bluuebunny/crossref_metadata_2025 huggingface dataset:
The Strength of the Orienting Response during Blocking
Authors: Kaye Helen , Pearce John M.
Published: October 2014

In two experiments rats initially received appetitive Pavlovian conditioning with an auditory conditioned stimulus (CS). Subsequently this stimulus was presented in compound with a novel light and paired with the same appetitive reinforcer. In keeping with the outcome of many such experiments on blocking, there was very little evidence of appetitive conditioning during subsequent independent presentations of the light. Of main concern in the present experiments, however, was the influence of this training on the strength of the orienting response directed towards the light. When the light was first presented it elicited a strong orienting response. The strength of this response declined rapidly when the light was presented in compound with the previously trained auditory CS but more slowly when it was paired with the reinforcer either by itself or in conjunction with an initially neutral auditory stimulus. It is suggested that the extent to which the events following the light are accurately predicted determines the strength of orientation towards this stimulus.
One-Trial Object Recognition by Rats
Authors: Aggleton J. P.
Published: October 2014

Four experiments examined the ability of rats to solve problems analogous to those used with primates, where they were required to remember an object seen on a single trial. In the first experiment, rats were rewarded for selecting the novel of two goal boxes in a Y-maze (nonmatching). Different pairs of goal boxes were used for every trial within a session in order to increase the salience of the positive stimulus and to exclude the use of odour trails. The animals rapidly learnt this one-trial object recognition task and performed well above chance after retention intervals as long as 120 sec. A control experiment confirmed that the rats could not use spatial cues to solve the task. A third experiment showed that rats could also learn to select the familiar of two boxes in a one-trial test of object matching. In the final experiment the rats were unable to acquire a win–stay/lose–shift strategy when tested in a comparable manner.
Matching and Oddity Learning in the Pigeon: Transfer Effects and the Absence of Relational Learning
Authors: Wilson Bundy , Mackintosh N. J. , Boakes R. A.
Published: October 2014

Three experiments examined the extent to which pigeons trained on a matching or oddity discrimination with one pair of colours showed transfer when tested on a new matching or oddity discrimination with a new pair of colours. Experiment 1 examined the effects of key spacing and a delay procedure and replicated previous reports that in the transfer stage subjects given the same kind of problem (Non-shift condition) in general learn more rapidly than those given the opposite problem (Shift condition). However, this difference appeared only when pigeons given matching in both training and transfer stages were compared to those shifted from oddity to matching; it did not appear in birds transferred to oddity. Transfer was not significantly affected by key spacing or by the delay.

Experiments 2 and 3 examined transfer from a non-relational conditional discrimination based on one set of colours to a subsequent matching or oddity task based on two new colours. Both a comparison between the results of Experiment 1 and 2 and the corresponding within-experiment comparison from Experiment 3 showed that transfer from conditional training to matching was as great as from prior training on matching, while prior training on oddity produced negative transfer on shift to matching. It was suggested that this negative transfer occurs because pigeons trained on oddity have not learned to override an initial bias towards the odd stimulus in an array. Whatever the correct explanation; the present results provide no support for the claim that pigeons solve matching or oddity discriminations relationally.
Transfer of Relational Rules in Matching and Oddity Learning by Pigeons and Corvids
Authors: Wilson Bundy , Mackintosh N. J. , Boakes R. A.
Published: October 2014

Three experiments compared the performance of pigeons and corvids when they were given the opportunity to transfer the relational rule underlying matching or oddity discriminations to new sets of stimuli. In the first, pigeons and jackdaws were initially trained either on a matching or on a non-relational conditional discrimination and then transferred to a new matching discrimination. In the second, pigeons and jays were trained on a series of three matching (or oddity) discriminations with three different pairs of colours and finally tested, either with the same or the reversed rule, on matching or oddity to line orientations. In the third, pigeons and rooks were trained to perform one response when two coloured panels were the same and a different response when the two colours were different and then transferred, either with the same or the reversed rule, to a new set of colour stimuli. All three experiments produced the same result: no evidence of transfer of the relational rule by pigeons, but substantial and significant transfer by corvids.
Algorithmic Responding on the Radial Maze in Rats does not Always Imply Absence of Spatial Encoding
Authors: Foreman Nigel
Published: October 2014

