Miracle-dz/UniFAR-FTUs huggingface dataset:
Heart Structure-Specific Transcriptomic Atlas Reveals Conserved microRNA-mRNA Interactions

MicroRNAs are short non-coding RNAs that regulate gene expression at the post-transcriptional level and play key roles in heart development and cardiovascular diseases. Here, we have characterized the expression and distribution of microRNAs across eight cardiac structures (left and right ventricles, apex, papillary muscle, septum, left and right atrium and valves) in rat, Beagle dog and cynomolgus monkey using microRNA sequencing. Conserved microRNA signatures enriched in specific heart structures across these species were identified for cardiac valve (miR-let-7c, miR-125b, miR-127, miR-199a-3p, miR-204, miR-320, miR-99b, miR-328 and miR-744) and myocardium (miR-1, miR-133b, miR-133a, miR-208b, miR-30e, miR-499-5p, miR-30e*). The relative abundance of myocardium-enriched (miR-1) and valve-enriched (miR-125b-5p and miR-204) microRNAs was confirmed using in situ hybridization. MicroRNA-mRNA interactions potentially relevant for cardiac functions were explored using anti-correlation expression analysis and microRNA target prediction algorithms. Interactions between miR-1/Timp3, miR-125b/Rbm24, miR-204/Tgfbr2 and miR-208b/Csnk2a2 were identified and experimentally investigated in human pulmonary smooth muscle cells and luciferase reporter assays. In conclusion, we have generated a high-resolution heart structure-specific mRNA/microRNA expression atlas for three mammalian species that provides a novel resource for investigating novel microRNA regulatory circuits involved in cardiac molecular physiopathology.
Early Event-related Potential Effects of Syllabic Processing during Visual Word Recognition

A number of behavioral studies have suggested that syllables might play an important role in visual word recognition in some languages. We report two event-related potential (ERP) experiments using a new paradigm showing that syllabic units modulate early ERP components. In Experiment 1, words and pseudowords were presented visually and colored so that there was a match or a mismatch between the syllable boundaries and the color boundaries. The results showed color-syllable congruency effects in the time window of the P200. Lexicality modulated the N400 amplitude, but no effects of this variable were obtained at the P200 window. In Experiment 2, high-and low-frequency words and pseudowords were presented in the congruent and incongruent conditions. The results again showed congruency effects at the P200 for low-frequency words and pseudowords, but not for high-frequency words. Lexicality and lexical frequency effects showed up at the N400 component. The results suggest a dissociation between syllabic and lexical effects with important consequences for models of visual word recognition.
Genetic Regulation of Atherosclerotic Plaque Size and Morphology in the Innominate Artery of Hyperlipidemic Mice

Objective—We sought to determine the genetic factors contributing to atherosclerotic plaque size and cellular composition in the innominate artery, a murine model of advanced atherosclerosis. Methods and Results—We examined genetic contributions to innominate atherosclerotic plaque size and cellular composition in an intercross between C57BL/6J.Apoe−/−, a strain susceptible to aortic lesions, and C3H/HeJ.Apoe−/−, a strain resistant to aortic lesions. Surprisingly, total innominate lesion size was similar in the two strains. Genetic analyses identified one novel locus on Chromosome 2 for innominate artery lesion size, a significant locus for fibrous cap thickness on Chromosome 15, and several suggestive loci for cellular composition, all distinct from loci influencing aortic lesions. The Chromosome 2 locus contains a candidate, CD44. We show that CD44 is expressed in the innominate artery and differs strikingly in expression between the parental strains. Conclusion—Multiple aspects of innominate lesion composition are genetically determined, but in a manner largely independent of the genetic contributions to aortic lesions.
Addressing Sexual Assault within Social Systems: System Justification as a Barrier to College Prevention Efforts

