Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for an ester linkage between the labile binding site of C3b and receptive surfaces.

The labile binding site of C3b interacts with receptive surfaces by way of a covalent bond. We report here experiments directed toward elucidating the nature of the linkage. 125I-C3b was bound to zymosan (Z) carrying C3-convertase activity on its surface. The resulting zymosan-C3b particles (Z-C3b) were washed free of noncovalently bound proteins with 1% SDS. The Z-C3b particles were incubated at different pH's, and it was found that C3b can be released under alkaline conditions but not acidic conditions. Release of C3b can also be observed at alkaline pH in the presence of 1 M hydroxylamine. The kinetics of the release of C3b from Z were studied at pH 7.5 in 1 M hydroxylamine and at pH 10 in 0.1 M NaHCO3. The second order rate constants for the release of C3b from Z were found to be 0.0026 ± 0.003 M-1 min-1 in hydroxylamine at neutral pH, and 37 ± 3 M-1 min-1 at pH 10. These values are comparable to the rate constants for the hydroxylaminolysis and hydrolysis of compounds containing esters such as benzoyl glycine ethyl ester, acetylcholine, and N,O-diacetylserinamide. They are significantly different, however, from the values obtained for the hydroxylaminolysis and hydrolysis of compounds containing thioesters, tyrosyl esters, and acylimidazole. The results of these experiments are consistent with the hypothesis that the bond between C3b and receptive surfaces is an ester. Further evidence for an ester linkage between C3b and receptive surfaces was obtained by analyzing the products of the release of C3d from zymosan by hydroxylamine. If the bond is indeed an ester, the release of C3d from Z with hydroxylamine will yield an hydroxamate that either associates with C3d or with Z. We were able to detect 0.66 ± 0.12 moles of hydroxamate per mole of C3d peptide, suggesting that the bond between C3b and receptive surfaces (RS) takes the form of RS-O-CO-C3b.
Phased psoralen cross-links do not bend the DNA double helix.

Although the chemical reaction of psoralens with nucleic acids is well understood, the structure of psoralen-DNA cross-linked products is still not clear. Model building studies base on the crystal structure of the psoralen-thymine monoadduct suggest that each cross-link bends the DNA double helix by 46.5 degrees [Pearlman, D. A. , Holbrook, S. R. , Pirkle, D. H. , & Kim, S. -H. (1985) Science (Washington, D.C.) 227, 1304-1308]. On the other hand, Sinden and Hagerman [Sinden, R. R. , & Hagerman, P. J. (1984) Biochemistry 23, 6299-6303] find that, in solution, psoralen cross-linked DNA is not bent. Here we use gel electrophoresis to test the validity of the current models. We have synthesized a series of DNA fragments (21-24 base pairs in length), each containing one unique T-A site for 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) cross-linking. Because of an estimated 28 degrees unwinding of the helix by HMT [Wiesehahn, G. , & Hearst, J. E. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 2703-2707], one expects that the 22-bp cross-linked fragment will be repeated nearly in phase with the average helical screw when multimerized. In that sequence ligation will maximally amplify any deformation to the double helix. We find that the ligated multimers of cross-linked DNA migrate close to the multimers of non-cross-linked DNA on polyacrylamide gels. Our observations place an upper limit of 10 degrees on DNA bending induced by psoralen cross-linking and indicate unwinding by about 1 bp, as well as stiffening of the double helix. These properties are not unexpected for classical intercalators.
Exploring Optimal Voting in Native Language Identification

We describe the submissions entered by the National Research Council Canada in the NLI-2017 evaluation. We mainly explored the use of voting, and various ways to optimize the choice and number of voting systems. We also explored the use of features that rely on no linguistic preprocessing. Long ngrams of characters obtained from raw text turned out to yield the best performance on all textual input (written essays and speech transcripts). Voting ensembles turned out to produce small performance gains, with little difference between the various optimization strategies we tried. Our top systems achieved accuracies of 87% on the essay track, 84% on the speech track, and close to 92% by combining essays, speech and i-vectors in the fusion track.
Accuracy Evaluation of GEM 5 Simulator System