Two experiments were conducted to determine whether consistent algorithmic response patterning on 8- and 10-arm versions of the radial maze is independent of spatial encoding. On the 8-arm version well-trained hooded rats were tested in darkness, after maze rotation that rendered room cues ambiguous with respect to arm positions, or with room cues unsystematically relocated. Ambiguous maze rotation was also used with well-trained subjects on the 10-arm version. If algorithmic patterning is a learned, non-spatial strategy, animals using it consistently ought not to have been affected by changes in the spatial layout of the test environment, and the type of pattern used by each subject would have remained constant. On the 8-arm radial maze, responses were most often made to arms 2 or 3 from that just visited. In many animals patterns were interchangeable, switching occurring between preferred angles of turn from day to day. Performance fell when animals were tested in darkness and upon ambiguous maze rotation early (but not later) in training. Testing in darkness increased the angle through which animals turned when responding, perhaps due to the disturbance of intramaze cue use. On the 10-arm maze the “consecutive arm” pattern was used persistently by several animals and appeared to protect their performance from disruption by ambiguous maze rotation. Animals not using rigid patterning were adversely affected. However, on both mazes animals using patterning correctly identified maze arms that had been omitted from otherwise patterned choice sequences. Animals adopted continuous patterning only when spatial encoding had been established. Response patterning appears to serve a mnemonic function and in rats complements rather than replaces the use of a spatial representation of the environment. It was concluded that a complex, flexible relationship exists between spatial functioning and its expression via motor responses.
A Comparison of the Effects of Partial Reinforcement Schedules using a Within-Subject Serial Autoshaping Procedure
Authors: Pearce John M. , Kaye Helen , Collins Louis
Published: October 2014

Three experiments, each using a single group of pigeons, are reported. In Experiment 1 subjects were initially trained with two stimuli, one of which was always followed by food, the other being reinforced according to a 50% partial reinforcement schedule. Subsequently a serial procedure was adopted in which an additional stimulus, C, was consistently followed by the partially reinforced CS. A second additional stimulus, A, was followed on half of its occurrences by the continuously reinforced CS, its remaining presentations being followed by nothing. The rate of autoshaped keypecking was substantially greater during A than during C. In the remaining experiments subjects received first-order conditioning with a single stimulus that was either partially (Experiment 2) or continuously (Experiment 3) reinforced. The stimuli A and C were then again introduced for serial autoshaping. Stimulus A was occasionally paired with the CS and occasionally followed by nothing, whereas stimulus C was always followed by the CS. As in Experiment 1, the rate of responding during A was greater than during C. It is proposed that one influence on the rate of autoshaped keypecking during a CS is the accuracy with which the immediate consequences of that CS are predicted.
Forward and Backward Blocking in Human Contingency Judgement
Authors: Shanks David R.
Published: October 2014

Three experiments investigated whether a process akin to Kamin's (1969) blocking effect would occur with human contingency judgements in the context of a video game. Subjects were presented with sets of trials on each of which they could perform a particular action and observe whether the action produced a particular outcome in a situation in which there was an alternative potential cause of the outcome. In Experiment 1 it was found that prior observation of the relationship between the alternative cause and the outcome did indeed block or reduce learning about the subsequent action-outcome relationship. However, exposure to the relationship between the alternative cause and the outcome after observing the association between the action and the outcome also reduced judgements of the action–outcome contingency (backward blocking), a finding at variance with conditioning theory. In Experiment 2 it was found that, just as is the case with forward blocking, the degree of backward blocking depended on how good a predictor of the outcome the alternative cause was. Finally, in Experiment 3 it was shown that the backward blocking effect was not the result of greater forgetting about the action–outcome relationship in the experimental than in the control condition. These results cast doubt upon the applicability of contemporary theories of conditioning to human contingency judgement.
Associability of a Previously Conditioned Stimulus as a Function of Qualitative Changes in the US
Authors: Kasprow Wesley J. , Schachtman Todd R. , Miller Ralph R.
Published: October 2014

Hall and Pearce (1979) reported retarded manifestation of conditioned responding to repeated CS–strong shock pairings as a result of prior CS–weak shock pairings. These authors suggested that a latent inhibition (LI)-like process reduced the associability of the CS during weak shock conditioning despite excitatory associations between CS and weak shock being formed. The present experiments examined the possibility that the negative transfer from CS–weak shock conditioning in Stage 1 to CS–strong shock conditioning in Stage 2 observed by Hall and Pearce was due at least in part to the similarity between weak and strong shock rather than, or in addition to, a general loss of CS associability. Specifically, the transfer of decreased associability to conditioning with a dissimilar US was investigated. Consistent with Hall and Pearce, who gave multiple training trials in Stage 2, Experiment 1 found the development of conditioned responding owing to a single CS–strong shock pairing in Stage 2 to be retarded by prior CS–weak shock pairings and compared this effect to conventional LI. In Experiment 2, partial attenuation of the negative transfer following CS–weak shock was obtained by substituting ice water immersion for strong shock, that is, by making the strong US qualitatively dissimilar from the weak US. In contrast, conventional LI resulting from preconditioning CS-only exposures was equivalent for strong shock in Experiment 1 and ice water immersion in Experiment 2. A possible mechanism for the sensitivity to qualitative US changes of the observed negative transfer is discussed.
Maternal Discrimination and the Development of Sex Differences in Exploratory Behaviour in Infant Spiny Mice (Acomys Cahirinus)
Authors: Birke Lynda I.A. , Sadler Dawn
Published: October 2014

