bluuebunny/crossref_metadata_2025_split huggingface dataset:
A case-control study of post-operative endophthalmitis diagnosed at a Spanish hospital over a 13-year-period
Authors: ASENCIO M. A. , HUERTAS M. , CARRANZA R. , TENIAS J. M. , CELIS J. , GONZALEZ-DEL VALLE F. 
Published: March 2014

SUMMARYA retrospective case-control study of patients who had undergone cataract extraction at a Spanish hospital over a 13-year period was conducted to identify the risk factors for developing post-operative endophthalmitis (POE). During the study period, the type of antibiotic prophylaxis was changed from subconjunctival gentamicin to the addition of both vancomycin and gentamicin to the irrigating solution. The overall incidence of POE was 0·19% (35 cases/18 287 operations). For the period prior to the change in antibiotic prophylaxis, the incidence rate of POE was 3·4 cases/1000 operations while in the latter period the incidence rate decreased to 0·34 cases/1000 operations. All patients who presented a virulent microorganism had a final visual acuity worse than 20/200. The only significant risk factor identified was the type of prophylaxis used (odds ratio 1·97, 95% confidence interval 0·94–4·14, P = 0·07). There were no significant differences between cases and controls although choice of surgeon approached significance.
Pituitary gland volume in at-risk mental state for psychosis: a longitudinal MRI analysis
Authors: Walter Anna , Studerus Erich , Smieskova Renata , Tamagni Corinne , Rapp Charlotte , Borgwardt Stefan J. , Riecher-Rössler Anita 
Published: March 2014

IntroductionPituitary enlargement has been reported in individuals with schizophrenic psychosis or an at-risk mental state for psychosis (ARMS). In a previous study, our group could show pituitary volume increase in first episode and ARMS patients with later transition to psychosis (ARMS-T). However, there are no longitudinal studies on this issue so far. We therefore examined longitudinally whether transition to psychosis would be accompanied by a further increase of pituitary volume in antipsychotic-naïve ARMS patients.MethodsMagnetic resonance imaging (MRI) data were acquired from 23 antipsychotic-naïve individuals with an ARMS. Ten subjects developed psychosis (ARMS-T) and 13 did not (ARMS-NT). ARMS-T were re-scanned after the onset of psychosis, and ARMS-NT were re-scanned at the end of the study period.ResultsThere was no significant difference of the pituitary volume between ARMS-T and ARMS-NT in our sample, and there were no significant pituitary volume changes over time.DiscussionLongitudinally, we could not detect any further volumetric changes in the pituitary volume with transition to psychosis.ConclusionsThis, together with the result of our previous study, could indicate that the perceived level of stress in ARMS patients is constantly high from very early onward.
Who decides the rules for network use? A ‘common pool’ analysis of gas network regulation
Authors: HALLACK MICHELLE , VAZQUEZ MIGUEL 
Published: March 2014

Abstract:Gas sector liberalization is based on opening networks to different players, so they become common pool resources. Different players using the same resources can give rise to “commons’ dilemmas”. To avoid them, rules must be established to constrain players’ use of the network. We build on the concept of common's pool resources to analyze the logic for and consequences of different institutional settings governing the use of gas pipelines. We show that rules based on regulation imply ex ante decisions that preclude players to choose the preferred output. This limitation may be removed by rules designed by market players. We also show that the mechanism to define the rules is based on the definition of network use property rights. The practical implications of our approach are stressed by comparing the US mechanism (negotiated rules) and the EU mechanism (regulated rules).
Integrated Training for Aphasia: An Application of Part–Whole Learning to Treat Lexical Retrieval, Sentence Production, and Discourse-Level Communications in Three Cases of Nonfluent Aphasia
Authors: Milman Lisa , Vega-Mendoza Mariana , Clendenen Deanna 
Published: March 2014

Purpose
The purpose of this study was to evaluate integrated training for aphasia (ITA), a multicomponent language-production treatment based on part–whole learning that systematically trains lexical retrieval, sentence production, and discourse-level communications. Specific research objectives were to evaluate acquisition of target structures, statistical parameters associated with learning variables, treatment generalization, and the efficacy of individual treatment components.

