Miracle-dz/UniFAR-FTUs huggingface dataset:
Linking Fold, Function and Phylogeny: A Comparative Genomics View on Protein (Domain) Evolution

Domains are the building blocks of all globular proteins and present one of the most useful levels at which protein function can be understood. Through recombination and duplication of a limited set of domains, proteomes evolved and the collection of protein superfamilies in an organism formed. As such, the presence of a shared domain can be regarded as an indicator of similar function and evolutionary history, but it does not necessarily imply it since convergent evolution may give rise to similar gene functions as well as architectures. Through the wealth of sequences and annotation data brought about by genomics, evolutionary links can be sought for via homology relationships and comparative genomics, structural modeling and phylogenetics. The goal hereby is not only to predict the function of newly discovered proteins, but also to spell out their pathway of evolution and, possibly, identify their most likely origin. This can ultimately help to understand protein function and functional relationships of protein families. Additionally, through comparison with transcriptional data, evolutionary data can be linked to gene (and genome) activity and thus allow for the identification of common principles behind fast evolving proteins and relatively stable ones. In this review, we describe the basic principles of studying protein (domain) evolution and illustrate recent developments in molecular evolution and give valuable new insights in the field of comparative genomics. As an example, we include here molecular models of the multiple PDZ domain protein MUPP-1 and present a simple comparative genomic view on its structural course of evolution.
The Role of Knowledge in Lowering Barriers to Internationalisation

Using a merged data set for Scotland comprising the Scottish Global Connections Survey (GCS) and the Annual Respondents Database (ARD), we demonstrate that exporters and those engaged in outward FDI have a productivity advantage over those firms that do not internationalise (both preand post-entry). We then consider the factors that determine which firms in Scotland operate in overseas markets, and specifically the role of knowledge-based assets in overcoming barriers to internationalisation. This allows us to consider whether firms that export are ‘better’ and would experience higher productivity even if they did not export, and thus if the post-entry positive impact of exporting on productivity is upward biased because of the self-selection of such firms into overseas markets. We find that such firms are indeed better, but when we use a ‘matching estimator’ approach we still find a post-entry productivity advantage which can be attributed to a ‘learning-by-exporting’ effect. Because the information in the GCS-ARD is limited with respect to firms’ assets, we also consider another source of information (Community Innovation Survey data) that allows us to understand better the importance of knowledge assets in determining internationalisation. Various policy conclusions are then considered based on our findings.
DNA Binding Features of Human POT1

The human telomeric protein POT1 is known to bind single-stranded telomeric DNA in vitro and to participate in the regulation of telomere maintenance by telomerase in vivo. We examined the in vitro DNA binding features of POT1. We report that deleting the oligosaccharide/oligonucleotide-binding fold of POT1 abrogates its DNA binding activity. The minimal binding site (MBS) for POT1 was found to be the telomeric nonamer 5′-TAGGGTTAG-3′, and the optimal substrate is [TTAGGG]n (n ≥ 2). POT1 displays exceptional sequence specificity when binding to MBS, tolerating changes only at position 7 (T7A). Whereas POT1 binding to MBS or [TTAGGG]2 was enhanced by the proximity of a 3′ end, POT1 was able to bind to a [TTAGGG]5 array when positioned internally. These data indicate that POT1 has a strong sequence preference for the human telomeric repeat tract and predict that POT1 can bind both the 3′ telomeric overhang and the displaced TTAGGG repeats at the base of the t-loop.
‘Affordance’ detection by mid-level physical parts

Derived from ecological psychology, the term `affordance' refers to the functional classification of objects. It simply means the set of actions a subject (i.e. humans and anthropomorphic agents) can possibly perform with an object. There are several paradigms in the researches regarding the approaches of affordance detection. These approaches include considering other contexts like the subject, ambient environment, scene etc. along with the object to detect the affordance. But the core challenge, which is to identify the affordance of an object with mere its visual features is still open ended. The orthodox approaches often used the fine level image features (i.e. HOG, SIFT) and perform bottom up processing to detect affordance. In this paper, we propose an effective methodology of using `mid-level physical parts' of objects as features for affordance detection. It is a multi-layered detection problem, where the simple image features are used to detect mid-level physical parts of an object and subsequently those parts are used to detect affordance. Our experiment results show the effectiveness of our method over the current affordance detection techniques. Moreover since the parts may be shared between different object classes, the method is also proficient in generality.
PowerTOSSIM z: realistic energy modelling for wireless sensor network environments