The present paper reports sex differences in exploratory behaviour by infant Spiny Mice, Acomys cahirinus, that may, in part, be related to differences in maternal behaviour towards pups; like some other rodents, mother Acomys differentiate behaviourally between male and female pups. In Experiment 1 infant Acomys were allowed to explore a novel arena. This experiment showed that even by Day 3 (the day of birth=Day 1) female Acomys explored a novel environment more than males; they entered the arena sooner than males and spent more time in contact with a novel object. Experiment 2 showed that infant females were more active than males when observed in the home cage in the presence of their parents and made more approaches to the mother. Mothers, on the other hand, directed more licking behaviour towards males. Experiment 3 focused on the exploratory behaviour of individual pups in the presence of the mother. Given access to a large, complex arena, female pups explored more than males. The results also showed that mothers direct more of their social interactions towards sons than daughters, particularly when pups are about a week old. Some mothers appear to “direct” the movement of their offspring, by blocking their forward movement; this was done more often to male than to female pups. The data suggest that the previously observed changes in exploratory behaviour at this time, and the emergence of sex differences in exploration, may in part depend upon the mothers’ reactions to pups by sex.
Long-Term Memory of Pigeons for Stimulus-Outcome Associations Involving Multiple Stimuli, each Seen in a Single Brief Trial
Authors: Macphail Euan M. , Reilly Steve , Good Mark
Published: October 2014

Experiment 1 explored performance of pigeons in two versions of a shortterm recognition memory procedure. In one version responding to entirely novel slides was rewarded, and responding to familiar slides (slides seen once, for 10 sec) was not rewarded; in the other version, responding to familiar slides was rewarded. Performance was initially below chance in both versions of the procedure. This result indicated that in this procedure associations were formed between the slides and the outcome (reward or non-reward) that followed their presentation. The result also suggested that the true capacity of pigeon recognition memory cannot be assessed using these procedures, as performance is inevitably disrupted by the bird's associative memory. The tendency of pigeons to form one-trial associations was exploited in Experiment 2. Phase 1 consisted of 16 two-session cycles: in Session 1 of each cycle, birds were shown 20 novel slides and were rewarded for responding to 10 of those slides; in Session 2, the same slides were shown again, with the same reinforcement contingencies. The birds showed significant overnight retention of the one-trial associations formed in Session 1 of each cycle. Phase 2 showed significant retention over periods of more than 20 days of associations involving 320 slides seen twice only. Phase 3 re-exposed for nine daily sessions one of the sets of 20 slides used in Phases 1 and 2; a high level of discrimination emerged rapidly and 4 (of 8) birds showed, by the end of training, no overlap in response rates to positive and negative slides. Comparative implications of the results are discussed.
Dimensional Shift and the Transfer of Attention
Authors: Whitney Lynne , White K. Geoffrey
Published: October 2014

Dimensional shift was examined by generating gradients of two-dimensional stimulus generalization for intradimensional and extradimensional transfer of attention. Undergraduates discriminated between lines varying in length and orientation. Stimulus values were relevant on one dimension and irrelevant on another. For intradimensional transfer, the Phase 2 transfer task involved discriminating between new values on the dimension that was relevant in Phase 1. For extradimensional transfer, Phase 2 involved discriminating between new values on the dimension that was irrelevant in Phase 1. Extradimensional transfer was learned in twice the number of trials that were required for intradimensional transfer. In Experiment 1, generalization gradients obtained at different stages of Phase 2 training showed that control by the relevant dimension was maintained throughout the intradimensional transfer. In the extradimensional transfer, however, control by the previously relevant dimension was gradually lost before control by the new relevant dimension was acquired. Experiment 2 showed that the advantage of intradimensional over extradimensional transfer could not be attributed to cue-specific stimulus generalization. Experiment 3 showed that in extradimensional transfer the irrelevant dimension in Phase 1 retarded acquisition of control by the new relevant dimension in Phase 2. Experiment 4 showed that the irrelevant dimension masked control by the relevant dimension in the generalization test, but verified the conclusion from Experiment 3 that learned irrelevance contributed to the intradimensional-extra-dimensional transfer difference.
Effects of Exposure to a To-Be-Shocked Environment upon the Rat's Freezing Response: Evidence for Facilitation, Latent Inhibition, and Perceptual Learning
Authors: Kiernan M. J. , Westbrook R. F.
Published: October 2014

Three experiments used the freezing response of rats to examine the effects of pre-exposure to an environment upon (1) its associability with shock and (2) its discriminability from a second environment. Experiments 1 and 2 demonstrated that freezing was proportional to the interval between exposure to the environment at time T1 and the occurrence of shock at T2. This function was shifted by pre-exposure to the to-be-shocked environment, with brief pre-exposures increasing (facilitation) and extended pre-exposures decreasing (latent inhibition) the impact of a given T1-T2 interval on freezing. Experiment 3 provided evidence that the facilitatory and latent inhibitory effects resulting from brief and extended exposures to the to-be-shocked environment were accompanied by an increase in discriminability. The results were taken to have supported the claim that pre-exposure changes associability as well as discriminability (Hall & Honey, 1989) and were discussed in terms of the model for perceptual learning proposed by McLaren, Kaye, and Mackintosh (1990).
Pre-Extinction of Sensory Preconditioned Electrodermal Activity
Authors: Vansteenwegen Debora , Crombez Geert , Baeyens Frank , Hermans Dirk , Eelen Paul
Published: October 2014

In the present study, sensory preconditioning of human electrodermal activity was demonstrated. In the first phase of the experiment, two pairs of neutral pictures of human faces were presented (A/B and C/D) sequentially. In the second phase, one picture of one pair was immediately followed by an electrocutaneous stimulus (B+), and one picture of the other pair was not (D−). In the third phase the other picture of each pair (A and C) was tested. The effect of A and C alone presentations (pre-extinction) between the first and the second phase was investigated. When only those participants that showed reliable B+/D− differentiation were considered, the extinction group did not show stronger conditioned electrodermal activity to A than to C, whereas the control group did. These findings suggest that sensory preconditioning of anticipatory/preparatory responding only occurs when the pre-conditioned stimulus (A) actually predicts the conditioned stimulus (B).
Choice Biases in Delayed Matching-to-Sample Duration with Pigeons: Manipulations of ITI and Delayillumination
Authors: Kelly Ronald , Spetch Marcia L.
Published: October 2014

Two experiments investigated the effects of similarity between intertrial interval (ITI) and delay illumation on the choose-short effect. Different groups of pigeons learned to match “short” (2 s) and “long” (6 or 8 s) food samples to green and red test stimuli in a matchingto-sample procedure with a 5-s training delay. Subsequent 10- and 20-s delay tests revealed choose-short effects if the ITI and delay were both illuminated (i.e., group ON-ON), if the ITI and delay were both dark (i.e., group OFF-OFF), and if the ITI was illuminated and the delay was dark (i.e., group ON-OFF). In addition, either a choose-short effect or a chooselong effect was observed if the ITI was dark and the delay was illuminated (i.e., group OFF-ON). Results are incompatible with the confusion/instructional failure view of the choose-short effect.
Effects of Reinforcement Magnitude and Ratio Values on Behaviour Maintained by a Cyclic Ratio Schedule of Reinforcement
Authors: Leslie Julian C. , Boyle Christine , Shaw David
Published: October 2014

In Experiments 1 and 2, lever pressing by rats was reinforced on a cyclic ratio schedule of food reinforcement, comprising a repeated sequence of fixed-ratio component schedules. Reinforcement magnitude was varied, on occasional sessions in Experiment 1 and across blocks of sessions in Experiment 2, from one to two or three 45-mg food pellets. In the one-pellet condition, post-reinforcement pauses increased with component schedule value. At higher magnitudes, post-reinforcement pauses increased, and overall response rates declined. Response rate on component schedules was a decreasing linear function of the obtained rate of reinforcement in all conditions. Plotted against component schedule value, response rate increased exponentially to an asymptote that decreased when reinforcement magnitude increased. These findings are consistent with regulatory accounts of food reinforced behaviour. In Experiment 3, rats were trained under a cyclic ratio schedule comprising fixed-ratio components including higher values, and some inverted U-shaped response functions were obtained. Those rats that did not showthis relationship were trained on cyclic ratios with even higher values, and all showed inverted U-shaped response functions. This suggests that behaviour on cyclic ratio schedules can reflect activating of reinforcement as well as the satiating effects seen in Experiments 1 and 2.
The Role of Nonreinforcement in the Learning of Honeybees
Authors: Couvillon P.A. , Ablan C.D. , Ferreira T.P. , Bitterman M.E.
Published: October 2014

Two series of experiments with honeybees were designed to test the assumption that inhibition is generated by nonreinforcement as a function of the excitatory value of the context. In the first series (Experiments 1–3), summation tests with B were made after A+/C-/AB- as compared to A+/C-/CB- training, with precautions taken to minimize the possibility of a masking effect of excitatory within-compound conditioning on AB trials; responding to B did not vary with training procedure. In the second series (Experiments 4–5), retardation tests rather than summation tests were used, in the belief that they might be more sensitive; after A+/AB-/CD- training, acquisition in a B+/D- problem was found to be no less rapid than in a D+/B- problem. A third series of experiments (Experiments 6–9) was designed to test the more general assumption that the effectiveness of nonreinforcement increases with the excitatory value of the context; response to B was found to be no different after A+/B+/C- training followed by A+/AB- training than after A+/B+/C- training followed by A+/CB- training. The results are compatible with the view that the role of nonreinforcement in honeybees is not to generate inhibition, but only to reduce excitation in a manner independent of the excitatory value of the context.
Evidence for Inhibitory Associations between the Unique Elements of two Compound Flavours
Authors: Dwyer D.M. , Bennett C.H. , MacKintosh N.J.
Published: October 2014

In each of two experiments, rats were pre-exposed to two flavoured solutions, saline-lemon and sucrose-lemon. For group ALT, trials with one solution alternated with trials with the other. Group BLK received all trials with one solution in a block, before any trials with the other. An associative theory suggests that the alternating, but not the blocked, schedule would establish an inhibitory association between sucrose and saline. To provide a retardation test of this inhibition, some animals in each group were then given a single pairing of saline and sucrose, experienced sodium depletion, and were finally tested for their consumption of sucrose. Sodium depletion increased consumption of sucrose more in group BLK than in group ALT. In groups given no saline-sucrose pairing, sodium depletion had only a small effect on sucrose consumption, which was the same in both groups. After multiple pairings of saline and sucrose, sodium depletion had an equally large effect on sucrose consumption in both ALT and BLK groups. These results imply that alternating pre-exposure to two compound solutions does establish an inhibitory association between their unique elements, and thus provide support for an associative theory of perceptual learning.
Interference with Judgements of Control and Learning as a Result of Prior Exposure to Controllable and Uncontrollable Feedback during Concept-Learning Tasks
Authors: Reed Phil , Frasquillo Frank , Colkin Clare , Liemann Victoria , Colbert Susie
Published: October 2014

Two experiments examined whether exposure to an uncontrollable relationship between an action and its outcome during a nonaversive pretreatment phase would attenuate subsequent ratings of control given to actions emitted by subjects. In Experiment 1, such an interference effect was demonstrated relative to a group that received prior training with a controllable action-outcome relationship, and relative to a group not exposed to any prior relationship. In Experiment 2, these effects were replicated, and interference was also found to occur when learning a maze task. Thus, the effects of helplessness were shown to be quite general, to be produced by a nonaversive induction procedure, and to occur most readily when the current contingency between action and outcome was weakest.
Mediated Conditioning and Retrospective Revaluation with LiCl then Flavour Pairings
Authors: Dwyer D.M.
Published: October 2014

It is becoming accepted that the associative strength of a cue can change in its absence, despite this being difficult to explain using existing theories of Pavlovian conditioning. To investigate the influence of timing on learning about the representation of an absent cue, lithium chloride (LiCl) or a flavour previously paired with LiCl was presented in a distinctive context that had previously been paired with a neutral target flavour. The former treatment produced an aversion to the target flavour whether the LiCl was presented 10 min before, or immediately after, exposure to the context. However, presenting the flavour associate of LiCl created an aversion to the target flavour only if it had been presented 10 min after LiCl during initial training. This pattern of results cannot be explained in the terms of a simple timing account, and it is proposed that an explanation will require different associative rules operating in simultaneous and successive training schedules.
Multiple mechanisms determine the order of APC/C substrate degradation in mitosis
Authors: Lu Dan , Hsiao Jennifer Y. , Davey Norman E. , Van Voorhis Vanessa A. , Foster Scott A. , Tang Chao , Morgan David O.
Published: October 2014

The ubiquitin protein ligase anaphase-promoting complex or cyclosome (APC/C) controls mitosis by promoting ordered degradation of securin, cyclins, and other proteins. The mechanisms underlying the timing of APC/C substrate degradation are poorly understood. We explored these mechanisms using quantitative fluorescence microscopy of GFP-tagged APC/CCdc20 substrates in living budding yeast cells. Degradation of the S cyclin, Clb5, begins early in mitosis, followed 6 min later by the degradation of securin and Dbf4. Anaphase begins when less than half of securin is degraded. The spindle assembly checkpoint delays the onset of Clb5 degradation but does not influence securin degradation. Early Clb5 degradation depends on its interaction with the Cdk1–Cks1 complex and the presence of a Cdc20-binding “ABBA motif” in its N-terminal region. The degradation of securin and Dbf4 is delayed by Cdk1-dependent phosphorylation near their Cdc20-binding sites. Thus, a remarkably diverse array of mechanisms generates robust ordering of APC/CCdc20 substrate destruction.
How mitosis keeps itself in order
Authors: Short Ben
Published: October 2014

Researchers describe how multiple mechanisms ensure that mitotic proteins are degraded in the correct sequence.
The AP-1 transcription factor Fra1 inhibits follicular B cell differentiation into plasma cells
Authors: Grötsch Bettina , Brachs Sebastian , Lang Christiane , Luther Julia , Derer Anja , Schlötzer-Schrehardt Ursula , Bozec Aline , Fillatreau Simon , Berberich Ingolf , Hobeika Elias , Reth Michael , Wagner Erwin F. , Schett Georg , Mielenz Dirk , David Jean-Pierre
Published: October 2014