Design space exploration (DSE) of complex embedded systems that combine a number of CPUs, dedicated hardware and software is a tedious task for which a broad range of approaches exists, from the use of high-level models to hardware prototyping. Each of these entails different simulation speed/accuracy tradeoffs, and thereby enables exploring a certain subset of the design space in a given time. Some simulation frameworks devoted to CPU-centric systems have been developed over the past decade, that either feature near real-time simulation speed or moderate to high speed with quasi-cycle level accuracy, often by means of instruction-set simulators or binary translation techniques. This paper presents an evaluation in term of accuracy in modeling real systems using the GEM5 simulator that belong to the first class. Performance figures of a wide range of benchmarks (e.g. in domains such as scientific computing and media applications) are captured and compared to results obtained on real hardware.
Medium-term electricity demand forecasting based on MARS

The paper proposes use of multivariate adaptive regression splines (MARS) method to perform monthly electricity demand forecasting for medium-term. The model is developed based on specific example of Turkey; however is applicable to any other system. Performance of the proposed method is compared to that of multiple linear regression (MLR), generalized additive model (GAM), and artificial neural networks (ANN) methods. The validation process shows that the proposed model outperforms the other ones by test error and shows stable error performance.
Meditation improves self‐regulation over the life span

The use of meditation to improve emotion and attention regulation has a long history in Asia and there are many practitioners in Western countries. Much of the evidence on the effectiveness of meditation is either anecdotal or a comparison of long‐term meditators with controls matched in age and health. Recently, it has been possible to establish changes in self‐regulation in undergraduate students after only 5 days of meditation practice, allowing randomized trials comparing effects of meditation with other self‐control methods such as relaxation training. Early studies took place in Chinese universities; however, similar effects have been obtained with U.S. undergraduates, and with Chinese children aged 4.5 years and older Chinese participants aged 65 years. Studies using neuroimaging techniques have shown that meditation improves activation and connectivity in brain areas related to self‐regulation, and these findings may provide an opportunity to examine remediation of mental disorders in a new light.
The planning and experience of time and space in three gestural media: theatre, film and interactive film

Human bodily gestures are now clearly present as a factor in human– computer interface design extending interactor experiences into designed space, in particular as interactive film, where the interactor may have gestural and emotional experiences with on-screen material. This paper describes the organisation of time and space in three media forms where gestures are prominent, namely theatre, film and interactive film, showing their interrelation, where interactive film absorbs processes of the first two media and is experienced as a game. The plan processes of the media is the focus of discussion, in particular the plan from the interactive gestural film game, To be or not to be, an original artwork designed and evaluated for practice-based research. A summary of gestural evaluation is also included.
Devices and Input Vectors are Shaping von Neumann Multiplexing

This paper starts by reviewing many of the gate-level reliability analyses of von Neumann multiplexing (vN-MUX). It goes on to detail very accurate device-level (CMOS technology specific) analyses of vN-MUX with respect to threshold voltage variations, taking into account both the gates' topology as well as the input vectors. Such results are essential for a clear understanding of vN-MUX when considering the unreliable behavior of future nanodevices. These analyses should change the “view from the top” as revealing a different picture from the well-known gate-level theoretical and simulation results. The findings presented here are also able to explain certain apparently abnormal behaviors of vN-MUX reported based on Monte Carlo simulations, and should have implications for the appraisal and the design of future fault-tolerant nanoarchitectures.
Characterization of sensory and corticothalamic excitatory inputs to rat thalamocortical neurones in vitro

