bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioconjugation and stabilisation of biomolecules in biosensors
Authors: Liébana Susana , Drago Guido A. 
Published: June 2016

Suitable bioconjugation strategies and stabilisation of biomolecules on electrodes is essential for the development of novel and commercially viable biosensors. In the present review, the functional groups that comprise the selectable targets for practical bioconjugation methods are discussed. We focus on describing the most common immobilisation techniques used in biosensor construction, which are classified into irreversible and reversible methods. Concerning the stability of proteins, the two main types of stability may be defined as (i) storage or shelf stability, and (ii) operational stability. Both types of stability are explained, as well as the introduction of an electrophoretic technique for predicting protein–polymer interactions. In addition, solution and dry stabilisation as well as stabilisation using the covalent immobilisation of proteins are discussed including possible factors that influence stability. Finally, the integration of nanomaterials, such as magnetic particles, with protein immobilisation is discussed in relation to protein stability studies.
Acoustic biosensors
Authors: Fogel Ronen , Limson Janice , Seshia Ashwin A. 
Published: June 2016

Resonant and acoustic wave devices have been researched for several decades for application in the gravimetric sensing of a variety of biological and chemical analytes. These devices operate by coupling the measurand (e.g. analyte adsorption) as a modulation in the physical properties of the acoustic wave (e.g. resonant frequency, acoustic velocity, dissipation) that can then be correlated with the amount of adsorbed analyte. These devices can also be miniaturized with advantages in terms of cost, size and scalability, as well as potential additional features including integration with microfluidics and electronics, scaled sensitivities associated with smaller dimensions and higher operational frequencies, the ability to multiplex detection across arrays of hundreds of devices embedded in a single chip, increased throughput and the ability to interrogate a wider range of modes including within the same device. Additionally, device fabrication is often compatible with semiconductor volume batch manufacturing techniques enabling cost scalability and a high degree of precision and reproducibility in the manufacturing process. Integration with microfluidics handling also enables suitable sample pre-processing/separation/purification/amplification steps that could improve selectivity and the overall signal-to-noise ratio. Three device types are reviewed here: (i) bulk acoustic wave sensors, (ii) surface acoustic wave sensors, and (iii) micro/nano-electromechanical system (MEMS/NEMS) sensors.
Mnemonic convergence in social networks: The emergent properties of cognition at a collective level
Authors: Coman Alin , Momennejad Ida , Drach Rae D. , Geana Andra 
Published: June 2016

Significance
Human memory is highly malleable. Because of this malleability, jointly remembering the past along with another individual often results in increased similarity between the conversational partners’ memories. We propose an approach that examines the conversation between a pair of participants as part of a larger network of social interactions that has the potential to reveal how human communities form collective memories. Empirical evidence indicating that dyadic-level conversational alignment processes give rise to community-wide shared memories is presented. We find that individual-level memory updating phenomena and social network structure are two fundamental factors that contribute to the emergence of collective memories.
Accounting for pairwise distance restraints in FFT-based protein–protein docking
Authors: Xia Bing , Vajda Sandor , Kozakov Dima 
Published: June 2016

Abstract
Summary: ClusPro is a heavily used protein–protein docking server based on the fast Fourier transform (FFT) correlation approach. While FFT enables global docking, accounting for pairwise distance restraints using penalty terms in the scoring function is computationally expensive. We use a different approach and directly select low energy solutions that also satisfy the given restraints. As expected, accounting for restraints generally improves the rank of near native predictions, while retaining or even improving the numerical efficiency of FFT based docking.
Availability and Implementation: The software is freely available as part of the ClusPro web-based server at http://cluspro.org/nousername.php
Contact: midas@laufercenter.org or vajda@bu.edu
Supplementary information : Supplementary data are available at Bioinformatics online.
Local versus global biological network alignment
Authors: Meng Lei , Striegel Aaron , Milenković Tijana 
Published: June 2016

