (admission minus discharge), C-reactive protein (CRP) on admission to and discharge from ICU, length of ICU stay, and mortality were recorded. COPD subjects were grouped according to eosinophil levels (>2% or ≤2%) (group 1, eosinophilic; group 2, non-eosinophilic). These groups were compared with the recorded data. Results Over the study period, 647 eligible COPD subjects were enrolled (62 [40.3% female] in group 1 and 585 [33.5% female] in group 2). Group 2 had significantly higher C-reactive protein, neutrophils, NLR, delta NLR, and hemoglobin, but a lower lymphocyte, monocyte, and platelet count than group 1, on admission to and discharge from the ICU. Median (interquartile range) length of ICU stay and mortality in the ICU in groups 1 and 2 were 4 days (2–7 days) vs 6 days (3–9 days) (P<0.002), and 12.9% vs 24.9% (P<0.034), respectively. Conclusion COPD exacerbations with acute respiratory failure requiring ICU admission had a better outcome with a peripheral eosinophil level >2%. NLR and peripheral eosinophilia may be helpful indicators for steroid and antibiotic management.
Tightly regulated, beta-estradiol dose-dependent expression system for yeast.

We have refined the regulated expression of UASGAL1, 10-driven genes in yeast by modifying a vector encoding the beta-estradiol inducible activator, GAL4.ER. VP16 (GEV). The expression of GEV was placed under the regulation of the low-level, constitutive MRP7 promoter, and beta-estradiol-regulated expression was monitored by the expression of an integrated UASGAL10-lacZ reporter and by immunoblot analysis of a UASGAL1-regulated gene product. Target gene expression regulated by low levels of GEV has several advantages over the standard galactose-inducible expression systems. (i) Most importantly, the target gene expression is undetectable in the absence of hormone; (ii) target gene expression is beta-estradiol dose-dependent, and variable levels of target gene expression from low to several hundred-fold induction can be achieved; and (iii) induction or depletion studies can be conducted independent of carbon source in gal4 delta strains. In addition, any UASGAL1,10 expression construct can be used without modification of the target gene or many gal4 delta host strains, and GEV vectors are compatible with other inducible yeast expression systems. This method may be useful to researchers investigating the functions of essential genes, dominant negative mutants, mitochondrial genes, and viral, plant, and mammalian genes in yeast assay systems.
Simplex NPs Clustered by Head: A Method for Identifying Significant Topics Within a Document

This paper discusses 'head clustering', a novel, linguistically-motivated method for representing the aboutness of a document. First, a list of candidate significant topics consisting all simplex NPs is extracted from the document. Next, these NPs are clustered by head. Finally, a significance measure is obtained by ranking frequency of heads: those NPs with heads that occur with greater frequency in the document are more significant than NPs whose head occurs less frequently. An important strength of this technique is that it i s in principle domain-general. Furthermore, the output can be filtered in a variety of ways, both for automatic processing and for presentation to users. In order to evaluate the head clustering method, an experiment was conducted in which judges were asked to rate three lists as to whether they conveyed a sense of the content of the article. The judges agreed that the list of simplex NPs with repeated heads was more helpful in representing the content of the full document than a list of keywords with a frequency of greater than one or than a list of repeated word sequences.
On the Importance of Synchronization Primitives with Low Consensus Numbers

The consensus number of a synchronization primitive is the maximum number of processes for which the primitive can solve consensus. This has been the traditional measure of power of a synchronization primitive. Thus, the compare-and-swap primitive, which has infinite consensus number, is considered most powerful and has been the primitive of choice for implementing concurrent data structures. In this work, we show that the synchronization primitives with low consensus numbers can also be potentially powerful by using them along with the compare-and-swap primitive to design an O (√n) time wait-free and linearizable concurrent queue. The best known time bound for a wait-free and linearizable concurrent queue using only the compare-and-swap primitive is O(n). Here, n is the total number of processes that can access the queue. The queue object maintains a sequence of elements and supports the operations enqueue(x) and dequeue(). The wait-free property implies that every call to enqueue(x) and dequeue() finishes in a bounded number of steps irrespective of the schedule of other n --1 processes. The linearizable property implies that the enqueue(x) and dequeue() calls appear to be instantaneously applied within the duration of respective calls. We design a wait-free and a linearizable concurrent queue using shared memory registers that support the compare-and-swap primitive and two other primitives of consensus number one and two respectively. The enqueue(x) and dequeue() operations take O (√n) steps each. The total number of registers required are O(nm) of O (max{log n, log m }) bits each, where m is a bound on the total number of enqueue(x) operations.
Developing your organization with models and simulations

Purpose – This paper discusses how simulations can be used to improve organizations.Design/methodology/approach – The paper provides an overview of three major simulation methods – Petri nets, system dynamics, and agent based modeling.Findings – The overview shows that while each method has different complexity levels and more appropriate areas for implementation, all can be used better understand organizational processes.Originality/value – This paper provides a unique comparison of simulation methods in a developmental context.
Randomized Controlled Comparison of Cognitive Behavior Therapy with Rogerian Supportive Therapy in Chronic Post-Traumatic Stress Disorder: A 2-Year Follow-Up

Background: To date, there have been no studies comparing cognitive behavior therapy (CBT) with Rogerian therapy in post-traumatic stress disorder. Method: Sixty outpatients with DSM-IV chronic post-traumatic stress disorder were randomized into two groups for 16 weekly individual sessions of CBT or Rogerian supportive therapy (ST) at two centers. No medication was prescribed. Measures included the Post-Traumatic Stress Disorder Checklist Scale (PCLS), the Hamilton Anxiety Scale, Beck Depression Inventory, and Quality of Life. The general criterion of improvement (GCI) was a score of less than 44 on the PCLS. Results: Forty-two patients were evaluated at post-test, 38 at week 52 and 25 at week 104. At post-test, the rate of patients leaving the trial due to worsening or lack of effectiveness was significantly higher in the ST group (p = 0.004). At this point, no between-group difference was found on the GCI and any of the rating scales. Intent-to-treat analysis found no difference for the GCI, but patients in the CBT group showed greater improvement on the PCLS and Hamilton Anxiety Scale. Naturalistic follow-up showed sustained improvement without between-group differences at weeks 52 and 104. Conclusions: CBT retained significantly more patients in treatment than ST, but its effects were equivalent to those of ST in the completers. CBT was better in the dimensional intent-to-treat analysis at post-test.
From the Cover : Semiotic dynamics and collaborative tagging

www.pnas. org/cgi/content/full/104/5/1461#otherarticles This article has been cited by other articles: E-mail Alerts . click here at the top right corner of the article or Receive free email alerts when new articles cite this article sign up in the box Rights & Permissions www.pnas. org/misc/rightperm.shtml To reproduce this article in part (figures, tables) or in entirety, see: Reprints www.pnas. org/misc/reprints.shtml To order reprints, see: