bluuebunny/crossref_metadata_2025_split huggingface dataset:
Auditory Brainstem Response Altered in Humans With Noise Exposure Despite Normal Outer Hair Cell Function
Authors: Bramhall Naomi F. , Konrad-Martin Dawn , McMillan Garnett P. , Griest Susan E. 
Published: November 2016

Objectives:
Recent animal studies demonstrated that cochlear synaptopathy, a partial loss of inner hair cell-auditory nerve fiber synapses, can occur in response to noise exposure without any permanent auditory threshold shift. In animal models, this synaptopathy is associated with a reduction in the amplitude of wave I of the auditory brainstem response (ABR). The goal of this study was to determine whether higher lifetime noise exposure histories in young people with clinically normal pure-tone thresholds are associated with lower ABR wave I amplitudes.

Design:
Twenty-nine young military Veterans and 35 non Veterans (19 to 35 years of age) with normal pure-tone thresholds were assigned to 1 of 4 groups based on their self-reported lifetime noise exposure history and Veteran status. Suprathreshold ABR measurements in response to alternating polarity tone bursts were obtained at 1, 3, 4, and 6 kHz with gold foil tiptrode electrodes placed in the ear canal. Wave I amplitude was calculated from the difference in voltage at the positive peak and the voltage at the following negative trough. Distortion product otoacoustic emission input/output functions were collected in each participant at the same four frequencies to assess outer hair cell function.

Results:
After controlling for individual differences in sex and distortion product otoacoustic emission amplitude, the groups containing participants with higher reported histories of noise exposure had smaller ABR wave I amplitudes at suprathreshold levels across all four frequencies compared with the groups with less history of noise exposure.

Conclusions:
Suprathreshold ABR wave I amplitudes were reduced in Veterans reporting high levels of military noise exposure and in non Veterans reporting any history of firearm use as compared with Veterans and non Veterans with lower levels of reported noise exposure history. The reduction in ABR wave I amplitude in the groups with higher levels of noise exposure cannot be accounted for by sex or variability in outer hair cell function. This change is similar to the decreased ABR wave I amplitudes observed in animal models of noise-induced cochlear synaptopathy. However, without post mortem examination of the temporal bone, no direct conclusions can be drawn concerning the presence of synaptopathy in the study groups with higher noise exposure histories.
Mannose-Binding Lectin Levels in Critically Ill Children With Severe Infections*
Authors: Madsen Erik C. , Levy Emily R. , Madden Kate , Agan Anna A. , Sullivan Ryan M. , Graham Dionne A. , Randolph Adrienne G. 
Published: November 2016

Objectives:
Low mannose-binding lectin levels and haplotypes associated with low mannose-binding lectin production have been associated with infection and severe sepsis. We tested the hypothesis that mannose-binding lectin levels would be associated with severe infection in a large cohort of critically ill children.

Design:
Prospective cohort study.

Setting:
Medical and Surgical PICUs, Boston Children’s Hospital.

Patients:
Children less than 21 years old admitted to the ICUs from November 2009 to November 2010.

Interventions:
None.

Measurements and Main Results:
We measured mannose-binding lectin levels in 479 of 520 consecutively admitted children (92%) with severe or life-threatening illness. We genotyped 213 Caucasian children for mannose-binding lectin haplotype tagging variants and assigned haplotypes. In the univariate analyses of mannose-binding lectin levels with preadmission characteristics, levels were higher in patients with preexisting renal disease. Patients who received greater than 100 mL/kg of fluids in the first 24 hours after admission had markedly lower mannose-binding lectin, as did patients who underwent spinal fusion surgery. Mannose-binding lectin levels had no association with infection status at admission, or with progression from systemic inflammatory response syndrome to sepsis or septic shock. Although mannose-binding lectin haplotypes strongly influenced mannose-binding lectin levels in the predicted relationship, low mannose-binding lectin–producing haplotypes were not associated with increased risk of infection.

Conclusions:
Mannose-binding lectin levels are largely genetically determined. This relationship was preserved in children during critical illness, despite the effect of large-volume fluid administration on mannose-binding lectin levels. Previous literature evaluating an association between mannose-binding lectin levels and severe infection is inconsistent; we found no relationship in our PICU cohort. We found that mannose-binding lectin levels were lower after aggressive fluid resuscitation and suggest that studies of mannose-binding lectin in critically ill patients should assess mannose-binding lectin haplotypes to reflect preillness levels.
A Multilevel Analysis of U.S. Hospital Patient Safety Culture Relationships With Perceptions of Voluntary Event Reporting
Authors: Burlison Jonathan D. , Quillivan Rebecca R. , Kath Lisa M. , Zhou Yinmei , Courtney Sam C. , Cheng Cheng , Hoffman James M. 
Published: November 2016

Objectives
Patient safety events offer opportunities to improve patient care, but, unfortunately, events often go unreported. Although some barriers to event reporting can be reduced with electronic reporting systems, insight on organizational and cultural factors that influence reporting frequency may help hospitals increase reporting rates and improve patient safety. The purpose of this study was to evaluate the associations between dimensions of patient safety culture and perceived reporting practices of safety events of varying severity.