1 Using an in vitro slice preparation of the rat dorsal lateral geniculate nucleus (dLGN), the properties of retinogeniculate and corticothalamic inputs to thalamocortical (TC) neurones were examined in the absence of GABAergic inhibition. 2 The retinogeniculate EPSP evoked at low frequency (<= 0.1 Hz) consisted of one or two fast‐rising (0.8 ± 0.1 ms), large‐amplitude (10.3 ± 1.6 mV) unitary events, while the corticothalamic EPSP had a graded relationship with stimulus intensity, owing to its slower‐rising (2.9 ± 0.4 ms), smaller‐amplitude (1.3 ± 0.3 mV) estimated unitary components. 3 The retinogeniculate EPSP exhibited a paired‐pulse depression of 60.3 ± 5.6 % at 10 Hz, while the corticothalamic EPSP exhibited a paired‐pulse facilitation of > 150 %. This frequency‐dependent depression of the retinogeniculate EPSP was maximal after the second stimulus, while the frequency‐dependent facilitation of the corticothalamic EPSP was maximal after the fourth or fifth stimulus, at interstimulus frequencies of 1‐10 Hz. 4 There was a short‐term enhancement of the <= 0.1 Hz corticothalamic EPSP (64.6 ± 9.2 %), but not the retinogeniculate EPSP, following trains of stimuli at 50 Hz. 5 The <= 0.1 Hz corticothalamic EPSP was markedly depressed by the non‐NMDA antagonist 1‐(4‐amino‐phenyl)‐4‐methyl‐7,8‐methylene‐dioxy‐5H‐2,3‐benzodiazepine (GYKI 52466), but only modestly by the NMDA antagonist 3‐((RS)‐2‐carboxypiperazin‐4‐yl)‐propyl‐1‐phosphonic acid ((RS)‐CPP), and completely blocked by the co‐application of GYKI 52466, 6‐cyano‐7‐nitroquinoxaline‐2,3‐dione (CNQX), (RS)‐CPP and (5R,10S)‐(+)‐5‐methyl‐10,11‐dihydro‐5H‐dibenzo[a,d]cyclohepten‐5,10‐imine (MK‐801). Likewise, the corticothalamic responses to trains of stimuli (1‐500 Hz) were greatly reduced by this combination of ionotropic glutamate receptor antagonists. 6 In the presence of GYKI 52466, CNQX, (RS)‐CPP and MK‐801, residual corticothalamic responses and slow EPSPs, with a time to peak of 2‐10 s, could be generated following trains of five to fifty stimuli. Neither of these responses were occluded by 1S,3R‐1‐aminocyclopentane‐1,3‐dicarboxylic acid (1S,3R‐ACPD), suggesting they are not mediated via group I and II metabotropic glutamate receptors.
Behavioral Approach System and Behavioral Inhibition System sensitivities and bipolar spectrum disorders: prospective prediction of bipolar mood episodes.

OBJECTIVES Research has found that bipolar spectrum disorders are associated with Behavioral Approach System (BAS) hypersensitivity and both unipolar and bipolar depression are associated with high Behavioral Inhibition System (BIS) sensitivity, but prospective studies of these relationships are lacking. We tested whether BAS and BIS sensitivities prospectively predicted the time to new onsets of major depressive and hypomanic and manic episodes in bipolar spectrum individuals. METHODS We followed 136 bipolar II or cyclothymic and 157 demographically matched normal control individuals prospectively for an average of 33 months. Participants completed the BIS/BAS scales and symptom measures at Time 1 and semi-structured diagnostic interviews every four months of follow-up. RESULTS The bipolar spectrum group exhibited higher Time 1 BAS, but not BIS, scores than the normal controls, controlling for Time 1 symptoms. Among bipolar spectrum participants, high BAS sensitivity prospectively predicted a shorter time to onset of hypomanic and manic episodes, whereas high BIS sensitivity predicted less survival time to major depressive episodes, controlling for initial symptoms. CONCLUSIONS Consistent with the BAS hypersensitivity model of bipolar disorder, a highly responsive BAS provides vulnerability to onsets of (hypo)manic episodes. In addition, a highly sensitive BIS increases risk for major depressive episodes.
Caregiver outcomes and interventions: a systematic scoping review of the traumatic brain injury and spinal cord injury literature