Method
ITA was administered to 3 individuals with nonfluent aphasia following a multiple-baseline, across-behaviors design. Effect size and correlational coefficients were computed to assess acquisition, generalization, and maintenance of target structures. Standardized tests and a treatment efficacy questionnaire were also completed.

Results
A significant treatment effect was found in 2 of the 3 participants. In addition, as is seen in normal skill acquisition, practice time and error rate were significantly correlated. All participants demonstrated evidence of generalization on standardized language measures. Only 1 participant improved, however, on the communication measures. Results of the treatment component analysis revealed significant differences in the perceived efficacy of individual therapy tasks.

Conclusions
Findings add to the evidence supporting multicomponent aphasia treatments, provide preliminary support for ITA and the application of a part–whole learning approach, and suggest that specific treatment components may contribute differentially to outcomes and generalization effects.

Supplemental Material

https://doi.org/10.23641/asha.6170210
Electrostatics of proteins in dielectric solvent continua. II. Hamiltonian reaction field dynamics
Authors: Bauer Sebastian , Tavan Paul , Mathias Gerald 
Published: March 2014

In Paper I of this work [S. Bauer, G. Mathias, and P. Tavan, J. Chem. Phys. 140, 104102 (2014)] we have presented a reaction field (RF) method, which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of polarizable molecular mechanics (MM) force fields. Building upon these results, here we suggest a method for linearly scaling Hamiltonian RF/MM molecular dynamics (MD) simulations, which we call “Hamiltonian dielectric solvent” (HADES). First, we derive analytical expressions for the RF forces acting on the solute atoms. These forces properly account for all those conditions, which have to be self-consistently fulfilled by RF quantities introduced in Paper I. Next we provide details on the implementation, i.e., we show how our RF approach is combined with a fast multipole method and how the self-consistency iterations are accelerated by the use of the so-called direct inversion in the iterative subspace. Finally we demonstrate that the method and its implementation enable Hamiltonian, i.e., energy and momentum conserving HADES-MD, and compare in a sample application on Ac-Ala-NHMe the HADES-MD free energy landscape at 300 K with that obtained in Paper I by scanning of configurations and with one obtained from an explicit solvent simulation.
Role of substrate unbinding in Michaelis–Menten enzymatic reactions
Authors: Reuveni Shlomi , Urbakh Michael , Klafter Joseph 
Published: March 2014

Significance
Enzymes are biological catalysts vital to all life processes, and the quest to determine their inner workings continues to attract and fascinate scientists over a broad range of disciplines. With the advent of high-resolution methods of single-molecule spectroscopy, it is now possible to directly observe and manipulate the behavior of individual enzymes in the course of a chemical reaction. Chemistry at the single-molecule level is, however, inherently stochastic and, at times, extremely unintuitive. In this paper, we explain why, and under what circumstances, an increase in the rate at which an enzyme unproductively departs from a bound substrate will—unexpectedly—lead to an acceleration in the rate of product formation. The far-reaching implications of this effect are discussed.
Out-of-body–induced hippocampal amnesia
Authors: Bergouignan Loretxu , Nyberg Lars , Ehrsson H. Henrik 
Published: March 2014

Significance
Transformation of experiences into long-term memory is a remarkable capability. However, some experiences are so extreme that they are not translated into coherent or lasting memories. Clinical reports suggest that one potential mechanism for memory disturbance could be “dissociative experiences,” in which events are experienced in a distance from the body (out-of-body). Here, we experimentally induced an illusory out-of-body experience on healthy participants while they were experiencing life events. Remarkably, participants had an episodic impairment for events encoded out-of-body. Out-of-body encoding specifically impacted the activation of the left posterior hippocampus during retrieval. These findings establish that hippocampus-based episodic memory depends on the perception of the world from within one's own body, and that a dissociative experience during encoding blocks the memory-forming mechanism.
Binding of the histone chaperone ASF1 to the CBP bromodomain promotes histone acetylation
Authors: Das Chandrima , Roy Siddhartha , Namjoshi Sarita , Malarkey Christopher S. , Jones David N. M. , Kutateladze Tatiana G. , Churchill Mair E. A. , Tyler Jessica K. 
Published: March 2014

