bluuebunny/crossref_metadata_2025_split huggingface dataset:
A National Survey on the Use of Immersive Simulation for Interprofessional Education in Physical Therapist Education Programs
Authors: Stockert Brad , Ohtake Patricia J. 
Published: May 2017

Introduction
There is growing recognition that collaborative practice among healthcare professionals is associated with improved patient outcomes and enhanced team functioning, but development of collaborative practitioners requires interprofessional education (IPE). Immersive simulation, a clinically relevant experience that deeply engages the learner in realistic clinical environments, is used increasingly for IPE. The purpose of this study was to assess the use of immersive simulation as a strategy for IPE in physical therapist (PT) education programs.

Methods
During fall 2014 and spring 2015, we contacted all 214 Commission on Accreditation in Physical Therapy Education accredited PT education programs in the United States and invited a faculty member to participate in our online survey.

Results
One hundred fourteen PT programs responded (53% response rate). Eighty responding programs (70%) identified themselves as users of immersive simulation, and 45 programs (39%) used simulation for IPE. Of these 45 programs, more than 90% included Interprofessional Education Collaborative competency learning objectives of roles/responsibilities, interprofessional communication, and teams/teamwork and 51% reported learning objectives for values/ethics for interprofessional practice. Interprofessional simulations with PT students commonly included nursing (91%). In programs using immersive simulation for IPE, 91% included debriefing and 51% included debriefing by interprofessional teams.

Conclusions
Eighty accredited PT programs (70%) that responded to the survey use immersive simulation, and 45 programs (39%) use simulation for IPE. Most programs conduct simulations consistent with recognized best practice, including debriefing and Interprofessional Education Collaborative competency learning objectives for promoting interprofessional collaborative practice. We anticipate an increase in the use of immersive simulation for IPE as an educational strategy to comply with the revised Commission on Accreditation in Physical Therapy Education accreditation standards related to interprofessional collaborative practice that will become effective on January 1, 2018.
Expanding the computable reactome inPseudomonas putidareveals metabolic cycles providing robustness
Authors: Nogales Juan , Gudmundsson Steinn , Duque Estrella , Ramos Juan Luis , Palsson Bernhard O. 
Published: May 2017

AbstractGenome-scale network reconstructions are organism-specific representations of metabolism and powerful tools for analyzing systemic metabolic properties. The use of reconstructions is limited by the lack of coverage of the metabolic reactome. We present an exhaustive and validated reconstruction of the biotechnologically relevant bacteriumPseudomonas putidaKT2440, greatly expanding its computable metabolic states. The reconstruction,iJN1411, represents a significant expansion over other reconstructed bacterial metabolic networks. Computations based on the reconstruction exhibit high accuracy in predicting nutrient sources, growth rates, carbon flux distributions, and gene essentiality, thus providing a deep understanding ofPseudomonasmetabolism.iJN1411 was used for: i) the assessment of the metabolic capabilities ofP. putidaas a species through multi-strain modeling, ii) deciphering the molecular mechanisms underlying metabolic robustness, and iii) identification of metabolic “capacitors” based on ATP-fueled metabolic cycles. This study represents the most complete and comprehensive bacterial metabolic reconstruction built to date, while providing computational and experimental evidence about how bacteria increase metabolic robustness, paving the way for engineering more robust biocatalysts and searching for drug targets in robust pathogens.
Simultaneous activation of parallel sensory pathways promotes a grooming sequence inDrosophila
Authors: Hampel Stefanie , McKellar Claire E. , Simpson Julie H. , Seeds Andrew M. 
Published: May 2017

AbstractA central model that describes how behavioral sequences are produced features a neural architecture that readies different movements simultaneously, and a mechanism where prioritized suppression between the movements determines their sequential performance. We previously described a model whereby suppression drives aDrosophilagrooming sequence that is induced by simultaneous activation of different sensory pathways that each elicit a distinct movement (Seeds et al. 2014). Here, we confirm this model using transgenic expression to identify and optogenetically activate sensory neurons that elicit specific grooming movements. Simultaneous activation of different sensory pathways elicits a grooming sequence that resembles the naturally induced sequence. Moreover, the sequence proceeds after the sensory excitation is terminated, indicating that a persistent trace of this excitation induces the next grooming movement once the previous one is performed. This reveals a mechanism whereby parallel sensory inputs can be integrated and stored to elicit a delayed and sequential grooming response.
Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data
Authors: Farmery James HR , Smith Mike L ,   NIHR BioResource - Rare Diseases, Lynch Andy G 
Published: May 2017

ABSTRACTTelomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, technical replicates, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype.
ALPK1 and TIFA dependent innate immune response triggered by the Helicobacter pylori type IV secretion system
Authors: Zimmermann Stephanie , Pfannkuch Lennart , Al-Zeer Munir A. , Bartfeld Sina , Koch Manuel , Liu Jianping , Rechner Cindy , Soerensen Meike , Sokolova Olga , Zamyatina Alla , Kosma Paul , Mäurer André P. , Glowinski Frithjof , Pleissner Klaus-Peter , Schmid Monika , Brinkmann Volker , Naumann Michael , Rother Marion , Machuy Nikolaus , Meyer Thomas F. 
Published: May 2017

SummaryActivation of transcription factor NF-κB is a hallmark of infection with the gastric pathogenHelicobacter pyloriand associated with inflammation and carcinogenesis. Genome-wide RNAi screening revealed numerous hits involved inH. pylori-, but not IL-1β- and TNF-α- dependent NF-κB regulation. Pathway analysis including CRISPR/Cas9-knockout and recombinant protein technology, immunofluorescence microscopy, immunoblotting, mass spectrometry and mutantH. pyloristrains, identified theH. pylorimetabolite D-glycero-β-D-manno-heptose1,7-bisphosphate (βHBP) as a cagPAI type IV secretion system (T4SS)-dependent effector of NF-κB activation in infected cells. Upon pathogen-host cell contact, TIFA forms large complexes (TIFAsomes) including interacting host factors, such as TRAF2. NF-κB activation, TIFA phosphorylation as well as TIFAsome formation depended on a functional ALPK1 kinase, highlighting the ALPK1-TIFA axis as core of a novel innate immune pathway. ALPK1-TIFA-mediated NF-κB activation was independent of CagA protein translocation, indicating that CagA translocation and HBP delivery to host cells are distinct features of the pathogen’s T4SS.
STRIDE: Species Tree Root Inference from Gene Duplication Events
Authors: Emms David M. , Kelly Steven 
Published: May 2017

AbstractThe correct interpretation of a phylogenetic tree is dependent on it being correctly rooted. A gene duplication event at the base of a clade of species is synapamorphic, and thus excludes the root of the species tree from that clade. We present STRIDE, a fast, effective, and outgroup-free method for species tree root inference from gene duplication events. STRIDE identifies sets of well-supported gene duplication events from cohorts of gene trees, and analyses these events to infer a probability distribution over an unrooted species tree for the location of the true root. We show that STRIDE infers the correct root of the species tree for a large range of simulated and real species sets. We demonstrate that the novel probability model implemented in STRIDE can accurately represent the ambiguity in species tree root assignment for datasets where information is limited. Furthermore, application of STRIDE to inference of the origin of the eukaryotic tree resulted in a root probability distribution that was consistent with, but unable to distinguish between, leading hypotheses for the origin of the eukaryotes. In summary, STRIDE is a fast, scalable, and effective method for species tree root inference from genome scale data.
Functional role of lanthanides in enzymatic activity and transcriptional regulation of PQQ-dependent alcohol dehydrogenases in Pseudomonas putida KT2440
Authors: Wehrmann Matthias , Billard Patrick , Meriadec Audrey Martin , Zegeye Asfaw , Klebensberger Janosch 
Published: May 2017

ABSTRACTThe oxidation of alcohols and aldehydes is crucial for detoxification and efficient catabolism of various volatile organic compounds (VOCs). Thus, many Gram-negative bacteria have evolved periplasmic oxidation systems, based on pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ-ADHs), which are often functionally redundant. Using purified enzymes from the soil-dwelling model organism Pseudomonas putida KT2440, the present study reports the first description and characterization of a lanthanide-dependent PQQ-ADH (PedH) in a non-methylotrophic bacterium. PedH exhibits enzyme activity on a similar substrate range as its Ca2+-dependent counterpart PedE, including linear and aromatic primary and secondary alcohols as well as aldehydes, however, only in the presence of lanthanide ions including La3+, Ce3+, Pr3+, Sm3+ or Nd3+. Reporter assays revealed that PedH not only has a catalytic function, but is also involved in the transcriptional regulation of pedE and pedH, most likely acting as a sensory module. Notably, the underlying regulatory network is responsive to as little as 1 – 10 nM of lanthanum, a concentration assumed to be of ecological relevance. The present study further demonstrates that the PQQ-dependent oxidation system is crucial for efficient growth with a variety of volatile alcohols. From these results we conclude that functional redundancy and inverse regulation of PedE and PedH represents an adaptive strategy of P. putida KT2440 to optimize growth with volatile alcohols in response to different lanthanide availability.IMPORTANCEDue to their low bioavailability, lanthanides have long been considered as biologically inert. In recent years however, the identification of lanthanides as a cofactor in methylotrophic bacteria has attracted tremendous interest among various biological fields. The present study reveals that one of the two PQQ-ADHs produced by the model organism P. putida KT2440 also utilizes lanthanides as a cofactor, thus expanding the scope of lanthanide employing bacteria beyond the methylotrophs. Similar to methyloptrophic bacteria, a complex regulatory network is involved in the lanthanide-responsive switch between the two PQQ-ADHs encoded by P. putida KT2440. We further show that functional production of at least one of the enzymes is crucial for efficient growth with several volatile alcohols. Overall, our study provides a novel understanding for the redundancy of PQQ-ADHs observed in many organisms and further highlights the importance of lanthanides for bacterial metabolism, particularly in soil environments.
A Theta Band Network Involving Prefrontal Cortex Unique to Human Episodic Memory
Authors: Young James J , Rudebeck Peter H , Marcuse Lara V , Fields Madeline C , Yoo Ji Yeoun , Panov Fedor , Ghatan Saadi , Fazl Arash , Mandelbaum Sarah , Baxter Mark G 
Published: May 2017