Abstract
Motivation: Network alignment (NA) aims to find regions of similarities between species’ molecular networks. There exist two NA categories: local (LNA) and global (GNA). LNA finds small highly conserved network regions and produces a many-to-many node mapping. GNA finds large conserved regions and produces a one-to-one node mapping. Given the different outputs of LNA and GNA, when a new NA method is proposed, it is compared against existing methods from the same category. However, both NA categories have the same goal: to allow for transferring functional knowledge from well- to poorly-studied species between conserved network regions. So, which one to choose, LNA or GNA? To answer this, we introduce the first systematic evaluation of the two NA categories.
Results: We introduce new measures of alignment quality that allow for fair comparison of the different LNA and GNA outputs, as such measures do not exist. We provide user-friendly software for efficient alignment evaluation that implements the new and existing measures. We evaluate prominent LNA and GNA methods on synthetic and real-world biological networks. We study the effect on alignment quality of using different interaction types and confidence levels. We find that the superiority of one NA category over the other is context-dependent. Further, when we contrast LNA and GNA in the application of learning novel protein functional knowledge, the two produce very different predictions, indicating their complementarity. Our results and software provide guidelines for future NA method development and evaluation.
Availability and implementation: Software: http://www.nd.edu/~cone/LNA_GNA
Contact: tmilenko@nd.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Network-based pathway enrichment analysis with incomplete network information
Authors: Ma Jing , Shojaie Ali , Michailidis George 
Published: June 2016

AbstractMotivation: Pathway enrichment analysis has become a key tool for biomedical researchers to gain insight into the underlying biology of differentially expressed genes, proteins and metabolites. It reduces complexity and provides a system-level view of changes in cellular activity in response to treatments and/or in disease states. Methods that use existing pathway network information have been shown to outperform simpler methods that only take into account pathway membership. However, despite significant progress in understanding the association amongst members of biological pathways, and expansion of data bases containing information about interactions of biomolecules, the existing network information may be incomplete or inaccurate and is not cell-type or disease condition-specific.Results: We propose a constrained network estimation framework that combines network estimation based on cell- and condition-specific high-dimensional Omics data with interaction information from existing data bases. The resulting pathway topology information is subsequently used to provide a framework for simultaneous testing of differences in expression levels of pathway members, as well as their interactions. We study the asymptotic properties of the proposed network estimator and the test for pathway enrichment, and investigate its small sample performance in simulated and real data settings.Availability and Implementation: The proposed method has been implemented in the R-package netgsa available on CRAN.Contact: jinma@upenn.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Translating evidence to practice in the health professions: a randomized trial of Twitter vs Facebook
Authors: Tunnecliff Jacqueline , Weiner John , Gaida James E , Keating Jennifer L , Morgan Prue , Ilic Dragan , Clearihan Lyn , Davies David , Sadasivan Sivalal , Mohanty Patitapaban , Ganesh Shankar , Reynolds John , Maloney Stephen 
Published: June 2016

Objective: Our objective was to compare the change in research informed knowledge of health professionals and their intended practice following exposure to research information delivered by either Twitter or Facebook.
Methods: This open label comparative design study randomized health professional clinicians to receive “practice points” on tendinopathy management via Twitter or Facebook. Evaluated outcomes included knowledge change and self-reported changes to clinical practice.
Results: Four hundred and ninety-four participants were randomized to 1 of 2 groups and 317 responders analyzed. Both groups demonstrated improvements in knowledge and reported changes to clinical practice. There was no statistical difference between groups for the outcomes of knowledge change (P = .728), changes to clinical practice (P = .11) or the increased use of research information (P = .89). Practice points were shared more by the Twitter group (P &lt; .001); attrition was lower in the Facebook group (P &lt; .001).
Conclusion: Research information delivered by either Twitter or Facebook can improve clinician knowledge and promote behavior change. No differences in these outcomes were observed between the Twitter and Facebook groups. Brief social media posts are as effective as longer posts for improving knowledge and promoting behavior change. Twitter may be more useful in publicizing information and Facebook for encouraging course completion.
Stakeholders
Authors: Harrison Jeffrey S. 
Published: June 2016

