bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lung Ultrasound After Transbronchial Biopsy for Pneumothorax Screening in Post–Lung Transplant Patients
Authors: Bensted Karen , McKenzie Jane , Havryk Adrian , Plit Marshall , Ben-Menachem Erez 
Published: October 2017

Background:
Lung ultrasound has been suggested as an alternative to routine chest radiography (CXR) to screen for pneumothorax after transbronchial lung biopsy. In post–lung transplant patients, who may have altered anatomy and pleural adhesions, the validity of lung ultrasound to screen for postbiopsy pneumothoraces has not been investigated.

Methods:
Lung ultrasound using an ultraportable handheld device was performed in a standardized manner 2-hour after biopsy in post–lung transplant patients. Ultrasound assessment was then compared with CXR performed immediately after lung ultrasound.

Results:
In total, 165 patients were enrolled in the study. Eight pneumothoraces were diagnosed by image intensifier or CXR before lung ultrasound. There were 8 pneumothoraces diagnosed on CXR 2-hour postbiopsy. Lung ultrasound had a sensitivity of 75% and specificity of 93%. Positive predictive value was 35% and negative predictive value was 99%. The mean number of biopsies taken in patients with and without a pneuomothorax on CXR was 10.6 (±3.1) and 10.9 (±2.1), respectively (P=0.79). The overall pneumothorax rate was 9.7%.

Conclusions:
Lung ultrasound is a valid tool in excluding penumothoraces after lung biopsy. Ultrasound scans with features of a pneumothorax or patients with symptoms should still undergo CXR. The high false positive rate may be due to small pneumothoraces being seen or the presence of pleural adhesions and altered lung anatomy in post–lung transplant patients.
Endobronchial Ultrasound Transbronchial Needle Aspiration for the Diagnosis of Lymphoma
Authors: Gandotra Sheetal , Dotson Travis , Lamar Zanetta , Bellinger Christina 
Published: October 2017

Background:
Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) presents a minimally invasive way to evaluate abnormal mediastinal and hilar adenopathy. Although EBUS has been established as an effective modality to diagnose lung cancer, its sensitivity for the diagnosis of lymphoma has been demonstrated to be lower. Because of these lower yields uncertainty persists about the ability of EBUS-TBNA to reliably diagnose lymphoma and questions remain regarding the utility of EBUS-TBNA as a first-line biopsy modality for patients suspected of having lymphoma.

Methods:
We conducted a review of our database (n=806 EBUS-TBNAs) for patients undergoing EBUS-TBNA for mediastinal and/or hilar lymphadenopathy over an 8-year span to identify patients diagnosed with lymphoma.

Results:
Twenty patients (2.3%) who underwent EBUS-TBNA were ultimately diagnosed with lymphoma. In total, 17 of the 20 patients with lymphoma obtained a diagnosis using EBUS-TBNA. The overall sensitivity of EBUS-TBNA for lymphoma was 85%. The sensitivity for de novo diagnosis was 78% (7/9), and sensitivity for recurrence was 91% (10/11). All patients who achieved a diagnosis by EBUS-TBNA could be adequately subtyped, allowing treatment recommendations.

Conclusion:
Although the sensitivity of EBUS-TBNA for the diagnosis of lymphoma did not reach values of published data for non–small cell lung cancer, EBUS-TBNA can be considered as a first-line diagnostic tool for patients with mediastinal and/or hilar lymphadenopathy suspected to be lymphoma. Because of the inherent limitations in small volume needle biopsies it is essential that negative samples obtained in the setting of high clinical suspicion warrant further evaluation.
How Was Your Otology Training? A Survey of Recent Otolaryngology Residents
Authors: Montague Phillip , Bennett Donald , Kellermeyer Brian 
Published: October 2017

Objective:
To survey graduating residents or recent graduates of otolaryngology residency programs to evaluate their Otology/Neurotology (ON) experience in residency and discern if they had received adequate training in time to decide whether to pursue a fellowship in Otology or Neurotology.

Study Design:
Internet-based survey.

Methods:
A survey was distributed to all US otolaryngology residency programs to distribute to 5th year residents and recent graduates in last 4 years. The survey assessed satisfaction in ON experience, presence of ON fellows, adequacy of experience to decide on ON fellowship, post-graduate year (PGY) year at which residents observed, performed, and proficiently performed five procedures (tympanoplasty, mastoidectomy, ossiculoplasty, stapedectomy, and cochlear implant), and plan for performing these surgeries in practice.

