bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utility of Flexible Bronchoscopic Cryobiopsy for Diagnosis of Diffuse Parenchymal Lung Diseases
Authors: Lentz Robert J. , Taylor Trevor M. , Kropski Jonathan A. , Sandler Kim L. , Johnson Joyce E. , Blackwell Timothy S. , Maldonado Fabien , Rickman Otis B. 
Published: August 2017

Background:
Initial reports of transbronchial cryobiopsy for diffuse parenchymal lung disease (DPLD) suggest the diagnostic yield approaches that of surgical lung biopsy (SLB) with an excellent safety profile. Centers performing cryobiopsy differ significantly in procedure technique; an optimal technique minimizing complications but still capable of diagnosing a wide range of DPLDs has not been established. We evaluated our practice of flexible bronchoscopic cryobiopsy in a primarily outpatient setting for patients who required a tissue diagnosis for DPLD of uncertain etiology.

Methods:
Consecutive patients with indeterminate DPLD who underwent bronchoscopic cryobiopsy at a large academic medical center from January 2012 to August 2015 were retrospectively analyzed. Rates of confident histopathologic diagnosis, confident multidisciplinary consensus diagnosis, management change, and complications were determined.

Results:
One hundred four cases were identified. Confident histopathologic diagnoses were established in 44% (46/104) and confident multidisciplinary consensus diagnoses in 68% (71/104). Usual interstitial pneumonia (19/104) and idiopathic pulmonary fibrosis (22/104) were the most common histopathologic and consensus diagnoses, respectively. Five subjects proceeded to SLB after cryobiopsy which was diagnostic in 3. Results of cryobiopsies changed management in 70% (73/104). Complications occurred in 8 cases with no death.

Conclusions:
Cryobiopsy during outpatient flexible bronchoscopy facilitated confident multidisciplinary consensus diagnosis of DPLD in more than two thirds of cases, and appears sufficient to establish the histopathologic diagnosis of usual interstitial pneumonia, with a complication rate that compares favorably to that reported for SLB.
Audiometric Outcomes Following Endoscopic Ossicular Chain Reconstruction
Authors: Yawn Robert J. , Hunter Jacob B. , O’Connell Brendan P. , Wanna George B. , Killeen Daniel E. , Wick Cameron C. , Isaacson Brandon , Rivas Alejandro 
Published: August 2017

Objective:
To evaluate the audiometric outcomes following endoscopic ossicular chain reconstruction (OCR).

Study Design:
Retrospective case series.

Setting:
Two tertiary referral centers.

Patients:
Sixty two ears with ossicular discontinuity.

Intervention(s):
Endoscopic and microscopic OCR in patients with ossicular discontinuity.

Main Outcome Measures:
Bone and air pure-tone averages (PTA), air-bone gap (ABG), and word recognition scores (WRS).

Results:
Sixty two ears were included for analysis. Patients that underwent ossiculoplasty were subdivided based on prosthesis type (total ossicular replacement prosthesis [TORP] and partial ossicular replacement prosthesis [PORP], primary and staged ossiculoplasties, and surgical approach [microscopic and total endoscopic]). Forty two ears required PORP reconstructions, while 20 ears required TORP reconstructions. The microscope was used to reconstruct the ossicular chain in 31 cases, while an exclusive endoscopic approach was used in the remaining 31 patients. Controlling for the prosthesis, there were no significant postoperative differences in bone PTA, air PTA, and ABG between primary and staged ossiculoplasties, or surgical approach.

Conclusions:
Controlling for the type of prosthesis, there were no significant differences in hearing outcomes with respect to staged ossicular chain reconstruction or whether the endoscope or microscope was used for visualization. Thus, in this series, endoscopic OCR yields similar audiometric outcomes when compared with microscopic OCR.
The Seasonal Variation of Benign Paroxysmal Positional Vertigo
Authors: Meghji Sheneen , Murphy Declan , Nunney Ian , Phillips John S. 
Published: August 2017

Objective:
Benign paroxysmal positional vertigo (BPPV) is characterized by recurrent episodes of positional vertigo due to dislodged otoconia debris within the semicircular canals. Many studies have proposed a correlation between Vitamin-D deficiency and recurrent BPPV. In the UK, serum Vitamin-D falls during the winter, reaching its lowest level in May and it is highest level in September. We hypothesize that if there is a relationship between BPPV and Vitamin-D levels, one would expect to see a seasonal variation in the incidence of BPPV among UK residents.