Methods
We conducted a cross-sectional survey study using previously collected data from The Agency for Healthcare Research and Quality Hospital Survey of Patient Safety Culture as predictors and outcome variables. The dataset included health-care professionals in U.S. hospitals, and data were analyzed using multilevel modeling techniques.

Results
Data from 223,412 individuals, 7816 work areas/units, and 967 hospitals were analyzed. Whether examining near miss, no harm, or potential for harm safety events, the dimension feedback about error accounted for the most unique predictive variance in the outcome frequency of events reported. Other significantly associated variables included organizational learning, nonpunitive response to error, and teamwork within units (all P < 0.001). As the perceived severity of the safety event increased, more culture dimensions became significantly associated with voluntary reporting.

Conclusions
To increase the likelihood that a patient safety event will be voluntarily reported, our study suggests placing priority on improving event feedback mechanisms and communication of event-related improvements. Focusing efforts on these aspects may be more efficient than other forms of culture change.
The Monarch Initiative: An integrative data and analytic platform connecting phenotypes to genotypes across species
Authors: Mungall Christopher J , McMurry Julie A , Köhler Sebastian , Balhoff James P. , Borromeo Charles , Brush Matthew , Carbon Seth , Conlin Tom , Dunn Nathan , Engelstad Mark , Foster Erin , Gourdine JP , Jacobsen Julius O.B. , Keith Daniel , Laraway Bryan , Lewis Suzanna E. , Nguyen Xuan Jeremy , Shefchek Kent , Vasilevsky Nicole , Yuan Zhou , Washington Nicole , Hochheiser Harry , Groza Tudor , Smedley Damian , Robinson Peter N. , Haendel Melissa A 
Published: November 2016

AbstractThe principles of genetics apply across the whole tree of life: on a cellular level, we share mechanisms with species from which we diverged millions or even billions of years ago. We can exploit this common ancestry at the level of sequences, but also in terms of observable outcomes (phenotypes), to learn more about health and disease for humans and all other species. Applying the range of available knowledge to solve challenging disease problems requires unified data relating genomics, phenotypes, and disease; it also requires computational tools that leverage these multimodal data to inform interpretations by geneticists and to suggest experiments. However, the distribution and heterogeneity of databases is a major impediment: databases tend to focus either on a single data type across species, or on single species across data types. Although each database provides rich, high-quality information, no single one provides unified data that is comprehensive across species, biological scales, and data types. Without a big-picture view of the data, many questions in genetics are difficult or impossible to answer. The Monarch Initiative (https://monarchinitiative.org) is an international consortium dedicated to providing computational tools that leverage a computational representation of phenotypic data for genotype-phenotype analysis, genomic diagnostics, and precision medicine on the basis of a large-scale platform of multimodal data that is deeply integrated across species and covering broad areas of disease.
All or Nothing: the False Promise of Anonymity
Authors: Walker Neil 
Published: November 2016

AbstractIn early 2016, the International Committee of Medical Journal Editors (ICMJE) proposed that responsible sharing of de-identified individual-level data be required for clinical trials published in their affiliated journals. There would be a delay in implementing this policy to allow for the necessary informed consents to work their way through ethical review. Meanwhile, some researchers and policy makers have conflated the notions of de-identification and anonymity. The former is a process that seeks to mitigate disclosure risk though careful application of rules and statistical analysis, while the latter is an absolute state. The consequence of confusing the process and the state is profound. Extensions to the ICMJE proposal based on the presumed anonymity of data include: sharing unconsented data; sharing data without managing access, as Open Data; and proposals to sell data. This essay aims to show that anonymity (the state) cannot be guaranteed by de-identification (the process), and so these extensions to the ICMJE proposal should be rejected on governance grounds, if no other. This is not as negative a position as it might seem, as other disciplines have been aware of these limitations and concomitant responsibilities for many years. The essay concludes with an example from social science of managed access strategies that could be adopted by the medical field.
The lexical categorization model: A computational model of left-ventral occipito-temporal cortex activation in visual word recognition
Authors: Gagl Benjamin , Richlan Fabio , Ludersdorfer Philipp , Sassenhagen Jona , Eisenhauer Susanne , Gregorova Klara , Fiebach Christian J. 
Published: November 2016