Stakeholders are groups and individuals that have an interest in the actions and outcomes of an organization and upon whom the organization relies to achieve its own objectives. Note in this definition that there is a two-way interdependent relationship. It is not enough for a particular group or individual to claim a “stake” in the firm, such as suppliers, financiers, customers, shareholders, and communities. Genuine stakeholders are those that either contribute to or have the ability to undermine the productive activities of an organization. Because of its breadth, stakeholder theory holds multiple interpretations, but at its heart the theory suggests that firms that take excellent care of a broad group of these stakeholders (as opposed to focusing on one group, such as shareholders or customers) will gain benefits that are not available to other organizations. For example, employees are expected to work harder, customers to buy more, suppliers to provide the best resources and terms, financiers to offer the best interest rates, and so forth. These sorts of benefits lead an organization to create more value, which is then distributed back to the stakeholders that helped to create it. In spite of what many scholars and practitioners might think, this theory is not the same as corporate social responsibility (CSR), which tends to focus on social issues such as the environment or sustainability. While it may be true that firms that take exceptionally good care of their stakeholders may also be good corporate citizens, the objective behind stakeholder theory is on effective and efficient management in an increasingly turbulent business environment rather than pursuing social welfare for its own sake.
Homozygous loss of autism-risk geneCNTNAP2results in reduced local and long-range prefrontal functional connectivity
Authors: Liska Adam , Bertero Alice , Gomolka Ryszard , Sabbioni Mara , Galbusera Alberto , Barsotti Noemi , Panzeri Stefano , Scattoni Maria Luisa , Pasqualetti Massimo , Gozzi Alessandro 
Published: June 2016

AbstractFunctional connectivity aberrancies, as measured with resting-state fMRI (rsfMRI), have been consistently observed in the brain of autism spectrum disorders (ASD) patients. However, the genetic and neurobiological underpinnings of these findings remain unclear. Homozygous mutations in Contactin Associated Protein-like 2 (CNTNAP2), a neurexin-related cell-adhesion protein, are strongly linked to autism and epilepsy. Here we used rsfMRI to show that homozygous mice lackingCntnap2exhibit reduced long-range and local functional connectivity in prefrontal and midline brain “connectivity hubs”. Long-range rsfMRI connectivity impairments affected heteromodal cortical regions and were prominent between fronto-posterior components of the mouse default-mode network (DMN), an effect that was associated with reduced social investigation, a core “autism trait” in mice. Notably, viral tracing revealed reduced frequency of prefrontal-projecting neural clusters in the cingulate cortex ofCntnap2−/−mutants, suggesting a possible contribution of defective mesoscale axonal wiring to the observed functional impairments. Macroscale cortico-cortical white matter organization appeared to be otherwise preserved in these animals. These findings reveal a key contribution of ASD-associated gene CNTNAP2 in modulating macroscale functional connectivity, and suggest that homozygous loss-of-function mutations in this gene may predispose to neurodevelopmental disorders and autism through a selective dysregulation of connectivity in integrative prefrontal areas.
Characterization of Methicillin-resistantStaphylococcus aureusIsolates from Fitness Centers in Memphis Metropolitan Area, USA
Authors: Mukherjee Nabanita , Sulaiman Irshad M. , Banerjee Pratik 
Published: June 2016

AbstractIndoor skin-contact surfaces of public fitness centers may serve as reservoirs of potential human transmission of methicillin-resistantStaphylococcus aureus(MRSA). We found a high prevalence of multi-drug resistant (MDR)-MRSA of CC59 lineage harboring a variety of extracellular toxin genes from surface swab samples collected from inanimate surfaces of fitness centers in Memphis metropolitan area, USA. Our findings underscore the role of inanimate surfaces as potential sources of transmission of MDR-MRSA strains with considerable genetic diversity.
Simulations reveal increased fluctuations in estrogen receptor-alpha conformation upon antagonist binding
Authors: Ng Ho Leung 
Published: June 2016