Methods:
A retrospective review of clinic letters and general practitioner referrals for patients presenting to a University Otolaryngology department over a 4-year period. Patients were divided into two groups: those presenting during the months associated with low serum Vitamin-D levels, and those presenting during the months associated with high serum Vitamin-D levels.

Results:
Three hundred thirty-nine patients were identified with posterior canal BPPV as a consequence of having had a positive Dix-Hallpike maneuver recorded in the clinical notes between October 2012 and October 2016. A Wilcoxon rank-sum test demonstrated there to be a statistically significant difference between the low serum Vitamin-D group and the high serum Vitamin-D group (p
= 0.0367).

Conclusion:
The results confirm that there is a seasonal variation in the incidence of BPPV. This study is important as it adds to the mounting literature suggesting an association between serum Vitamin-D levels and BPPV. Second, it suggests a therapeutic strategy to improve outcomes in affected patients. Third, it adds significance to the hypothesized role of calcium metabolism for the development of inner ear disease.
Intracanalicular Vestibular Schwannomas: Initial Clinical Manifestation, Imaging Classification, and Risk Stratification for Management Proposal
Authors: Younes Elias , Montava Marion , Bachelard-Serra Mathilde , Jaloux Laurent , Salburgo Florent , Lavieille Jean Pierre 
Published: August 2017

Introduction:
There is no consensus about the use of observation as a therapeutic modality for intracanalicular vestibular schwannoma (ICVS). The objective of this study was to describe tumor evolution, its correlation with initial size, stage of vestibular schwannoma, clinical presentation and to propose a risk classification for tumor growth with a therapeutic decision algorithm.

Methods:
Fifty-three patients with ICVS were followed prospectively from 2010 to 2015. The mean follow-up was 32 months. Patients underwent clinical examination, audiogram, magnetic resonance imaging at 6, 12, and then 12 months intervals within the first 5 years of initial diagnosis. We analyzed the patient's clinical course, audiologic changes, initial tumor location, and correlation of different parameters with ICVS growth.

Results:
Fourteen patients (26%) deteriorated their hearing level and 17 patients (27%) showed tumor growth during the follow-up period. Growth was noted during the first year of observation in 13 patients (76.5%). Considering initial presentation: tumor size, intracanalicular staging, and hearing level, patients with larger vestibular schwannoma, extension to the fundus regardless of tumor size, higher initial pure-tone average, and speech recognition test showed a significantly higher rate of tumor growth. ICVS evolution was not correlated with hearing deterioration with time.

Discussion:
We should consider observation a therapeutic modality. We valid the intrameatal staging as prognostic factor and propose a stratification of patients into low, moderate, or high risk for potential tumor growth to guide the initial management of ICVS.
A New Slim Modiolar Electrode Array for Cochlear Implantation: A Radiological and Histological Study
Authors: Iso-Mustajärvi Matti , Matikka Hanna , Risi Frank , Sipari Sini , Koski Teemu , Willberg Tytti , Lehtimäki Antti , Tervaniemi Jyrki , Löppönen Heikki , Dietz Aarno 
Published: August 2017

Hypothesis:
To explore the results of a new slim modiolar electrode array (SMA) with respect to intracochlear placement and trauma evaluated by detailed radiologic imaging and histology.

Background:
Hearing and structure preservation is the goal of cochlear implantation for advanced hearing outcomes. Currently, this is most consistently achieved with thin lateral wall electrodes. Modiolar electrodes are located nearer the modiolus and may provide some electrophysiological advantages, but have a greater tendency for causing insertion trauma.

Methods:
The SMA was implanted in 20 fresh-frozen human temporal bones (TB). All TBs were scanned pre- and postoperatively with cone beam computed tomography. For atraumatic insertion, the round window approach was preferred. Scalar localization and trauma were analyzed by three-dimensional image fusion reconstructions of the pre- and postimplant scans. The TBs underwent histologic examination to validate the radiologic findings.