AbstractTo characterize the left-ventral occipito-temporal cortex (lvOT) role during reading in a quantitatively explicit and testable manner, we propose the lexical categorization model (LCM). The LCM assumes that lvOT optimizes linguistic processing by allowing fast meaning access when words are familiar and filter out orthographic strings without meaning. The LCM successfully simulates benchmark results from functional brain imaging. Empirically, using functional magnetic resonance imaging, we demonstrate that quantitative LCM simulations predict lvOT activation across three studies better than alternative models. Besides, we found that word-likeness, which is assumed as input to LCM, is represented posterior to lvOT. In contrast, a dichotomous word/non-word contrast, which is assumed as the LCM’s output, could be localized to upstream frontal brain regions. Finally, we found that training lexical categorization results in more efficient reading. Thus, we propose a ventral-visual-stream processing framework for reading involving word-likeness extraction followed by lexical categorization, before meaning extraction.
A novel restraint device for injection ofGalleria mellonellalarvae that minimises the risk of accidental operator needle stick injury
Authors: Dalton J.P. , Uy B. , Swift S. , Wiles S. 
Published: November 2016

AbstractLarvae of the insectGalleria mellonellaare increasingly being used for studying pathogenic microbes and their virulence mechanisms, and as a rapid model for screening novel antimicrobial agents. The larvae (waxworms) are most frequently infected by injection of pathogenic organisms into the haemocoel through the insect’s prolegs. The mostly widely used method for restraining the waxworms for injection is by grasping them between the operator’s fingers, which puts the operator at risk of needle stick injury, an important consideration when working with highly pathogenic and/or drug-resistant microorganisms. While use of a stab proof glove can reduce this risk of injury, it does so at the loss of manual dexterity and speed, resulting in a more labour-intensive and cumbersome assay. We describe a simple cost effective device (the so-called ‘GalleriaGrabber’) for restraining waxworms for injection that keeps the operator’s fingers clear of the needle thus reducing the risk of injury.
Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis
Authors: MacManes Matthew D. , Austin Suzanne H. , Booth Andrew , Austin April , Farrar Victoria , Calisi Rebecca M. 
Published: November 2016

ABSTRACTThe hypothalamic-pituitary-gonadal (HPG) axis is a key biological system required for reproduction and associated sexual behaviors to occur. In the avian reproductive model of the rock dove (Columba livia), we characterized the transcript community of each tissue of the HPG axis in both sexes, thereby significantly expanding our mechanistic insight into HPG activity. We report greater sex-biased differential expression in the pituitary as compared to the hypothalamus, with multiple genes more highly expressed in the male pituitary being related to secretory function, and multiple genes more highly expressed in the female pituitary being related to reproduction, growth, and development. We report tissue-specific and sex-biased expression in genes commonly investigated when studying reproduction, highlighting the need for sex parity in future studies. In addition, we uncover new targets of investigation in both sexes, which could potentially change our understanding of HPG function.
Feature-coding transitions to conjunction-coding with progression through human visual cortex
Authors: Cowell Rosemary A. , Serences John T. 
Published: November 2016

AbstractIdentifying an object and distinguishing it from similar items depends upon the ability to perceive its component parts as conjoined into a cohesive whole, but the brain mechanisms underlying this ability remain elusive. The ventral visual processing pathway in primates is organized hierarchically: Neuronal responses in its early stages are sensitive to the manipulation of simple visual features whereas neuronal responses in subsequent stages are tuned to increasingly complex stimulus attributes. It is widely assumed that feature-coding dominates in early visual cortex whereas later visual regions employ conjunction-coding in which object representations are different from the sum of their simple-feature parts. However, no study has demonstrated that putative object-level codes in higher visual cortex cannot be accounted for by feature-coding and that putative feature-codes in regions prior to ventral temporal cortex are not equally well characterized as object-level codes. Thus the existence of a transition from feature- to conjunction-coding in visual cortex remains unconfirmed, and, if a transition does occur, its location remains unknown. By employing multivariate analysis of human functional imaging data, we measure both feature-coding and conjunction-coding directly, using the same set of visual stimuli, and pit them against each other to reveal the relative dominance of one versus the other throughout cortex. We provide the first demonstration of a transition from feature-coding in early visual cortex to conjunction-coding in both inferior temporal and posterior parietal cortices. This novel method enables the use of experimentally controlled stimulus features to investigate population-level feature- and conjunction-codes throughout human cortex.
An evolving cancer instigates clonally unrelated neighboring cells to form distant metastases
Authors: Dong Jie , Darini Cedric , Kabeer Farhia , Dendievel Sarah , Min Junxia , Hambardzumyan Dolores , Gaboury Louis , Lenaerts Tom , Darrasse-Jèze Guillaume , Li Yi , Podsypanina Katrina 
Published: November 2016

