Miracle-dz/UniFAR-FTUs huggingface dataset:
Using homology relations within a database markedly boosts protein sequence similarity search

Significance In the field of protein structure prediction, identifying homology to known folds offers the most successful and practically useful strategy to provide protein spatial structure models. For protein sequence targets without closely related structures, even very distant homologs can provide reasonable templates for modeling. Despite significant progress in the field, remote sequence similarity search is far from perfection and fresh ideas are needed to extend detection limits. In computer science, the concept of utilizing internal relations within a database to improve similarity search was key to the success of search engines such as Google. Here, we show that similar consideration of the homology network within a protein database of structure templates can dramatically improve the accuracy of homology search. Inference of homology from protein sequences provides an essential tool for analyzing protein structure, function, and evolution. Current sequence-based homology search methods are still unable to detect many similarities evident from protein spatial structures. In computer science a search engine can be improved by considering networks of known relationships within the search database. Here, we apply this idea to protein-sequence–based homology search and show that it dramatically enhances the search accuracy. Our new method, COMPADRE (COmparison of Multiple Protein sequence Alignments using Database RElationships) assesses the relationship between the query sequence and a hit in the database by considering the similarity between the query and hit’s known homologs. This approach increases detection quality, boosting the precision rate from 18% to 83% at half-coverage of all database homologs. The increased precision rate allows detection of a large fraction of protein structural relationships, thus providing structure and function predictions for previously uncharacterized proteins. Our results suggest that this general approach is applicable to a wide variety of methods for detection of biological similarities. The web server is available at prodata.swmed. edu/compadre.
Performances of surface EMG and Ultrasound signals in recognizing finger motion

This paper compared the performances of the surface electromyography (sEMG) with Ultrasound(US) signals in finger motion recognition. Compared to traditional sEMG-based human machine interface (HMI), the ultrasound can provide some information about the morphological changes of muscles and has higher resolution. It is possible for the US-based HMI to recognize some more dexterous hand gesture especially for some finger motions. In the experiment, the subjects were instructed to perform 14 different finger motions. The sEMG signals and the ultrasound images were collected simultaneously. The 2-fold cross-validation with LDA classifier was used to analyze the accuracy. The mean accuracy of US-based HMI was nearly 96.37% while the sEMG was 92.41%. One-way ANOVA analysis showed that the US-based HMI had a significantly higher classification accuracy than sEMG-based HMI. What's more, the difference between individuals and finger motions of ultrasound was significantly smaller than that of sEMG. The US-based HMI performed better and more stable than sEMG, which may imply that ultrasound has a great potential to be an alternative method to sEMG regarding precise control, or it can corporate with sEMG to achieve a better HMI.
Household Decision Making Models And The Value Of Child Farm Safety

A number of studies have tested economic models of household decision-making, yet there is no consensus regarding which is most appropriate for practical application. One area where the choice of household decision model has potentially important implications is the valuation of child health or safety. Few child health valuation studies have investigated household decision-making models, typically adopting the simplifying unitary model. This study aims to determine the implications of household decision making models on the magnitude of a child safety premium. To achieve this, a stated preference survey is conducted amongst farm households in Northern Ireland to ascertain mothers' and fathers' individual preferences regarding the value of reducing the risk of non-fatal farm accidents to their child relative to themselves. A number of interesting results emerge. Firstly, no significant difference is found between child values elicited from mothers and fathers. Secondly, the premium, which suggests that fathers are willing to pay twice as much for their child than self, is consistent with previous findings. Finally, the affect of different household models on the value of the premium will be investigated. Results show that the premium magnitude varies, with midpoint values of 1.25 from the bargaining model, 1.5 from the collective model and 2 from the unitary model.
Right ventricular function after repair of tetralogy of Fallot: a comparison between bovine pericardium and porcine small intestinal extracellular matrix

