bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal Changes in Deceased Kidney Donor Characteristics in Australia
Authors: Chan Samuel , Campbell Scott B. , Clayton Phillip A. , Mudge David W. , Cho Yeoungjee , Hawley Carmel M. , Johnson David W. , Francis Ross S. 
Published: October 2016

Background
Demand for deceased donor kidneys has exceeded supply in Australia over the past 2 decades. With a desire to use as many donor organs as possible, the health characteristics of accepted donors may have changed over time.

Methods
All deceased kidney donors actually transplanted in Australia between January 1, 1994, and December 31, 2013, were retrospectively analyzed, using data from the Australian and New Zealand Organ Donor Registry.

Results
Of 4172 deceased donors, 57% were men. Mean donor age increased from 37.2 ± 16.8 years to 46.1 ± 17.7 years over time, and donor numbers increased from 162 in 1994 to 334 in 2013. As the primary cause of death, motor vehicle accidents decreased from 27% to 12%, whereas cerebral pathology persisted at 50%. There was an increase in the proportion of donors with hypertension (12% to 24%), diabetes (2% to 7%), and an increase in mean body mass index (24.4 ± 4.4 kg/m2 to 27.5 ± 6.3 kg/m2) between 1994 and 2013. These changes were reflected by an increase in the median kidney donor risk index from 1.08 (interquartile range, 0.85-1.25) to 1.32 (interquartile range, 0.95-1.53). The proportion of medically higher risk donors increased over time.

Conclusions
Because deceased kidney donor numbers have increased, the range of donor quality has broadened, with an increase in both the proportion and number of high-risk donors, as well as a decline in donor quality. These data highlight the need for kidney allocation algorithms to evolve to ensure appropriate allocation of deceased donor kidneys.
Temporary Lumbar Drain as Treatment for Pediatric Fulminant Idiopathic Intracranial Hypertension
Authors: Jiramongkolchai Kim , Buckley Edward G. , Bhatti M. Tariq , Muh Carrie R. , Wiggins Robert E. , Jiramongkolchai Pawina , El-Dairi Mays A. 
Published: October 2016

Abstract:
Fulminant idiopathic intracranial hypertension (FIIH) is a subtype of idiopathic intracranial hypertension (IIH) characterized by rapid, severe, progressive vision loss. Surgical intervention is often performed either as a cerebrospinal fluid (CSF) shunt procedure or an optic nerve sheath fenestration or, at times, both. These surgical procedures carry a significant risk of morbidity and failure. We present 2 patients in whom a temporary lumbar drain was successfully used in the management of medically undertreated pediatric FIIH, and circumvented the need for surgical intervention.
Comparing Hypertropia in Upgaze and Downgaze Distinguishes Congenital From Acquired Fourth Nerve Palsies
Authors: Ivanir Yair , Trobe Jonathan D. 
Published: October 2016

Background:
Isolated fourth nerve palsies are commonly caused by decompensation of a congenitally dysfunctional superior oblique muscle (“decompensated congenital palsies”). Distinguishing such palsies at initial presentation from palsies caused by presumed microvascular ischemia (“ischemic palsies”) has value for patient reassurance and in forestalling ancillary testing. Abnormally large vertical fusional amplitudes traditionally have been used to identify decompensated congenital palsies, but that may not be a reliable distinguishing feature. This study was undertaken to determine if the amount of hypertropia in upgaze and downgaze might be a more efficient separator. We also studied traumatic and tumorous fourth nerve palsies to see if they could be distinguished from decompensated congenital palsies by using this hypertropia comparison.

Methods:
Retrospective review of case records of patients diagnosed with isolated fourth nerve palsies at the University of Michigan Neuro-Ophthalmology Clinics over the past 15 years. We recorded the age, gender, vascular risk factors, duration of follow-up, cause, side of palsy, and alignment measurements in all patients.

