Miracle-dz/UniFAR-FTUs huggingface dataset:
Local alignment using the Four-Russians technique

Four-Russians is a method that can be used to improve the execution time of certain algorithms with a factor log(n) by precomputing common subproblems. Dan Gusfield adapted the original Four-Russians method to compute unit cost edit distances (a form of sequence alignment) in time O(n/ log(n)). ”Sequence” is a general term, and can contain many kinds of data. DNA, text strings, and so on. The input data itself has no real significance in this thesis. The focus is on the algorithms which take sequences as input. This thesis examines several aspects of the Four-Russians algorithm and its application. Gusfield’s method [1] for edit distances is used as a basis for the initial experiments, but the main focus is on local alignment. The challenges of adapting the Four-Russians method to local alignment has been analyzed and solved, which includes deriving a general formula for encoding arbitrary weighted scoring systems. In practice local alignment with Four-Russians has a clear advantage over the naive algorithm, even for slightly more complicated scoring systems. However, the gains of the method start to diminish once the encoding becomes more complex. The preprocessing step in Four-Russians method has also been addressed, and a simple algorithm for computing the lookup tables very quickly was designed, analyzed and tested. Despite substantial speedups of the preprocessing step using this algorithm, it was shown to have little relevance when combined with the much slower Four-Russians step. For completeness, speeding up local alignment backtracking using Hirschberg’s algorithm [6] in conjunction with Four-Russians has also been tested. The gains in backtracking are similar to the gain observed when computing the score of the alignment itself.
Perceived Shape Regularity Does Not Depend on Regularities along the Contour

In four experiments we investigated whether human observers are able to use certain regularities in polygons when they have to indicate which polygon they perceive as the more regular in a paired comparison task. From our results we conclude that regularities that are restricted to the contour do not play a role in judgments of regularity. For instance, equilateral polygons are not considered to be more regular than entirely random polygons. Only bilaterally symmetric polygons are consistently judged as regular. However, we show that this is caused by regularities across the polygon. These results are at odds with approaches that assume that regularities along the contour play an important part in visual perception.
Inhibition of Nonsense-mediated mRNA Decay by the Natural Product Pateamine A through Eukaryotic Initiation Factor 4AIII*

Nonsense-mediated mRNA decay (NMD) in mammalian cells is a key mechanism for the removal of mRNA containing premature stop codons and is mediated by the coordinated function of numerous proteins that dynamically associate with the exon junction complex. The information communicated by these interactions and the functional consequences from a mechanistic perspective, however, are not completely documented. Herein, we report that the natural product pateamine A (PatA) is capable of inhibiting NMD through direct interaction with eIF4AIII, which is independent of its inhibition of translation initiation. Furthermore, we have characterized the mechanisms by which PatA and cycloheximide modulate NMD. Unlike CHX, PatA was found to inhibit NMD by a novel mechanism that is independent of the phosphorylation of Up-frameshift protein 1.
Interactive Effects of the COMT Gene and Training on Individual Differences in Supervisory Control of Unmanned Vehicles

Objective: We examined whether a gene known to influence dopamine availability in the prefrontal cortex is associated with individual differences in learning a supervisory control task. Background: Methods are needed for selection and training of human operators who can effectively supervise multiple unmanned vehicles (UVs). Compared to the valine (Val) allele, the methionine (Met) allele of the COMT gene has been linked to superior executive function, but it is not known whether it is associated with training-related effects in multi-UV supervisory control performance. Method: Ninety-nine healthy adults were genotyped for the COMT Val158Met single nucleotide polymorphism (rs4680) and divided into Met/Met, Val/Met, and Val/Val groups. Participants supervised six UVs in an air defense mission requiring them to attack incoming enemy aircraft and protect a no-fly zone from intruders in conditions of low and high task load (numbers of enemy aircraft). Training effects were examined across four blocks of trials in each task load condition. Results: Compared to the Val/Met and Val/Val groups, Met/Met individuals exhibited a greater increase in enemy targets destroyed and greater reduction in enemy red zone incursions across training blocks. Conclusion: Individuals with the COMT Met/Met genotype can acquire skill in executive function tasks, such as multi-UV supervisory control, to a higher level and/or faster than other genotype groups. Application: Potential applications of this research include the development of individualized training methods for operators of multi-UV systems and selecting personnel for complex supervisory control tasks.
Response Surface Modeling and Optimization of Electrospun Nanofiber Membranes

