Miracle-dz/UniFAR-FTUs huggingface dataset:
Fold homology detection using sequence fragment composition profiles of proteins

The effectiveness of sequence alignment in detecting structural homology among protein sequences decreases markedly when pairwise sequence identity is low (the so‐called “twilight zone” problem of sequence alignment). Alternative sequence comparison strategies able to detect structural kinship among highly divergent sequences are necessary to address this need. Among them are alignment‐free methods, which use global sequence properties (such as amino acid composition) to identify structural homology in a rapid and straightforward way. We explore the viability of using tetramer sequence fragment composition profiles in finding structural relationships that lie undetected by traditional alignment. We establish a strategy to recast any given protein sequence into a tetramer sequence fragment composition profile, using a series of amino acid clustering steps that have been optimized for mutual information. Our method has the effect of compressing the set of 160,000 unique tetramers (if using the 20‐letter amino acid alphabet) into a more tractable number of reduced tetramers (∼15–30), so that a meaningful tetramer composition profile can be constructed. We test remote homology detection at the topology and fold superfamily levels using a comprehensive set of fold homologs, culled from the CATH database that share low pairwise sequence similarity. Using the receiver‐operating characteristic measure, we demonstrate potentially significant improvement in using information‐optimized reduced tetramer composition, over methods relying only on the raw amino acid composition or on traditional sequence alignment, in homology detection at or below the “twilight zone”. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Data analysis of social community reputation: Good questions vs. good answers

Developing an understanding of the behavior and reputation of community members, and the relationships between them, can help community developers and managers to build and maintain better communities. We analyzed Stack Overflow, currently one of the most popular Q&A communities for developers, in order to understand the relationship between user behavior and reputation. Our data analysis of user activities, as well as our analysis of the each behavior's reputation impact, has revealed that asking good questions is an important behavior in Stack Overflow. Good questioners have higher reputation, in spite of the reputation system's design, and they are also more likely to engage in other reputation-positive behavioral activities.
Eel migration to the Sargasso: remarkably high swimming efficiency and low energy costs

SUMMARY One of the mysteries of the animal kingdom is the long-distance migration (5000–6000 km) of the European eel Anguilla anguilla L. from the coasts of Europe to its spawning grounds in the Sargasso Sea. The only evidence for the location of the spawning site of the European eel in the Sargasso Sea is the discovery by Johannes Schmidt at the beginning of the previous century of the smallest eel larvae (leptocephali) near the Sargasso Sea. For years it has been questioned whether the fasting eels have sufficient energy reserves to cover this enormous distance. We have tested Schmidt's theory by placing eels in swim tunnels in the laboratory and allowing them to make a simulated migration of 5500 km. We find that eels swim 4–6 times more efficiently than non-eel-like fish. Our findings are an important advance in this field because they remove a central objection to Schmidt's theory by showing that their energy reserves are, in principle, sufficient for the migration. Conclusive proof of the Sargasso Sea theory is likely to come from satellite tracking technology.
Reduced Conductive EMI in Switched-Mode DC–DC Power Converters Without EMI Filters: PWM Versus Randomized PWM

This paper addresses improved electromagnetic compatibility (EMC) in switched-mode power converters (SMPCs), without using electromagnetic interference (EMI) filters. A practical solution is proposed for minimizing conductive EMI in a pulsewidth modulated (PWM), and random PWM dc-dc power converters. A comparative investigation is performed into the use of different random modulation schemes (driven by the DSP-2 board with the TMS320C32) as against the normal PWM. The effectiveness of randomization on spreading those dominating frequencies that normally exist in constant frequency PWM schemes is evaluated by power spectral density (PSD) estimations in the low-frequency range. Some parasitical- and topology-based EMI sources in devices are presented and frequency analysis is shown by using the discrete Fourier transform (DFT). SPICE simulations are also used to verify practical solutions for eliminating negative EMI sources and achieving EMC improvements. Finally, levels of conductive EMI are estimated with DFT, and experimentally verified to comply with the CISPR 25 (or EN 55025) regulations. Moreover, it is clearly shown, that limited speed PWM driving of the power switches with appropriate snubber circuits guarantees reduced conductive EMI. When considering the price and high EMC, in the final solution the power converter is driven by the mu-controller PIC16F876 with limited numerical and peripheral capabilities, where only normal PWM and randomized PWM can be implemented
Directing spatial attention to locations within remembered and imagined mental representations