AbstractMolecular dynamics (MD) simulations have been used to model dynamic fluctuations in the structure of estrogen receptor-alpha (ER-α) upon binding to the natural agonist 17β-estradiol (E2) and to the active metabolite of the breast cancer drug and antagonist, 4-hydroxytamoxifen (OHT). We present the most extensive MD simulations to date of ER-α with over 1 μs of combined simulations for the monomer and dimer forms. Simulations reveal that the antagonist-bound complex includes significant fluctuations while the agonist-bound complex is tightly restrained. OHT increases dynamic disorder in the loops located to either side of the tail H12 helix; H12 has been associated with the activation status of ER-α. We also report that fluctuations near H12 lead to greater conformational variation in the binding mode of the ethylamine tail of OHT. Both the agonist and antagonist conformations are stable throughout the 240 ns simulations, supporting the hypothesis that there are no transitions between these two states or into intermediate states. The stable position of H12 in the OHT-bound conformation suggests that OHT stabilizes a well-defined antagonist conformational ensemble rather than merely blocking the agonist-driven activation of ER-α. Simultaneously, the increased dynamic properties of the OHT-bound complex is a potential source of binding entropy.
FF12MC: A revised AMBER forcefield and new protein simulation protocol
Authors: Pang Yuan-Ping 
Published: June 2016

ABSTRACTSpecialized to simulate proteins in molecular dynamics (MD) simulations with explicit solvation, FF12MC is a combination of a new protein simulation protocol employing uniformly reduced atomic masses by tenfold and a revised AMBER forcefield FF99 with (i) shortened CH bonds, (ii) removal of torsions involving a nonperipheralsp3atom, and (iii) reduced 1-4 interaction scaling factors of torsionsϕandψThis article reports that in multiple, distinct, independent, unrestricted, unbiased, isobaric-isothermal, and classical MD simulations FF12MC can (i) simulate the experimentally observed flipping between left-and right-handed configurations for C14-C38 of BPTI in solution, (ii) autonomously fold chignolin, CLN025, and Trp-cage with folding times that agree with the experimental values, (iii) simulate subsequent unfolding and refolding of these miniproteins, and (iv) achieve a robust Z score of 1.33 for refining protein models TMR01, TMR04, and TMR07. By comparison, the latest general-purpose AMBER forcefield FF14SB locks the C14-C38 bond to the right-handed configuration in solution under the same protein simulation conditions. Statistical survival analysis shows that FF12MC folds chignolin and CLN025 in isobaric-isothermal MD simulations 2-4 times faster than FF14SB under the same protein simulation conditions. These results suggest that FF12MC may be used for protein simulations to study kinetics and thermodynamics of miniprotein folding as well as protein structure and dynamics.
Frequency-specific neuromodulation of local and distant connectivity in aging & episodic memory function
Authors: Davis Simon W. , Luber Bruce , Murphy David L. K. , Lisanby Sarah H. , Cabeza Roberto 
Published: June 2016