Energy continues to be the key constraint in wireless sensor networks. We review existing methods for estimating software power consumption and battery modelling, as applied to embedded systems such as Wireless Sensor Networks. We consider current developments in hardware and software technology, in particular the availability of high-fidelity simulators. Once such simulator, TOSSIM for TinyOS 1.x, models power consumption via a plugin, PowerTOSSIM. We complete the port of PowerTOSSIM to TinyOS 2.0 for the latest model of sensor node, the MICAz. Finally, we extend the simulator to model non-linear battery effects.
Impact on life expectancy of HIV-1 positive individuals of CD4+ cell count and viral load response to antiretroviral therapy

Objective:The objective of this study is to estimate life expectancies of HIV-positive patients conditional on response to antiretroviral therapy (ART). Methods:Patients aged more than 20 years who started ART during 2000–2010 (excluding IDU) in HIV clinics contributing to the UK CHIC Study were followed for mortality until 2012. We determined the latest CD4+ cell count and viral load before ART and in each of years 1–5 of ART. For each duration of ART, life tables based on estimated mortality rates by sex, age, latest CD4+ cell count and viral suppression (HIV-1 RNA <400 copies/ml), were used to estimate expected age at death for ages 20–85 years. Results:Of 21 388 patients who started ART, 961 (4.5%) died during 110 697 person-years. At start of ART, expected age at death [95% confidence interval (CI)] of 35-year-old men with CD4+ cell count less than 200, 200–349, at least 350 cells/&mgr;l was 71 (68–73), 78 (74–82) and 77 (72–81) years, respectively, compared with 78 years for men in the general UK population. Thirty-five-year-old men who increased their CD4+ cell count in the first year of ART from less than 200 to 200–349 or at least 350 cells/&mgr;l and achieved viral suppression gained 7 and 10 years, respectively. After 5 years on ART, expected age at death of 35-year-old men varied from 54 (48–61) (CD4+ cell count <200 cells/&mgr;l and no viral suppression) to 80 (76–83) years (CD4+ cell count ≥350 cells/&mgr;l and viral suppression). Conclusion:Successfully treated HIV-positive individuals have a normal life expectancy. Patients who started ART with a low CD4+ cell count significantly improve their life expectancy if they have a good CD4+ cell count response and undetectable viral load.
X-Check: A Novel Cross-Browser Testing Service Based on Record/Replay

With the advent of Web 2.0 application, and the increasing number of browsers and platforms on which the applications can be executed, cross-browser incompatibilities (XBIs) are becoming a serious problem for organizations to develop web-based software. Although some techniques and tools have been proposed to identify XBIs, they cannot assure the same execution when the application runs across different browsers as only explicit user activity is considered, and thus prone to generating both false positives and false negatives. To address this limitation, this paper describes X-Check, a platform that enables cross-browser testing as a service by leveraging record/replay technique. Comparing to existing techniques and tools, X-Check supports to detect cross-browser issues with high accuracy. It also provides useful support to developers for diagnosis and (eventually) elimination of XBIs. Our empirical evaluation shows that X-Check is effective, improves the state of the art.
Progressive Frequency Offset Compensation in Turbo Receivers

Based on the recently-proposed iterative receiver by Colavolpe et al., we extend it to further incorporate the mechanism of frequency offset compensation. As a progressive approach, the factor graph of a long frame is first divided into numerous subgraphs of short block, iterative decoding can successfully start its work as the effect of frequency offset can be well mitigated due to the small size of subgraph. As the iteration goes on, the extrinsic information from decoder can be employed to get finer estimate of the frequency offset. The system performance can be steadily improved as the block size is progressively expanded to the final frame size.
Can Phlorotannins Purified Extracts Constitute a Novel Pharmacological Alternative for Microbial Infections with Associated Inflammatory Conditions?

