Miracle-dz/UniFAR-FTUs huggingface dataset:
GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors

GPCR-ModSim (http://open.gpcr-modsim.org) is a centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs). 3D molecular models can be generated from amino acid sequence by homology-modeling techniques, considering different receptor conformations. GPCR-ModSim includes a membrane insertion and molecular dynamics (MD) equilibration protocol, which can be used to refine the generated model or any GPCR structure uploaded to the server, including if desired non-protein elements such as orthosteric or allosteric ligands, structural waters or ions. We herein revise the main characteristics of GPCR-ModSim and present new functionalities. The templates used for homology modeling have been updated considering the latest structural data, with separate profile structural alignments built for inactive, partially-active and active groups of templates. We have also added the possibility to perform multiple-template homology modeling in a unique and flexible way. Finally, our new MD protocol considers a series of distance restraints derived from a recently identified conserved network of helical contacts, allowing for a smoother refinement of the generated models which is particularly advised when there is low homology to the available templates. GPCR- ModSim has been tested on the GPCR Dock 2013 competition with satisfactory results.
Built-in jitter measurement methodology for spread-spectrum clock generators

In this paper, a built-in-self-test methodology for measuring frequency deviation and jitter of spread-spectrum clock generators is presented. It utilizes a phase detector to detect the clock phase of spread spectrum clock (SSC) and then measure the jitter by filtering out the low frequency component of the clock phase. Frequency of spread-spectrum clock can also be obtained by filtering out the high frequency component of the signal. The methodology is analyzed and verified with chip implementation and measurement. As an all digital design, the hardware overhead is very low.
Performance evaluation of the UK equity unit trusts : does active management add value?

Since Jensen (1968), performance evaluation of managed funds has been a popular topic in Finance. Whilst most of the studies have been focused on the US mutual funds, the evaluation of fund performance in the UK has been relatively few. This thesis investigates if active equity portfolio management can add value using a sample of UK unit trusts. Chapter 1 introduces the UK unit trust industry and the descriptive results of the data. Chapter 2 provides a literature review on performance evaluation. Chapter 3 explains the stochastic discount factor models and the generalized method of moments. It further explores the most fitted estimator with examinations of their small sample properties. Chapter 4 evaluates the conditioning performance of UK unit trusts within the framework of the stochastic discount factor models. Chapter 5 investigates style performance and presents the evidence of superior performance of style rotation strategies. Chapter 6 examines performance persistence. Chapter 7 concludes.
Better Deterministic Online Packet Routing on Grids

We consider the following fundamental routing problem. An adversary inputs packets arbitrarily at sources, each packet with an arbitrary destination. Traffic is constrained by link capacities and buffer sizes, and packets may be dropped at any time. The goal of the routing algorithm is to maximize throughput, i.e., route as many packets as possible to their destination. Our main result is an O(log n)-competitive deterministic algorithm for an n-node uni-directional line network (i.e., 1-dimensional grid), requiring only that buffers can store at least 5 packets, and that links can deliver at least 5 packets per step. We note that O(log n) is the best ratio known, even for randomized algorithms, even when allowed large buffers and wide links. The best previous deterministic algorithm for this problem with constant-size buffers and constant-capacity links was O(log5 n)-competitive. Our algorithm works like admission-control algorithms in the sense that if a packet is not dropped immediately upon arrival, then it is "accepted" and guaranteed to be delivered. We also show how to extend our algorithm to a polylog-competitive algorithm for any constant-dimension uni-directional grid.
Liu Zhi-qing, Dou Qing

Computer programs of GO, because of enormous complexities of the game, are typically constructed using a knowledge-based approach with heuristics and pattern matching. In this approach, quantity, quality and consistency of patterns used in computer programs of GO determine, to a large extent, the strengths of the programs. This paper presents an effective method to automatically acquire comprehensive GO patterns from large collections of game records. Statistical usages of the patterns ensure consistency and quality of the patterns, which, in turn, can help improve the strengths of computer GO programs. Additionally, statistical usages of patterns from different sources of game records clearly show subtle and significant discrepancies among various types of GO players, and clarify certain myths in the playing of GO.
Interactive visual analysis of families of curves using data aggregation and derivation