Results:
Inclusion criteria were met by 118 patients. Hypertropia was equal or greater in upgaze than downgaze in 50 of the 58 decompensated congenital palsies (86%) in whom those data were recorded. Hypertropia was never greatest in upgaze in the 15 patients with traumatic palsies. Vertical fusional amplitudes were increased in only 15 of 27 patients (56%) with decompensated palsies in whom those data were recorded. Torsional misalignment on double Maddox rod testing was present in 16 (94%), 13 (87%), and 3 (100%) patients with ischemic, traumatic, and tumorous palsies, but also in 19 patients (54%) with decompensated congenital palsies in whom those data were recorded.

Conclusions:
Hypertropia greater in upgaze than downgaze or equal in upgaze and downgaze was an efficient separator of congenital from ischemic and tumorous fourth nerve palsies, being characteristic of patients with decompensated congenital palsies and never present in patients with ischemic, traumatic, or tumorous palsies. Vertical fusional amplitudes and torsional misalignment did not effectively differentiate between the patient groups. Comparing the hypertropia in upgaze and downgaze improved differential diagnosis and reduces the potential for unnecessary ancillary tests.
A compound that directly and selectively stalls PCSK9 translation
Authors: Lintner Nathanael G. , McClure Kim F. , Petersen Donna , Londregan Allyn T. , Piotrowski David W. , Wei Liuqing , Xiao Jun , Bolt Michael , Loria Paula M. , Maguire Bruce , Geoghegan Kieran F. , Huang Austin , Rolph Tim , Liras Spiros , Doudna Jennifer A. , Dullea Robert G. , Cate Jamie H.D. 
Published: October 2016

AbstractProprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) plays a key role in regulating the levels of plasma low density lipoprotein cholesterol (LDL-C). Here we demonstrate that the compound PF-06446846 inhibits translation of PCSK9 by inducing the ribosome to stall around codon 34, mediated by the sequence of the nascent chain within the exit tunnel. We further show that PF-06446846 reduces plasma PCSK9 and total cholesterol levels in rats following oral dosing. Using ribosome profiling, we demonstrate that PF-06446846 is highly selective for the inhibition of PCSK9 translation. The mechanism of action employed by PF-06446846 reveals a previously unexpected tunability of the human ribosome, which allows small molecules to specifically block translation of individual transcripts.One Sentence SummaryA small-molecule PCSK9 inhibitor targets the human ribosome and selectively prevents PCSK9 synthesis.
Extremely fast and incredibly close: co-transcriptional splicing in budding yeast
Authors: Wallace Edward W.J. , Beggs Jean D. 
Published: October 2016

AbstractRNA splicing, an essential part of eukaryotic pre-messenger RNA processing, can be simultaneous with transcription by RNA polymerase II. Here, we compare and review independent next-generation sequencing methods that quantify co-transcriptional splicing in budding yeast. Splicing in yeast is fast, taking place within seconds of intron transcription, while polymerase is within a few dozens of nucleotides of the 3’ splice site. Ribosomal protein mRNAs are spliced particularly fast and co-transcriptionally. Intron-mediated regulation of some genes is also likely to be co-transcriptional. We suggest that intermediates of the splicing reaction, missing from current datasets, may hold key information about splicing kinetics.TrendsIndependent next-generation sequencing methods quantify co-transcriptional splicing in budding yeastRibosomal protein mRNAs are spliced particularly fast and co-transcriptionallyIntron-mediated regulation ofDBP2andRPS9Ais likely co-transcriptionalSplicing intermediates, missing from current datasets, may hold key information
Experimental and Computational Investigation of the Structure of Peptide Monolayers on Gold Nanoparticles
Authors: Colangelo Elena , Chen Qiubo , Davidson Adam M. , Paramelle David , Sullivan Michael B. , Volk Martin , Lévy Raphaël 
Published: October 2016

