Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural elements and allosteric mechanisms governing regulation and catalysis of CSK-family kinases and their inhibition of Src-family kinases

C-terminal Src kinase (CSK) and CSK-homologous kinase (CHK) are endogenous inhibitors constraining the activity of the oncogenic Src-family kinases (SFKs) in cells. Both kinases suppress SFKs by selectively phosphorylating their consensus C-terminal regulatory tyrosine. In addition to phosphorylation, CHK can suppress SFKs by a unique non-catalytic inhibitory mechanism that involves tight binding of CHK to SFKs to form stable complexes. In this review, we discuss how allosteric regulators, phosphorylation, and inter-domain interactions interplay to govern the activity of CSK and CHK and their ability to inhibit SFKs. In particular, based upon the published results of structural and biochemical analysis of CSK and CHK, we attempt to chart the allosteric networks in CSK and CHK that govern their catalysis and ability to inhibit SFKs. We also discuss how the published three-dimensional structure of CSK complexed with an SFK member sheds light on the structural basis of substrate recognition by protein kinases.
An Adaptive OpenMP Loop Scheduler for Hyperthreaded SMPs

Hyperthreaded (HT) and simultaneous multithreaded (SMT) processors are now available in commodity workstations and servers. This technology is designed to increase throughput by executing multiple concurrent threads on a single physical processor. These multiple threads share the processor’s functional units and on-chip memory hierarchy in an attempt to make better use of idle resources. This work focuses on tuning the behavior of OpenMP applications executing on SMPs with SMT processors. We propose a self-tuning OpenMP loop scheduler designed to react to behavior caused by inter-thread data locality, instruction mix and SMT-related load imbalance. This adaptive loop scheduler automatically selects the number of threads that should be used for each parallel loop and a good scheduling policy for the iterations. It is shown that this scheduler outperforms all other OpenMP schedulers, and because it can dynamically select the number of threads to use for each region, it even outperforms the best combination of runtime schedulers for any fixed number of threads.
An intermediate report of TrakMark WG - international voluntary activities on establishing benchmark test schemes for AR/MR geometric registration and tracking methods

In the study of AR/MR field, tracking and geometric registration methods are very important topics that are actively discussed. Especially, the study on tracking is flourishing and many algorithms are being proposed every year. With this trend in mind, we, the TrakMark WG, had proposed benchmark test schemes for geometric registration and tracking in AR/MR at ISMAR 2009 [1]. This paper is an intermediate report of the TrakMark WG, which describes its activities and the first proposal on benchmarking image sequences.
Assessment of Risks introduced to Safety Critical Software by Agile Practices - a Software Engineer's Perspective

In this article we investigate the problem of applying agile practices into safety- critical projects. The goal of our research is to investigate potential benefits from introducing agile practices into safety-critical environment and to present a solution providing for balancing agile approach with more disciplined assurance techniques, bringing the best of the two worlds together. In this article we present the supporting ideas such as assurance argument patterns along with a case study. The case study investigates how software engineers perceive risks associated with the introduction of agile practices and collect their ideas on how these risks could be mitigated.
Temperature-induced elevation of basal metabolic rate does not affect testis growth in great tits

SUMMARY The timing of reproduction varies from year to year in many bird species. To adjust their timing to the prevailing conditions of that year, birds use cues from their environment. However, the relative importance of these cues, such as the initial predictive (e.g. photoperiod) and the supplemental factors (e.g. temperature), on the seasonal sexual development are difficult to distinguish. In particular, the fine-tuning effect of temperature on gonadal growth is not well known. One way temperature may affect timing is via its strong effect on energy expenditure as gonadal growth is an energy-demanding process. To study the interaction of photoperiod and temperature on gonadal development, we first exposed 35 individually housed male great tits (Parus major) to mid-long days (after 6 weeks of 8 h L:16 h D at 15°C, photoperiod was set to 13 h L:11 h D at 15°C). Two weeks later, for half of the males the temperature was set to 8°C, and for the other half to 22°C. Unilateral laparotomies were performed at weeks 5 (i.e one week before the birds were transferred to mid-long days), 8 and 11 to measure testis size. Two measures of basal metabolic rate (BMR) were performed at the end of the experiment (weeks 11 and 12). Testis size increased significantly during the course of the experiment, but independently of the temperature treatment. BMR was significantly higher in birds exposed to the cold treatment. These results show that temperature-related elevation of BMR did not impair the long-day-induced testis growth in great tits. As a consequence, temperature may not be a crucial cue and/or constraint factor in the fine-tuning of the gonadal recrudescence in male great tits, and testis growth is not a high energy-demanding seasonal process.
Aluminized silicious sorbent and water purification device incorporating the same