Sexual assault perpetrated by men against women is a distressingly common occurrence, particularly on college campuses. One of the barriers to assault prevention efforts is the general perception of violence against women as an unwanted yet implicitly tolerated aspect of the status quo. Drawing on system justification theory, a concept used to explain why individuals accept aspects of their social systems that are objectively unjust, the mechanisms that perpetuate sexual assault are examined. Furthermore, this theory is used to examine current prevention efforts on college campuses and suggestions for modifications to these programs will be made.
Robust State Estimation for Neural Networks With Discontinuous Activations

Discontinuous dynamical systems, particularly neural networks with discontinuous activation functions, arise in a number of applications and have received considerable research attention in recent years. In this paper, the robust state estimation problem is investigated for uncertain neural networks with discontinuous activations and time-varying delays, where the neuron-dependent nonlinear disturbance on the network outputs are only assumed to satisfy the local Lipschitz condition. Based on the theory of differential inclusions and nonsmooth analysis, several criteria are presented to guarantee the existence of the desired robust state estimator for the discontinuous neural networks. It is shown that the design of the state estimator for such networks can be achieved by solving some linear matrix inequalities, which are dependent on the size of the time derivative of the time-varying delays. Finally, numerical examples are given to illustrate the theoretical results.
An experience in integrating automated unit testing practices in an introductory programming course

Unit testing is one of the core practices in the Extreme Programming lightweight software development method, and it is usually carried out with the help of software frameworks that ease the construction of test cases as an integral part of programming tasks. This work describes our first results in studying the integration of automated unit testing practices in conventional 'introduction to programming' laboratories. Since the work used a classical procedural language in the course's assignments, we had to design a specific testing framework called tpUnit. The results of the experiment points out that a straightforward approach for the integration of unit testing in first-semester courses do not result in the expected outcomes in terms of student's engagement in the practice.
Ayres, Sensory Integration and Learning Disorders: A Question of Theory and Practice

SynopsisBefore new remedial education techniques are widely tried with learning disabled children, the theories on which they are based should be verified by careful research. Many recently developed theories in Special Education have not yet been confirmed by research, but techniques derived from them are being used in teaching children with learning problems. To date, research has not confirmed theories concerned with perceptual-motor processes and there is no clear evidence that their training methods work. Doubts are expressed about the increasing use of sensory integration training for treatment of children with learning problems, in Australia, when alternate, proven methods are available to help these children.
Elevated pulmonary artery pressure is a risk factor for primary graft dysfunction following lung transplantation for idiopathic pulmonary fibrosis.

BACKGROUND Idiopathic pulmonary fibrosis (IPF) is often associated with elevations in pulmonary artery pressures. Although primary pulmonary arterial hypertension (PAH) has been associated with primary graft dysfunction (PGD), the role of secondary PAH in mediating PGD risk in patients with IPF is incompletely understood. The purpose of this study was to evaluate the relationship between mean pulmonary artery pressure (mPAP) and PGD among patients with IPF. METHODS We performed a multicenter prospective cohort study of 126 lung transplant procedures performed for IPF between March 2002 and August 2007. The primary outcome was grade 3 PGD at 72 h after lung transplant. The mPAP was measured as the initial reading following insertion of the right-sided heart catheter during lung transplant. Multivariable logistic regression was used to adjust for confounding variables. RESULTS The mPAP for patients with PGD was 38.5 ± 16.3 mm Hg vs 29.6 ± 11.5 mm Hg for patients without PGD (mean difference, 8.9 mm Hg [95% CI, 3.6-14.2]; P = .001). The increase in odds of PGD associated with each 10-mm Hg increase in mPAP was 1.64 (95% CI, 1.18-2.26; P = .003). In multivariable models, this relationship was independent of confounding by other clinical variables, although the use of cardiopulmonary bypass partially attenuated the relationship. CONCLUSIONS Higher mPAP in patients with IPF is associated with the development of PGD.
Role of the beta-lactamase of Campylobacter jejuni in resistance to beta-lactam agents