Spatial attention enables us to enhance the processing of items at target locations, at the expense of items presented at irrelevant locations. Many studies have explored the neural correlates of these spatial biases using event-related potentials (ERPs). More recently some studies have shown that these ERP correlates are also present when subjects search visual short-term memory (VSTM). This suggests firstly that this type of mental representation retains a spatial organization that is based upon that of the original percept, and secondly that these attentional biases are flexible and can act to modulate remembered as well as perceptual representations. We aimed to test whether it was necessary for subjects to have actually seen the memoranda at those spatial locations, or whether simply imagining the spatial layout was sufficient to elicit the spatial attention effects. On some trials subjects performed a “visual” search of an array held in VSTM, and upon other trials subjects imagined the items at those spatial locations. We found ERP markers of spatial attention in both the memory-search and the imagery-search conditions. However, there were differences between the conditions, the effect in the memory-search began earlier and included posterior electrode sites. By contrast the ERP effect in the imagery-search condition was apparent only over fronto-central electrode sites and emerged slightly later. Nonetheless, our data demonstrate that it is not necessary for subjects to have ever seen the items at spatial locations for neural markers of spatial attention to be elicited; searching an imaginary spatial layout also triggers spatially-specific attention effects in the ERP data.
Neural-based control and stability analysis of a class of nonlinear systems: Base-excited inverted pendulums

This paper presents a novel application of multilayer neural networks for online control of a class of base-excited inverted pendulums. The pendulum has two degrees of rotational freedom and its base-point moves freely in three-dimensional space. The goal is to apply control torques to keep the pendulum in a desired orientation, in spite of disturbing base-point movement. Four three-layered neural networks are trained online to represent the inverse dynamics of the plant within a controller. The conditions of training accuracy, to guarantee the stability of such a non-autonomous closed-loop system, are established using Lyapunov stability theory. The proposed neural controller is examined through simulations. Its performance is also compared with the performance of a Lyapunov controller from the most recent published work. It is shown that the proposed control scheme is simple in implementation in the sense that it does not require a mathematical model of the target pendulum or the measurement of the base-point movement. At the same time, it produces fast, yet well-damped responses with smooth control torques. The work presented here can benefit practical problems such as the study of stable locomotion of the human upper-body and bipedal robots.
Towards local resource redirection across thin client protocols

In this paper we discuss the design, implementation and testing of amount, a package to support the use of client side hot-pluggable storage devices across thin client protocols in a Linux environment. Many third level institutions utilise thin client and remote access protocols, and as the use of portable storage devices continues to increase, there is a strong case for the development of such a tool. Several existing thin client implementations lack the ability' to manipulate client side file systems when working on the server side, and consequently restrict users productivity. By modifying the existing thin client computing model and creating a supplemental package for existing thin client protocols, we can eliminate these barriers, and support redirection of local peripheral devices from the client to the server. While existing support for local peripheral redirection is often platform or protocol dependent, our approach is independent of either. Moreover, we demonstrate that our approach improves on existing implementations in certain aspects of performance.
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Cerebral Hemodynamic and Metabolic Studies in Patients with Congestive Heart Failure: I. Observations in Lucid Subjects

MEASUREMENTS of cerebral blood flow and metabolism in subjects with congestive heart failure have yielded conflicting results.13 Scheinberg1 compared the values in 14 persons with congestive heart failure of unstated severity with those in normal young men and concluded that cerebral blood flow was significantly decreased in subjects with cardiac decompensation. Novak and co-workers,2 on the other hand, compared their findings in 15 decompensated cardiac patients with the values in a "similar arteriosclerotic group " and concluded that the cerebral eireulation was not affected by the congestive state. In 20 hypertensive individuals with congestive heart failure Moyer and associates3 found no significant diminution in cerebral perfusion, nor was there any significant change following treatment; cerebral blood flow, however, was apparently diminished in 6 subjects with valvular heart disease and congestive failure. In addition, Moyer's group4 reported that the administration of aminophylline to persons with congestive heart failure resulted in a decline in cerebral blood flow. In an attempt to resolve the existing confusion, the present study was undertaken. The design of the study permits comparison of cerebral blood flow in 2 types of patients with cardiac decompensation: those with mild forms and those with severe congestive failure. In addition, many patients were studied prior to treatment and again after compensation had been achieved. This experimental design was promnpted by prelimninary observa-
Evidence, regulation and 'rational' prescribing: the case of gabapentin for neuropathic pain.