규산질 재료, 알루미늄 금속 및 수용액의 반응 생성물이 개시된다. 상기 반응 생성물은 생물학적 물질, 염료, 가용성 금속, 비소 또는 방사성 원소와 같은 오염물의 정수에 이용되는 흡수제의 형성에 사용될 수 있다. 흡수제의 수착량을 더 개선시키기 위해 첨가제를 반응 생성물에 첨가할 수 있다. 흡수제를 갖는 정수 장치도 개시된다.
Wizard of Oz Experiments on Speech Dialogue Systems Design and Realisation with a New Integrated Simulation Environment

The Wizard of Oz simulation technique is an approved aid for designing speech dialogue systems. There are a number of tools for simulation which have been used successfully, but which are inflexible in terms of the application domain, support for additional modalities, or integration with existing dialogue design tools. This thesis describes the design and realisation of Wizard of Oz experiments with a new, application-independent simulation environment which is fully integrated into the dialogue design process. First, the Wizard of Oz technique is presented in detail along with a thorough review of prior art in this field to collect requirements for the new simulation environment. The process of designing and conducting a Wizard of Oz study is then analysed, before the new environment and the underlying concepts are introduced. Apart from the application-independence, extensibility, and integration into the dialogue design process, the main innovation is a new dialogue structure representation for Wizard of Oz experimentation which is based on hierarchies instead of the commonly used graphs. In two evaluations, the new environment is tested, critically reviewed, and confirmed to be usable. Finally, useful extensions to the simulation environment and the dialogue representation are discussed and ideas for future work are collected.
Sutureless Vitrectomy

The introduction of pars plana vitrectomy was a revolution in ophthalmic surgery which allowed successful treatment of many previously untreatable conditions. After rapid early technical development, 3-port 20-gauge vitrectomy became established as the norm. Recent years have seen the introduction of new and innovative systems for performing vitrectomy without the need for sutures. This article describes the history of sutureless vitrectomy, and reviews the literature addressing the advantages and disadvantages of each technique.
Incident depression increases medical utilization in Medicaid patients with hypertension

Hypertension is an important risk factor for cardiovascular disease and occurs disproportionately among patients with depression. Few studies have rigorously examined outcomes specifically among hypertensive patients with newly diagnosed comorbid depression. Aim: We hypothesized that incident depression would exacerbate hypertensive disease and that this would be evident through greater utilization of medical services than would otherwise occur in the absence of depression. Methods: Claims data for hypertensive patients enrolled in Maryland Medicaid (2005–2010) were used to estimate the change in annualized utilization following incident depression, compared to a matched cohort of hypertensive patients never diagnosed with depression. Multivariate regression was used to adjust for changes in antihypertensive medications, adherence and comorbidity that followed depression onset. Results: While medical utilization increased after incident depression, additional encounters tended to be for nonacute medical care and there was no significant increase in encounters specifically for cardiovascular or hypertension-related conditions. Discussion: The results contribute to the discussion on the relationship between depression and cardiovascular disease and will inform future studies that aim to look at longer term outcomes in patients with hypertension.
A Random-Model Approach to QTL Mapping in Multiparent Advanced Generation Intercross (MAGIC) Populations

Most standard QTL mapping procedures apply to populations derived from the cross of two parents. QTL detected from such biparental populations are rarely relevant to breeding programs because of the narrow genetic basis: only two alleles are involved per locus. To improve the generality and applicability of mapping results, QTL should be detected using populations initiated from multiple parents, such as the multiparent advanced generation intercross (MAGIC) populations. The greatest challenges of QTL mapping in MAGIC populations come from multiple founder alleles and control of the genetic background information. We developed a random-model methodology by treating the founder effects of each locus as random effects following a normal distribution with a locus-specific variance. We also fit a polygenic effect to the model to control the genetic background. To improve the statistical power for a scanned marker, we release the marker effect absorbed by the polygene back to the model. In contrast to the fixed-model approach, we estimate and test the variance of each locus and scan the entire genome one locus at a time using likelihood-ratio test statistics. Simulation studies showed that this method can increase statistical power and reduce type I error compared with composite interval mapping (CIM) and multiparent whole-genome average interval mapping (MPWGAIM). We demonstrated the method using a public Arabidopsis thaliana MAGIC population and a mouse MAGIC population.
Integrin Activation by Regulated Dimerization and Oligomerization of Platelet Endothelial Cell Adhesion Molecule (Pecam)-1 from within the Cell