We studied the role of the beta-lactamase of Campylobacter jejuni in resistance to beta-lactam agents. beta-Lactamase-positive strains were more resistant than beta-lactamase-negative strains to amoxicillin, ampicillin, and ticarcillin (P less than 0.05). With penicillin G, piperacillin, imipenem, and six cephalosporins, the susceptibility levels were similar for both beta-lactamase-positive and -negative strains. By using spectrophotometric and microbiological assays, the beta-lactamase from three strains hydrolyzed ampicillin, amoxicillin, penicillin G, cloxacillin, and, partially, cephalothin. Ticarcillin and piperacillin were partially hydrolyzed in the microbiological assay. There was no activity against five other cephalosporins or imipenem. Isoelectric focusing of the enzyme showed a pI of 8.8. Tazobactam was the best inhibitor of the enzyme, followed by clavulanic acid, sulbactam, and cefoxitin, while EDTA and p-chloromercuribenzoate had no activity. All beta-lactamase-positive strains became susceptible to amoxicillin and ampicillin with 1 micrograms of clavulanic acid per ml. With the same inhibitor, there was a reduced but significant effect for ticarcillin but no effect for penicillin G or piperacillin. Sulbactam had no effect and tazobactam was effective only at 2 micrograms/ml on amoxicillin and ampicillin. The beta-lactamase of C. jejuni seems to be a penicillinase with a role in resistance for only amoxicillin, ampicillin, and ticarcillin.
Consensus or dissensus? Stakeholders’ views on the role of play in learning

Across cultures and eras, children have engaged in play as part of the process of growing and maturing into adulthood. Play has been recognized as an effective form of pedagogy to promote learning in the early years. However, beliefs about what play is and how it should be practiced vary across Hong Kong and in other countries. Because Chinese culture places a heavy emphasis on academic achievement, a play-based curriculum has not been widely implemented in the region. Through classroom observations and interviews with key stakeholders in early childhood education, namely parents, teachers, and principals, this study reveals the complexity of views on this matter and uncovers the root cause of the difficulties in supporting play in the Hong Kong kindergartens. These findings may help promote the play-based curriculum in Hong Kong and other countries where play is in crisis.
An Unusual Member of the Papain Superfamily: Mapping the Catalytic Cleft of the Marasmius oreades agglutinin (MOA) with a Caspase Inhibitor

Papain-like cysteine proteases (PLCPs) constitute the largest group of thiol-based protein degrading enzymes and are characterized by a highly conserved fold. They are found in bacteria, viruses, plants and animals and involved in a number of physiological and pathological processes, parasitic infections and host defense, making them interesting targets for drug design. The Marasmius oreades agglutinin (MOA) is a blood group B-specific fungal chimerolectin with calcium-dependent proteolytic activity. The proteolytic domain of MOA presents a unique structural arrangement, yet mimicking the main structural elements in known PLCPs. Here we present the X-ray crystal structure of MOA in complex with Z-VAD-fmk, an irreversible caspase inhibitor known to cross-react with PLCPs. The structural data allow modeling of the substrate binding geometry and mapping of the fundamental enzyme-substrate interactions. The new information consolidates MOA as a new, yet strongly atypical member of the papain superfamily. The reported complex is the first published structure of a PLCP in complex with the well characterized caspase inhibitor Z-VAD-fmk.
Conscious access to fear-relevant information is mediated by threshold

The present report proposed a model of access consciousness to fear-relevant information according to which there is a threshold for emotional perception beyond that the subject makes hits with no false alarm. The model was examined by having the participants performed a confidence-ratings masking task with fearful faces. Measures of the thresholds for conscious access were taken by looking at the receiver operating characteristics (ROC) curves generated from a three-state lowand high-threshold (3-LHT) model by Krantz. Indeed, the analysis of the masking data revealed that the ROCs had threshold-like-nature (a two-limb shape) rather continuous (a curvilinear shape) challenging in this fashion the classical signal-detection view on perceptual processing. Moreover, the threshold ROC curve exhibited the specific y-intercepts relevant to conscious access performance. The study suggests that the threshold can be an intrinsic property of conscious access, mediating emotional contents between perceptual states and consciousness.
Architecture of virtual machines