Results:
89/106 (84%) of respondents felt they had adequate training in Otology in time to decide whether or not to pursue a fellowship and were found to observe and perform surgeries significantly earlier in training by PGY including: mastoidectomy (observed PGY 1.9 versus PGY 2.3, performed PGY 2.9 versus PGY 3.5), ossiculoplasty (observed 2.1 versus 3.0, performed 3.6 versus 4.3), stapedectomy (observed 2.3 versus 3.0, performed 3.9 versus 4.5), and cochlear implant (observed 2.1 versus 2.8, performed 3.4 versus 4.1) all p < 0.05. There were 19/106 (17.9%) respondents who came from programs with fellowships and 78.9% thought fellows were beneficial to their ON experience.

Conclusions:
Early exposure to ON surgeries may aid in residents’ decision to pursue a fellowship in ON. The presence of fellows appears to facilitate residents’ ON experience.
Transarterial chemoembolization for hepatocellular carcinoma: development and external validation of the Munich-TACE score
Authors: op den Winkel Mark , Nagel Dorothea , op den Winkel Philip , Trojan Jörg , Paprottka Philipp M. , Steib Christian J. , Schmidt Laura , Göller Markus , Stieber Petra , Göhring Peter , Herbst Andreas , Rentsch Markus , De Toni Enrico N. , Göke Burkhard , Gerbes Alexander L. , Kolligs Frank T. 
Published: October 2017

Background
Allocation of patients with hepatocellular carcinoma (HCC) to the adequate therapy is determined by both tumor burden and liver function. The Barcelona Clinic Liver Cancer (BCLC) staging system and therapeutic algorithm recommends transarterial chemoembolization (TACE) based on the best evidence available to patients with intermediate-stage HCC (BCLC-B). However, many centers also treat subgroups of patients outside these recommendations and with more advanced disease by TACE. The purpose of this study was to identify prognostic factors in a TACE cohort, including BCLC-B patients, as well as patients treated outside of BCLC-B, to test the prognostic capabilities of published staging systems and to optimize prognostication for TACE patients.

Patients and methods
A cohort of 186 first-line TACE patients was analyzed. Independent prognostic factors were identified and used to construct the Munich-TACE score (M-TACE). M-TACE was tested against established staging systems (including BCLC and two recently published TACE-specific scores) and a ranking using concordance index and Akaike Information Criterion was performed. Finally, an external validation in an independent TACE cohort (n=71) was conducted.

Results
Bilirubin, Quick/international normalized ratio, C-reactive protein, creatinine, α-feto protein, and tumor extension were identified as independent prognostic factors and used to construct M-TACE. M-TACE identifies three distinct subgroups (P<0.0001) with median survival times of 35.2, 16.9, and 8.6 months, respectively. Compared with established staging systems, M-TACE showed the best prognostic capabilities in both cohorts of patients (cohort 1: c-index, 0.71; Akaike Information Criterion: 1276; cohort 2: c-index, 0.754).

Conclusion
We identified independent risk factors for patients treated with TACE. The newly constructed M-TACE score is superior to established staging systems and might prove helpful to identify patients who are most suitable for TACE.
Evaluation of the Cardiac Morphologic Alterations Secondary to Autoimmune Thyroid Disorder Using Cardiac Magnetic Resonance Imaging
Authors: Zandieh Shahin , Schuck Linus , Mirzaei Siroos , Haller Joerg , Hergan Klaus , Bernt Reinhard 
Published: October 2017

Purpose:
Thyroid functional disease is associated with clinically significant cardiovascular changes. The aim of this study was to assess changes in the cardiac magnetic resonance imaging of patients with autoimmune thyroid disorders (AITs).

Materials and Methods:
Forty patients with AIT (12 men, 28 women; age range, 20 to 82 y; mean age, 59 y) were identified and included in our study. In addition, 20 controls (12 men, 8 women; age range, 21 to 76 y; mean age, 50 y) without AIT or cardiac disorders were included.

Results:
In patients with AIT, the mean value calculated for the end diastolic volume was 161.2 mL, the mean end systolic volume value was 95.3 mL, and the mean left ventricular ejection fraction value was 45.2%. In comparing AIT patients with the control group, we found a significant difference in the end systolic volume, ejection fraction, stroke index, cardiac output, cardiac index, and left ventricular diameter (P<0.05).