The experimental design and response surface methodology (RSM) have been used to develop predictive mod- els for simulation and optimization of electrospun polyvinylidene fluoride non-woven membranes. The objective is to prepare electrospun fibers with small diameters and narrow diameter distribution. The factors considered for experimental design were the polymer dope solution flow rate, the applied electric voltage and the distance between the needle tip and the collector. A full factorial design was considered. The obtained electrospun fibers were characterized by scanning elec- tron microscopy. The response for the model was the quality loss function that takes into account the quadratic effects of both the weighted arithmetic mean of the fibers diameter and the standard deviation. Minimal output response has been predicted and confirmed experimentally. The optimum operating conditions guarantying a small polyvinylidene fluoride nanofiber diameter with a narrow distribution were a voltage of 24.1 kV, an air gap of 27.7 cm and a polymer flow rate of 1.23 mL/h. The fabricated optimum membrane was characterized by different techniques and applied for desalination by membrane distillation. The obtained permeate fluxes in this study are higher than those reported so far for electrospun nanofibrous membranes.
Rezension des “NEO-Persönlichkeitsinventar nach Costa und McCrae (NEO-PI-R)“ von F. Ostendorf und A. Angleitner

Zusammenfassung. Das Funf-Faktoren-Modell in seiner Konzeption und Operationalisierung von Costa und McCrae (1992) gilt derzeit als das elaborierteste Eigenschaftsmodell der Personlichkeit. Es ist hierarchisch strukturiert und unterscheidet - neben den funf varianzstarken Personlichkeitsfaktoren (Neurotizismus, Extraversion, Offenheit fur Erfahrungen, Vertraglichkeit und Gewissenhaftigkeit) - auf einer spezifischeren Ebene 30 Facetten, von denen je sechs einem Personlichkeitsbereich zugeordnet werden. Das NEO-PI-R in der hier vorliegenden Ubersetzung von Ostendorf und Angleitner (2004) bildet die Originalstruktur in hervorragender Weise nach. Alle Kennwerte sprechen fur eine gelungene Ubertragung in den deutschen Sprachraum. Lediglich fehlende kriteriumsbezogene Validitatsbefunde truben das ansonsten positive Bild. Hier kann allerdings auf die Forschung mit dem US-amerikanischen Original verwiesen werden. Fur die Organisationspsychologie im Allgemeinen und die Berufseignungsdiagnostik im Besonderen stellt.
Viewer Attention to ESPN's Mosaic Screen: An Eye-Tracking Investigation

Sports broadcasters have traditionally pioneered innovative techniques for the broadcast of media sports. One recent technique is a mosaic screen, which presents multiple streams of video simultaneously. This study used eye tracking to examine how viewer attention is distributed among multiple screen elements. Attention varied as a function of element size, game play, and repeated exposure. In addition, participants with greatest interest in sports evaluated the format more positively than those with less interest in sports.
Functional electrical stimulation improves endothelial function and reduces peripheral immune responses in patients with chronic heart failure

