Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the interaction between the bacterial superantigen streptococcal pyrogenic exotoxin A (SpeA) and the human T‐cell receptor

Streptococcus pyogenes that produces the bacterial superantigen streptococcal pyrogenic exotoxin A (SpeA) is associated with outbreaks of streptococcal toxic shock syndrome (STSS) in the United States and Europe. SpeA stimulates Vβ2.1, 12.2, 14.1, and 15.1‐positive T cells, and the lymphokine production from the activated T cells is believed to result in the symptoms associated with STSS. The T‐cell receptor (TCR)–SpeA interaction is crucial for superantigenic activity, and studies were undertaken to determine regions of both SpeA and the TCR involved in the formation of MHC/SpeA/TCR complexes. Previously, recombinant toxins encoded by speA alleles 1, 2, and 3 as well as toxins resulting from 19 distinct point mutations in speA1 were generated. Here, these 22 toxin forms were incubated with human peripheral blood mono‐ nuclear cells (PBMCs), and the percentages of T‐cell blasts bearing Vβ chains 2.1, 12.2, and 14.1 were quantified by flow cytometry. The analysis indicates that the residues of SpeA needed for a productive TCR interaction differ for each Vβ chain examined. An amino acid substitution at only one site significantly affected the toxin’s ability to stimulate Vβ2.1‐expressing T cells, three individual amino acid substitutions resulted in significant loss of ability to stimulate Vβ12.2‐expressing T cells, and substitution at 13 individual sites significantly affected the ability to stimulate Vβ14.1‐expressing T cells. To elucidate the regions of the Vβ chains that interacted with SpeA, synthetic peptides representative of the human Vβ12.2 complementary‐determining regions (CDRs) 1, 2, and 4 were used to block the SpeA‐mediated proliferation of human PBMCs. The CDR1, CDR2 and CDR4 peptides were each able to block proliferation, with the activity of CDR1 > CDR2 > CDR4. Combinations of CDR1 peptide with CDR2 or CDR4 peptides allosterically enhanced the ability of each to block proliferation, suggesting SpeA has distinct binding sites for the CDR loops.
Two parameters extension of quartic Bézier curve and its applications

A set of quintic polynomial basis functions with two parameters are presented. Based on these basis functions, the quintic Bezier curve with two parameters which is called λμ -Bezier curves is defined. λμ -Bezier curves produces a closer fit to the guiding polygon than does the Bézier curves. We can attain local shape control of quintic λμ − B spline curve by modifying the shape parameters exactly to ensure two quintic λμ -Bezier curves segment satisfying C<sup>1</sup>-continuity at the common endpoint without affecting other parts. Finally,we present a example to illustrate the validity of the modification methods.
The visual hallucinatory response to flickering polychromatic light.

Our understanding of human visual perception generally rests on the assumption that conscious visual states represent, in some qualitative fashion, a complex interaction between spatially structured variations in the ambient optic array and our visual nervous systems. The existence of visual hallucinations in a number of pathologies (e. g. Kolmel, 1984) as well as in experimental contexts (Fechner, 1838; Benham, 1895; Herrmann & Elliott, 2001; Knoll & Kugler, 1959) questions the assumption that what we see in the environment is necessarily determined by spatial structure in the distal stimulus. Here we show that complex colour and form hallucinations are evoked by flickering light and that the type of hallucination varies with flicker frequency flicker phase and the occurrence of other flicker induced hallucinations. This evidence supports theories of consciousness that stress temporal aspects of perceptual processing. Contemporary perspectives hold conscious experience as an emergent property arising from synchronous oscillations at widely dispersed brain areas (Tononi & Edelman, 2002). Nevertheless, the question of whether or not the mechanisms responsible for conscious content depend upon precise temporal coding remains a problem of considerable complexity. It has been shown that an hallucinatory experience of visual percepts might be brought about through electrical stimulation (Knoll & Kugler, 1959) or by means of photic driving, that is as a function of exposure to high frequency flicker (Eichmeier & Hofer, 1974; Herrmann & Elliott, 2001). A hallucinatory experience involves the perception of an external object or event in the absence of object-related information in the ambient optic array. Pure visual hallucinations are thus conscious states that appear to occur solely as a function of our visual nervous systems and with no obvious spatial reference in the visual world. If hallucinatory experience can arise solely as a function of intermittent stimulation, the possibility to describe conscious visual states exclusively in terms of variations in the temporal patterning of stimulation seemed highly promising.
Quantifying cortical surface asymmetry via logistic discriminant analysis