AbstractEpisodic memory, everyday memory for events, is fundamental to our lives. We tested patients undergoing intracranial electroencephalography (intracranial EEG) monitoring for the localization of medically-refractory epilepsy on a well-characterized paradigm that requires episodic memory. Here we report that an anatomically diffuse network characterized by thetaband (4-7 Hz) coherence is activated at the time of a choice that requires episodic memory. This distinct network pattern of oscillatory activity is absent in situations that do not require episodic memory. The episodic network we identified spans prefrontal and temporal lobes and coherence between these areas was greatest during memory encoding. Our data provide novel empirical evidence for a set of brain areas that supports episodic memory in humans.Significance StatementSynchronous oscillations of electrical fields are thought to support brain processes such as language, movement, memory and learning. However, little is known about which types of synchronous oscillations are needed for which process. We performed invasive recordings of electrical activity in patients undergoing surgical management for epilepsy while they perform different types of memory tasks. We found synchronous oscillations in the theta band (4-7 Hz) correlate with performance in an episodic memory. This pattern of oscillations activates a distinct network of brain regions from a task that does not require episodic memory. This finding advances our understanding of the brain systems that support each process.
mTORC2/AKT/HSF1/HuR constitute a feed-forward loop regulating Rictor expression and tumor growth in glioblastoma
Authors: Holmes Brent , Benavides-Serrato Angelica , Freeman Ryan S. , Landon Kenna A. , Bashir Tariq , Nishimura Robert N. , Gera Joseph 
Published: May 2017

ABSTRACTOverexpression of Rictor has been demonstrated to result in increased mTORC2 nucleation and activity leading to tumor growth and increased invasive characteristics in glioblastoma multiforme (GBM). However the mechanisms regulating Rictor expression in these tumors is not clearly understood. In this report, we demonstrate that Rictor is regulated at the level of mRNA translation via HSF1-induced HuR activity. HuR is shown to directly bind the 3′ UTR of the Rictor transcript and enhance translational efficiency. Moreover, we demonstrate that mTORC2/AKT signaling activates HSF1 resulting in a feed-forward cascade in which continued mTORC2 activity is able to drive Rictor expression. RNAi-mediated blockade of AKT, HSF1 or HuR is sufficient to downregulate Rictor and inhibit GBM growth and invasive characteristicsin vitroand suppresses xenograft growth in mice. We further demonstrate that constitutive overexpression of HuR is able to maintain Rictor expression under conditions of AKT or HSF1 loss. In an additional level of regulation,miR-218, a known Rictor targeting miRNA is shown to be subject to mTORC2/STAT3-mediated repression. The expression of these components is also examined in patient GBM samples and correlative associations between the relative expression of these factors support the presence of these signaling relationships in GBM. These data support a role for a feed-forward loop mechanism by which mTORC2 activity stimulates Rictor translational efficiency and suppressesmiR-218resulting in enhanced mTORC2 activity in these tumors.
TDG regulates cell cycle progression in human neural progenitors
Authors: Germanguz I , Park J , Cinkornpumin J , Soloman A , Ohashi M , Lowry WE 
Published: May 2017

AbstractAs cells divide, they must replicate both their DNA and generate a new set of histone proteins. The newly synthesized daughter strands and histones are unmodified and must therefore be covalently modified to allow for transmission of important epigenetic marks to daughter cells. Human pluripotent stem cells (hPSCs) display a unique cell cycle profile, and control of the cell cycle is known to be critical for their proper differentiation and survival. A major unresolved question is how hPSCs regulate their DNA methylation status through the cell cycle, namely how passive and active demethylation work to maintain a stable genome. TDG, an embryonic essential gene, has been recently implicated as a major enzyme involved in demethylation1. Here we present new data showing that TDG regulates cell cycle related gene expression in human neural progenitors (NPCs) derived from hPSCs and controls their capacity for neural differentiation. These observations suggest that TDG and active demethylation play an important role in hPSC cell cycle regulation and differentiation.
Cooperative Accumulation of Dynein-Dynactin at Microtubule Minus-Ends Drives Microtubule Network Reorganization
Authors: Tan Ruensern , Foster Peter J. , Needleman Daniel J. , McKenney Richard J. 
Published: May 2017