Results:
Insertion through the round window was performed in 19 TBs and through a cochleostomy in one TB. In one TB trauma in the form of scala translocation was identified radiologically and histologically. In the remaining TBs there was no insertion trauma. Adequate modiolar localization of the SMA was found in 19 of 20 TBs. The mean angular insertion depth was 400 degrees without correlation to cochlea size. There was no significant statistical difference between the radiological and histological measurements of electrode localization.

Conclusion:
The SMA showed consistent and atraumatic insertion results in TBs. Pre- and postimplant cone beam computed tomography with image fusion was shown to be very accurate for the assessment of electrode position and insertion trauma.
Nurse Manager Engagement
Authors: Conley Karen A. 
Published: August 2017

OBJECTIVE
This study provided insight into the level of engagement of nurse managers (NMs) and strategies used to achieve and sustain engagement in acute care settings.

BACKGROUND
Nurse managers have a significant role in staff satisfaction and unit outcomes and therefore need to be engaged in their work to influence others. Little is known about the level of individual NM engagement and strategies they use to remain engaged.

METHODS
A mixed methods approach was used to elicit information about NM engagement. This study used a sample of 47 NMs to measure their level of engagement, and for those achieving scores indicating high levels of engagement, interviews were conducted, and a content analysis was completed to identify themes.

RESULTS
Results showed that there were significantly higher levels of NM engagement among those managers who had been practicing as nurse leaders for a longer period and also those who had advanced degrees. Qualitative review revealed the themes of expert communication, autonomy, and influence as the key factors driving NM engagement.

CONCLUSIONS
The role of the nurse executive in NM engagement is significant in supporting educational advancement and retention, both of which proved to have an impact on the level of engagement.
Diffusion Basis Spectral Imaging Detects Ongoing Brain Inflammation in Virologically Well-Controlled HIV+ Patients
Authors: Strain Jeremy F. , Burdo Tricia H. , Song Sheng-Kwei , Sun Peng , El-Ghazzawy Omar , Nelson Brittany , Westerhaus Elizabeth , Baker Laurie , Vaida Florin , Ances Beau M. 
Published: August 2017

Abstract:
Inflammation occurs after HIV infection and persists, despite highly active antiretroviral therapy (HAART). Diffusion tensor imaging (DTI) measures HIV-associated white matter changes, but can be confounded by inflammation. Currently, the influence of inflammation on white matter integrity in well-controlled HIV+ patients remains unknown. We used diffusion basis spectral imaging (DBSI)-derived cellularity to isolate restricted water diffusion associated with inflammation separated from the anisotropic diffusion associated with axonal integrity. Ninety-two virologically suppressed HIV+ patients on HAART and 66 HIV uninfected (HIV−) controls underwent neuropsychological performance (NP) testing and neuroimaging. NP tests assessed multiple domains (memory, psychomotor speed, and executive functioning). DTI- and DBSI-derived fractional anisotropy (FA) maps were processed with tract-based spatial statistics for comparison between both groups. Cellularity was assessed regarding age, HIV status, and NP. Within the HIV+ cohort, cellularity was compared with clinical (HAART duration) and laboratory measures of disease (eg, CD4 cell current and nadir). NP was similar for both groups. DTI-derived FA was lower in HIV+ compared with HIV− individuals. By contrast, DBSI-derived FA was similar for both groups. Instead, diffuse increases in cellularity were present in HIV+ individuals. Observed changes in cellularity were significantly associated with age, but not NP, in HIV+ individuals. A trend level association was seen between cellularity and HAART duration. Elevated inflammation, measured by cellularity, persists in virologically well-controlled HIV+ individuals. Widespread cellularity changes occur in younger HIV+ individuals and diminish with aging and duration of HAART.
Biogeochemical modelling of dissolved oxygen in a changing ocean
Authors: Andrews Oliver , Buitenhuis Erik , Le Quéré Corinne , Suntharalingam Parvadha 
Published: August 2017