Abstract Background The porcine small intestinal extracellular matrix reportedly has the potential to differentiate into viable myocardial cells. When used in tetralogy of Fallot repair, it may improve right ventricular function. We evaluated right ventricular function after repair of tetralogy of Fallot with extracellular matrix versus bovine pericardium. Method Subjects with non-transannular repair of tetralogy of Fallot with at least 1 year of follow-up were selected. The extracellular matrix and bovine pericardium groups were compared. We used three-dimensional right ventricular ejection fraction, right ventricle global longitudinal strain, and tricuspid annular plane systolic excursion to assess right ventricular function. Results The extracellular matrix group had 11 patients, whereas the bovine pericardium group had 10 patients. No differences between the groups were found regarding sex ratio, age at surgery, and cardiopulmonary bypass time. The follow-up period was 28±12.6 months in the extracellular matrix group and 50.05±17.6 months in the bovine pericardium group (p=0.001). The mean three-dimensional right ventricular ejection fraction (55.7±5.0% versus 55.3±5.2%, p=0.73), right ventricular global longitudinal strain (−18.5±3.0% versus −18.0±2.2%, p=0.44), and tricuspid annular plane systolic excursions (1.59±0.16 versus 1.59±0.2, p=0.93) were similar in the extracellular matrix group and in the bovine pericardium group, respectively. Right ventricular global longitudinal strain in healthy children is reported at −29±3% in literature. Conclusion In a small cohort of the patients undergoing non-transannular repair of tetralogy of Fallot, there was no significant difference in right ventricular function between groups having extracellular matrix versus bovine pericardium patches followed-up for more than 1 year. Lower right ventricular longitudinal strain noted in both the groups compared to healthy children.
Schizophrenia and personality disorder patients’ adherence to music therapy

Background: Music therapy is used in psychiatric treatment of severe psychiatric conditions such as schizophrenia, depression and personality disorder. Aim: To investigate adherence and predictors for adherence to music therapy treatment in patients diagnosed with schizophrenia or personality disorder. Method: Demographic, psychiatric and therapeutic data were collected for 27 patients receiving music therapy treatment over a 1-year observation period and a 1-year follow-up period. Predictors for adherence to music therapeutic treatment were determined by means of regression analysis. Results: Drop-out from treatment was low (11.5%) and none of the variables significantly predicted adherence. Lack of significance may be because of type 2 error. Conclusion: Patients with severe mental disorder may adhere to music therapy treatment.
Passive Image-Splicing Detection by a 2-D Noncausal Markov Model

In this paper, a 2-D noncausal Markov model is proposed for passive digital image-splicing detection. Different from the traditional Markov model, the proposed approach models an image as a 2-D noncausal signal and captures the underlying dependencies between the current node and its neighbors. The model parameters are treated as the discriminative features to differentiate the spliced images from the natural ones. We apply the model in the block discrete cosine transformation domain and the discrete Meyer wavelet transform domain, and the cross-domain features are treated as the final discriminative features for classification. The support vector machine which is the most popular classifier used in the image-splicing detection is exploited in our paper for classification. To evaluate the performance of the proposed method, all the experiments are conducted on public image-splicing detection evaluation data sets, and the experimental results have shown that the proposed approach outperforms some state-of-the-art methods.
Optimal Portfolio for CRRA Utility Functions When Risky Assets are Exponential Additive Processes

In this paper, we analyse a market where the risky assets follow exponential additive processes, which can be viewed as time-inhomogeneous generalizations of geometric Levy processes. In this market we show that, when an investor wants to maximize a CRRA utility function of his/her terminal wealth, his/her optimal strategy consists in keeping proportions of wealth in the risky assets which depend only on time but not on the current wealth level or on the prices of the risky assets. In the time-homogeneous case, the optimal strategy is to keep constant proportions of wealth, a result already found by Kallsen which extends the classical Merton’s result to this market. While the one-dimensional case has been extensively treated and the multidimensional case has been treated only in the time-homogeneous case Callegaro and Vargiolu (2009), Kallsen (2000), and Korn et al. (2003) to the authors’ knowledge this is the first time that such results are obtained for exponential additive processes in the multidimensional case. We use these results to show that the optimal solution in the presence of jumps has the form of the analogous one without jumps but with the asset yields vector reduced by suitable quantities: in the one-dimensional case, we extend a result by Benth et al. (2001). We conclude with four examples.
Co-domain Embedding using Deep Quadruplet Networks for Unseen Traffic Sign Recognition

Recent advances in visual recognition show overarching success by virtue of large amounts of supervised data. However, the acquisition of a large supervised dataset is often challenging. This is also true for intelligent transportation applications, i.e., traffic sign recognition. For example, a model trained with data of one country may not be easily generalized to another country without much data. We propose a novel feature embedding scheme for unseen class classification when the representative class template is given. Traffic signs, unlike other objects, have official images. We perform co-domain embedding using a quadruple relationship from real and synthetic domains. Our quadruplet network fully utilizes the explicit pairwise similarity relationships among samples from different domains. We validate our method on three datasets with two experiments involving one-shot classification and feature generalization. The results show that the proposed method outperforms competing approaches on both seen and unseen classes.
Understanding Evaluation in Nonprofit Organizations