Background Previous studies have shown beneficial effects of functional electrical stimulation (FES) on muscle performance and exercise capacity of patients with chronic heart failure. This study evaluates the impact of FES on endothelial function and peripheral markers of immune activation in patients with moderate to severe heart failure. Methods Twenty-four patients with a left ventricular ejection fraction of less than 40% and New York Heart Association class II-III symptoms, undergoing optimized drug therapy, were randomly assigned (2:1) to a 6-week training programme of FES (n = 16) or served as controls (n = 8). Endothelial function was assessed by Doppler flow-mediated dilatation (FMD) of the brachial artery before and after the training programme. Peripheral pro-inflammatory/anti-inflammatory markers such as tumour necrosis factor (TNF)-α, interleukin (IL)-6, soluble intercellular adhesion molecule (sICAM)-1, soluble vascular cell adhesion molecule (sVCAM)-1 and IL-10 were also measured before and after training. Results A significant improvement on the 6-min walk test (7.5 ± L3.3%), Minnesota Living Score (18.2 ± 8.6%) and FMD (38.5 ± 15.1%) was observed only in the FES-treated group. FES also causes a significant reduction of TNF-α (−11.5 ± 8.9%), sICAM-1 (−13.1 ± 9.8%), and sVCAM-1 (−10.6 ± 6.6%), as well as a respective increase in the ratio IL-10/TNF-α (37.1 ± 29.4%). In the FES group, the percentage improvement in the Minnesota Living Score was significantly correlated with respective changes in circulating TNF-α (r = 0.624, P<0.01), sVCAM-1 (r = 0.665, P<0.001) and the ratio IL-10/TNF-α (r = −0.641, P<0.01). Conclusion FES is an exercise training programme that improves endothelial function in patients with chronic heart failure, and also has anti-inflammatory effects.
The changing power of 'explanations': directors, academics and their sensemaking from 1989 to 2000

This paper is based on empirical research conducted with directors in large UK organizations, first in 1987-89, and again in 1998-2000. While the time frame has changed, the focus of the inquiry has remained constant - how do you "run" a large organization - and data gathered reflect significant changes over time as to how the question is answered. This paper addresses one particular aspect of this complex material: the changing power of practitioner and academic explanations across the decade, highlighted by comparing and contrasting this data and its analysis over time. The paper illustrates a surprising degree of consistency (in contrast to 1987-89 findings) in practitioners' contemporary explanations of their organizing: all talk of strategic focus, shareholder value and corporate governance, phrases previously never mentioned. This reflects a variety of changes across the decade, including an important concentration of power amongst investors. As well as the methodological implications of "repeating" this study, the changing power of academics' explanations "on" organization is also discussed as conceptual frameworks gain and lose their resonance with the times. The paper concludes that sensemaking (Weick, 1995) offers the most appropriate perspective by which such shifts in the power of explanations may best be appreciated.
Combining 2D Mapping and Low Density Elevation Data in a GIS for GNSS Shadow Prediction

The number of satellites visible to a Global Navigation Satellite System (GNSS) receiver is important for high accuracy surveys. To aid with this, there are software packages capable of predicting GNSS visibility at any location of the globe at any time of day. These prediction packages operate by using regularly updated almanacs containing positional data for all navigation satellites; however, one issue that restricts their use is that most packages assume that there are no obstructions on the horizon. In an attempt to improve this, certain planning packages are now capable of modelling simple obstructions whereby portions of the horizon visible from one location can be blocked out, thereby simulating buildings or other vertical structures. While this is useful for static surveys, it is not applicable for dynamic surveys when the GNSS receiver is in motion. This problem has been tackled in the past by using detailed, high-accuracy building models and designing novel methods for modelling satellite positions using GNSS almanacs, which is a time-consuming and costly approach. The solution proposed in this paper is to use a GIS to combine existing, freely available GNSS prediction software to predict pseudo satellite locations, incorporate a 2.5D model of the buildings in an area created with national mapping agency 2D vector mapping and low density elevation data to minimise the need for a full survey, thereby providing savings in terms of cost and time. Following this, the ESRI ArcMap viewshed tool was used to ascertain what areas exhibit poor GNSS visibility due to obstructions over a wide area, and an accuracy assessment of the procedure was made.
Old techniques for new join algorithms: A case study in RDF processing