Bacterial and fungal infections and the emerging multidrug resistance are driving interest in fighting these microorganisms with natural products, which have generally been considered complementary to pharmacological therapies. Phlorotannins are polyphenols restricted to brown seaweeds, recognized for their biological capacity. This study represents the first research on the antibacterial, antifungal, anti-inflammatory and antioxidant activity of phlorotannins purified extracts, which were obtained from ten dominant brown seaweeds of the occidental Portuguese coast. Phlorotannins content was determined by the specific dimethoxybenzaldehyde (DMBA) method and a yield between 75 and 969 mg/Kg phloroglucinol units (dry matter) was obtained. Fucus spiralis ranked first, followed by three Cystoseira species. The anti-inflammatory potential of the purified extracts was assessed via inhibitory effect on nitric oxide (NO) production by lipopolysaccharide-stimulated RAW 264.7 macrophage cells, Cystoseira tamariscifolia being the one showing promising activity for the treatment of inflammation. NO scavenging ability was also addressed in cell free systems, F. spiralis being the species with highest capacity. The antimicrobial potential of the extracts was checked against five Gram-positive and four Gram-negative bacteria and three fungi strains, that commonly colonize skin and mucosa and are responsible for food contamination. The different extracts were more effective against Gram-positive bacteria, Staphylococcus epidermidis being the most susceptible species. Concerning antifungal activity, Trichophyton rubrum was the most sensitive species. Although the molecular mechanisms underlying these properties remain poorly understood, the results obtained turn phlorotannins purified extracts a novel and potent pharmacological alternative for the treatment of a wide range of microbial infections, which usually also present an inflammatory component. In addition to the biological properties demonstrated herein, phlorotannins extracts may also be preferred, in order to avoid side effects and allergic reactions commonly associated with synthetic drugs.
Five-day regimen of intramuscular or subcutaneous self-administered adrenocorticotropic hormone gel for acute exacerbations of multiple sclerosis: a prospective, randomized, open-label pilot trial

Background: Despite over 50 years of experience with adrenocorticotropic hormone (ACTH) as a treatment for acute exacerbations of multiple sclerosis, there have been no trials examining the options of the 2–3-week dosing regimen or intramuscular injection protocol used in the original trials. At our clinic, we performed a small, prospective, randomized pilot study to examine the efficacy and safety of, and patient satisfaction with, a short (five-day) self-administered ACTH dosing protocol for exacerbations of multiple sclerosis, and to compare the subcutaneous and intramuscular routes of administration. Methods: Patients for this study were recruited from an outpatient treatment clinic. Each patient self-administered natural ACTH gel 80 U/day by subcutaneous or intramuscular injection for five consecutive days and was evaluated at baseline and on days 7 and 14. Patient feedback was collected using the Patient Global Impression of Change (PGI-C, the primary efficacy measure), a patient global visual analog scale, the Expanded Disability Status Scale, a timed walk, the Nine-hole Peg Test, and the Clinical Global Impression of Change. Results: Of the 20 enrolled patients (mean age 39.5 years), 19 completed the study. On day 14, 61.1% of patients (11 of 18 with day 14 scores) were treatment responders, and rated their condition as “very much improved” or “much improved” on the PGI-C. The intramuscular group had numerically more responders, but there was no significant difference in the proportion of responders between the intramuscular and subcutaneous groups at day 14 (P = 0.3). The intramuscular route of injection was associated with more injection site pain than the subcutaneous route. Conclusion: A shorter five-day course of intramuscular or subcutaneous ACTH gel may improve symptoms associated with acute exacerbations of multiple sclerosis. Larger studies with standard of care controls are needed to confirm whether this shorter course of intramuscular or subcutaneous ACTH gel is effective and could potentially be substituted for the standard 14-day treatment.
Local control mechanisms in six-legged walking

Walknet, a biological inspired neural network, has been proposed to control walking of a 6-legged; 18 DoF walker. Control of stance movement is difficult because all legs in stance are mechanically coupled. Based on the idea of velocity feedback, recently a specific revision, local positive velocity feedback, has been proposed to solve this problem using an extremely decentralised architecture. In this control scheme the locally measured joint velocity of an elastic joint is fed into the same joint in the next time step to maintain the movement. At the same time an additional part of the same joint controller observes the mechanical joint power to confine the positive feedback. In this paper, we show that this principle can actually be successfully applied to move a complete 6-legged system. This is tested using a dynamic simulation.
The DEEP Groth Strip Survey. II. Hubble Space Telescope Structural Parameters of Galaxies in the Groth Strip

The quantitative morphological classification of distant galaxies is essential to the understanding of the evolution of galaxies over the history of the universe. This paper presents Hubble Space Telescope WFPC2 F606W and F814W photometric structural parameters for 7450 galaxies in the "Groth Strip. " These parameters are based on a two-dimensional bulge + disk surface brightness model and were obtained using an automated reduction and analysis pipeline described in detail here. A first set of fits was performed separately in each bandpass, and a second set of fits was performed simultaneously on both bandpasses. The information produced by these two types of fits can be used to explore different science goals. Systematic and random fitting errors in all structural parameters as well as bulge and disk colors are carefully characterized through extensive sets of simulations. The results of these simulations are given in catalogs similar to the real science catalogs so that both real and simulated measurements can be sampled according to the same selection criteria to show biases and errors in the science data subset of interest. The effects of asymmetric structures on the recovered bulge+disk fitting parameters are also explored through simulations. The full multidimensional photometric survey selection function of the Groth Strip is also computed. This selection function, coupled to bias maps from simulations, provides a complete and objective reproduction of the observational limits, and these limits can be applied to theoretical predictions from galaxy evolution models for direct comparisons with the data.
The origami of thioredoxin‐like folds