Time-series data are regularly collected and analyzed in a wide range of domains. Multiple simulation runs or multiple measurements of the same physical quantity result in ensembles of curves which we call families of curves. The analysis of time-series data is extensively studied in mathematics, statistics, and visualization; but less research is focused on the analysis of families of curves. Interactive visual analysis in combination with a complex data model, which supports families of curves in addition to scalar parameters, represents a premium methodology for such an analysis. In this paper we describe the three levels of complexity of interactive visual analysis we identified during several case studies. The first two levels represent the current state of the art. The newly introduced third level makes extracting deeply hidden implicit information from complex data sets possible by adding data derivation and advanced interaction. We seamlessly integrate data derivation and advanced interaction into the visual exploration to facilitate an in-depth interactive visual analysis of families of curves. We illustrate the proposed approach with typical analysis patterns identified in two case studies from automotive industry.
Remote rendering of High Dynamic Range graphics content

A large amount of computer graphics content is now regularly rendered in High Dynamic Range (HDR). The computational requirements of this are such that this rendering is typically done remotely. As the data requirements of HDR are large, compression is required if the resultant HDR frames are to be streamed efficiently to where they are required on existing ICT infrastructure. This paper investigates augmenting video streaming of computer generated HDR graphics using metadata available from the rendering engine which is not typically accessible for real-world HDR video streaming. In particular depth, geometry and motion information is used to produce an efficient stream for transmission. This is combined with state-of-the-art techniques for encoding HDR video to produce a highly efficient means of steaming HDR video of graphics content.
Upper Tract Urothelial Carcinomas in Patients with Chronic Kidney Disease: Relationship with Diagnostic Challenge

Chronic kidney disease and upper tract urothelial carcinomas display a bidirectional relationship. Review of the literature indicates that early diagnosis and correct localization of upper tract urothelial carcinomas in dialysis patients and kidney transplant recipients are important but problematic. Urine cytology and cystoscopy have limited sensitivity for the diagnosis of upper tract urothelial carcinomas in dialysis patients. Enhanced computed tomography and magnetic resonance imaging could prove useful for the detection and staging of upper tract urothelial carcinomas in dialysis patients. Renal ultrasound can detect hydronephrosis caused by upper tract urothelial carcinomas in kidney transplant recipients but cannot visualize the carcinomas themselves. High detection rates for upper tract urothelial carcinomas in kidney transplant recipients have recently been demonstrated using computed tomography urography, which appears to be a promising tool. To detect carcinomas in dialysis patients and kidney transplant recipients as early as possible, regular screening in asymptomatic patients and diagnostic work-up in symptomatic patients should be performed using a combination of urological and imaging methods. Careful assessment of subsequent recurrence within the contralateral upper urinary tract and the urinary bladder is necessary for dialysis patients and kidney transplant recipients with upper tract urothelial carcinomas.
Glycolipids and transmembrane signaling: antibodies to galactocerebroside cause an influx of calcium in oligodendrocytes