Secular decreases in dissolved oxygen concentration have been observed within the tropical oxygen minimum zones (OMZs) and at mid- to high latitudes over the last approximately 50 years. Earth system model projections indicate that a reduction in the oxygen inventory of the global ocean, termed ocean deoxygenation, is a likely consequence of on-going anthropogenic warming. Current models are, however, unable to consistently reproduce the observed trends and variability of recent decades, particularly within the established tropical OMZs. Here, we conduct a series of targeted hindcast model simulations using a state-of-the-art global ocean biogeochemistry model in order to explore and review biases in model distributions of oceanic oxygen. We show that the largest magnitude of uncertainty is entrained into ocean oxygen response patterns due to model parametrization ofpCO2-sensitive C : N ratios in carbon fixation and imposed atmospheric forcing data. Inclusion of apCO2-sensitive C : N ratio drives historical oxygen depletion within the ocean interior due to increased organic carbon export and subsequent remineralization. Atmospheric forcing is shown to influence simulated interannual variability in ocean oxygen, particularly due to differences in imposed variability of wind stress and heat fluxes.This article is part of the themed issue ‘Ocean ventilation and deoxygenation in a warming world’.
Identification of different putative outer membrane electron conduits necessary for Fe(III) citrate, Fe(III) oxide, Mn(IV) oxide, or electrode reduction byGeobacter sulfurreducens
Authors: Otero Fernanda Jiménez , Chan Chi Ho , Bond Daniel R. 
Published: August 2017

AbstractAt least five gene clusters in theGeobacter sulfurreducensgenome encode putative ‘electron conduits’ implicated in electron transfer across the outer membrane, each containing a periplasmic multihemec-type cytochrome, integral outer membrane anchor, and outer membrane redox lipoprotein(s). Markerless single gene cluster deletions and all possible multiple deletion combinations were constructed and grown with soluble Fe(III) citrate, Fe(III)- and Mn(IV)-oxides, and graphite electrodes poised at +0.24 V and −0.1 V vs. SHE. Different gene clusters were necessary for reduction of each electron acceptor. During metal oxide reduction, deletion of the previously describedomcBCcluster caused defects, but deletion of additional components in an ΔomcBCbackground, such asextEFG, were needed to produce defects greater than 50% compared to wild type. Deletion of all five gene clusters abolished all metal reduction. During electrode reduction, only the ΔextABCDmutant had a severe growth defect at both redox potentials, while this mutation did not affect Fe(III)-oxide, Mn(IV)-oxide, or Fe(III) citrate reduction. Some mutants containing only one cluster were able to reduce particular terminal electron acceptors better than wild type, suggesting routes for improvement by targeting specific electron transfer pathways. Transcriptomic comparisons between fumarate and electrode-based growth showed all of theseextclusters to be constitutive, and transcriptional analysis of the triple-deletion strain containing onlyextABCDdetected no significant changes in expression of known redox proteins or pili components. These genetic experiments reveal new outer membrane conduit complexes necessary for growth ofG. sulfurreducens, depending on the available extracellular electron acceptor.
dRNA-seq implicates sulfide as master regulator of S(0) metabolism inChlorobaculum tepidumand other green sulfur bacteria
Authors: Hilzinger Jacob M. , Raman Vidhyavathi , Shuman Kevin E. , Eddie Brian J. , Hanson Thomas E. 
Published: August 2017