In this paper we develop a model which represents the addressing of resources by processes executing on a virtual machine. The model distinguishes two maps: the ø-map which represents the map visible to the operating system software running on the virtual machine, and the f-map which is invisible to that software but which is manipulated by the virtual machine monitor running on the real machine. The ø-map maps process names into resource names and the f-map maps virtual resource names into real resource names. Thus, a process running on a virtual machine addresses its resources under the composed map f o ø. In recursive operation, f maps from one virtual machine level to another and we have f o f o . o f o ø. The model is used to describe and characterize previous virtual machine designs. We also introduce and illustrate a general approach for implementing virtual machines which follows directly from the model. This design, the Hardware Virtualizer, handles all process exceptions directly within the executing virtual machine without software intervention. All resource faults (VM-faults) generated by a virtual machine are directed to the appropriate virtual machine monitor without the knowledge of processes on the virtual machine (regardless of the level of recursion).
Searchable symmetric encryption: Sequential scan can be practical

The proliferation of cloud computing highlights the importance of techniques that allow both securing sensitive data and flexible data management at the same time. One line of research with this double motivation is the study of Searchable Symmetric Encryption (SSE) that has provided several outstanding results in the recent years. These solutions allow sublinear keyword search in huge databases by using various data structures to store keywords and document identifiers. In this work, we focus on certain scenarios in which search over the whole database is not necessary and show that the otherwise inefficient sequential scan (in linear time) can be very practical. This is due to the fact that adding new entries to the database comes for free in this case while updating a complex data structure without information leakage is rather complicated. To demonstrate the practicality of our approach we build a simple SSE scheme based on bilinear pairings and prove its security against adaptive chosen-keyword attacks in the standard model under the widely used Symmetric eXternal Diffie-Hellman (SXDH) assumption.
Global CLF Stabilization of Nonlinear Systems. Part I: A Geometric Approach - Compact Strictly Convex CVS

The aim of this paper is to design regular feedback controls for the global asymptotic stabilization (GAS) of affine control systems with compact (convex) control value sets (CVS) $U\subset\mathbb{R}^{m}$ with $0\in\mathrm{int}U$, in the framework of Artstein--Sontag's control Lyapunov function (CLF) approach. Convex analysis allows us to reveal the intrinsic geometry involved in the CLF stabilization problem, and to solve it, if an optimal control $\overline{\omega}(x)$ exists. The study of its existence, uniqueness, and continuity, in terms of properties of $U$, yields that $\overline{\omega}(x)$ is gradient-based, and leads to the generic class $\mathcal{U}(\mathbb{R}^{m})$ of compact strictly convex CVS. Moreover, higher regularity is attained via the geometry (curvature) of $U$ (illustrated for the $p,r$-weighted balls). However, since $\overline{\omega}(x)$ is singular, we consider a general form of admissible feedback controls for the GAS of a system, provided a CLF is known. For $U\in\mathcal{U}(\.
Gender differences in symptoms in partial responders to proton pump inhibitors for gastro-oesophageal reflux disease

Background Gender differences may exist in the symptom experience of patients with gastro-oesophageal reflux disease (GERD) who have a partial response to proton pump inhibitors (PPIs). Objective The purpose of this study was to analyse gender differences in partial responders to PPIs. Methods Patients with GERD who responded partially to PPIs (n = 580; NCT00703534) completed the Reflux Symptom Questionnaire 7-day recall (RESQ-7) and the Gastrointestinal Symptom Rating Scale (GSRS). Anxiety and depression were evaluated using the Hospital Anxiety and Depression Scale. Results Women had significantly higher RESQ-7 domain scores than men for Heartburn (frequency: 4.3 vs 3.9; intensity: 3.1 vs 2.8), Burping (frequency: 4.9 vs 4.4; intensity: 3.1 vs 2.8) and Hoarseness, cough and difficulty swallowing (frequency: 2.6 vs 2.2; intensity: 1.8 vs 1.5), and had higher GSRS domain discomfort scores than men for Abdominal pain (3.51 vs 3.23), Indigestion (3.80 vs 3.45) and Constipation (2.69 vs 2.17) (all p < 0.05). Anxiety and depression were significantly more prevalent in women than in men. Conclusion In this population of partial responders, women had more frequent/intense heartburn and extra-oesophageal symptoms and more discomfort from abdominal pain, indigestion and constipation than men. Comorbid anxiety and depression may contribute to the increased symptom burden in women.
A proposal of multi-agent system development framework for cooperative problem solving and its experimental evaluation