We present a computational framework for analyzing brain hemispheric asymmetry without any kind of image flipping. In almost all previous literature, to perform brain asymmetry analysis, it was necessary to flip 3D magnetic resonance images (MRI) and establish the hemispheric correspondence by registering the original image to the flipped image. The difference between the original and the flipped images is then used as a measure of cerebral asymmetry. Instead of physically flipping MRI and performing image registration, we construct the global algebraic representation of cortical surface using the weighted spherical harmonics. Then using the inherent angular symmetry present in the spherical harmonics, image flipping is done by changing the sign of the asymmetric part in the representation. The surface registration between hemispheres and different subjects is done algebraically within the representation itself without any time consuming numerical optimization. The methodology has been applied in localizing the abnormal cortical asymmetry pattern of a group of autistic subjects using the logistic discriminant analysis that avoids the traditional hypothesis driven statistical paradigm.
HashNet: Deep Learning to Hash by Continuation

Learning to hash has been widely applied to approximate nearest neighbor search for large-scale multimedia retrieval, due to its computation efficiency and retrieval quality. Deep learning to hash, which improves retrieval quality by end-to-end representation learning and hash encoding, has received increasing attention recently. Subject to the ill-posed gradient difficulty in the optimization with sign activations, existing deep learning to hash methods need to first learn continuous representations and then generate binary hash codes in a separated binarization step, which suffer from substantial loss of retrieval quality. This work presents HashNet, a novel deep architecture for deep learning to hash by continuation method with convergence guarantees, which learns exactly binary hash codes from imbalanced similarity data. The key idea is to attack the ill-posed gradient problem in optimizing deep networks with non-smooth binary activations by continuation method, in which we begin from learning an easier network with smoothed activation function and let it evolve during the training, until it eventually goes back to being the original, difficult to optimize, deep network with the sign activation function. Comprehensive empirical evidence shows that HashNet can generate exactly binary hash codes and yield state-of-the-art multimedia retrieval performance on standard benchmarks.
"Afsluiting" na die verlies van 'n kind : 'n narratiewe pastorale studie van 'n moeder(s) se belewenis(se)

The purpose of this research is to explore and interpret the experience of mourning and the process of closure for mothers after the loss of a child. The research is founded in Practical Theology and researched from postmodernity as paradigm with a social constructionistic discourse as epistemological point of departure. Principles underlining Participatory Action Research, as part of a qualitative research method are utilised. The research is informed by using mechanisms of the narrative approach. This correlated well with the principles underlying Participatory Action Research that are operasionalised in the reserach. A "conversation-and-time approach" is formulated in the article to describe a possible pastoral conversational engagement to accompany mothers in mourning.
Do Banks Matter? A Credit View Model for Small Open Economies

The Mundell-Fleming model is expanded to include a "credit channel" by adding a market for bank loans. In contrast to the predictions of the traditional Mundell-Fleming model, asset shifts in bank portfolios between bonds and bank loans produce aggregate demand effects in our credit-channel model. We test this hypothesis with an empirical growth model estimated with data from small open economies: the U.S. states. The evidence supports our "credit view" model's prediction that variations in bank lending decisions can produce economically significant fluctuations in aggregate demand, and may initiate or amplify economic contractions and expansions.
Outcome Measures for Low Back Pain Research: A Proposal for Standardized Use

Study Design. An international group of back pain researchers considered recommendations for standardized measures in clinical outcomes research in patients with back pain. Objectives. To promote more standardization of outcome measurement in clinical trials and other types of outcomes research, including meta‐analyses, cost‐effectiveness analyses, and multicenter studies. Summary of Background Data. Better standardization of outcome measurement would facilitate comparison of results among studies, and more complete reporting of relevant outcomes. Because back pain is rarely fatal or completely cured, outcome assessment is complex and involves multiple dimensions. These include symptoms, function, general well‐being, work disability, and satisfaction with care. Methods. The panel considered several factors in recommending a standard battery of outcome measures. These included reliability, validity, responsiveness, and practicality of the measures. In addition, compatibility with widely used and promoted batteries such as the American Academy of Orthopaedic Surgeons Lumbar Cluster were considered to minimize the need for changes when these instruments are used. Results. First, a six‐item set was proposed, which is sufficiently brief that it could be used in routine care settings for quality improvement and for research purposes. An expanded outcome set, which would provide more precise measurement for research purposes, includes measures of severity and frequency of symptoms, either the Roland or the Oswestry Disability Scale, either the SF‐12 or the EuroQol measure of general health status, a question about satisfaction with symptoms, three types of "disability days," and an optional single item on overall satisfaction with medical care. Conclusion. Standardized measurement of outcomes would facilitate scientific advances in clinical care. A short, 6‐item questionnaire and a somewhat expanded, more precise battery of questionnaires can be recommended. Although many considerations support such recommendations, more data on responsiveness and the minimally important change in scores are needed for most of the instruments.
Sensor Systems Based on FPGAs and Their Applications: A Survey