Significance
The Creb-binding protein (CBP) transcriptional coactivator contains a histone acetyl transferase domain and a bromodomain. Bromodomains bind to acetylated lysines, and their function as previously understood was limited to mediating recruitment to chromatin via binding to acetylated proteins. Here we show that the acetyl lysine-binding activity of the CBP bromodomain has unexpected roles in CBP-mediated acetylation of nonchromatin bound histones, and we show that the interaction between a bromodomain and acetyl lysine is stimulated by autoacetylation. Furthermore, we find that the histone chaperone anti-silencing function 1 binds to the bromodomain of CBP to present free histones correctly for efficient acetylation. Through a combination of structural, biochemical, and cell-based analyses, these studies enhance our understanding of bromodomain function and regulation.
Exchange of ADP with ATP in the CII ATPase domain promotes autophosphorylation of cyanobacterial clock protein KaiC
Authors: Nishiwaki-Ohkawa Taeko , Kitayama Yohko , Ochiai Erika , Kondo Takao 
Published: March 2014

Significance
The circadian clock protein KaiC cyclically phosphorylates and dephosphorylates itself with a periodicity of ∼24 h. Unlike the reactions mediated by conventional protein phosphatases, dephosphorylation of KaiC occurs via reversal of the phosphorylation reaction. This unusual mechanism suggests that the KaiC phosphorylation rhythm is sustained by periodic shifts in the equilibrium of the reversible autophosphorylation reaction, the molecular basis of which has never been elucidated. In this study, we found that KaiA promoted the forward reaction by stimulating exchange of KaiC-bound ADP for exogenous ATP. KaiB inhibited KaiA, promoting retention of KaiC-bound ADP, and thereby facilitating the reverse reaction. We propose that KaiA and KaiB sustain the circadian oscillation by regulating this reversible reaction at the level of substrate availability.
Structural polymorphism in the N-terminal oligomerization domain of NPM1
Authors: Mitrea Diana M. , Grace Christy R. , Buljan Marija , Yun Mi-Kyung , Pytel Nicholas J. , Satumba John , Nourse Amanda , Park Cheon-Gil , Madan Babu M. , White Stephen W. , Kriwacki Richard W. 
Published: March 2014

Significance
Nucleophosmin (NPM1) is a multifunctional protein with critical roles in ribosome biogenesis, centrosome duplication, and tumor suppression. Despite the established importance of NPM1 as a tumor marker and potential drug target, little is currently known about the molecular mechanisms that govern its various functions. Our manuscript describes that the N-terminal domain of NPM1 (Npm-N) exhibits phosphorylation-dependent structural polymorphism along a broad conformational landscape between two extreme states: a stable, folded pentamer and a globally disordered monomer. We propose that phosphorylation-induced “regulated unfolding” of Npm-N provides a means to modulate NPM1 function and subcellular localization. Our findings will drive future structure-based studies on the roles of regulated unfolding in NPM1 biology and will provide a foundation for NPM1-targeted anticancer drug development.
Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)
Authors: Mommen Geert P. M. , Frese Christian K. , Meiring Hugo D. , van Gaans-van den Brink Jacqueline , de Jong Ad P. J. M. , van Els Cécile A. C. M. , Heck Albert J. R. 
Published: March 2014