Platelet endothelial cell adhesion molecule (PECAM)-1 is a 130-kD transmembrane glycoprotein having six Ig homology domains within its extracellular domain and an immunoreceptor tyrosine–based inhibitory motif within its cytoplasmic domain. Previous studies have shown that addition of bivalent anti–PECAM-1 mAbs to the surface of T cells, natural killer cells, neutrophils, or platelets result in increased cell adhesion to immobilized integrin ligands. However, the mechanism by which this occurs is not clear, and it is possible that anti–PECAM-1 mAbs elicit this effect by simply sequestering PECAM-1, via antibody-induced patching and capping, away from stimulatory receptors that it normally regulates. To determine whether dimerization or oligomerization of PECAM-1 directly initiates signal transduction pathways that affect integrin function in an antibody-independent manner, stable human embryonic kidney-293 cell lines were produced that expressed chimeric PECAM-1 cDNAs containing one or two FK506-binding protein (FKBP) domains at their COOH terminus. Controlled dimerization initiated by addition of the bivalent, membrane-permeable FKBP dimerizer, AP1510, nearly doubled homophilic binding capacity, whereas AP1510-induced oligomers favored cis PECAM-1/PECAM-1 associations within the plane of the plasma membrane at the expense of trans homophilic adhesion. Importantly, AP1510-induced oligomerization resulted in a marked increase in both adherence and spreading of PECAM/FKBP-2–transfected cells on immobilized fibronectin, a reaction that was mediated by the integrin α5β1. These data demonstrate that signals required for integrin activation can be elicited by clustering of PECAM-1 from inside the cell, and suggest that a dynamic equilibrium between PECAM-1 monomers, dimers, and oligomers may control cellular activation signals that influence the adhesive properties of vascular cells that express this novel member of the immunoreceptor tyrosine–based inhibitory motif family of regulatory receptors.
Effect of twist and porosity on the electrical conductivity of carbon nanofiber yarns

This study focuses on the effect of twist and porosity on the electrical conductivity of carbon nanofiber (CNF) yarns. The process of fabrication of CNF yarns included the synthesis of aligned ribbons of polyacrylonitrile (PAN) nanofibers via electrospinning. The PAN ribbons were twisted into yarns with twist levels ranging from zero twist to high twists of 1300 turn per meter (tpm). The twist imposed on the ribbons substantially improved the interactions between nanofibers and reduced the porosity. The PAN yarns were subsequently stabilized in air, and then carbonized in nitrogen at 1100 ° C for 1 h. Compressive stresses developed between the PAN nanofibers as a result of twist promoted interfusion between neighboring nanofibers, which was accelerated by heating the yarns during stabilization to temperatures above the glass transition of PAN. The electrical conductivity of the yarns was measured with a four point probe measurement technique. Although increasing the twist promotes electrical conductivity between nanofibers by forming junctions between them, our results indicate that the electrical conductivity does not continuously increase with increasing twist, but reaches a threshold value after which it starts to decrease. The causes for this behavior were studied through experimental techniques and further explored using a yarn-equivalent electrical circuit model.
Errors in optical computation of correlation coefficients.

A variety of methods have been proposed for solving pat­ tern recognition problems using optical methods. Some of these involve generating a synthetic discriminant function that is a weighted combination of the functions available as training data. The weights for the combination are obtained either from the principal component of the data set or by imposing different deterministic constraints that ensure the separation of the classes. Caulfield has shown that these problems can be unified as solving the following matrix-vector equation:
How Do People Stop Non-Suicidal Self-Injury? A Systematic Review

The current paper reviews extant quantitative and qualitative literature into how Non-Suicidal Self-Injury cessation occurs, and individuals’ experiences of stopping. Specific search criteria utilizing a PRISMA format were used across 5 databases, which resulted in 454 papers being identified. After utilizing exclusion criteria and then review, nine of the 454 papers identified were retained for extensive synthesis and critique. Results: Results from 8 of the identified papers indicated that both intra and inter personal factors can influence self-injury cessation. These include: family support, self-esteem, emotional regulation, and professional help. Only 1 paper articulated a cessation process, describing it as a procedural event of developing interpersonal strength, then implementing alternative coping strategies. Limitations and implications of the studies are reported, concluding that further research is warranted to inform effective prevention and treatment strategies to ameliorate this growing public health concern.
Solution of Second-Order Ordinary Differential Equations via Simulated Annealing

In this paper, we approach the problem of obtaining approximate solution of second-order initial value problems by converting it to an optimization problem. It is assumed that the solution can be approximated by a polynomial. The coefficients of the polynomial are then optimized using simulated annealing technique. Numerical examples with good results show the accuracy of the proposed approach compared with some existing methods.
BlueCache: A Scalable Distributed Flash-based Key-value Store