The cornerstone of humoral immunity is the differentiation of B cells into antibody-secreting plasma cells. This process is tightly controlled by a regulatory gene network centered on the transcriptional repressor B lymphocyte–induced maturation protein 1 (Blimp1). Proliferation of activated B cells is required to foster Blimp1 expression but needs to be terminated to avoid overshooting immune reactions. Activator protein 1 (AP-1) transcription factors become quickly up-regulated upon B cell activation. We demonstrate that Fra1, a Fos member of AP-1, enhances activation-induced cell death upon induction in activated B cells. Moreover, mice with B cell–specific deletion of Fra1 show enhanced plasma cell differentiation and exacerbated antibody responses. In contrast, transgenic overexpression of Fra1 blocks plasma cell differentiation and immunoglobulin production, which cannot be rescued by Bcl2. On the molecular level, Fra1 represses Blimp1 expression and interferes with binding of the activating AP-1 member c-Fos to the Blimp1 promoter. Conversely, overexpression of c-Fos in Fra1 transgenic B cells releases Blimp1 repression. As Fra1 lacks transcriptional transactivation domains, we propose that Fra1 inhibits Blimp1 expression and negatively controls plasma cell differentiation through binding to the Blimp1 promoter. In summary, we demonstrate that Fra1 negatively controls plasma cell differentiation by repressing Blimp1 expression.
Thermal effects on the switching kinetics of silver/manganite memristive
systems
Authors: Stoliar P , Sánchez M J , Patterson G A , Fierens P I
Published: October 2014

We investigate the switching kinetics of oxygen vacancy (Ov) diffusion in
La(5/8-y)Pr(y)Ca(3/8)MnO(3)-Ag (LPCMO–Ag) memristive interfaces by performing experiments
on the temperature dependence of the high resistance state under thermal cycling. Experimental
results are well reproduced by numerical simulations based on thermally activated Ov diffusion
processes and fundamental assumptions relying on a recent model proposed to explain bipolar
resistive switching in manganite-based cells. The confident values obtained for activation
energies and the diffusion coefficient associated to Ov dynamics constitute a validation test
for both model predictions and Ov diffusion mechanisms in memristive interfaces.
Classification of subdivision rules for geometric groups of low dimension
Authors: Rushton Brian
Published: October 2014

Subdivision rules create sequences of nested cell structures on CW-complexes, and they frequently arise from groups. In this paper, we develop several tools for classifying subdivision rules. We give a criterion for a subdivision rule to represent a Gromov hyperbolic space, and show that a subdivision rule for a hyperbolic group determines the Gromov boundary. We give a criterion for a subdivision rule to represent a Euclidean space of dimension less than 4. We also show that Nil and Sol geometries cannot be modeled by subdivision rules. We use these tools and previous theorems to classify the geometry of subdivision rules for low-dimensional geometric groups by the combinatorial properties of their subdivision rules.
Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions
Authors: Schmidt Ralf , Waschina Silvio , Boettger-Schmidt Daniela , Kost Christian , Kaleta Christoph
Published: October 2014

Motivation : Genome-scale metabolic network reconstructions have been established as a powerful tool for the prediction of cellular phenotypes and metabolic capabilities of organisms. In recent years, the number of network reconstructions has been constantly increasing, mostly because of the availability of novel (semi-)automated procedures, which enabled the reconstruction of metabolic models based on individual genomes and their annotation. The resulting models are widely used in numerous applications. However, the accuracy and predictive power of network reconstructions are commonly limited by inherent inconsistencies and gaps.

Results : Here we present a novel method to validate metabolic network reconstructions based on the concept of autocatalytic sets. Autocatalytic sets correspond to collections of metabolites that, besides enzymes and a growth medium, are required to produce all biomass components in a metabolic model. These autocatalytic sets are well-conserved across all domains of life, and their identification in specific genome-scale reconstructions allows us to draw conclusions about potential inconsistencies in these models. The method is capable of detecting inconsistencies, which are neglected by other gap-finding methods. We tested our method on the Model SEED, which is the largest repository for automatically generated genome-scale network reconstructions. In this way, we were able to identify a significant number of missing pathways in several of these reconstructions. Hence, the method we report represents a powerful tool to identify inconsistencies in large-scale metabolic networks.

Availability and implementation : The method is available as source code on http://users.minet.uni-jena.de/∼m3kach/ASBIG/ASBIG.zip .

Contact : christoph.kaleta@uni-jena.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data
Authors: Bastien Philippe , Bertrand Frédéric , Meyer Nicolas , Maumy-Bertrand Myriam
Published: October 2014

Motivation : A vast literature from the past decade is devoted to relating gene profiles and subject survival or time to cancer recurrence. Biomarker discovery from high-dimensional data, such as transcriptomic or single nucleotide polymorphism profiles, is a major challenge in the search for more precise diagnoses. The proportional hazard regression model suggested by Cox (1972), to study the relationship between the time to event and a set of covariates in the presence of censoring is the most commonly used model for the analysis of survival data. However, like multivariate regression, it supposes that more observations than variables, complete data, and not strongly correlated variables are available. In practice, when dealing with high-dimensional data, these constraints are crippling. Collinearity gives rise to issues of over-fitting and model misidentification. Variable selection can improve the estimation accuracy by effectively identifying the subset of relevant predictors and enhance the model interpretability with parsimonious representation. To deal with both collinearity and variable selection issues, many methods based on least absolute shrinkage and selection operator penalized Cox proportional hazards have been proposed since the reference paper of Tibshirani. Regularization could also be performed using dimension reduction as is the case with partial least squares (PLS) regression. We propose two original algorithms named sPLSDR and its non-linear kernel counterpart DKsPLSDR, by using sparse PLS regression (sPLS) based on deviance residuals. We compared their predicting performance with state-of-the-art algorithms on both simulated and real reference benchmark datasets.