SignificanceThe surface presentation of peptides by human leukocyte antigen (HLA) class I molecules is essential for adaptive immune responses against pathogens and tumors. To date, the repertoire of HLA class I peptides remains largely unexplored, although their identity could lead to new targets for vaccine development or cancer immunotherapy. Here, we demonstrate that recent developments in mass spectrometry (MS)-based sequencing technology can expand the detectable peptide repertoire to an unprecedented depth, revealing unique features in the antigen presentation machinery. Our data include a variety of posttranslational modifications for which evidence is accumulating that they play important roles in human diseases. Hence, next-generation MS-based sequencing can make the important step into the discovery of disease-related HLA class I antigens.
Episodic simulation and episodic memory can increase intentions to help others
Authors: Gaesser Brendan , Schacter Daniel L. 
Published: March 2014

Significance
Humans are readily willing to help individuals in need, in part because they can adopt the thoughts and feelings of others. Here, we provide evidence of an additional mechanism facilitating empathic responses. Our experiments revealed that, when presented with a situation depicting another person’s plight, participants who imagined an event in which they help the person (episodic simulation) or remembered a related past event of actually helping others (episodic memory) showed increased prosocial intentions. The findings reported here provide a starting point for research that could be used to develop new strategies targeted at episodic mechanisms for promoting empathy, as well as to guide research that attempts to characterize and improve empathic deficits in patient populations.
Protective role of miR-155 in breast cancer through
RAD51
targeting impairs homologous recombination after irradiation
Authors: Gasparini Pierluigi , Lovat Francesca , Fassan Matteo , Casadei Lucia , Cascione Luciano , Jacob Naduparambil K. , Carasi Stefania , Palmieri Dario , Costinean Stefan , Shapiro Charles L. , Huebner Kay , Croce Carlo M. 
Published: March 2014

Significance
Cell survival after DNA damage relies on DNA repair, the abrogation of which causes genomic instability and development of cancer. DNA double-strand breaks are lesions induced by ionizing radiation (IR) and can be efficiently repaired by DNA homologous recombination, a system that requires RAD51 recombinase (RAD51). Here we show that overexpression of miR-155 in human breast cancer cells reduces the levels of RAD51 and affects the cellular response to IR. High miR-155 levels were associated with lower RAD51 expression and with better overall survival of patients in a large series of triple-negative breast cancers. Testing triple-negative breast cancer patients for miR-155 expression may be a useful prognostic tool to identify who will benefit from an IR-based therapeutic approach.
Predicting premature termination with alliance at sessions 1 and 3: an exploratory study
Authors: Yoo Hana , Bartle‐Haring Suzanne , Gangamma Rashmi 
Published: March 2014

Research has demonstrated that the therapeutic alliance is associated with termination status and treatment outcomes regardless of therapy models and the number of people involved in the treatment. Compared to individual therapy, however, relatively less attention has been paid to the therapeutic alliance as a predictor of premature termination of couple and family therapy. In the current study, videotape recordings of two samples of couples in therapy – one in the first session and the other in the third session – were analysed to examine the association between the therapeutic alliance and termination status. A total of 34 videotapes were analysed in this exploratory study. All the tapes were rated for the therapeutic alliance using the Vanderbilt therapeutic alliance scale, which allowed observers to code behaviour and interactions between couples and their therapist. The results of this study, though preliminary, suggested that the therapeutic alliance measured at the first session was more predictive of premature termination than was the alliance at the third session, which somewhat challenges findings from studies of individual psychotherapy.Practitioner points
Assessing the therapeutic alliance in the first couple therapy session may be more important in predicting later premature termination than in the third session.
In particular, new therapists in training may need to pay special attention to their alliance with clients from the very beginning of therapy.
A Springtime Journey to the Soviet Union: Postwar Planning and Policy Mobilities through the Iron Curtain
Authors: Cook Ian R. , Ward Stephen V. , Ward Kevin 
Published: March 2014