Conclusions:
We conclude that our data show that there is a correlation between thyroid function and cardiac function, as evaluated with cardiac magnetic resonance imaging. This can be useful in the diagnosis of cardiovascular changes associated with AIT.
Users Guide to Pitfalls and Lessons Learned About HBOC-201 During Clinical Trials, Expanded Access, and Clinical Use in 1,701 Patients
Authors: Mackenzie Colin F. , Dubé Gregory P. , Pitman Arkaidy , Zafirelis Melissa 
Published: October 2017

ABSTRACT
Lessons learned during 1,701 clinical uses of HBOC-201, a polymerized bovine hemoglobin-based oxygen carrier (HBOC), were identified to provide management lessons and training material for future clinical trials and use. HBOC-201 contains 13 g/dL hemoglobin (Hb), is iso-oncotic, stable at 2°C to 30°C with shelf-life of 3 years, requires no cross-matching with half-life of 19 h, and plasma volume distribution. Adverse effects include increased blood pressure, oliguria, gastrointestinal (GI) symptoms, yellow skin and scleral discoloration, decreased pulse oximetry measurements, and transient increases in methemoglobin, hepatic, and pancreatic enzymes. There was no cardiotoxicity. Elevations in blood pressure were transient and were managed with vasodilators. Oliguria was of limited duration. GI symptoms were treated with smooth muscle relaxants. Yellow skin and sclera were self-limiting, caused by Hb metabolism. The most important clinical management errors were lack of understanding of volume expansion effects and the half-life properties of HBOC-201, and failure to repeat infusions. Early use of HBOC-201 for Expanded Access when Hb less than 5 g/dL optimized survival and minimized advanced resource utilization. For phase 3 trials, there was transfusion avoidance of 96% for 24 h, 70% for 1 week, with no difference in serious adverse events or mortality whether patients received at most 10 bags HBOC-201 or at most 3 units blood. More nonserious events occurred with HBOC-201. Age, history of cardiac disease, and Hb deficit, but not randomization to HBOC-201, were significantly predictive of cardiac ischemic events. Administration of HBOC-201 in1,701 humans showed it was well tolerated in a wide range of doses and clinical settings. HBOC-201 should be considered when blood is not available or an option.
Managing high blood pressure during acute ischemic stroke and intracerebral hemorrhage
Authors: Appiah Karen O. , Minhas Jatinder S. , Robinson Thompson G. 
Published: October 2017

Purpose of review
Blood pressure (BP) elevations above premorbid levels are observed in at least 60% of acute ischemic and hemorrhagic stroke patients, within the first 24 h of symptom onset. A number of potential causes have been hypothesized, and high BP may be associated with poor stroke outcome. This review discusses management strategies of high BP in acute stroke, in the context of current guidelines.

Recent findings
Excessive BP elevation can impact acute stroke therapeutic strategies, particularly in modifying intervention safety and efficacy. Currently, guidance on BP management in acute ischemic stroke and intracerebral hemorrhage (ICH) exists in a limited number of specific clinical presentations, including spontaneous ICH and continuing versus stopping preexisting antihypertensive therapy. However, ongoing clinical trials will further investigate the safety and efficacy of urgent BP-lowering therapy for other indications.

Summary
There are clear national and international guidelines on BP lowering for specific indications, as well as ongoing clinical trials aiming to address common clinical scenarios in which the evidence-base is lacking and uncertain. This is specifically in important stroke subgroups previously excluded from trials, patients requiring mechanical thrombectomy and nonvitamin K antagonist-associated ICH reversal.
Non-invasive imaging reveals conditions that impact distribution and persistence of cells after in vivo administration
Authors: Scarfe Lauren , Taylor Arthur , Sharkey Jack , Harwood Rachel , Barrow Michael , Comenge Joan , Beeken Lydia , Astley Cai , Santeramo Ilaria , Hutchinson Claire , Ressel Lorenzo , Smythe Jon , Austin Eric , Levy Raphael , Rosseinsky Matthew J. , Adams Dave J. , Poptani Harish , Park B. Kevin , Murray Patricia , Wilm Bettina 
Published: October 2017