RATIONALE, AIMS AND OBJECTIVES In 2004, the pharmaceutical company Warner-Lambert paid US $430 million to resolve criminal and civil legal liability for aggressive off-label marketing of gabapentin. Perhaps surprisingly, however, regulatory and legal concerns regarding the marketing of gabapentin has not significantly impacted upon the attitude of doctors towards using gabapentin for neuropathic pain. In this paper, we attempt to understand the reasons for this discrepancy between clinical practice and regulatory/legal concerns through an analysis of published discussions about gabapentin prescribing. METHODS We performed a qualitative empirical analysis of the published clinical debate surrounding the use of gabapentin for the management of neuropathic pain. RESULTS The ongoing use of gabapentin for neuropathic pain was primarily driven by the perception that it was a safe, non-addictive drug with few drug interactions, by possible similarities between the physiology of chronic pain and other neurological conditions, by the well-established clinical precedent of using antiepileptic drugs in pain management, and by the lack of alternative options available in the market. Emerging evidence of lack of effectiveness and controversies about the integrity of the scientific record appeared to be of relatively little importance to practising clinicians. CONCLUSIONS Those who want to promote 'rational' prescribing need to recognize that prescribing is driven by many factors other than epidemiological data and regulatory indications and that even intensely negative publicity about medicines may not penetrate clinical reasoning. This suggests that a range of measures may be needed to 'incentivize' rational prescribing and to promote research integrity. Regulators must be more sensitive to the contextual issues that are relevant to clinical practice when evaluating drugs for approval and developing guidelines.
Stability of the interstitial matrix after crystalloid fluid loading studied by volume kinetic analysis.

To investigate if fluid therapy changes the prerequisites for the development of oedema, four i.v. infusions of Ringer's solution 25 ml kg-1 were given over 15 or 30 min in a randomized crossover study to 10 healthy male volunteers, aged 28-40 (mean 31) yr. Blood haemoglobin concentration, measured every 5 min for 90 min, and urinary excretion were used as input data for volume kinetic analysis. The results showed that the elimination rate constant (kr) was higher when another infusion had been given earlier on the same day (208 vs 140 ml min-1; P < 0.002) and the size of V1 was larger during the 15-min infusions (4.7 vs 3.2 litre; P < 0.02). However, the size of V2 and the rate constant for the exchange of fluid between V1 and V2 were similar during all infusions. We conclude that a fluid challenge makes elimination of further infused fluid more effective but does not change compliance with volume expansion in healthy volunteers.
Central pupillary light reflex circuits in the cat: I. The olivary pretectal nucleus

The central pathways subserving the feline pupillary light reflex were examined by defining retinal input to the olivary pretectal nucleus (OPt), the midbrain projections of this nucleus, and the premotor neurons within it. Unilateral intravitreal wheat germ agglutinin–conjugated horseradish peroxidase (WGA–HRP) injections revealed differences in the pattern of retinal OPt termination on the two sides. Injections of WGA–HRP into OPt labeled terminals bilaterally in the anteromedian nucleus, and to a lesser extent in the supraoculomotor area, centrally projecting Edinger–Westphal nucleus, and nucleus of the posterior commissure. Labeled terminals, as well as retrogradely labeled multipolar cells, were present in the contralateral OPt, indicating a commissural pathway. Injections of WGA–HRP into the anteromedian nucleus labeled fusiform premotor neurons within the OPt, as well as multipolar cells in the nucleus of the posterior commissure. Connections between retinal terminals and the pretectal premotor neurons were characterized by combining vitreous chamber and anteromedian nucleus injections of WGA–HRP in the same animal. Fusiform‐shaped, retrogradely labeled cells fell within the anterogradely labeled retinal terminal field in the OPt. Ultrastructural analysis revealed labeled retinal terminals containing clear spherical vesicles. They contacted labeled pretectal premotor neurons via asymmetric synaptic densities. These results provide an anatomical substrate for the pupillary light reflex in the cat. Pretectal premotor neurons receive direct retinal input via synapses suggestive of an excitatory drive, and project directly to nuclei containing preganglionic motoneurons. These projections are concentrated in the anteromedian nucleus, indicating its involvement in the pupillary light reflex. J. Comp. Neurol. 522:3960–3977, 2014. © 2014 Wiley Periodicals, Inc.
Acetate Dose-Dependently Stimulates Milk Fat Synthesis in Lactating Dairy Cows.