AbstractThis article builds upon a relatively small but growing literature in geography, planning and cognate disciplines that seeks to understand the variegated geographies and histories of policy mobilities. The article uses a case study of an exchange trip between town planners in the Soviet Union and the UK between 1957 and 1958. It focuses on the experiences of the British planners in the Soviet Union and sets the tour within the wider context of a fluctuating and sometimes turbulent history of Anglo‐Soviet politics, travels and connections. In doing this, the article makes three arguments: first, there is much to be gained by bringing together the geography‐dominated policy mobilities literature with that on exchanges and visits by architects, engineers and planners. Secondly, the greater sensitivity to the histories of policy mobilities allows contemporary studies to be contextualized in the longer history of organized learning between different urban professions. Thirdly, despite the long history of policy mobilities, what differentiates the current era from previous eras is the prominent ‘knowledge intermediary’ roles now played by consultancies and think tanks. As the article will demonstrate, it was branches of government and professional bodies, rather than consultancies and think tanks, that tended to dominate such roles previously.
Monitoring temporal change of bird communities with dissimilarity acoustic indices
Authors: Lellouch Laurent , Pavoine Sandrine , Jiguet Frédéric , Glotin Hervé , Sueur Jérôme 
Published: March 2014

Summary

A part of biodiversity assessment and monitoring consists in the estimation and track of the changes in species composition and abundance of animal communities. Such a task requires an important sampling over a broad‐scale time that is difficult to reach with classical survey methods. Acoustics may offer an alternative to usual techniques by recording the sound produced by vocal animals. Animal species that use sound for communication (sing and/or call) establish an acoustic community when they sing at the same time and at a particular place. The estimation of the acoustic community dynamics could provide indirect cues on what drives changes in community composition and species abundance.

Here, new methods were developed to estimate the changes in bird communities recorded at three woodland temperate sites in France. Both field recordings and simulated data were used to test whether acoustic dissimilarity indices can be used to estimate changes in the composition of the community. Four dissimilarity indices found in the literature, and a new one named Dcf were tested on auditory spectra after transformation to the Mel scale, rather than on classical Fourier frequency spectra. All indices were compared with each other and with compositional indices.

The results show that bird communities occurring at the three sites were dynamic with changes of composition with time. Dissimilarities computed on simulated acoustic communities were correlated with compositional dissimilarity but those computed on field‐recorded communities could not be considered as faithful estimators of community composition variations. However, the indices indicate important dates in community changes around mid‐April that were also seen in the composition dynamics.

Acoustic dissimilarity indices failed to track accurately changes in species composition of the bird communities. However, these indices, which are easy to compute, still provide information on the acoustic dynamics of bird community. Acoustics might not be considered as a proxy of compositional diversity but rather as another facet of animal diversity that needs to be studied and preserved on its own.
Cognitive deficits in youth with familial and clinical high risk to psychosis: a systematic review and meta‐analysis
Authors: Bora E. , Lin A. , Wood S. J. , Yung A. R. , McGorry P. D. , Pantelis C. 
Published: March 2014

ObjectiveIt is likely that cognitive deficits are vulnerability markers for developing schizophrenia, as these deficits are already well‐established findings in first‐episode psychosis. Studies at‐risk adolescents and young adults are likely to provide information about cognitive deficits that predate the onset of the illness.MethodWe conducted meta‐analyses of studies comparing familial‐high risk (FHR) or ultra‐high risk (UHR; n = 2113) and healthy controls (n = 1748) in youth studies in which the mean age was between 15 and 29.ResultsCompared with controls, high risk subjects were impaired in each domain in both UHR (d = 0.34–0.71) and FHR (d = 0.24–0.81). Heterogeneity of effect sizes across studies was modest, increasing confidence to the findings of the current meta‐analysis (I2 = 0–0.18%). In both risk paradigms, co‐occurrence of genetic risk with attenuated symptoms was associated with more severe cognitive dysfunction. In UHR, later transition to psychosis was associated with more severe cognitive deficits in all domains (d = 0.31–0.49) except sustained attention. However, cognitive impairment has a limited capacity to predict the outcome of high‐risk patients.ConclusionCognitive deficits are already evident in adolescents and young adults who have familial or clinical risk for psychosis. Longitudinal developmental studies are important to reveal timing and trajectory of emergence of such deficits.