This is the first study to provide evidence that one function for the surface glycolipid galactocerebroside (GalC) is participation in the opening of Ca2+ channels in oligodendroglia in culture. This glycolipid is a unique differentiation marker for myelin-producing cells; antibodies to GalC have been shown to markedly alter oligodendroglial morphology via disruption of microtubules (Dyer, C. A., and J. A. Benjamins. 1988. J. Neurosci. 8:4307-4318). This study demonstrates that extracellular EGTA blocks anti-GalC-induced disassembly of microtubules in oligodendroglial membrane sheets, demonstrating that an influx of extracellular Ca2+ mediates the cytoskeletal changes. The Ca2+ influx was examined directly by loading oligodendroglia with the fluorescent dye Indo-1 in defined medium, and measuring changes in Ca2+ in individual cells with a laser cytometer. Upon addition of anti-GalC IgG, a marked sustained increase in intracellular Ca2+ occurred in 80% of the oligodendroglia observed. EGTA blocked the increase, indicating the increase is due to an influx of extracellular Ca2+, and not due to release from intracellular stores. The effect is specific, since Ca2+ levels remain normal in oligodendroglia treated with nonimmune IgG; astrocytes do not respond to the anti-GalC. The Ca2+ response in oligodendrocytes is dependent on concentration of antibody and GalC on the oligodendroglial membrane surface. The Ca2+ influx is not mediated by voltage-sensitive Ca2+ channels: it is not blocked by cadmium, and depolarization with K+ does not mimic the response. The kinetics of the response suggest that second messenger-mediated opening of Ca2+ channels is involved.
Flammability as a biological concept.

Studies examining plant flammability descriptors as fire-adaptive traits (e.g., Schwilk, 2003; Scarff & Westoby, 2006; Cowan & Ackerly, 2010; Saura-Mas et al., 2010; Pausas et al., 2012) are normally formulated within the framework of inclusive fitness theory. In such framework, flammabilityenhancing traits are considered to favour individuals if the elevated flammability confers fitness benefits. In post-fire seeder species (i.e., those with fire-stimulated germination from a persistent seed bank), higher flammability could increase the recruitment opportunities for the offspring of the individual with enhanced flammability by increasing the chance of opening spaces and by producing the necessary cues for triggering germination from the seedbank (‘kill thy neighbour’ hypothesis; Bond & Midgley, 1995). This might be specially relevant in non-resprouting (obligate) seeders with strong spatial population structure (e.g., with short-distance dispersal). Because there is some evidence of heritability for both seed dormancy (e.g., Baskin et al., 2000; Huang et al., 2010) and flammability-enhancing traits (e.g. Sampedro et al., 2010), we would expect a selection for higher flammability with repeated fires.
Studies on the biosynthesis of neurofilament proteins

To determine whether the triplet polypeptides of neurofilaments arise by degradation of precursor, we studied the biosynthesis of neurofilament polypeptides both in vivo and in cell-free systems. Neurofilament-enriched fractions and polyribosomes were prepared from the same rabbit spinal cord homogenates. At 1 h after intracisternal administration of [34S]methionine, radiolabeled neurofilament proteins were detected in spinal cord homogenates as well as in isolated filaments. When polyribosomes from rabbit spinal cord were allowed to incorporate [35S]methionine into protein, triplet polypeptides were among the proteins labeled. Addition of spinal cord polyribosomes to rabbit reticulocyte lysates led to several cycles of translation of the spinal cord mRNA; the three neurofilament polypeptides were among the proteins synthesized in this system. The results demonstrate that the triplet polypeptides of neurofilaments are synthesized as such in the course of individual translational events and do not arise from degradation of P200 or a larger precursor.
The Supersymmetric Parameter Space in Light of $B^-$ physics Observables and Electroweak Precision Data

Indirect information about the possible scale of supersymmetry (SUSY) breaking is provided by B-physics observables (BPO) as well as electroweak precision observables (EWPO). We combine the constraints imposed by recent measurements of the BPO BR(b → sγ), BR(Bs → μ+μ−), BR(Bu → τντ) and ΔMBs with those obtained from the experimental measurements of the EWPO MW, sin2 θeff, ΓZ, (g−2)μ and Mh, incorporating the latest theoretical calculations of these observables within the Standard Model and supersymmetric extensions. We perform a χ2 fit to the parameters of the constrained minimal supersymmetric extension of the Standard Model (CMSSM), in which the SUSY-breaking parameters are universal at the GUT scale, and the non-universal Higgs model (NUHM), in which this constraint is relaxed for the soft SUSY-breaking contributions to the Higgs masses. Assuming that the lightest supersymmetric particle (LSP) provides the cold dark matter density preferred by WMAP and other cosmological data, we scan over the remaining parameter space. Within the CMSSM, we confirm the preference found previously for a relatively low SUSY-breaking scale, though there is some slight tension between the EWPO and the BPO. In studies of some specific NUHM scenarios compatible with the cold dark matter constraint we investigate (MA, tan β) planes and find preferred regions that have values of χ2 somewhat lower than in the CMSSM.
Desperately Seeking Systems Thinking in the Information Systems Discipline