Background: Acetate is a short-chain fatty acid (FA) that is especially important to cows because it is the major substrate for de novo FA synthesis. However, the effect of acetate supply on mammary lipid synthesis is not clear.Objective: The objective of this experiment was to determine the effect of increasing acetate supply on milk fat synthesis in lactating dairy cows.Methods: Six multiparous lactating Holstein cows were randomly assigned to treatments in a replicated design to investigate the effect of acetate supply on milk fat synthesis. Treatments were 0 (control), 5, 10, and 15 mol acetate/d continuously infused into the rumen for 4 d. Rumen short-chain FAs, plasma hormones and metabolites, milk fat concentration, and milk FA profile were analyzed on day 4 of each treatment. Polynomial contrasts were used to test the linear and quadratic effects of increasing acetate supply.Results: Acetate increased milk fat yield quadratically (P < 0.01) by 7%, 16%, and 14% and increased milk fat concentration linearly (P < 0.001) by 6%, 9%, and 11% for 5, 10, and 15 mol acetate/d, respectively, compared with the control treatment. Increased milk fat yield predominantly was due to a linear increase in 16-carbon FAs (P < 0.001) and a quadratic increase in de novo synthesized FAs (<16-carbon FAs; P < 0.01), indicating that there was stimulation of de novo synthesis pathways. Apparent transfer of acetate to milk fat was 33.4%, 36.2%, and 20.6% for 5, 10, and 15 mol/d, respectively. Acetate infusion linearly increased the relative concentration of rumen acetate (P < 0.001) before feeding, but not after feeding. Acetate linearly increased plasma ß-hydroxybutyric acid by 29%, 50%, and 78%, respectively, after feeding compared with the control treatment (P < 0.01). Conclusions: Increasing acetate supply to lactating cows increases milk fat synthesis, suggesting that nutritional strategies that increase ruminal acetate absorption would be expected to increase milk fat by increasing de novo FA synthesis.
A Family of G Protein βγ Subunits Translocate Reversibly from the Plasma Membrane to Endomembranes on Receptor Activation*

The present model of G protein activation by G protein-coupled receptors exclusively localizes their activation and function to the plasma membrane (PM). Observation of the spatiotemporal response of G protein subunits in a living cell to receptor activation showed that 6 of the 12 members of the G protein γ subunit family translocate specifically from the PM to endomembranes. The γ subunits translocate as βγ complexes, whereas the α subunit is retained on the PM. Depending on the γ subunit, translocation occurs predominantly to the Golgi complex or the endoplasmic reticulum. The rate of translocation also varies with the γ subunit type. Different γ subunits, thus, confer distinct spatiotemporal properties to translocation. A striking relationship exists between the amino acid sequences of various γ subunits and their translocation properties. γ subunits with similar translocation properties are more closely related to each other. Consistent with this relationship, introducing residues conserved in translocating subunits into a non-translocating subunit results in a gain of function. Inhibitors of vesicle-mediated trafficking and palmitoylation suggest that translocation is diffusion-mediated and controlled by acylation similar to the shuttling of G protein subunits (Chisari, M., Saini, D. K., Kalyanaraman, V., and Gautam, N. (2007) J. Biol. Chem. 282, 24092–24098). These results suggest that the continual testing of cytosolic surfaces of cell membranes by G protein subunits facilitates an activated cell surface receptor to direct potentially active G protein βγ subunits to intracellular membranes.
Confidence Intervals

The National Institute has a long history of analysing its forecasting record; recent Reviews have contained accounts of the accuracy of our forecasts of inflation (February 1984) and GDP (Savage 1983). Earlier studies include Brooks and Cuthbertson (1981) and Osborn and Teal (1979). Such studies ask two fundamental questions: how good have our forecasts been in the past, and how much confidence can we hold for our forecasts for the future? In the case of the first question the above-mentioned studies provide an almost complete answer. The second question can only be answered by such studies on the assumption that our past record will be maintained in the future. This note approaches the second question from an entirely different viewpoint. An estimate of confidence bands for the National Institute's Model 7 will be derived by the use of stochastic simulations of the model. Just as the earlier studies offer only a partial guide to the accuracy of our forecasting ability in the future, so this note is also only a partial answer to the question. This is because our forecasts do not consist simply of a mechanical model run; instead the basic model forecast is supplemented by much other information. A good example of this is the recent miners' strike which could not have been included in the forecast on the basis of a purely mechanical model forecast. We would therefore expect the model to have a larger error bound than our final published forecasts. The scope of this note, it must be stressed, is strictly only applicable to the model we use to forecast and not to the finally published forecasts.
Patch-based nonlocal dynamic MRI reconstruction with low-rank prior

Compressed sensing utilizes the sparsity of Magnetic resonance (MR) images to obtain accurate reconstructions from undersampled k-space data. In this paper, a novel nonlocal dynamic MRI reconstruction method with low-rank regularization is developed to exploit the spatiotemporal structural sparsity of a MRI sequence. The nonlocal prior and low rank prior are combined organically by grouping similar patches in both spatial and temporal domain. The low-rank regularization can be approximated by nuclear norm minimization solved by a singular value thresholding (SVT) method with adaptive thresholds estimation. The objective function is divided into several sub-problems that are easier to solve by alternative direction multiplier method (ADMM). Extensive experiments show that the new method outperforms commonly used classical dynamic MRI reconstruction algorithms.