ABSTRACTThe self-assembly and self-organization of small molecules at the surface of nanoparticles constitute a potential route towards the preparation of advanced protein-like nanosystems. However, their structural characterization, critical to the design of bio-nanomaterials with well-defined biophysical and biochemical properties, remains highly challenging. Here, a computational model for peptide-capped gold nanoparticles is developed using experimentally characterized CALNN-and CFGAILSS-capped gold nanoparticles as a benchmark. The structure of CALNN and CFGAILSS monolayers is investigated by both structural biology techniques and molecular dynamics simulations. The calculations reproduce the experimentally observed dependence of the monolayer secondary structure on peptide capping density and on nanoparticle size, thus giving us confidence in the model. Furthermore, the computational results reveal a number of new features of peptide-capped monolayers, including the importance of sulfur movement for the formation of secondary structure motifs, the presence of water close to the gold surface even in tightly packed peptide monolayers, and the existence of extended 2D parallel β-sheet domains in CFGAILSS monolayers. The model developed here provides a predictive tool that may assist in the design of further bio-nanomaterials.
Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells
Authors: Danko Charles G. , Choate Lauren A. , Marks Brooke A. , Rice Edward J. , Wang Zhong , Chu Tinyi , Martins Andre L. , Dukler Noah , Coonrod Scott A. , Wojno Elia D. Tait , Lis John T. , Kraus W. Lee , Siepel Adam 
Published: October 2016

AbstractTranscriptional regulatory changes have been shown to contribute to phenotypic differences between species, but many questions remain about how gene expression evolves. Here we report the first comparative study of nascent transcription in primates. We used PRO-seq to map actively transcribing RNA polymerases in resting and activated CD4+ T-cells in multiple human, chimpanzee, and rhesus macaque individuals, with rodents as outgroups. This approach allowed us to measure transcription separately from post-transcriptional processes. We observed general conservation in coding and non-coding transcription, punctuated by numerous differences between species, particularly at distal enhancers and non-coding RNAs. We found evidence that transcription factor binding sites are a primary determinant of transcriptional differences between species, that stabilizing selection maintains gene expression levels despite frequent changes at distal enhancers, and that adaptive substitutions have driven lineage-specific transcription. Finally, we found strong correlations between evolutionary rates and long-range chromatin interactions. These observations clarify the role of primary transcription in regulatory evolution.
An Optimized Approach for Annotation of Large Eukaryotic Genomic Sequences using Genetic Algorithm
Authors: Chowdhury Biswanath , Garai Arnav , Garai Gautam 
Published: October 2016

ABSTRACTDetection of important functional and/or structural elements and identifying their positions in a large eukaryotic genome is an active research area. Gene is an important functional and structural unit of DNA. The computation of gene prediction is essential for detailed genome annotation. In this paper, we propose a new gene prediction technique based on Genetic Algorithm (GA) for determining the optimal positions of exons of a gene in a chromosome or genome. The correct identification of the coding and non-coding regions are difficult and computationally demanding. The proposed genetic-based method, named Gene Prediction with Genetic Algorithm (GPGA), reduces this problem by searching only one exon at a time instead of all exons along with its introns. The advantage of this representation is that it can break the entire gene-finding problem into a number of smaller subspaces and thereby reducing the computational complexity. We tested the performance of the GPGA with some benchmark datasets and compared the results with the well-known and relevant techniques. The comparison shows the better or comparable performance of the proposed method (GPGA). We also used GPGA for annotating the human chromosome 21 (HS21) using cross species comparison with the mouse orthologs.
Tempo and timing of ecological trait divergence in bird speciation
Authors: McEntee Jay P. , Tobias Joseph A. , Sheard Catherine , Burleigh J. Gordon 
Published: October 2016

Summary paragraphOrganismal traits may evolve either gradually or in rapid pulses followed by periods of stasis, but the relative importance of these evolutionary models in generating biodiversity has proven difficult to resolve1,2. In addition, while it is often assumed that pulses of trait evolution are associated with speciation events, few studies have explicitly examined how the tempo of trait divergence varies with respect to different geographical phases of speciation. Thus, we still know little about the trajectories of trait divergence over timescales relevant to speciation, or the extent to which these trajectories are shaped by variation in geographical isolation and overlap (sympatry) among incipient species. Here, we combine divergence time estimates, trait measurements, and geographic range data for avian sister species pairs worldwide to examine the tempo and timing of trait divergence during allopatric speciation. We show that divergence in two important ecological traits—?body mass and beak morphology—is best explained by a model including pulses of divergence and periods of relative stasis. We also infer that trait divergence pulses often precede sympatry, and that pulses leading to greater trait disparity are associated with earlier transitions to sympatry. These findings suggest that early pulses of trait divergence promote subsequent transitions to sympatry, rather than such pulses occurring after sympatry has been established, for example via character displacement3. Incorporating pulsed divergence models into allopatric speciation theory helps to resolve some apparently contradictory observations, including widespread instances of both rapid sympatry and prolonged geographical exclusion4-6.
The Effect of Compositional Context on Synthetic Gene Networks
Authors: Yeung Enoch , Dy Aaron J. , Martin Kyle B. , Ng Andrew H. , Del Vecchio Domitilla , Beck James L. , Collins James J. , Murray Richard M. 
Published: October 2016