AbstractBased on the clonal evolution theory of cancer formation, a single cell within a tissue gains a cancer-driving mutation and thus a growth advantage. From this expanded cellular mass, another cell gains a new mutation allowing this newly mutated cell to gain new competitive advantage and to expand in number (thus clonal expansion). Another clone then emerges. Eventually all required mutations are gained, and a cancer forms. Consequently, while a primary lesion may harbor divergent subclones, all the subclones within the primary cancer as well as all metastatic growths in secondary organs share at least the very first oncogenic mutation that initiates the primary cancer. However, by tracking genetically marked mammary epithelial cells that suffered the initiating oncogenic mutation—and their neighboring mammary cells that did not-in several mouse models of human breast cancer, we found that genetically unrelated mammary epithelial cells can be colluded by neighboring mutated cells to disseminate, and that they can even undergode novotumorigenic transformation and form distant metastases. Therefore, clonally unrelated epithelial cells may contribute to cancer progression and to the heterogeneity of the systemic disease. The non-linear cancer spread has important implications in cancer prevention, treatment, and therapeutic resistance.
Inferring the role of habitat dynamics in driving diversification: evidence for a species pump in Lake Tanganyika cichlids
Authors: Janzen Thijs , Etienne Rampal S. 
Published: November 2016

ABSTRACTGeographic isolation that drives speciation is often assumed to slowly increase over time, for instance through the formation of rivers, the formation of mountains or the movement of tectonic plates. Cyclic changes in connectivity between areas may occur with the advancement and retraction of glaciers, with water level fluctuations in seas between islands or in lakes that have an uneven bathymetry. These habitat dynamics may act as a driver of allopatric speciation and propel local diversity. Here we present a parsimonious model of the interaction between cyclical (but not necessarily periodic) changes in the environment and speciation, and provide an ABC-SMC method to infer the rates of allopatric and sympatric speciation from a phylogenetic tree. We apply our approach to the posterior sample of an updated phylogeny of theLamprologini, a tribe of cichlid fish from Lake Tanganyika where such cyclic changes in water level have occurred. We find that water level changes play a crucial role in driving diversity in Lake Tanganyika. We note that if we apply our analysis to the Most Credible Consensus (MCC) tree, we do not find evidence for water level changes influencing diversity in theLamprologini, suggesting that the MCC tree is a misleading representation of the true species tree. Furthermore, we note that the signature of habitat dynamics is found in the posterior sample despite the fact that this sample was constructed using a species tree prior that ignores habitat dynamics. However, in other cases this species tree prior might erase this signature. Hence we argue that in order to improve inference of the effect of habitat dynamics on biodiversity, phylogenetic reconstruction methods should include tree priors that explicitly take into account such dynamics.
Using the Volta phase plate with defocus for cryo-EM single particle analysis
Authors: Danev Radostin , Tegunov Dimitry , Baumeister Wolfgang 
Published: November 2016

AbstractPreviously, we reported an in-focus data acquisition method for cryo-EM single particle analysis with the Volta phase plate (VPP) (Danev and Baumeister, 2016). Here, we extend the technique to include a small amount of defocus which enables contrast transfer function measurement and correction. This hybrid approach simplifies the experiment and increases the data acquisition speed. It also enables 3D reconstructions with resolutions in the 2 Å range, demonstrating that, in practice, there are no resolution limitations imposed by the VPP.
Dynamical modelling of the heat shock response inChlamydomonas reinhardtii
Authors: Magni Stefano , Succurro Antonella , Skupin Alexander , Ebenhöh Oliver 
Published: November 2016

AbstractGlobal warming is exposing plants to more frequent heat stress, with consequent crop yield reduction. Organisms exposed to large temperature increases protect themselves typically with a heat shock response (HSR). To study the HSR in photosynthetic organisms we present here a data driven mathematical model describing the dynamics of the HSR in the model organismChlamydomonas reinhartii. Temperature variations are sensed by the accumulation of unfolded proteins, which activates the synthesis of heat shock proteins (HSP) mediated by the heat shock transcription factor HSF1. Our dynamical model employs a system of ordinary differential equations mostly based on mass-action kinetics to study the time evolution of the involved species. The signalling network is inferred from data in the literature, and the multiple experimental data-sets available are used to calibrate the model, which allows to reproduce their qualitative behaviour. With this model we show the ability of the system to adapt to temperatures higher than usual during heat shocks longer than three hours by shifting to a new steady state. We study how the steady state concentrations depend on the temperature at which the steady state is reached. We systematically investigate how the accumulation of HSPs depends on the combination of temperature and duration of the heat shock. We finally investigate the system response to a smooth variation in temperature simulating a hot day.