This study uses organizational theory to explore why nonprofit organizations conduct evaluations and how they use evaluation information. According to rational choice theory, managers of nonprofit organizations will conduct evaluations to make sure they are making good decisions about how to improve their services and achieve their goals. Yet, according to data gathered about the experiences of 31 nonprofit organizations, this assumption about the evaluation practices of nonprofits rarely holds true. Rather, other organizational theories, such as agency theory, institutional theory, resource dependence theory, and stewardship theory, which make different assumptions about how organizations operate and how managers behave, provide a more accurate description of why nonprofits engage in evaluation and how they use evaluation information. The findings from this study are important because they help to identify strategies that would encourage nonprofit organizations to use evaluation in more productive and meaningful ways.
The Medicago truncatula E3 Ubiquitin Ligase PUB1 Interacts with the LYK3 Symbiotic Receptor and Negatively Regulates Infection and Nodulation[W][OA]

Partner specificity in legume-rhizobia symbiosis involves perception of rhizobial signals by plant lysin motif receptor-like kinases (LysM-RLKs) leading to the formation of nitrogen-fixing root nodules. This work describes PUB1, a protein interactor of LYK3 LysM-RLK, which is involved in regulating the specificity of interaction between Medicago truncatula and Sinorhizobium meliloti. LYK3 is a lysin motif receptor-like kinase of Medicago truncatula, which is essential for the establishment of the nitrogen-fixing, root nodule symbiosis with Sinorhizobium meliloti. LYK3 is a putative receptor of S. meliloti Nod factor signals, but little is known of how it is regulated and how it transduces these symbiotic signals. In a screen for LYK3-interacting proteins, we identified M. truncatula Plant U-box protein 1 (PUB1) as an interactor of the kinase domain. In planta, both proteins are localized and interact in the plasma membrane. In M. truncatula, PUB1 is expressed specifically in symbiotic conditions, is induced by Nod factors, and shows an overlapping expression pattern with LYK3 during nodulation. Biochemical studies show that PUB1 has a U-box–dependent E3 ubiquitin ligase activity and is phosphorylated by the LYK3 kinase domain. Overexpression and RNA interference studies in M. truncatula show that PUB1 is a negative regulator of the LYK3 signaling pathway leading to infection and nodulation and is important for the discrimination of rhizobia strains producing variant Nod factors. The potential role of PUB E3 ubiquitin ligases in controlling plant–microbe interactions and development through interacting with receptor-like kinases is discussed.
On non-saturation regime in IEEE 802.11p based VANET with mobile nodes

In this paper, we investigate the IEEE 802.11p based Vehicular Ad-hoc Network transition between non-saturation and saturation regimes with mobile nodes. We combine vehicular traffic theory, queuing model and Markov chain to evaluate the performance of the network under spatial or networking saturation for mutiple data classes over control and service channels with different transmission rates depending on the vehicle's distance from the roadside unit (RSU). Our results show that the vehicle density growth can result in saturation of wireless medium around the RSU, further resulting in buffer overflows at on board units.
Warfarin persistence among atrial fibrillation patients - why is treatment ended?

BACKGROUND AND AIM Warfarin treatment discontinuation is significant among patients with atrial fibrillation (AF). Studies mainly focused on whether the proportion of warfarin persistence and discontinuation are clinically appropriate are absent. This study evaluates warfarin persistence with focus on predictors for, and reasons to, warfarin discontinuation in AF patients. METHODS From the national quality register AuriculA, all AF patients in Sundsvall, Sweden, on warfarin treatment on January 1, 2010 were included. These 478 patients were followed until discontinuation or study-stop, December 31, 2013. By going through each patient's medical record, risk factors for thromboembolism, bleeding, and causes of discontinuation were obtained. RESULTS Proportion of warfarin persistence was 0.91 (95% confidence interval [CI] 0.89-0.93) after 1 year and 0.73 (95% CI: 0.69-0.77) after 4 years. Previous intracranial bleeding, excessive alcohol use, anemia, and pulmonary or peripheral emboli were each associated with over two times higher risk of discontinuation (hazard ratio [HR] 5.66, CI 2.23-14.36; HR 2.54, CI 1.48-4.37; HR 2.40, CI 1.38-4.17; and HR 2.13, CI 1.02-4.46). Among patients discontinuing, 50.5% were due to questionable causes, such as sinus rhythm (33.9%), patients demand (10.1%), and falls (8.2%). The majority (43.1%) of treatment discontinuers were changed to aspirin, while 40.4% of them were left without medical stroke prophylaxis. CONCLUSIONS Although persistence to warfarin among AF patients proves higher than previously reported, there is room for improvement since half of the discontinuers have questionable reasons for treatment stop and the majority of them receive no other efficient stroke prophylaxis.
(Dis)connected communities and sustainable place-making