In this manuscript, we present a survey of designs and implementations of research sensor nodes that rely on FPGAs, either based upon standalone platforms or as a combination of microcontroller and FPGA. Several current challenges in sensor networks are distinguished and linked to the features of modern FPGAs. As it turns out, low-power optimized FPGAs are able to enhance the computation of several types of algorithms in terms of speed and power consumption in comparison to microcontrollers of commercial sensor nodes. We show that architectures based on the combination of microcontrollers and FPGA can play a key role in the future of sensor networks, in fields where processing capabilities such as strong cryptography, self-testing and data compression, among others, are paramount.
Calibration Accuracy Evaluation with Stereo Reconstruction

During SPECT imaging, a patient must remain motionless for 20 minutes or more. Without compensation, patient motion can compromise diagnostic accuracy. As the first step in compensation, we propose stereo-optical tracking of retro-reflective spheres attached to stretchy bands wrapped about the patients to estimate patient motion. Camera calibration is a crucial step in stereo- imaging, which ultimately determines the accuracy of tracking. The two leading methods of camera calibration are: 1) phantom-based calibration, and 2) grid board-based calibration. They both use the Tsai camera model, but use different input data and methods of calculation. Thus, the two methods will show different sensitivities to system modeling and input data inaccuracies. We evaluated the relationship between inaccuracies using two error measures. The first was the residual error or the difference between the input center location of spheres in the 2D optical images and the centers estimated using the calibration parameters. The second was stereo error or the difference between the input 3D location of the center of spheres in the calibration phantom and the centers estimated by stereo imaging. We observed that the grid board-based calibration is more stable, and that for both methods the stereo error increases with distance away from the center of the measurement volume.
Visual illness narratives of asthma: explanatory models and health-related behavior.

OBJECTIVE To examine explanatory models of asthma and health-related behaviors. METHODS Children and adolescents with poorly controlled asthma used Video Intervention/Prevention Assessment (VIA) to generate visual illness narratives. Visual narratives were logged, structured using ATLAS.ti software, and coded for asthma-related beliefs and behaviors. RESULTS Participants' knowledge of asthma reflected biomedical models they had been taught, but explanatory models of its origin, natural history, and prognosis were more responsive to personal experience, anecdote, and cultural beliefs. Self-management and behavior were more powerfully affected by these models than by knowledge. CONCLUSION Understanding and responding to explanatory models of asthma management may be more important than education to improve asthma-related behaviors and adherence to medical plans.
Towards protein function annotations for matching remote homologs

Motivation: Identifying functional homologs from their protein structures is an important problem in biology. One way to approach this is to discover their common local structures (i.e. motif) among protein families. Unfortunately, most of the motif models are inadequate to characterize the structural diversities, especially when the proteins are distantly related. In this study, we first introduce a statistical model, together with a semi-supervised refinement method, to perform post-processing on the motif obtained from a motif discovery algorithm or from motif database. Our model makes use of Markov Random Fields (MRF), which provide a large search space to optimize the motif while preserving the dependencies among neighbor elements. The resulting model not only can better represent the underlying patterns for different protein families, but also can enable the power of functional annotation from a set of unknown proteins using probability approximations. In addition, we develop two filter approaches (three methods) to further eliminate the false positives introduced by any motif models. By considering the local environment around the active sites of each family, the filters reject proteins to match with the model without similar environment profiles. Results: Our experimental results, as evaluated in five sets of enzyme families
Pretreatment with AQP4 and NKCC1 Inhibitors Concurrently Attenuated Spinal Cord Edema and Tissue Damage after Spinal Cord Injury in Rats