A key-value store (KVS), such as memcached and Redis, is widely used as a caching layer to augment the slower persistent backend storage in data centers. DRAM-based KVS provides fast key-value access, but its scalability is limited by the cost, power and space needed by the machine cluster to support a large amount of DRAM. This paper offers a 10X to 100X cheaper solution based on flash storage and hardware accelerators. In BlueCache key-value pairs are stored in flash storage and all KVS operations, including the flash controller are directly implemented in hardware. Furthermore, BlueCache includes a fast interconnect between flash controllers to provide a scalable solution. We show that BlueCache has 4.18X higher throughput and consumes 25X less power than a flash-backed KVS software implementation on x86 servers. We further show that BlueCache can outperform DRAM-based KVS when the latter has more than 7.4% misses for a read-intensive aplication. BlueCache is an attractive solution for both rack-level appliances and data-center-scale key-value cache.
Tree Kernel Usage in Naive Bayes Classifiers

We present a novel approach in machine learning by combining naBayes classifiers with tree kernels. Tree kernel methods produce promising results in machine learning tasks containing tree- structured attribute values. These kernel methods are used to compare two tree-structured attribute values recursively. Up to now tree kernels are only used in kernel machines like Support Vector Machines or Perceptrons. In this paper, we show that tree kernels can be utilized in a naBayes classifier enabling the classifier to handle tree-structured values. We evaluate our approach on three datasets contain- ing tree-structured values. We show that our approach using tree-structures delivers signifi- cantly better results in contrast to approaches us- ing non-structured (flat) features extracted from the tree. Additionally, we show that our approach is significantly faster than comparable kernel ma- chines in several settings which makes it more useful in resource-aware settings like mobile de- vices.
Towards an implantable brain-machine interface based on epicortical field potentials

Today, a major challenge in neuro-engineering is to develop a brain-machine interface (BMI) suitable to restore communication and motor control in paralyzed patients. One fundamental, unresolved question is which neuronal signal type should be recorded and decoded for such purposes. Here we review work on neuronal population activity, i.e. the ensemble activity of local groups of neurons, as a control signal for BMIs. Further, we propose a BMI approach based on population activity recorded directly from the human cortical surface. Using a finger movement task, we evaluate movement related changes in epicortical potentials across a broad frequency range and we show that the side of index finger flexions can be inferred from primary motor cortex population activity with up to 100% accuracy from single trial data.
STUDY ON WAFER REWORK STRATEGIES AND DISPATCHING RULES AT THE PHOTOLITHOGRAPHY STAGE

ABSTRACT Due to the high costs of wafer materials and machines, it is feasible to apply rework to increase wafer yield at the photolithography stage. At the same time, in order to maintain good fabrication quality, shorten the process time and meet the required due date, it is absolutely necessary to have good rework strategies for wafer rework so as to make up the wafer defects in the photolithography area. In order to find the best fabrication control combination, this paper studied rework strategies to be applied in coordination with some commonly used dispatching rules at the photolithography stage. By applying simulation, combination models between the foregoing rework strategies and the five commonly used dispatching rules, including FIFO, SPT, EDD, SRPT and CR+, were analyzed individually to find the most suitable rework model for each specific production goal.
Surface modification on polycaprolactone electrospun mesh and human decalcified bone scaffold with synovium-derived mesenchymal stem cells-affinity peptide for tissue engineering.

Synovium-derived mesenchymal stem cells (SMSC) have been studied for over a decade since first being successfully isolated in 2001. These cells demonstrate the most promising therapeutic efficacy for musculoskeletal regeneration of the MSC family, particularly for cartilage regeneration. However, the mobilization and transfer of MSCs to defective or damaged tissues and organs in vivo with high accuracy and efficiency has been a major problem in tissue engineering (TE). In the present study, we identified a seven amino acid peptide sequence [SMSCs-affinity peptide (LTHPRWP; L7)] through phage display technology that has a high specific affinity to SMSCs. Our analysis suggested that L7 efficiently and specifically interacted with SMSCs without any species specificity. Thereafter, L7 was covalently conjugated onto both polycaprolactone (PCL) electrospun meshes and human decalcified bone scaffolds (hDBSc) to investigate its TE applications. After 24 h coculture with human SMSCs (hSMSCs), L7-conjugated PCL electrospun meshes had significantly more adherent hSMSCs than the control group, and the cells expanded well. Similar results were obtained using hDBSs. These results suggest that the novel L7 peptide sequence has a high specific affinity to SMSCs. Covalently conjugating this peptide to either artificial polymer material (PCL mesh) or natural material (hDBS) significantly enhances the adhesion of SMSCs. This method is applicable to a wide range of potential SMSC-based TE applications, particularly to cartilage regeneration, via surface modification on various type of materials.