Aim: To identify factors reported with negative and positive outcomes for caregivers of the traumatic brain injury and spinal cord injury cohorts, to investigate what interventions have been studied to support carers and to report what effectiveness has been found. Methods: Scoping systematic review. Electronic databases and websites were searched from 1990 to December 2015. Studies were agreed for inclusion using pre-defined criteria. Relevant information from included studies was extracted and quality assessment was completed. Data were synthesised using qualitative methods. Results: A total of 62 studies reported caregiver outcomes for the traumatic brain injury cohort; 51 reported negative outcomes and 11 reported positive outcomes. For the spinal cord injury cohort, 18 studies reported caregiver outcomes; 15 reported negative outcomes and three reported positive outcomes. Burden of care was over-represented in the literature for both cohorts, with few studies looking at factors associated with positive outcomes. Good family functioning, coping skills and social support were reported to mediate caregiver burden and promote positive outcomes. A total of 21 studies further described interventions to support traumatic brain injury caregivers and four described interventions to support spinal cord injury caregivers, with emerging evidence for the effectiveness of problem-solving training. Further research is required to explore the effects of injury severity of the care recipient, as well as caregiver age, on the outcome of the interventions. Conclusion: Most studies reported negative outcomes, suggesting that barriers to caregiving have been established, but not facilitators. The interventions described to support carers are limited and require further testing to confirm their effectiveness.
Consistency of orthodontic treatment planning decisions.

OBJECTIVE (i) To analyse the consistency of a group of orthodontists' treatment decisions and (ii) to identify factors that may influence this consistency. DESIGN Cross-sectional observational study. SUBJECTS Ten orthodontists. METHODS The orthodontists examined 60 case vignettes and recorded their treatment decisions on two separate occasions. MAIN MEASURE Inter- and intra-examiner agreement was evaluated with the Kappa statistic. RESULTS The consistency within each orthodontist was moderate. However, between-orthodontist consistency was poor. CONCLUSION It appears that there is marked variation between orthodontists in treatment planning decisions and this may reflect the lack of evidence for the effectiveness of competing treatments.
Developmental origins of life history: Growth, productivity, and reproduction

There is now much evidence that early life undernutrition elevates risk of diseases like cardiovascular disease. Less clear is whether the underlying developmental plasticity in metabolism and physiology evolved to serve an adaptive function, beyond these effects on pathophysiology. This review builds from principles of life history theory to propose a functional model linking early environments with adult biology. An organism has metabolic potential in excess of survival requirements, called productivity, that supports growth before being shunted into reproduction after growth ceases. This concept from inter‐specific studies leads to the prediction that plasticity in growth rate will be positively correlated with components of future adult reproductive expenditure. Consistent with this idea, evidence is reviewed that early nutrition or growth rate predict offspring size in females, and increased somatic investment related to reproductive strategy in males. Thus, population birth weight and sexual size dimorphism are predicted to increase in response to improvements in early nutrition. A striking feature of the continuity of metabolic production is its perpetuation not merely during the lifecycle but across generations: in females, growth rate predicts future nutritional investment in reproduction, which in turn determines fetal growth rate in the next generation. Growth and reproduction serve as mutually‐defining templates, thus creating a phenotypic bridge allowing ecologic information to be maintained during ontogeny and transmitted to offspring. Resetting of metabolic production in response to maternal nutritional cues may serve a broader goal of integrating nutritional information within the matriline, thus providing a more reliable basis for adjusting long‐term strategy. Am. J. Hum. Biol., 2007. © 2007 Wiley‐Liss, Inc.
A case study of Google Search Engine and Bigtable : Distributed Systems

Interaction of autonomous computers on a network so as to achieve a common goal is called a “distributed system” [8]. The goal of distributed system is to divide resources/tasks among different machines on a network either to solve or to achieve the same objective with fewer burdens on machines with maintenance of the high performance of systems so that these free resources can handle other users at same time. Similarly, a very famous search engine “Google” uses the same concept of distributed system to answer the queries of its over 10 billion users a month [1] maintaining its speed. Projects like Google earth, Google maps, Google finance, and many other projects of Google need the independent big storage place; and Bigtable, a distributed storage system, functions to provide sufficient storage to all projects of Google by using its Google App engine. Keywords—DistributedSystem, Google, Search Engine,
The hypervariable C-terminal tail of the Sendai paramyxovirus nucleocapsid protein is required for template function but not for RNA encapsidation