The research and development results of agent technology are awaited as the software solution with autonomy and social ability, which can provide the way to realize social activities on the Internet. However, the current status of the agent research is that many researches are for a specific application domain and are lacking in generality, and it is hard to apply the framework of the existing research to other fields. Moreover, it is thought that practical usage of agent is in immature state that there are few practical application examples and the system development methodology is not sufficient. In this research, the cooperative problem solving system by the multi-agent is first shown as an application development framework by the agents. Then, we present usage of templates of the agent model and the task model as the development support technique. And the evaluation according to an application construction experiment in a planning problem or the field of network community support is discussed.
Selection of memory strategy and brain activity during metamemory process

Metamemory refers to knowledge and monitoring of our own memory. This evaluation can be measured by a judgment of learning (JOL), which is a subjective judgment regarding our confidence in whether a learned item will be remembered in the future. We examined the effects on people's judgments of learning of a different kind of relatedness, which occurs in a list organized into sets of categorically related words and unrelated words. Then, we investigated how metamemory is involved in memory strategy. Furthermore, we examined the hypothesis of neural mechanism that the frontal cortex is critically involved in monitoring and control processes, which are central components of metamemory. Participants were thirteen healthy Japanese adults, and were instructed to memorize a list of words consisted of four exemplars from each of four categories (categorical list condition) or a list of unrelated words (unrelated list condition). The JOLs were made immediately after each learning. During the words learning and JOLs, we also measured oxygenated hemoglobin changes [oxyHb] using the near-infrared spectroscopy (NIRS). The results showed that JOL would be more accurate in the categorical list condition compared with the unrelated list condition, and categorization in memory strategy would be more used in the categorical list condition rather than the unrelated list condition. The results of NIRS showed that [oxyHb] changes in dorsolatere prefrontal area were more increased in the categorical list condition rather than the unrelated list condition, while [oxyHb] changes in medial prefrontal area were more increased in the unrelated list condition rather than the categorical list condition. These findings demonstralte metamemory is involved in an efficient memory strategy and distinct neural mechanisms supporting metamemory processes. It suggests that dorsolateral prefrontal area plays an important role in cognitive control, while medial prefrontal area does it in cognitive monitoring.
Structural Analysis of Recombinant Human Preproinsulins by Structure Prediction, Molecular Dynamics, and Protein-Protein Docking

More effective production of human insulin is important, because insulin is the main medication that is used to treat multiple types of diabetes and because many people are suffering from diabetes. The current system of insulin production is based on recombinant DNA technology, and the expression vector is composed of a preproinsulin sequence that is a fused form of an artificial leader peptide and the native proinsulin. It has been reported that the sequence of the leader peptide affects the production of insulin. To analyze how the leader peptide affects the maturation of insulin structurally, we adapted several in silico simulations using 13 artificial proinsulin sequences. Three-dimensional structures of models were predicted and compared. Although their sequences had few differences, the predicted structures were somewhat different. The structures were refined by molecular dynamics simulation, and the energy of each model was estimated. Then, protein-protein docking between the models and trypsin was carried out to compare how efficiently the protease could access the cleavage sites of the proinsulin models. The results showed some concordance with experimental results that have been reported; so, we expect our analysis will be used to predict the optimized sequence of artificial proinsulin for more effective production.