Miracle-dz/UniFAR-FTUs huggingface dataset:
A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure.

Representative genomes from each of the three kingdoms of life are compared in terms of protein structure, in particular, those of Haemophilus influenzae (a bacteria), Methanococcus jannaschii (an archaeon), and yeast (a eukaryote). The comparison is in the form of a census (or comprehensive accounting) of the relative occurrence of secondary and tertiary structures in the genomes, which particular emphasis on patterns of supersecondary structure. Comparison of secondary structure shows that the three genomes have nearly the same overall secondary-structure content, although they differ markedly in amino acid composition. Comparison of super-secondary structure, using a novel "frequent-words" approach, shows that yeast has a preponderance of consecutive strands (e.g. beta-beta-beta patterns), Haemophilus, consecutive helices (alpha-alpha-alpha), and Methanococcus, alternating helix-strand structures (beta-alpha-beta). Yeast also has significantly more helical membrane proteins than the other two genomes, with most of the differences concentrated in proteins containing two transmembrane segments. Comparison of tertiary structure (by sequence matching and domain-level clustering) highlights the substantial duplication in each genome (approximately 30% to 50%), with the degree of duplication following similar patterns in all three. Many sequence families are shared among the genomes, with the degree of overlap between any two genomes being roughly similar. In total, the three genomes contain 148 of the approximately 300 known protein folds. Forty-five of these 148 that are present in all three genomes are especially enriched in mixed super-secondary structures (alpha/beta). Moreover, the five most common of these 45 (the "top-5") have a remarkably similar super-secondary structure architecture, containing a central sheet of parallel strands with helices packed onto at least one face and beta-alpha-beta connections between adjacent strands. These most basic molecular parts, which, presumably, were present in the last common ancestor to the three Kingdoms, include the TIM-barrel, Rossmann, flavodoxin, thiamin-binding, and P-loop-hydrolase folds.
Comparing Dry Electrode Materials for Long-term ECG Monitoring - Evaluation of a New Method

Studies prove, that ECG monitoring over longer periods of time can significantly improve the diagnosis of heart failure. Dry electrodes are a valuable alternative to conventional wet electrodes, if the monitoring period is longer than one week, because they are more stable and cause less skin irritations. One drawback however is the minor signal quality compared to wet electrodes. As there are different electrode materials for dry electrodes available, a qualitative comparison concerning signal quality is carried out in this work. The signal quality of well known dry-electrode-materials used in fitness-heart belts are compared with metal dry electrodes. All electrodes are assembled in an identical mechanical electrode-setup. A parcours-based field trial with 13 subjects is carried out in two stages. In order to estimate the reproducibility of the parcours, the first stage is used to benchmark the differences in signal quality of consecutive measurements not originating from the electrode material. In the second stage however, the actual measurement takes place. The accuracy of the method is presented and the comparison results are discussed.
A Natural Language Translation Neural Network

proper translation by a user without any expert knowledge of how the computer stores and represents rules. This paper demonstrates the utility of neural networks in precisely this area on a small scale translation problem. We have tested the ability of neural networks to perform natural language translation. Our results have shown a greatly improved translation accuracy in comparison to the work of R.B. Allen (1987) in translating English into Spanish. A neural network was trained on a set of 10,000 sentences from a total of 24,750 sentences using a novel training algorithm. On a test set of 100 sentences the neural network showed a 98% sentence accuracy. The neural network had 48 input nodes, 70 nodes in the first hidden layer, 1 node in the third hidden layer, and 36 nodes in the output layer (48-701-36). A fully connected architecture was used. Connectionist NLP Research has already shown the usefulness of neural networks in various natural language processing tasks: (Allen, 1987), (Jain, 1991), (Waibel, 1988) and (Waibel et al, 1991).
Exploration of vertical MOSFET and tunnel FET device architecture for Sub 10nm node applications

A vertical device architecture having -40% density improvement over planar for sub-10nm technology node has been evaluated for Si NMOS and III-V HTFET with Lg=16nm. For LOP applications including the effect of parasitic elements, the HTFET presents superior energy efficiency and desired low-power analog performance for VDD<;0.6V, while MOSFET is superior for VDD>;0.6V. To further improve MOSFET performance, ION needs to be improved with higher injection velocity materials (e.g. III-V). For delay reduction, the parasitic capacitances (Cov and Cg,fringe) and contact resistance need to be further engineered for both MOSFETs and TFETs.
IL-27 Modulates Chemokine Production in TNF-α -Stimulated Human Oral Epithelial Cells