Results : sPLSDR and DKsPLSDR compare favorably with other methods in their computational time, prediction and selectivity, as indicated by results based on benchmark datasets. Moreover, in the framework of PLS regression, they feature other useful tools, including biplots representation, or the ability to deal with missing data. Therefore, we view them as a useful addition to the toolbox of estimation and prediction methods for the widely used Cox’s model in the high-dimensional and low-sample size settings.

Availability and implementation : The R-package plsRcox is available on the CRAN and is maintained by Frédéric Bertrand. http://cran.r-project.org/web/packages/plsRcox/index.html .

Contact : pbastien@rd.loreal.com or fbertran@math.unistra.fr .

Supplementary information : Supplementary data are available at Bioinformatics online.
Chimera: a Bioconductor package for secondary analysis of fusion products
Authors: Beccuti Marco , Carrara Matteo , Cordero Francesca , Lazzarato Fulvio , Donatelli Susanna , Nadalin Francesca , Policriti Alberto , Calogero Raffaele A.
Published: October 2014

Summary:  Chimera is a Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools; current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion and STAR. The core of Chimera is a fusion data structure that can store fusion events detected with any of the aforementioned tools. Fusions are then easily manipulated with standard R functions or through the set of functionalities specifically developed in Chimera with the aim of supporting the user in managing fusions and discriminating false-positive results.

Availability and implementation:  Chimera is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at bioconductor.org.

Contact:  raffaele.calogero@unito.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
Partial differential equation models in macroeconomics
Authors: Achdou Yves , Buera Francisco J. , Lasry Jean-Michel , Lions Pierre-Louis , Moll Benjamin
Published: October 2014

The purpose of this article is to get mathematicians interested in studying a number of partial differential equations (PDEs) that naturally arise in macroeconomics. These PDEs come from models designed to study some of the most important questions in economics. At the same time, they are highly interesting for mathematicians because their structure is often quite difficult. We present a number of examples of such PDEs, discuss what is known about their properties, and list some open questions for future research.
Thermococcus eurythermalis sp. nov., a conditional piezophilic, hyperthermophilic archaeon with a wide temperature range for growth, isolated from an oil-immersed chimney in the Guaymas Basin
Authors: Zhao Weishu , Zeng Xianping , Xiao Xiang
Published: October 2014

A conditional piezophilic, hyperthermophilic archaeon showing growth over a wide range of temperature, pH and pressure was isolated from an oil-immersed hydrothermal chimney at a depth of 2006.9 m in the Guaymas Basin. Enrichment and isolation of strain A501T were performed at 80 °C at 0.1 MPa. Cells of isolate A501T were irregular motile cocci with a polar tuft of flagella and generally 0.6–2.6 µm in diameter. Growth was detected over the range 50–100 °C (optimal growth at 85 °C) at atmospheric pressure and was observed at 102 °C at a pressure of 10 MPa. At 85 °C, growth was observed at a pressure of 0.1–70 MPa (optimum pressure 0.1 MPa–30 MPa), while at 95 °C, the pressure allowing growth ranged from 0.1 MPa to 50 MPa (optimum pressure 10 MPa). Cells of strain A501T grew at pH 4–9 (optimum pH 7.0) and a NaCl concentration of 1.0–5.0 % (w/v) (optimum concentration 2.5 % NaCl). This isolate was an anaerobic chemo-organoheterotroph and was able to utilize yeast extract, peptone, tryptone and starch as the single carbon source for growth. Elemental sulfur and cysteine stimulated growth; however, these molecules were not necessary. The DNA G+C content of the complete genome was 53.47 mol%. The results of 16S rRNA gene sequence analysis indicated that strain A501T belongs to the genus

Thermococcus

. There was no significant similarity between strain A501T and the phylogenetically related species of the genus

Thermococcus

based on complete genome sequence alignments and calculation of the average nucleotide identity and the tetranucleotide signature frequency correlation coefficient. These results indicate that strain A501T represents a novel species, Thermococcus eurythermalis sp. nov. The type strain is A501T ( = CGMCC 7834T = JCM 30233T).
Cross-protective effect of a novel multi-antigen-chimeric vaccine against Streptococcus and Staphylococcus aureus infection in mice
Authors: Yu Liquan , Fan Ziyao , Ma Jinzhu , Tong Chunyu , Song Baifen , Zhu Zhanbo , Cui Yudong
Published: October 2014