Recently there has been significant interest around designing specialized RDF engines, as traditional query processing mechanisms incur orders of magnitude performance gaps on many RDF workloads. At the same time researchers have released new worst-case optimal join algorithms which can be asymptotically better than the join algorithms in traditional engines. In this paper we apply worst-case optimal join algorithms to a standard RDF workload, the LUBM benchmark, for the first time. We do so using two worst-case optimal engines: (1) LogicBlox, a commercial database engine, and (2) EmptyHeaded, our prototype research engine with enhanced worst-case optimal join algorithms. We show that without any added optimizations both LogicBlox and EmptyHeaded outperform two state-of-the-art specialized RDF engines, RDF-3X and TripleBit, by up to 6× on cyclic join queries-the queries where traditional optimizers are suboptimal. On the remaining, less complex queries in the LUBM benchmark, we show that three classic query optimization techniques enable EmptyHeaded to compete with RDF engines, even when there is no asymptotic advantage to the worst-case optimal approach. We validate that our design has merit as EmptyHeaded outperforms MonetDB by three orders of magnitude and LogicBlox by two orders of magnitude, while remaining within an order of magnitude of RDF-3X and TripleBit.
Home Camera-Based Fall Detection System for the Elderly

Falls are the leading cause of injury and death in elderly individuals. Unfortunately, fall detectors are typically based on wearable devices, and the elderly often forget to wear them. In addition, fall detectors based on artificial vision are not yet available on the market. In this paper, we present a new low-cost fall detector for smart homes based on artificial vision algorithms. Our detector combines several algorithms (background subtraction, Kalman filtering and optical flow) as input to a machine learning algorithm with high detection accuracy. Tests conducted on over 50 different fall videos have shown a detection ratio of greater than 96%.
Evaluation of Calibration for Optical See-Through Augmented Reality Systems

A crucial aspect in the implementation of an augmented reality (AR) system is determining its accuracy. The accuracy of a system determinies the applications it can be used for. The aim of our research is measuring the overall accuracy of an arbitrary AR system. Once measurements of a system are made, they can be analyzed for structure and used to track down sources of error. From the analysis it may also be possible to improve the methods used to calibrate and register the virtual to the real. This paper describes an online method for measuring the registration accuracy of optical see-through AR systems. By online, we mean that the user can measure the registration error they are experiencing while they are using the system. We overcome the difficulty of not having retinal access by having the user indicate the projection of a perceived object on a planar measurement device. Our method provides information which can be used to analyze the structure of the system error in two or three dimensions. The results of the application of our method to two monocular optical see-through AR systems are shown.
Tracing the Interdependencies between Architecture and Organization in Goal-Oriented Extensible Models

Architectural decisions, such as choosing an appropriate technology or an effective decomposition into subsystems, are interacting with organizational influence factors, e.g.: diverging technology skills of project participants, the structure within development teams or even their geographical distribution. Our goal is to formalize these interdependencies, to detect potential conflicts and to propose solution patterns on both, the organizational and the architectural side. The prerequisite for that is a meta-model which captures the organizational context and supports a bidirectional tracing to architectural elements. The range of architecture-relevant influence factors differs on a project-by-project basis, therefore the meta-model needs to be adaptable. For the given purpose, this work provides a goal-oriented approach. GRL is a suitable notation to model organizational dependency-structures. Architectural deliverables, the means for their realization and the involved contributors, are represented in a three-layered GRL-based basic-model. The project-specific adaption is attained by the utilization of expansion-models which cover particular organizational viewpoints like the aforementioned skill profiles. Our work is based on our experience and exemplary applications in a joint research project and in an ongoing e-commerce project.
“The Rock I Cling To”

A growing body of research—much of which has focused on male inmates—suggests that religion ameliorates many pains and problems of imprisonment. The purpose of this study is to examine the effects of religious engagement on prison adjustment among a sample of 214 females serving life sentences in a Southern state prison system. Results of multivariate analyses indicate that religious engagement is indirectly related to prison adjustment; however, the role that religious engagement plays seems to be through helping women deal with feelings of depression. Women’s personal accounts of prison adjustment corroborate these findings.
A Reconfigurable 40-to-67 dB SNR, 50-to-6400 Hz Frame-Rate, Column-Parallel Readout IC for Capacitive Touch-Screen Panels