AbstractBackgroundCell-based regenerative medicine therapies are now frequently tested in clinical trials. In many conditions, cell therapies are administered systemically, but there is little understanding of their fate, and adverse events are often under-reported. Currently, it is only possible to assess safety and fate of cell therapies in preclinical studies, specifically by monitoring animals longitudinally using multimodal imaging approaches. Here, using a suite of in vivo imaging modalities to explore the fate of a range of human and murine cells, we investigate how route of administration, cell type and host immune status affect the fate of administered cells.MethodsWe applied a unique imaging toolkit combining bioluminescence, optoacoustic and magnetic resonance imaging modalities to assess the safety of different human and murine cell types by following their biodistribution and persistence in mice following administration into the venous or arterial system. Results: Longitudinal imaging analyses (i) suggested that the intra-arterial route may be more hazardous than intravenous administration for certain cell types; (ii) revealed that the potential of a mouse mesenchymal stem/stromal cell (MSC) line to form tumours, depended on administration route and mouse strain; and (iii) indicated that clinically tested human umbilical cord (hUC)-derived MSCs can transiently and unexpectedly proliferate when administered intravenously to mice.ConclusionsIn order to perform an adequate safety assessment of potential cell-based therapies, a thorough understanding of cell biodistribution and fate post administration is required. The non-invasive imaging toolbox used here can expose not only the general organ distribution of these therapies, but also a detailed view of their presence within different organs and, importantly, tumourigenic potential. Our observation that the hUC-MSCs but not the human bone marrow (hBM)-derived MSCs persisted for a period in some animals, suggests that therapies with these cells should proceed with caution.
Dynamics of pollen tube growth and embryo sac development in Pozna Plava plum cultivar related to fruit set
Authors: Đorđević Milena , Cerović Radosav , Radičević Sanja , Nikolić Dragan , Milošević Nebojša , Glišić Ivana , Marić Slađana , Lukić Milan 
Published: October 2017

AbstractA newly released, late ripening plum cultivar Pozna Plava sets fruit poorly, although it produces high quality fruit. This study aimed to evaluate which factors in the reproductive process could be related to the lack of fruit set. In two consecutive years, establishment of a suitable polleniser and the stage of ovule development at anthesis as well as initial and final fruit set have been studied. In addition to this, the impact made by temperature fluctuations on the interaction between male gametophytes and female sporophytes was also analysed. Growth of the pollen tubes in the style and penetration into the nucellus as well as fruit set were more effective in cross-pollination than in open and self-pollination. A relative delay in ovule development was observed, and most ovules had an embryo sac with eight nuclei. Considering the results of the quantitiative parameter study of pollen tube growth in the ovary as well as the results of the stage of ovule development, a conclusion can be made that this cultivar is characterised by an extremely short effective period of pollination.
QTLseqr: An R package for bulk segregant analysis with next-generation sequencing
Authors: Mansfeld Ben N. , Grumet Rebecca 
Published: October 2017

1AbstractNext Generation Sequencing Bulk Segregant Analysis (NGS-BSA) is efficient in detecting quantitative trait loci (QTL). Despite the popularity of NGS-BSA and the R statistical platform, no R packages are currently available for NGS-BSA. We present QTLseqr, an R package for NGS-BSA that identifies QTL using two statistical approaches: QTL-seq and G’. These approaches use a simulation method and a tricube smoothed G statistic, respectively, to identify and assess statistical significance of QTL. QTLseqr, can import and filter SNP data, calculate SNP distributions, relative allele frequencies, G’ values, and log10(p-values), enabling identification and plotting of QTL. The source code is available at https://github.com/bmansfeld/QTLseqr.Core ideasAn R package that performs Next Generation Sequencing Bulk Segregant Analysis was developedTwo methods for analysis are provided: QTL-seq and G’The QTLseqr package is quick and produces publication quality figures and tables
Cadmium exposure inhibits branching morphogenesis and causes alterations consistent with HIF-1α inhibition in human primary breast organoids
Authors: Rocco Sabrina A. , Koneva Lada , Middleton Lauren Y. M. , Thong Tasha , Solanki Sumeet , Karram Sarah , Nambunmee Kowit , Harris Craig , Rozek Laura S. , Sartor Maureen A. , Shah Yatrik M. , Colacino Justin A. 
Published: October 2017