The paramyxovirus nucleocapsid proteins (NPs) are relatively well conserved, except for the C-terminal 20% (or ca. 100 amino acids), referred to as the tail. We have examined whether this hypervariable tail is required for genome synthesis, both in vitro, where synthesis is predominantly from the input templates, and in vivo, where multiple rounds of amplification occur. In these viruses, genome synthesis and assembly of the nascent chain are coupled. We find that the tail is required in vivo but not in vitro. Closer examination of the in vivo system showed that the tailless NP could encapsidate the genome chain but that amplification did not occur. We interpret these results as indicating that the tail is not required for RNA assembly but is required for the template to function in RNA synthesis. Relatively small deletions within the conserved N-terminal 80% of the protein, on the other hand, rendered the protein nonfunctional in either system. The possible functions of the tail in RNA synthesis are discussed.
Functional organization and networ resilience in self-organizing clustered neuronal cultures

Desvelar la relacion entre la red de conexiones anatomica y su emergente dinamica es uno de los grandes desafios de la neurociencia actual. En este sentido, los cultivos neuronales han tomado un papel muy importante para entender esta cuestion, ya que fenomenologias fundamentales pueden ser estudiadas a escalas mas tratables. Los cultivos neuronales se obtienen tipicamente a base de disociar tejido neuronal de una parte especifica del cerebro, corteza cerebral de rata en nuestro caso, y su cultivo en un medio adecuado. Neuronas en cultivo constituyen en 1-2 semanas una red nueva con una actividad espontanea rica. Una de las preparaciones in vitro que ofrece mayor potencial es las 'redes clusterizadas'. Estas redes se auto-organizan de forma natural, formando grupos de neuronas (clusteres) interconectados a traves de axones. La caracterizacion de la dinamica de estas redes clusterizadas, asi como su sensibilidad a perturbaciones, ha sido el objetivo principal de esta tesis. Asi, hemos caracterizado la red funcional del cultivo a partir de su dinamica espontanea, desarrollando para ello un novedoso modelo fisicomatematico. Hemos observado que las redes tienen una conectividad modular, donde clusteres tienden a conectarse fuertemente en pequenos grupos, los cuales a su vez se conectan entre ellos. Ademas, las redes funcionales muestran propiedades topologicas clave, en especial asortatividad (interconexion preferente de clusteres con numero similar de conexiones) y la existencia de un 'rich club' (grupo de clusteres con una interconectividad tan destacada que forman el nucleo fundamental de la red). Estas propiedades confieren una gran robustez y flexibilidad a la red. Por esta razon, en la tesis hemos investigado diferentes perturbaciones fisicas y bioquimicas, demostrando que las redes clusterizadas son mucho mas resistentes a dano que otras configuraciones, lo que refuerza la relacion entre las propiedades topologicas descritas y resistencia al dano. Ademas, observamos que las redes presentaron diferentes mecanismos de reforzamiento entre conexiones para preservar la actividad de la red. Por ello, las redes clusterizadas constituyen una plataforma ideal para estudiar resistencia en redes o como sistema modelo aplicado a estudios de enfermedades neurodegenerativas, como por ejemplo Alzheimer.
Regulation of mouse satellite DNA replication time.

The satellite DNA sequences located near the centromeric regions of mouse chromosomes replicate very late in S in both fibroblast and lymphocyte cells and are heavily methylated at CpG residues. F9 teratocarcinoma cells, on the other hand, contain satellite sequences which are undermethylated and replicate much earlier in S. DNA methylation probably plays some role in the control of satellite replication time since 5‐azacytidine treatment of RAG fibroblasts causes a dramatic temporal shift of replication to mid S. In contrast to similar changes accompanying the inactivation of the X‐chromosome, early replication of satellite DNA is not associated with an increase in local chromosomal DNase I sensitivity. Fusion of F9 with mouse lymphocytes caused a dramatic early shift in the timing of the normally late replicating lymphocyte satellite heterochromatin, suggesting that trans‐activating factors may be responsible for the regulation of replication timing.