Background/Aims: Interleukin-27 (IL-27) is a cytokine which belongs to the IL-12 family. However, the role of IL-27 in the pathogenesis of periodontal disease is uncertain. The aim of this study was to examine the effect of IL-27 on chemokine production in TNF-α-stimulated human oral epithelial cells (TR146). Methods: We measured chemokine production in TR146 by ELISA. We used western blot analysis to detect the phosphorylation levels of signal transduction molecules, including STAT1 and STAT3 in TR146. We used inhibitors to examine the role of STAT1 and STAT3 activation. Results: IL-27 increased CXCR3 ligands production in TNF-α-stimulated TR146. Meanwhile, IL-27 suppressed IL-8 and CCL20 production induced by TNF-α. STAT1 phosphorylation level in IL-27 and TNF-α-stimulated TR146 was enhanced in comparison to TNF-α-stimulated TR146. STAT3 phosphorylation level in IL-27-treated TR146 did not change by TNF-α. Both STAT1 inhibitor and STAT3 inhibitor decreased CXCR3 ligands production. STAT1 inhibitor overrode the inhibitory effect of IL-27 on IL-8 and CCL20 production in TNF-α-stimulated TR146. Meanwhile, STAT3 inhibitor did not modulate IL-8 and CCL20 production. Conclusion: IL-27 might control leukocyte migration in periodontal lesion by modulating chemokine production from epithelial cells.
Pragmatic primitives for non-blocking data structures

We define a new set of primitive operations that greatly simplify the implementation of non-blocking data structures in asynchronous shared-memory systems. The new operations operate on a set of Data-records, each of which contains multiple fields. The operations are generalizations of the well-known load-link (LL) and store-conditional (SC) operations called LLX and SCX. The LLX operation takes a snapshot of one Data-record. An SCX operation by a process p succeeds only if no Data-record in a specified set has been changed since p last performed an LLX on it. If successful, the SCX atomically updates one specific field of a Data-record in the set and prevents any future changes to some specified subset of those Data-records. We provide a provably correct implementation of these new primitives from single-word compare-and-swap. As a simple example, we show how to implement a non-blocking multiset data structure in a straightforward way using LLX and SCX.
Tars: Timeliness-Aware Adaptive Replica Selection for Key-Value Stores

In current large-scale distributed key-value stores, a single end-user request may lead to key-value access across tens or hundreds of servers. The tail latency of these key-value accesses is crucial to the user experience and greatly impacts the revenue. To cut the tail latency, it is crucial for clients to choose the best replica server as much as possible for the service of each key-value access. Aware of the challenges on the time-varying performance across servers and the herd behaviors, an adaptive replica selection scheme C3 is proposed recently. In C3, feedback from individual servers is brought into replica ranking to reflect the time-varying performance of servers, and the distributed rate control and backpressure mechanism is invented. Despite of C3's good performance, we reveal the timeliness issue of C3, which has large impacts on both the replica ranking and the rate control, and propose the Tars (timeliness-aware adaptive replica selection) scheme. Following the same framework as C3, Tars improves the replica ranking by taking the timeliness of the feedback information into consideration, as well as revises the rate control of C3. Simulation results confirm that Tars outperforms C3.
Evidence and Credibility: Full Bayesian Significance Test for Precise Hypotheses

A Bayesian measure of evidence for precise hypotheses is presented. The inte n- tion is to give a Bayesian alternative to significance tests or, equivalently, to p-values. In fact, a set is defined in the parameter space and the posterior probability, its credibility, is evaluated. This set is the "Highest Posterior Density Region" that is "tangent" to the set that defines the null hypothesis. Our measure of evidence is the complement of the credibility of the "tangent" region.
Search in Peer-to-Peer File-Sharing System: Like Metasearch Engines, But Not Really

Peer-to-peer information systems have gained prominence of late with applications such as file sharing systems and grid computing. However, the information retrieval component of these systems is still limited because traditional techniques for searching and ranking are not directly applicable. This work compares search in peer-to-peer information systems to that in metasearch engines, and describes how they are unique. Many works describing advances in peer-to-peer information retrieval are cited.
A Stable and Real-Time Nonlinear Elastic Approach to Simulating Guidewire and Catheter Insertions Based on Cosserat Rod

Interventional Radiology procedures (e.g., angioplasty, embolization, stent graft placement) provide minimally invasive therapy to treat a wide range of conditions. These procedures involve the use of flexible tipped guidewires to advance diagnostic or therapeutic catheters into a patient's vascular or visceral anatomy. This paper presents a real-time physically based hybrid modeling approach to simulating guidewire insertions. The long, slender body of the guidewire shaft is simulated using nonlinear elastic Cosserat rods, and the shorter flexible tip composed of a straight, curved, or angled design is modeled using a more efficient generalized bending model. Therefore, the proposed approach efficiently computes intrinsic dynamic behaviors of guidewire interactions within vascular structures. The efficacy of the proposed method is demonstrated using detailed numerical simulations inside 3-D blood vessel structures derived from preprocedural volumetric data. A validation study compares positions of four physical guidewires deployed within a vascular phantom, with the co-ordinates of the corresponding simulated guidewires within a virtual model of the phantom. An optimization algorithm is also implemented to further improve the accuracy of the simulation. The presented simulation model is suitable for interactive virtual reality-based training and for treatment planning.
Large Capacity of Conscious Access for Incidental Memories in Natural Scenes