SUMMARYIt is well known that synthetic gene expression is highly sensitive to how comprising genetic elements (promoter structure, spacing regions between promoter and coding sequences, ribosome binding sites, etc.) are spatially configured. An important topic that has received far less attention is how the physical layout of entire genes within a synthetic gene network affects their individual expression levels. In this paper we show, both quantitatively and qualitatively, that compositional context can significantly alter expression levels in synthetic gene networks. We also show that these compositional context effects are pervasive both at the transcriptional and translational level. Further, we demonstrate that key characteristics of gene induction, such as ultra-sensitivity and dynamic range, are heavily dependent on compositional context. We postulate that supercoiling can be used to explain these interference effects and validate this hypothesis through modeling and a series ofin vitrosupercoiling relaxation experiments. On the whole, these results suggest that compositional context introduces feedback in synthetic gene networks. As an illustrative example, we show that a design strategy incorporating compositional context effects can improve threshold detection and memory properties of the toggle switch.
Large-scale meta-analysis suggests low regional modularity in lateral frontal cortex
Authors: de la Vega Alejandro , Yarkoni Tal , Wager Tor D. , Banich Marie T. 
Published: October 2016

AbstractExtensive fMRI study of human lateral frontal cortex (LFC) has yet to yield a consensus mapping between discrete anatomy and psychological states, partly due to the difficulty of inferring mental states in individual studies. Here, we used a data-driven approach to generate a comprehensive functional-anatomical mapping of LFC from 11,406 neuroimaging studies. We identified putatively separable LFC regions on the basis of whole-brain co-activation, revealing 14 clusters organized into three whole-brain networks. Next, we used multivariate classification to identify the psychological states that best predicted activity in each sub-region, resulting in preferential psychological profiles. We observed large functional differences between networks, suggesting brain networks support distinct modes of processing. Within each network, however, we observed low functional specificity, suggesting discrete psychological states are not modularly organized. Our results are consistent with the view that individual LFC regions work as part of highly parallel, distributed networks to give rise to flexible, adaptive behavior.
Casein Kinase II is Required for Proper Cell Division and Acts as a Negative Regulator of Centrosome Duplication inC. elegansEmbryos
Authors: Medley Jeffrey C. , Kabara Megan M. , Stubenvoll Michael D. , DeMeyer Lauren E. , Song Mi Hye 
Published: October 2016

Summary statementThe conserved protein kinase CK2 negatively regulates centrosome assembly and is required for proper cell cycle progression and cytokinesis in earlyC. elegansembryos.AbstractCentrosomes are the primary microtubule-organizing centers that orchestrate microtubule dynamics during the cell cycle. The correct number of centrosomes is pivotal for establishing bipolar mitotic spindles that ensure accurate segregation of chromosomes. Thus, centrioles must duplicate once per cell cycle, one daughter per mother centriole, the process of which requires highly coordinated actions among core factors and modulators. Protein phosphorylation is shown to regulate the stability, localization and activity of centrosome proteins. Here, we report the function of Casein Kinase II (CK2) in earlyC. elegansembryos. The catalytic subunit (KIN-3/CK2α) of CK2 localizes to nuclei, centrosomes and midbodies. Inactivating CK2 leads to cell division defects, including chromosome missegregation, cytokinesis failure and aberrant centrosome behavior. Furthermore, depletion or inhibiting kinase activity of CK2 results in elevated ZYG-1 levels at centrosomes, restoring centrosome duplication and embryonic viability tozyg-1mutants. Our data suggest that CK2 functions in cell division and negatively regulates centrosome duplication in a kinase-dependent manner.
Creating sustainable cities through knowledge exchange
Authors: Hope Alex 
Published: October 2016

Purpose
The purpose of this paper is to examine the use of knowledge transfer partnership (KTP)as a means for universities to generate and exchange knowledge to foster sustainable cities and societies.