Although called systems, information systems in organizations are often viewed as tools that “users” use. IS success is often gauged as though it were about acceptance and usage of a tool. System development is often conceived as building computerized tools that satisfy information requirements of idealized business processes. Frequent IS disappointments and occasional failures are often attributed to inadequate user involvement, and even users involved in the projects often admit difficulty contributing fully to these technical discussions. This paper argues that the current balance between tool thinking and systems thinking in IS practice and research is slanted toward tool thinking, and that the IS discipline has done far too little to exploit the system nature of systems in organizations. Progress in that direction would fully recognize the sociotechnical nature of systems in organizations, thereby encouraging richer systems thinking than is possible in practice or in research when largely social entities and largely technical entities are treated separately. A long-term effort toward richer systems thinking in the IS field is the attempt to develop the work system method, a systems analysis method for business professionals. To date, this effort has generated innovations that may have valuable implications for systems analysis, IS pedagogy, and the development of a body of knowledge for the IS field. Many research issues for the future have also emerged.
Sources of Infant Pertussis Infection in the United States

BACKGROUND: Pertussis is poorly controlled, with the highest rates of morbidity and mortality among infants. Although the source of infant pertussis is often unknown, when identified, mothers have historically been the most common reservoir of transmission. Despite high vaccination coverage, disease incidence has been increasing. We examined whether infant source of infection (SOI) has changed in the United States in light of the changing epidemiology. METHODS: Cases <1 year old were identified at Enhanced Pertussis Surveillance sites between January 1, 2006 to December 31, 2013. SOI was collected during patient interview and was defined as a suspected pertussis case in contact with the infant case 7 to 20 days before infant cough onset. RESULTS: A total of 1306 infant cases were identified; 24.2% were <2 months old. An SOI was identified for 569 cases. Infants 0 to 1 months old were more likely to have an SOI identified than 2- to 11-month-olds (54.1% vs 40.2%, respectively; P < .0001). More than 66% of SOIs were immediate family members, most commonly siblings (35.5%), mothers (20.6%), and fathers (10.0%); mothers predominated until the transition to siblings beginning in 2008. Overall, the SOI median age was 14 years (range: 0–74 years); median age for sibling SOIs was 8 years. CONCLUSIONS: In contrast to previous studies, our data suggest that the most common source of transmission to infants is now siblings. While continued monitoring of SOIs will optimize pertussis prevention strategies, recommendations for vaccination during pregnancy should directly increase protection of infants, regardless of SOI.
Production of Proteolytic Enzymes by a Keratin-Degrading Aspergillus niger

A fungal isolate with capability to grow in keratinous substrate as only source of carbon and nitrogen was identified as Aspergillus niger using the sequencing of the ITS region of the rDNA. This strain produced a slightly acid keratinase and an acid protease during cultivation in feather meal. The peak of keratinolytic activity occurred in 48 h and the maximum proteolytic activity in 96 h. These enzymes were partly characterized as serine protease and aspartic protease, respectively. The effects of feather meal concentration and initial pH on enzyme production were evaluated using a central composite design combined with response surface methodology. The optimal conditions were determined as pH 5.0 for protease and 7.8 for keratinase and 20 g/L of feather meal, showing that both models were predictive. Production of keratinases by A. niger is a less-exploited field that might represent a novel and promising biotechnological application for this microorganism.
On random generation of stable polynomials