This paper describes a capacitive touch-screen panel (TSP) readout IC that provides a reconfigurable SNR and frame rate with high noise immunity and touch sensitivity. The readout IC mitigates severe noise interference with a lock-in sensing architecture. In addition, a band-pass filtering effect by the TSP and charge amplifier further improves the noise immunity. A differential sensing scheme is employed to enhance the touch sensitivity and to reject a common-mode noise. A column-parallel incremental ΣΔ ADC is adopted to provide a high resolution and frame rate. Furthermore, a multiple sampling and averaging effect of the ADC enhances the noise immunity. The readout IC reconfigures its SNR and frame rate by adjusting the configurable resolution of the employed ADC. The test chip is fabricated in a 0.18 μm CMOS process and occupies a 2.2 mm 2 active area. The test chip achieves a 60 dB SNR and 200 Hz frame rate with a 12×8 TSP. The SNR can be adjusted from 40 dB to 67 dB, while the frame rate is then inversely scaled from 50 Hz to 6.4 kHz. The test chip supports a supply voltage range from 2.1 V to 3.3 V and consumes 6.26 mW from a 3.3 V supply.
An Orally Bioavailable Small Molecule Antagonist of CRTH2, Ramatroban (BAY u3405), Inhibits Prostaglandin D2-Induced Eosinophil Migration in Vitro

Ramatroban (Baynas, BAY u3405), a thromboxane A2(TxA2) antagonist marketed for allergic rhinitis, has been shown to partially attenuate prostaglandin (PG)D2-induced bronchial hyperresponsiveness in humans, as well as reduce antigen-induced early- and late-phase inflammatory responses in mice, guinea pigs, and rats. PGD2 is known to induce eosinophilia following intranasal administration, and to induce eosinophil activation in vitro. In addition to the TxA2 receptor, PGD2 is known as a ligand for the PGD2receptor, and the newly identified G-protein-coupled chemoattractant receptor-homologous molecule expressed on Th2 cells (CRTH2). To fully characterize PGD2-mediated inflammatory responses relevant to eosinophil activation, further analysis of the mechanism of action of ramatroban has now been performed. PGD2-stimulated human eosinophil migration was shown to be mediated exclusively through activation of CRTH2, and surprisingly, these effects were completely inhibited by ramatroban. This is also the first report detailing an orally bioavailable small molecule CRTH2 antagonist. Our findings suggest that clinical efficacy of ramatroban may be in part mediated through its action on this Th2-, eosinophil-, and basophil-specific chemoattractant receptor.
Cumulative Noise and 5.9 GHz DSRC Extensions for ns-2.28

The network simulator ns-2 is a widely used tool in the field of wired and wireless communications research. Although the ns-2 implementation is in constant evolution, it fails, for obvious reasons, to reflect all aspects related to the newest communication technologies. One example of such technology is 5.9GHz Direct Short Range Communications (DSRC) for vehicular environments, which is currently attracting attention due to its promises to reduce the amount of road fatalities and improve vehicular traffic efficiency on public roads. The IEEE 802.11p group is currently developing a standard to enable future 5.9GHz DSRC based inter-vehicle communications. In this report, we describe the modifications realized in ns-2 in order to model more accurately future wireless communications in vehicular environments. Section 2 reports the extensions performed to the PHY and MAC modules in order to include cumulative noise capabilities. Note that vehicular environments are specially sensible to the way interferences are modeled since safety related information will be commonly transmitted in a broadcast fashion. Section 3 describes the adjustments required to the MAC and PHY modules to reflect the behavior described in the current draft of IEEE 802.11p.
Depth in English grammar

Corpus data are used to investigate Yngve's claim that English usage avoids grammatical structures in which the number of left branches between any word and the root node of a sentence exceeds some fixed limit. The data do display a marked bias against left-branching, but the pattern of word-depths does not conform to Yngve's concept of a sharp limit. The bias could alternatively reflect a statistical invariance in the incidence of left-branching, but whether this is so depends on how left-branching is counted. Six nonequivalent measures are proposed; it turns out that one (and only one) of these yields strikingly constant figures for left-branching in real-life sentences over a wide range of lengths. This is not the measure suggested by Yngve's formulation; it is the measure whose invariance is arguably the most favourable for computational tractability.