Spinal cord injury (SCI) affects more than 2.5 million people worldwide. Spinal cord edema plays critical roles in the pathological progression of SCI. This study aimed to delineate the roles of aquaporin 4 (AQP4) and Na+-K+-Cl− cotransporter 1 (NKCC1) in acute phase edema and tissue destruction after SCI and to explore whether inhibiting both AQP4 and NKCC1 could improve SCI-induced spinal edema and damage. Rat SCI model was established by modified Allen's method. Spinal cord water content, cerebrospinal fluid lactose dehydrogenase (LDH) activity, AQP4 and NKCC1 expression, and spinal cord pathology from 30 min to 7 days after SCI were monitored. Additionally, aforementioned parameters in rats treated with AQP4 and/or NKCC1 inhibitors were assessed 2 days after SCI. Spinal cord water content was significantly increased 1 h after SCI while AQP4 and NKCC1 expression and spinal fluid LDH activity elevated 6 h after SCI. Spinal cord edema and spinal cord destruction peaked around 24 h after SCI and maintained at high levels thereafter. Treating rats with AQP4 inhibitor TGN-020 and NKCC1 antagonist bumetanide significantly reduced spinal cord edema, tissue destruction, and AQP4 and NKCC1 expression after SCI in an additive manner. These results demonstrated the benefits of simultaneously inhibiting both AQP4 and NKCC1 after SCI.
Performance Investigation of Capacity Enhancement Algorithm for IEEE 802.11 Wireless Ad-hoc Networks

The performance of IEEE 802.11 with different network densities and protocol configurations is of interest, particularly in distributed coordination function (DCF) mode. A mathematical model for single hop network IEEE 802.11 protocol was introduced by Bianchi [1] to analytically derive the saturated throughput. The ultimate goal is to enhance the capacity of Ad-hoc network closer to the analytical values of this model. As an attempt, the Receiver Based Capacity Enhancement Algorithm using Cross-Layer Design Approach (RCECLD) is proposed which dynamically adapts the data rate. It uses Signal-to-Noise Ratio (SNR) values calculated by Physical layer and exported to Medium Access Control (MAC) layer via the cross-layer interface to estimate the prevailing channel state. In RCECLD the receiver decides the transmission data rate by calculating the SNR value of received RTS (Readyto-Send), which is in turn an estimate of the prevailing channel state, and piggybacking it through CTS (Clear-to-Send) to the transmitter. Accordingly, transmitter transmits the data frame with adopted data rate. The capacity of the Ad-hoc network is enhanced with RCECLD. It is investigated through an extensive set of single hop and multi-hop simulations. The results indicate that the enhancement is very close to analytical values for smaller network size and it is about 2.5 times more than Auto-Rate Fallback (ARF) [2], inspite of fading and mobility effects in case of single hop, whereas in case of multi-hop with a chain of nodes it is almost doubled .
Improvements in cognition, quality of life, and physical performance with clinical Pilates in multiple sclerosis: a randomized controlled trial

[Purpose] The aim of this study was to determine the effects of clinical Pilates in multiple sclerosis patients. [Subjects and Methods] Twenty multiple sclerosis patients were enrolled in this study. The participants were divided into two groups as the clinical Pilates and control groups. Cognition (Multiple Sclerosis Functional Composite), balance (Berg Balance Scale), physical performance (timed performance tests, Timed up and go test), tiredness (Modified Fatigue Impact scale), depression (Beck Depression Inventory), and quality of life (Multiple Sclerosis International Quality of Life Questionnaire) were measured before and after treatment in all participants. [Results] There were statistically significant differences in balance, timed performance, tiredness and Multiple Sclerosis Functional Composite tests between before and after treatment in the clinical Pilates group. We also found significant differences in timed performance tests, the Timed up and go test and the Multiple Sclerosis Functional Composite between before and after treatment in the control group. According to the difference analyses, there were significant differences in Multiple Sclerosis Functional Composite and Multiple Sclerosis International Quality of Life Questionnaire scores between the two groups in favor of the clinical Pilates group. There were statistically significant clinical differences in favor of the clinical Pilates group in comparison of measurements between the groups. Clinical Pilates improved cognitive functions and quality of life compared with traditional exercise. [Conclusion] In Multiple Sclerosis treatment, clinical Pilates should be used as a holistic approach by physical therapists.
Turkish Paraphrase Corpus

Paraphrases are alternative syntactic forms in the same language expressing the same semantic content. Speakers of all languages are inherently familiar with paraphrases at different levels of granularity (lexical, phrasal, and sentential). For quite some time, the concept of paraphrasing is getting a growing attention by the research community and its potential use in several natural language processing applications (such as text summarization and machine translation) is being investigated. In this paper, we present, what is to our best knowledge, the first Turkish paraphrase corpus. The corpus is gleaned from four different sources and currently contains 1270 paraphrase pairs. All paraphrase pairs are carefully annotated by native Turkish speakers with the identified semantic correspondences between paraphrases. The work for expanding the corpus is still under way.