Staphylococcal and streptococcal species are the most common pathogens that cause bovine mastitis. Induction of a broad-spectrum protective immunity against staphylococci and streptococci by combining multiple antigens into a single vaccine is highlighted. To develop a universal vaccine candidate, a GapC1-tIsdB-TRAP (GIT) construct was generated. The GIT contained the truncated GapC from Streptococcus dysgalactiae, and truncated IsdB and full-length TRAP from Staphylococcus aureus. The humoral and cellular immune responses elicited by GIT were evaluated in mice. Antibody levels against GIT displayed a consistent tendency with antibody levels against GapC, IsdB and TRAP. The level of IFN-γ was higher in the GIT group than in the IsdB group (P<0.05), and the level of IL-4 was higher in the GIT group than in the GapC or TRAP groups (P<0.05). The GIT group showed an improved protection against Streptococcus in comparison with GapC group. A significant difference in S. aureus challenge test was detected between the GIT group and the IsdB or TRAP groups (P<0.05) in per cent survival of mice, and a synergistic immunoprotection against S. aureus or S. dysgalactiae was produced in the GIT group. These results suggested that the GIT would be a promising common vaccine candidate against S. aureus and Streptococcus.
Selective corticostriatal plasticity during acquisition of an auditory discrimination task
Authors: Xiong Qiaojie , Znamenskiy Petr , Zador Anthony M
Published: October 2014

Perceptual decisions are based on the activity of sensory cortical neurons, but how organisms learn to transform this activity into appropriate actions remains unknown. Projections from the auditory cortex to the auditory striatum carry information that drives decisions in an auditory frequency discrimination task1. To assess the role of these projections in learning, we developed a Channelrhodopsin-2-based assay to selectively probe for synaptic plasticity associated with corticostriatal neurons representing different frequencies. Here we report that learning this auditory discrimination preferentially potentiates corticostriatal synapses from neurons representing either high or low frequencies, depending on reward contingencies. We observed frequency-dependent corticostriatal potentiationin vivoover the course of training, andin vitroin striatal brain slices. Our findings suggest a model in which selective potentiation of inputs representing different components of a sensory stimulus enables the learned transformation of sensory input into actions.
Crystal structure of 2-(4-chlorophenyl)-2-oxoethyl 3-bromobenzoate
Authors: Khan Imtiaz , Ibrar Aliya , Hameed Shahid , White Jonathan M. , Simpson Jim
Published: October 2014

2-(4-Chlorophenyl)-2-oxoethyl 3-bromobenzoate, C15H10BrClO3, was synthesized in a single-step reaction by condensation of 3-bromobenzoic acid with 2-bromo-1-(4-chlorophenyl)ethanone in dimethylformamide in the presence of triethylamine as a catalyst. The structure consists of an aryl ketone moiety linked to an aryl ester unit by a methylene group. Both units are reasonably planar (r.m.s. deviations of 0.119 and 0.010 Å for the aryl ketone and aryl ester units, respectively) and are almost orthogonal, with an angle of 88.60 (3)° between them. In the crystal, molecules form five separate sets of inversion dimers. Three of these are generated by two C—H...O interactions and a C—H...Br contact, and form chains alongcand along theabcell diagonal. In addition, two inversion-related π–π stacking interactions between like aryl rings again form chains of molecules but in this instance along thebcdiagonal. These contacts generate infinite layers of molecules parallel to (011) and stack the molecules along thea-axis direction.
Crystal structure of (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]hydrazinecarbothioamide
Authors: Vimala G. , Govindaraj J. , Haribabu J. , Karvembu R. , SubbiahPandi A.
Published: October 2014

In the title compound, C12H11N3O2S, the dihedral angle between the 4H-chromen-4-one ring system and the –CH=N—NH—CS—NH– unit is 6.22 (1)°. In the crystal, inversion dimers linked by pairs of N—H...O hydrogen bonds generateR22(14) loops. The dimers are reinforced by a pair of C—H...O interactions, which generateR22(10) loops.
Investigation of short-range structural order in Zr69.5Cu12Ni11Al7.5and Zr41.5Ti41.5Ni17glasses, using X-ray absorption spectroscopy andab initiomolecular dynamics simulations
Authors: Lahiri Debdutta , Sharma Surinder M. , Verma Ashok K. , Vishwanadh B. , Dey G. K. , Schumacher Gerhard , Scherb Tobias , Riesemeier Heinrich , Reinholz Uwe , Radtke Martin , Banerjee S.
Published: October 2014

Short-range order has been investigated in Zr69.5Cu12Ni11Al7.5and Zr41.5Ti41.5Ni17metallic glasses using X-ray absorption spectroscopy andab initiomolecular dynamics simulations. While both of these alloys are good glass formers, there is a difference in their glass-forming abilities (Zr41.5Ti41.5Ni17> Zr69.5Cu12Ni11Al7.5). This difference is explained by inciting the relative importance of strong chemical order, icosahedral content, cluster symmetry and configuration diversity.