When searching a crowd, people can detect a target face only by direct fixation and attention. Once the target is found, it is consciously experienced and remembered, but what is the perceptual fate of the fixated nontarget faces? Whereas introspection suggests that one may remember nontargets, previous studies have proposed that almost no memory should be retained. Using a gaze-contingent paradigm, we asked subjects to visually search for a target face within a crowded natural scene and then tested their memory for nontarget faces, as well as their confidence in those memories. Subjects remembered up to seven fixated, nontarget faces with more than 70% accuracy. Memory accuracy was correlated with trial-by-trial confidence ratings, which implies that the memory was consciously maintained and accessed. When the search scene was inverted, no more than three nontarget faces were remembered. These findings imply that incidental memory for faces, such as those recalled by eyewitnesses, is more reliable than is usually assumed.
Assembly of the tight junction: the role of diacylglycerol

Extracellular Ca2+ triggers assembly and sealing of tight junctions (TJs) in MDCK cells. These events are modulated by G-proteins, phospholipase C, protein kinase C (PKC), and calmodulin. In the present work we observed that 1,2-dioctanoylglycerol (diC8) promotes the assembly of TJ in low extracellular Ca2+, as evidenced by translocation of the TJ-associated protein ZO-1 to the plasma membrane, formation of junctional fibrils observed in freeze-fracture replicas, decreased permeability of the intercellular space to [3H]mannitol, and reorganization of actin filaments to the cell periphery, visualized by fluorescence microscopy using rhodamine-phalloidin. In contrast, diC8 in low Ca2+ did not induce redistribution of the Ca-dependent adhesion protein E-cadherin (uvomorulin). Extracellular antibodies to E-cadherin block junction formation normally induced by adding Ca2+. diC8 counteracted this inhibition, suggesting that PKC may be in the signaling pathway activated by E-cadherin-mediated cell-cell adhesion. In addition, we found a novel phosphoprotein of 130 kD which coimmunoprecipitated with the ZO-1/ZO-2 complex. Although the assembly and sealing of TJs may involve the activation of PKC, the level of phosphorylation of ZO-1, ZO-2, and the 130-kD protein did not change after adding Ca2+ or a PKC agonist. The complex of these three proteins was present even in low extracellular Ca2+, suggesting that the addition of Ca2+ or diC8 triggers the translocation and assembly of preformed TJ subcomplexes.
Novel Molecular Approaches in Heart Failure: Seven Trans-Membrane Receptors Signaling in the Heart and Circulating Blood Leukocytes

Heart failure (HF) is the result of molecular, cellular, and structural changes induced by cardiac load or injury. A complex network of signaling pathways have been involved in the development and progression of cardiac dysfunction. In this review, we summarize the pivotal role of seven trans-membrane receptors (7TMRs), also called G-protein-coupled receptors (GPCRs), in HF. Moreover, we will discuss the current knowledge on the potential mirroring of 7TMR signaling between circulating blood leukocytes and the heart, and the related future possibilities in the management of HF patients.
Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding

Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping-by-sequencing (GBS) has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs.
Portable Memory Hierarchy Techniques For PDE Solvers : Part I

I am taking the unusual step of writing an editorial foreword for this article. The main reason is that the article, the first of two parts, is highly pedagogical and therefore atypical for this column. The content of this first part is required for a full understanding, and appreciation, of the more application-focused second part, which will appear in the next issue of SIAM News. Additionally, I feel that many readers will benefit from this exposition, especially those who are not familiar with the impact that caches can have on application performance. —GA
Real-time 3D interaction for augmented and virtual reality

We demonstrate a real-time 3-D augmented reality video-conferencing system. The observer sees the real world from his viewpoint, but modified so that the image of a remote collaborator is rendered into the scene. For each frame, we estimate the transformation between the camera and a fiducial marker using techniques developed in Kato and Billinghurst [1999]. We use a shape-from-silhouette algorithm to generate the appropriate view of the collaborator in real time. This is based on simultaneous measurements from fifteen calibrated cameras that surround the collaborator. The novel view is then superimposed upon the real world image and appropriate directional audio is added. The result gives the strong impression that the virtual collaborator is a real part of the scene.
Harmonic Elimination of Cascade Multilevel Inverters with Nonequal DC Sources Using Particle Swarm Optimization