AbstractA growing literature has focused on the brain’s ability to augment processing in local regions by recruiting distant communities of neurons in response to neural decline or insult. In particular, both younger and older adult populations recruit bilateral prefrontal cortex (PFC) as a means of compensating for increasing neural effort to maintain successful cognitive function. However, it remains unclear how local changes in neural activity affect the recruitment of this adaptive mechanism. To address this problem, we combined graph theoretical measures from functional MRI (fMRI) with diffusion weighted imaging (DWI) and repetitive transcranial magnetic stimulation (rTMS) in order to resolve a central hypothesis:how do aged brains flexibly adapt to local changes in cortical activity?Specifically, we applied neuromodulation to increase or decrease local activity in a cortical region supporting successful memory encoding (left dorsolateral prefrontal cortex or DLPFC) using 5Hz or 1Hz rTMS, respectively. We then assessed a region’s localwithin-module degree(WMD), or the distributedbetween-module degree(BMD) between distant cortical communities. We predicted that (1) local stimulation-related deficits may be counteracted by boosting BMD between bilateral PFC, and that this effect should be (2)positively correlatedwith structural connectivity. Both predictions were confirmed; 5Hz rTMS increased local success-related activity and local increases in PFC connectivity, while 1Hz rTMS decreases local activity and triggered a more distributed pattern of bilateral PFC connectivity to compensate for this local inhibitory effect. These results provide an integrated, causal explanation for the network interactions associated with successful memory encoding in older adults.
Post-mortem molecular profiling of three psychiatric disorders
Authors: Ramaker Ryne C. , Bowling Kevin M. , Lasseigne Brittany N. , Hagenauer Megan H. , Hardigan Andrew A. , Davis Nick S. , Gertz Jason , Cartagena Preston M. , Walsh David M. , Vawter Marquis P. , Jones Edward G. , Schatzberg Alan F. , Barchas Jack D. , Watson Stan J. , Bunney Blynn G. , Akil Huda , Bunney William E. , Li Jun Z. , Cooper Sara J. , Myers Richard M. 
Published: June 2016

AbstractBackgroundPsychiatric disorders are multigenic diseases with complex etiology contributing significantly to human morbidity and mortality. Although clinically distinct, several disorders share many symptoms suggesting common underlying molecular changes exist that may implicate important regulators of pathogenesis and new therapeutic targets.ResultsWe compared molecular signatures across brain regions and disorders in the transcriptomes of postmortem human brain samples. We performed RNA sequencing on tissue from the anterior cingulate cortex, dorsolateral prefrontal cortex, and nucleus accumbens from three groups of 24 patients each diagnosed with schizophrenia, bipolar disorder, or major depressive disorder, and from 24 control subjects, and validated the results in an independent cohort. The most significant disease differences were in the anterior cingulate cortex of schizophrenia samples compared to controls. Transcriptional changes were assessed in an independent cohort, revealing the transcription factorEGR1as significantly down regulated in both cohorts and as a potential regulator of broader transcription changes observed in schizophrenia patients. Additionally, broad down regulation of genes specific to neurons and concordant up regulation of genes specific to astrocytes was observed in SZ and BPD patients relative to controls. We also assessed the biochemical consequences of gene expression changes with untargeted metabolomic profiling and identified disruption of GABA levels in schizophrenia patients.ConclusionsWe provide a comprehensive post-mortem transcriptome profile of three psychiatric disorders across three brain regions. We highlight a high-confidence set of independently validated genes differentially expressed between schizophrenia and control patients in the anterior cingulate cortex and integrate transcriptional changes with untargeted metabolite profiling.
Members of the Scottish Parliament on Twitter: good constituency men (and women)?
Authors: Baxter Graeme , Marcella Rita , O'Shea Mary 
Published: June 2016

Purpose– The purpose of this paper is to explore the use of Twitter by Members of the Scottish Parliament (MSPs) for the provision of constituency-related information, or in support of their constituency service work.Design/methodology/approach– Content analysis of 10,411 tweets sent by the 105 MSPs on Twitter during four weeks in early-2014.Findings– While there was some evidence of MSPs on Twitter acting as a promoter of local community interests and as a conduit for information on local policy issues and events, their tweets were dominated by the wider, national, political agenda and by the Scottish independence debate. Compared with their online behaviour as parliamentary candidates three years earlier, MSPs placed an even greater emphasis on the one-way broadcast of information to their followers. They were reluctant to respond to contentious local policy questions, or to enter into any visible, meaningful, political debate with their constituents.Research limitations/implications– Although the research was conducted seven months before the Scottish independence referendum on 18 September 2014, the independence debate still dominated proceedings on Twitter. It might, therefore, be appropriate to revisit MSPs’ use of Twitter at some point during a truer “peacetime” period.Originality/value– This is the first systematic content analysis of tweets sent by all MSPs on Twitter. It allows the authors to compare their actual Twitter use with that envisaged by the Scottish Parliament, as a way of MSPs communicating about their work and engaging with their constituents.