Origami is the Japanese art of folding a piece of paper into complex shapes and forms. Much like origami of paper, Nature has used conserved protein folds to engineer proteins for a particular task. An example of a protein family, which has been used by Nature numerous times, is the thioredoxin superfamily. Proteins in the thioredoxin superfamily are all structured with a β‐sheet core surrounded with α‐helices, and most contain a canonical CXXC motif. The remarkable feature of these proteins is that the link between them is the fold; however, their reactivity is different for each member due to small variations in this general fold as well as their active site. This review attempts to unravel the minute differences within this protein family, and it also demonstrates the ingenuity of Nature to use a conserved fold to generate a diverse collection of proteins to perform a number of different biochemical tasks.
Research and applications: Ontology-guided organ detection to retrieve web images of disease manifestation: towards the construction of a consumer-based health image library

BACKGROUND Visual information is a crucial aspect of medical knowledge. Building a comprehensive medical image base, in the spirit of the Unified Medical Language System (UMLS), would greatly benefit patient education and self-care. However, collection and annotation of such a large-scale image base is challenging. OBJECTIVE To combine visual object detection techniques with medical ontology to automatically mine web photos and retrieve a large number of disease manifestation images with minimal manual labeling effort. METHODS As a proof of concept, we first learnt five organ detectors on three detection scales for eyes, ears, lips, hands, and feet. Given a disease, we used information from the UMLS to select affected body parts, ran the pretrained organ detectors on web images, and combined the detection outputs to retrieve disease images. RESULTS Compared with a supervised image retrieval approach that requires training images for every disease, our ontology-guided approach exploits shared visual information of body parts across diseases. In retrieving 2220 web images of 32 diseases, we reduced manual labeling effort to 15.6% while improving the average precision by 3.9% from 77.7% to 81.6%. For 40.6% of the diseases, we improved the precision by 10%. CONCLUSIONS The results confirm the concept that the web is a feasible source for automatic disease image retrieval for health image database construction. Our approach requires a small amount of manual effort to collect complex disease images, and to annotate them by standard medical ontology terms.
What Does Project Leadership Really Do

The objective of article is to explore the importance of project leadership which has become essential for managing projects in complex and challenging environment. The study aims highlight a question that "what does project leadership really do? " This paper also draw attention to significance of project leadership as there is a limited research in the area of project leadership even though calls have been made for more research. It is apprehended that there is a vital need of effective role which must be able to lead and manage simultaneously and project leadership is considered critical to overcome such challenges. The roles and functions of project leadership have been highlighted and it becomes important to understand the difference between leadership and management as well as difference between project leadership and project management to determine the effect on success or failure of projects. Future research has been suggested for effective project leadership.
Associations Between Parenting Practices and Decision-Making Competence inEmerging Adults: A Prospective Study

approved:_____________________________________________________ Joshua Weller Developmental research has suggested that parenting practices may impact the development of risk behaviors later in life. However, little evidence exists regarding how parenting may impact actual decision processes that precede poor choices. This study examined how parenting practices in early childhood influence the development of decision-making competence (DMC), a latent trait that reflects individual differences in rational responding, and has been linked with risk behaviors (i.e. drug use, unprotected sex, drinking) in later life outcomes. To answer this question, we utilized a longitudinal dataset that tracked children from ages 10-12 through early adulthood. We correlated scores from Loeber’s (1989) Parental Supervision/Monitoring scale and Schludermann, and Schludermann’s (1970) Child Report on Parenting Behavior Inventory with scores on the Youth Decision-Making Competence (Y-DMC) scale. Preliminary results suggest that there are significant correlations between parenting practices and DMC. Specifically, children whose parents engaged in greater supervision and parental monitoring demonstrated higher DMC. Additionally, parenting practices uniquely contributed to the variance in DMC scores, controlling for socioeconomic status, child’s gender, child’s self-control, and cognitive ability at age 10. The findings from this study can contribute to future research related to decision-making, highlighting environmental factors that might impact the development of advantageous decision-making.
Hybrid Recommender System Using Latent Features

This paper proposes a hybrid recommender system that utilizes latent features. The main problem discussed in this paper is the cold start problem. To handle this problem, the proposed system first extracts latent features from items represented by a multi-attributed record using a probabilistic model. Then, it calculates the similarity of users from their ratings. Both similarities between items and users are used for predicting unknown rating of a user to a item. We evaluate the proposed method using a movie data set and shows that the proposed method achieves good performance for small ratings information.