In this paper, various techniques for random generation of stable polynomials in discrete and continuous time are considered and presented in a unified framework. An attempt is made to present our “global vision” of the potentials of random generation techniques for stable polynomials. Moreover, their properties are discussed and compared, with a particular attention to the MATLAB implementation issues. Possible applications are indicated and illustrative results of simulations are provided.
Microbial experimental evolution as a novel research approach in the Vibrionaceae and squid-Vibrio symbiosis

The Vibrionaceae are a genetically and metabolically diverse family living in aquatic habitats with a great propensity toward developing interactions with eukaryotic microbial and multicellular hosts (as either commensals, pathogens, and mutualists). The Vibrionaceae frequently possess a life history cycle where bacteria are attached to a host in one phase and then another where they are free from their host as either part of the bacterioplankton or adhered to solid substrates such as marine sediment, riverbeds, lakebeds, or floating particulate debris. These two stages in their life history exert quite distinct and separate selection pressures. When bound to solid substrates or to host cells, the Vibrionaceae can also exist as complex biofilms. The association between bioluminescent Vibrio spp. and sepiolid squids (Cephalopoda: Sepiolidae) is an experimentally tractable model to study bacteria and animal host interactions, since the symbionts and squid hosts can be maintained in the laboratory independently of one another. The bacteria can be grown in pure culture and the squid hosts raised gnotobiotically with sterile light organs. The partnership between free-living Vibrio symbionts and axenic squid hatchlings emerging from eggs must be renewed every generation of the cephalopod host. Thus, symbiotic bacteria and animal host can each be studied alone and together in union. Despite virtues provided by the Vibrionaceae and sepiolid squid-Vibrio symbiosis, these assets to evolutionary biology have yet to be fully utilized for microbial experimental evolution. Experimental evolution studies already completed are reviewed, along with exploratory topics for future study.
Bilingual analysis of LOVE and HATRED emotional markers (SPSS-based approach)

This paper presents the results of GRID project which aimed at studying the semantics of 24 emotion terms in 23 languages belonging to 8 language families (Indo-European, IndoIranian, Afro-Asiatic, Altaic, Uralic, Japonic, Sino-Tibetan, Niger-Congo, and Unclassified). We limit ourselves in this article only to two Slavic languages – Slovak and Czech and to two emotion terms – love and hatred – and try show how greatly information technologies helped the psychologists first of all to obtain, and then to process large volume of information from a bit less than 5000 people, active project participants, who live in 30 countries.
Parental intentions to provide healthy diets for pre‐school children

The aim of this thesis was to investigate the factors that influence parental intention to provide their children with healthier diets. The study was conducted in three phases. Firstly, a two-part structured literature review was carried out. The review explored the influences on family and children’s diet using an ecological model. The second part reviewed the behavioural and psychological theories employed in studies related to parental behaviour for their children. The findings identified global, social and personal factors that influenced family-food environment and children’s diet. The theory of planned behaviour was identified as the most suitable model to examine the factors influencing parental behavioural intention to provide their children with healthier diets. The second phase explored qualitatively the factors influencing family and children’s diet. In-depth interviews were conducted with 15 parents living in different areas within NHS Tayside. The results revealed that various social and psychological factors influence the family food environment and parents’ food choices. The findings from the first and second phases of the study informed the design of the third phase. The third phase used the theory of planned behaviour to investigate the influence of attitude, subjective norm, perceived behavioural control, moral norm and nutrition knowledge on parental intention to provide their children with healthier diets. Parents (n=102) from areas with level of varying social deprivation participated. The results indicated that parental intention was positively predicted by attitude and moral norm. Subjective norm, perceived behavioural control and nutrition knowledge were not significant in predicting parental intention. This thesis concludes that parents have positive attitudes towards providing a healthy diet for their children and they intend to do so. From the findings of this thesis it may be suggested that interventions aimed at improving children’s diet could benefit from addressing the gap between intention and behaviour, perhaps through addressing the cost of healthier foods, sociocultural food practices and work-life balance policies.