ABSTRACTBackgroundDevelopmental cadmium exposure in vivo disrupts mammary gland differentiation, while exposure of breast cell lines to cadmium causes invasion consistent with the epithelial-mesenchymal transition (EMT). The effects of cadmium on normal human breast stem cell development have not been measured.ObjectiveThe objective of this study was to quantify the effects of cadmium exposure on normal breast stem cell proliferation and differentiation.MethodsWe tested the effects of two physiologically relevant doses of cadmium: 0.25µM and 2.5μM on reduction mammoplasty patient-derived breast cells using the mammosphere assay, organoid formation in 3D hydrogels, and tested for molecular alterations using RNA-seq. We functionally validated our RNA-seq findings with a HIF-1α transcription factor activity reporter line and pharmaceutical inhibition of HIF-1α in mammosphere and organoid formation assays.Results2.5μM cadmium reduced primary and secondary mammosphere formation and branching structure organoid formation rates by 33%, 40%, and 83%, respectively. Despite no changes in mammosphere formation, 0.25μM cadmium treatment inhibited branching organoid formation in hydrogels by 68%. RNA-seq revealed that cadmium treatment downregulated genes associated with extracellular matrix formation and EMT, while upregulating genes associated with metal response including metallothioneins and zinc transporters. In the RNA-seq data, cadmium treatment also downregulated HIF-1α target genes including LOXL2, ZEB1, and VIM. Cadmium treatment significantly inhibited HIF-1α activity in a luciferase assay, and the HIF-1α inhibitor acriflavine ablated mammosphere and organoid formation.DiscussionThese findings show that cadmium, at doses relevant to human exposure, inhibited human mammary gland development, potentially through disruption of HIF-1α activity. These findings do not support cadmium being a breast cancer initiator via induction of stem cell proliferation, but instead implicate cadmium as an inhibitor of mammary gland morphogenesis.
Molecular mechanism of cell-cell adhesion mediated by cadherin-23
Authors: Singaraju G. S. , Kumar A. , Samuel J. S. , Sagar A. , Hazra J. P. , Sannigrahi M. K. , Yennamalli R. M. , Ashish  , Rakshit S. 
Published: October 2017

AbstractAdherin-junctions are traditionally described by the homophilic-interactions of classical cadherin-proteins at the extracellular region. However, the role of long-chain non-classical cadherins like cadherin-23(Cdh23) is not explored as yet even though it is implicated in tissue-morphogenesis, cancer, and force-sensing in neuronal tissues. Here, we identified a novel antiparallel-binding interface of Cdh23 homodimer in solution by combining biophysical and computational methods, in-vitro cell-binding, and mutational modifications. The dimer consists of two electrostatic-based interfaces extended up to two terminal domains, atypical to classical-cadherins known so far, and forms the strongest interactions in cadherin-family as measured using single-molecule force-spectroscopy. We further identified single point-mutation, E78K, that completely disrupts this binding. Interestingly, the mutation, S77L, found in skin cancers falls within the binding interface of the antiparallel-dimer. Overall, we provide the molecular architecture of Cdh23 at the cell-cell junctions which are likely to have far-reaching applications in the fields of mechanobiology and cancer.
The Transcriptional Logic of Mammalian Neuronal Diversity
Authors: Sugino Ken , Clark Erin , Schulmann Anton , Shima Yasuyuki , Wang Lihua , Hunt David L. , Hooks Bryan M. , Tränkner Dimitri , Chandrashekar Jayaram , Picard Serge , Lemire Andrew , Spruston Nelson , Hantman Adam , Nelson Sacha B. 
Published: October 2017

AbstractThe mammalian nervous system is constructed of many cell types, but the principles underlying this diversity are poorly understood. To assess brain-wide transcriptional diversity, we sequenced the transcriptomes of the largest collection of genetically and anatomically identified neuronal classes. Using improved expression metrics that distinguish information content from signal-to-noise-ratio, we found that homeobox transcription factors contain the highest information about cell types and have the lowest noise. Genes that contribute the most to neuronal diversity tend to be long and enriched in factors specifically involved in neuronal function. Genome accessibility measurements reveal that long genes have more candidate regulatory elements arrayed in more distinct patterns. These elements frequently overlap interspersed repeats (mobile elements) and the pattern of repeats is predictive of gene expression. New regulatory sites resulting from elongation of neuronal genes by mobile elements may be an evolutionary force enhancing nervous system complexity.