In this paper, the elimination of harmonics in a cascade multilevel inverter by considering the nonequality of separated dc sources by using particle swarm optimization is presented. Solving a nonlinear transcendental equation set describing the harmonic-elimination problem with nonequal dc sources reaches the limitation of contemporary computer algebra software tools using the resultant method. The proposed approach in this paper can be applied to solve the problem in a simpler manner, even when the number of switching angles is increased and the determination of these angles using the resultant theory approach is not possible. Theoretical results are verified by experiments and simulations for an 11-level H-bridge inverter. Results show that the proposed method does effectively eliminate a great number of specific harmonics, and the output voltage is resulted in low total harmonic distortion.
Interobserver reliability of the Turkish version of the expanded and revised gross motor function classification system

Purpose: Cerebral palsy (CP) is the most common disability in childhood. The gross motor function classification system (GMFCS) has become an important tool to assess motor function in CP patient. In 2007, the expanded and revised (E&R) version of GMFCS which includes age band for youth 12–18 years of age was developed. The aim of this study was to evaluate reliability of Turkish version of expanded and revised GMCS. Methods: We assessed interobserver reliability between two physical medicine and rehabilitation specialists in 136 children with CP and test-retest reliability within a subgroup of 48 patients. Percent agreement, intraclass correlation coefficient (ICC) and μ statistics were used to evaluate reliability. Result: The ICC between two physicians was 0.97 and the total agreement was 89%. This result indicates excellent agreement. The overall weighted μ was 0.86. High test-retest reliability was found (ICC: 0.94 95% confidence interval) and the total agreement was 75% for test-retest reliability. Conclusion: The Turkish version of the E&R GMFCS is shown to be reliable and valid for assessment of Turkish CP children. Implications for Rehabilitation Cerebral palsy (CP) is the major developmental disability affecting function in children. Assessment of functional status of children with CP is important for planning treatment. The gross motor function classification system (GMFCS) can be considered to be a diagnostic tool for predicting motor development in children with CP based on self-initiated movement, emphasising on sitting, transfers and mobility. The expanded GMFCS includes an age band for youth 12–18 years of age.
The modulation of mucosal immune markers, URS, and psychological parameters following acute and chronic exercise

THE MODULATION OF MUCOSAL IMMUNE MARKERS, URS, AND PSYCHOLOGICAL PARAMETERS FOLLOWING ACUTE AND CHRONIC EXERCISE by CAROLE ANN SLOAN August 2014 Advisor: Dr. Hermann-J. Engels Major: Exercise and Sport Science Degree: Doctor of Philosophy The purpose of this dissertation was to evaluate changes in two antimicrobial markers, upper respiratory symptom (URS) variables, and mood state following participation in an acute (N = 93) and chronic (N = 88) observational study of college aerobic exercise, yoga exercise, and non-exercise classes. METHODS: Unstimulated whole saliva was collected pre/post-acute (50 minutes) and pre/midpoint/post-chronic (12 weeks) during the study period. Saliva was analyzed for salivary immunoglobulin A (SIgA) and salivary alpha amylase (SAA) using protocols and assay kits by Salimetrics, upper respiratory symptoms (URS) were evaluated using the Wisconsin Upper Respiratory Symptom Survey (WURSS), and mood states were evaluated by the Profile of Mood States (POMS) questionnaire. RESULTS: Analysis of the acute data revealed significant improvements for SIgA concentration in the aerobic exercise group (AEG) and the yoga exercise group (YEG) as well as SIgA secretion increases for all participants combined. No significant acute SAA concentration or secretion improvements were noted.
Handling Missing Values when Applying Classification Models

A method for analyzing various components in a natural gas pipeline with the aid of a computer controlled gas chromatograph comprising the steps of: (a) providing the computer control unit with a data base for operating the gas chromatograph including at least: (1) periodically causing a sample of the natural gas to be supplied to the gas chromatograph; (2) operating the gas chromatograph to analyze the various components in the natural gas stream; (3) computing the amount of the various components in the natural gas stream; and (4) reporting the amount of components in the natural gas stream.
Functional discretization of space using Gaussian processes for road intersection crossing

A framework for the discretization of navigable space within and around a cross intersection is proposed in this paper. The purpose of our approach is to capture the manner in which drivers manoeuvre in an intersection in order to facilitate and understand the decision-making tasks. Gaussian processes are used to learn and predict the most likely trajectories taken by multiple drivers in different situations. The merging and crossing areas are found by searching for the overlap between two predicted trajectories, whereas the area approaching the intersection is discretized by using the most probable occupancy. The generated areas are stored in the vehicle navigation map. The correlation between the proposed discretization and the driver's behaviour is demonstrated. The proposed framework enables also the discretization of the vehicle velocity profile, information that can be used to govern the decision-making function.