Design/methodology/approach
This paper reports on a series of separate yet interrelated KTPs between a university and the local authority in the North East of England, designed to enhance the environmental, social and economic performance of a large-scale urban housing procurement project.

Findings
Results from the partnerships indicate that KTPs may play a crucial role in developing capacity within local authorities tasked with creating sustainable cities and societies, whilst at the same time, enhancing skills and knowledge within the communities whom they represent and their industry partners.

Originality/value
The paper contributes an understanding as to how universities can act as a conduit for the generation and exchange of knowledge for sustainability. It presents a case study which examines how a series of KTPs can provide a useful mechanism for enhancing environmental, social and economic sustainability.
Finding the movement: the geographies of social movement scenes
Authors: Creasap Kimberly 
Published: October 2016

Purpose
A social movement scene is “a network of people who share a set of subcultural or countercultural beliefs, values, norms, and convictions as well as a network of physical spaces where members of that group are known to congregate” (Leach and Haunss 2009, p. 260, emphasis in the original). The purpose of this paper is to further develop theories of social movement scenes by examining the spatial dimensions of proximity, centrality, visibility, and accessibility, arguing that different scene configurations are shaped by gentrification processes.

Design/methodology/approach
This is an ethnographic study based on research conducted in Sweden over a five year period (2007-2012), including several summer research trips and a sustained fieldwork period of 14 months. Using snowball sampling, the author conducted semi-structured interviews with 38 activists involved in autonomous movement scenes. The author interviewed both men (n=26) and women (n=12) who ranged in age from 18 to 37, with most interviewees in their late 20s and early 30s.

Findings
Findings suggest that neighborhoods in the early stages of gentrification are most conducive to strong scenes. The author’s findings suggest that, while some of these conditions are locally specific, there were common structural conditions in each city, such as changes in the commercial landscape and housing tenure.

Originality/value
This paper contributes to the specificity of the concept of a social movement scene by presenting three spatial dimensions of scenes: centrality (relative to the Central Business District), concentration (clustering of scene places in one area of the city), and visibility (a visible presence communicated by signs and symbols). A second contribution of this paper is to offer a set of hypotheses about the urban conditions under which social movement scenes thrive (or fizzle).
How can organisations help employees thrive? The development of guidelines for promoting positive mental health at work
Authors: Davenport Lauren J. , Allisey Amanda F. , Page Kathryn M. , LaMontagne Anthony D. , Reavley Nicola J. 
Published: October 2016

PurposeBenefits of positive mental health have been demonstrated across work and non-work domains. Individuals reporting positive mental health experience better work performance, better social relationships and better physical health. Additionally, positive work environments can contribute to employee mental health. The purpose of this paper is to develop “expert” consensus regarding practical, actionable strategies that organisations can implement to promote positive mental health in the workplace.Design/methodology/approachA Delphi consensus method was used to establish expert consensus on strategies to promote positive workplace mental health. A 278-item questionnaire was developed and strategies were rated over three survey rounds by two panels comprising 36 workplace mental health practitioners and 36 employer representatives and employees (27 and 9, respectively), employees with experience of promoting positive mental health and well-being in the workplace (total – 72 panellists).FindingsIn total, 220/278 strategies were rated as essential or important by at least 80 per cent of both panels. Endorsed strategies covered the topics of: mental health and well-being strategy, work environment that promotes positive mental health, positive leadership styles, effective communication, designing jobs for positive mental health, recruitment and selection, supporting and developing employees, work-life balance, and positive mental health and well-being initiatives.Originality/valueThe guidelines arising from this study represent expert consensus on what is currently appropriate for promoting positive mental health at work from the perspectives of workplace mental health practitioners, employers and employees, and constitute a resource for translating the growing body of knowledge in this area into policy and practice.