AbstractThe green sulfur bacteria (Chlorobiaceae) are anaerobes that use electrons from reduced sulfur compounds (sulfide, S(0), and thiosulfate) as electron donors for photoautotrophic growth.Chlorobaculum tepidum, the model system for theChlorobiaceae, both produces and consumes extracellular S(0) globules depending on the availability of sulfide in the environment. These physiological changes imply significant changes in gene regulation, which has been observed when sulfide is added toCba. tepidumgrowing on thiosulfate. However, the underlying mechanisms driving these gene expression changes, i.e. specific regulators and promoter elements involved, have not yet been defined. Here, differential RNA-seq (dRNA-seq) was used to globally identify transcript start sites (TSS) that were present during growth on sulfide, biogenic S(0), and thiosulfate as sole electron donors. TSS positions were used in combination with RNA-seq data from cultures growing on these same electron donors to identify both basal promoter elements and motifs associated with electron donor dependent transcriptional regulation. These motifs were conserved across homologousChlorobiaceaepromoters. Two lines of evidence suggest that sulfide mediated repression is the dominant regulatory mode inCba. tepidum. First, motifs associated with genes regulated by sulfide overlap key basal promoter elements. Second, deletion of the gene CT1277, encoding a putative regulatory protein, leads to constitutive over-expression of the sulfide:quinone oxidoreductase CT1087 in the absence of sulfide. The results suggest that sulfide is the master regulator of sulfur metabolism inCba. tepidumand theChlorobiaceae. Finally, the identification of basal promoter elements with differing strengths will further the development of synthetic biology inCba. tepidumand perhaps otherChlorobiaceae.ImportanceElemental sulfur is a key intermediate in biogeochemical sulfur cycling. The photoautotrophic green sulfur bacteriumChlorobaculum tepidumboth produces and consumes elemental sulfur depending on the availability of sulfide in the environment. Our results reveal transcriptional dynamics ofChlorobaculum tepidumon elemental sulfur, and increase our understanding of the mechanisms of transcriptional regulation governing growth on different reduced sulfur compounds. This study identifies new genes and sequence motifs that likely play significant roles in the production and consumption of elemental sulfur. Beyond this focused impact, this study paves the way for the development of synthetic biology inChlorobaculum tepidumand otherChlorobiaceaeby providing a comprehensive identification of promoter elements to control gene expression, a key element of strain engineering.
Cpk2, a catalytic subunit of cyclic AMP-PKA, regulates growth and pathogenesis in rice blast
Authors: Selvaraj Poonguzhali , Shen Qing , Yang Fan , Naqvi Naweed I. 
Published: August 2017

SummaryThe cAMP-Protein Kinase A signalling, anchored on CpkA, is necessary for appressorium development and host penetration, but indispensable for infectious growth inMagnaporthe oryzae. In this study, we identified and characterized the gene encoding the second catalytic subunit,CPK2, whose expression was found to be lower compared toCPKAat various stages of pathogenic growth inM. oryzae. Deletion ofCPK2 caused no alterations in vegetative growth, conidiation, appressorium formation, or pathogenicity. Surprisingly, thecpkAΔcpk2Δ double deletion strain displayed significant reduction in growth rate and conidiation compared to the single deletion mutants. Interestingly, loss ofCPKAandCPK2resulted in morphogenetic defects in germ tubes (with curled/wavy and serpentine growth pattern) on hydrophobic surfaces, and a complete failure to produce appressoria therein, thus suggesting an important role forCPK2-mediated cAMP-PKA in surface sensing and response pathway.CPKApromoter-drivenCPK2expression partially suppressed the defects in host penetration and pathogenicity in thecpkAΔ. Such ectopicCPK2expressing strain successfully penetrated the rice leaves, but was unable to produce proper secondary invasive hyphae, thus underscoring the importance of CpkA in growth and differentiationin planta. The Cpk2-GFP localized to the nucleus and cytoplasmic vesicles in conidia and the germ tubes. The Cpk2-GFP colocalized with CpkA-mCherry on vesicles in the cytosol, but such overlap was not evident in the nucleus. Our studies indicate that CpkA and Cpk2 share overlapping functions, but also play distinct roles during pathogenesis-associated signalling and morphogenesis in the rice blast fungus.
Intrauterine position probabilities in mice, rats and gerbils
Authors: Mulley John F , Kuncheva Ludmila I 
Published: August 2017

ABSTRACTThe position of a developing embryo or foetus relative to members of the same or opposite sex can have profound effects on its resulting anatomy, physiology and behavior. Here we treat intrauterine position as a combinatorial problem and determine the theoretical probability of having 0, 1 or 2 adjacent foetuses of the opposite sex for species with random and biased distribution of genders in uterine horns (mice and gerbils), and where the influence of an “upstream” male has been proposed to be a factor (rats). As overall litter size increases the probabilities of having 0, 1, or 2 adjacent foetuses of the opposite sex approaches and eventually settles at 0.25, 0.5, 0.25 respectively. However, at biologically-relevant litter sizes probabilities are more variable and the general effect of an increase in litter size is to increase the probability that any particular foetus will be flanked by two members of the opposite sex. When gender ratios within a uterine horn are no longer balanced, the probability that there are 0 adjacent foetuses of the opposite sex increases.