SummaryCytoplasmic dynein-1 (dynein) is minus-end directed motor protein that transports cargo over long distances and organizes microtubules (MTs) during critical cellular processes such as mitotic spindle assembly. How dynein motor activity is harnessed for these diverse functions remains unknown. Here, we have uncovered a mechanism for how processive dynein-dynactin complexes drive MT-MT sliding, reorganization, and focusing, activities required for mitotic spindle assembly. We find that motors cooperatively accumulate, in limited numbers, at MT minus-ends. Minus-end accumulations drive MT-MT sliding, independent of MT orientation, and this activity always results in the clustering of MT minus-ends. At a mesoscale level, activated dynein-dynactin drives the formation and coalescence of MT asters. Macroscopically, dynein-dynactin activity leads to bulk contraction of millimeter-scale MT networks, demonstrating that minus-end accumulations produce network scale contractile stresses. Our data provides a model for how localized dynein activity is harnessed by cells to produce contractile stresses within the mitotic spindle.HighlightsProcessive dynein-dynactin complexes cooperatively form stable accumulations at MT minus-ends.Minus-end accumulations of motors slide MTs without orientation bias, leading to minus-end focusing.Minus-end accumulations of motors organize dynamic MTs into asters.Minus-end accumulations of motors drive bulk contractions of large-scale MT networks.
Badnaviruses of sweetpotato: symptomless co-inhabitants on a global scale
Authors: Kreuze Jan F. , Perez Ana , Galvez Marco , Cuellar Wilmer J. 
Published: May 2017

AbstractSweetpotato is among the most important root-crops worldwide, particularly in developing countries, and its production is affected severely by a variety of virus diseases. During the last decade a number of new viruses have been discovered in sweetpotatoes from different continents through next generation sequencing studies, among them belonging to the genusBadnavirusand collectively assigned to the speciesSweet potato pakkakuy virus(SPPV). We determined the complete genome sequence of two SPPV isolates and show the ubiquitous presence of similar viruses in germplasm and field material from around the globe. We show SPPV is not integrated into the sweetpotato genome, occurs only at extremely low titers but is nevertheless efficiently transmitted through seeds and cuttings. They are unaffected by virus elimination therapy and lack any discernible symptoms in sweetpotatoes or indicator host plants. Nevertheless, they show considerable variation in their nucleotide sequences and correspond to several genetic lineages. Studies of their interaction with the two most important sweetpotato viruses showed only limited synergistic increase in the titres of one of two SPPV isolates. We contend that these viruses may pose little threat to sweetpotato production and more likely represent a new type of persistent virus in a possibly commensal or mutualistic relationship with sweetpotato.ImportanceNext generation sequencing approaches have in the last few years led to the discovery of many virus like sequences in different crop plants including sweetpotatoes. The significance of such discoveries can sometimes be elusive when they have not been associated with specific symptoms due to mixed infections or have been found in apparently healthy plants. Badnavirus sequences found in sweetpotatoes provide a typical case. Considering they have now been reported globally, it was important to determine how common these viruses are and what their possible impact may be on sweetpotato production. The significance of our research lies in resolving the case of badnaviruses, providing evidence they represent a new type of vertically transmitted persistent and apparently harmless episomal viruses living in a state of commensalism with their host.
Comparison of US and UK rankings of LIS journals
Authors: Taylor Lynsey , Willett Peter 
Published: May 2017

Purpose
The purpose of this paper is to investigate UK academics’ views of the importance and prestige of journals relevant to library and information science (LIS) teaching and research.

Design/methodology/approach
A questionnaire, based on one used previously in the USA, was sent to UK academics involved in LIS teaching and research. The questionnaire asked respondents to rate the importance of 87 LIS journals, to suggest others that were of importance to them but that were not amongst the 87, and to identify the five most prestigious journals for promotion purposes. In addition, those journals were identified that had figured in institutional submissions to the LIS Unit of Assessment in Research Excellence Framework (REF).

Findings
While there was a fair measure of overall agreement between US and UK rankings of the 87 journals, with both highlighting the standing of the Journal of the Association for Information Science and Technology and of the Journal of Documentation, some substantial differences were also noted. Evidence is presented for a strong locational component to academics’ assessments of journal prestige, and analysis of the REF2014 submissions demonstrates the highly inter-disciplinary nature of LIS research in the UK.

Research limitations/implications
The sample size is small, comprising 30 completed responses.

Originality/value
This is the first study to report UK academics’ rankings of LIS journals, and to compare those with comparable data for US academics.