Why, despite a recent surge in the UK in “sustainable communities” policy discourse, do so many community-led sustainability initiatives remain fragmented, marginal and disconnected from local government strategies? How can community- and government-led sustainability initiatives be better integrated such that they add significantly to a denser matrix and cluster of sustainable places? These questions, we argue, lie at the heart of current sustainable place-making debates. With particular reference to two spatial scales of analysis and action, the small town of Stroud, England and the city of Cardiff, Wales, we explore the twin processes of disconnection and connection between community sustainability activists and local state actors. We conclude that whilst there will always remain a need for community groups to protect the freedom which comes from acting independently, for community activists and policy-makers alike, there are nevertheless a series of mutual benefits to be had from co-production. However, in setting out these benefits we also emphasise the dual need for local government to play a much more nuanced, integrative and facilitatory role, in addition to, but separate from, its more traditional regulatory role.
ISO 14001 and the Reduction of Toxic Emissions

ISO 14001 is an international standard for Environmental Management Systems, adopted by over 36,000 organizations worldwide. This paper attempts to determine the length of time after which a given company has implemented ISO 14001 experiences emission reduction. The sample used is a group of 264 manufacturing facilities in the USA, which represent 23 percent of all the ISO 14001 certified organizations in the US, analyzed throughout the period from 1996 to 2001. The results show that 75 percent of the companies experienced a reduction in their emissions, among which 53 percent had already done so just one year after obtaining ISO 14001.
Cast versus functional brace in the rehabilitation of patients treated non-operatively for a rupture of the Achilles tendon: protocol for the UK study of tendo achilles rehabilitation (UK STAR) multi-centre randomised trial

Introduction Achilles tendon rupture affects over 11 000 people yearly in the UK, and the incidence is increasing. Controversy remains with regard to the best rehabilitation strategy for these patients. In operatively treated patients, functional bracing provides better outcomes compared with plaster casts. However, the role of functional bracing in non-operatively managed patients is unclear. This is the protocol for a multicentre randomised trial of plaster cast immobilisation versus functional bracing for patients with a non-operatively managed Achilles tendon rupture. Methods and analysis All adults presenting with a primary rupture of the Achilles tendon will be screened. Non-operatively treated patients will be eligible to take part in the trial. Broad eligibility criteria will ensure that the results of the study can be generalised to the wider patient population. Randomisation will be on a 1:1 basis. Both rehabilitation strategies are widely used within the National Health Service. Standardised protocols will be followed, and details of plaster material and brace will be as per the site’s usual practice. A minimum of 330 patients will be randomised to obtain 90% power to detect a difference of 8 points in Achilles Tendon Total Rupture Score at 9 months. Quality of life and resource use will be collected at 3, 6 and 9 months. The differences between treatment groups will be assessed on an intention-to-treat basis. The results of the trial-based economic evaluation will be expressed in terms of incremental cost per quality-adjusted life-year gained. Ethics and dissemination The National Research Ethic Committee approved this study on 18 March 2016 (16/SC/0109). The National Institute for Health Research Health Technology Assessment monograph and a manuscript to a peer-reviewed journal will be submitted on completion of the trial (summer 2019). The results of this trial will substantially inform clinical practice on the clinical and cost-effectiveness of the treatment of this injury. This study has been registered on the International Standard Randomised Controlled Trial Number registry with reference no ISRCTN62639639.
Polyamide membranes with nanoscale Turing structures for water purification

Turing structures at the nanoscale Turing structures arise when imbalances in diffusion rates make a stable steady-state system sensitive to small heterogeneous perturbations. For example, Turing patterns occur in chemical reactions when a fast-moving inhibitor controls the motion of a slower-moving activator. Tan et al. grew polyamide membranes by using interfacial polymerization, where the reactions occur at the interface between oil and water layers. The addition of polyvinyl alcohol to the aqueous phase reduced the diffusion of the monomer. This process generates membranes with more bumps, voids, and islands, which prove to be better for water desalination. Science, this issue p. 518 Turing structures generated via diffusion-driven instabilities make polyamide membranes for water desalination. The emergence of Turing structures is of fundamental importance, and designing these structures and developing their applications have practical effects in chemistry and biology. We use a facile route based on interfacial polymerization to generate Turing-type polyamide membranes for water purification. Manipulation of shapes by control of reaction conditions enabled the creation of membranes with bubble or tube structures. These membranes exhibit excellent water-salt separation performance that surpasses the upper-bound line of traditional desalination membranes. Furthermore, we show the existence of high water permeability sites in the Turing structures, where water transport through the membranes is enhanced.