bluuebunny/crossref_metadata_2025_split huggingface dataset:
Osmotic Compounds Enhance Antibiotic Efficacy against Acinetobacter baumannii Biofilm Communities
Authors: Falghoush Azeza , Beyenal Haluk , Besser Thomas E. , Omsland Anders , Call Douglas R. 
Published: July 2017

ABSTRACT

Biofilm-associated infections are a clinical challenge, in part because a hydrated matrix protects the bacterial community from antibiotics. Herein, we evaluated how different osmotic compounds (maltodextrin, sucrose, and polyethylene glycol [PEG]) enhance antibiotic efficacy against
Acinetobacter baumannii
biofilm communities. Established (24-h) test tube biofilms (strain ATCC 17978) were treated with osmotic compounds in the presence or absence of 10× the MIC of different antibiotics (50 μg/ml tobramycin, 20 μg/ml ciprofloxacin, 300 μg/ml chloramphenicol, 30 μg/ml nalidixic acid, or 100 μg/ml erythromycin). Combining antibiotics with hypertonic concentrations of the osmotic compounds for 24 h reduced the number of biofilm bacteria by 5 to 7 log (
P
< 0.05). Increasing concentrations of osmotic compounds improved the effect, but there was a trade-off with increasing solution viscosity, whereby low-molecular-mass compounds (sucrose, 400-Da PEG) worked better than higher-mass compounds (maltodextrin, 3,350-Da PEG). Ten other
A. baumannii
strains were similarly treated with 400-Da PEG and tobramycin, resulting in a mean 2.7-log reduction in recoverable bacteria compared with tobramycin treatment alone. Multivariate regression models with data from different osmotic compounds and nine antibiotics demonstrated that the benefit from combining hypertonic treatments with antibiotics is a function of antibiotic mass and lipophilicity (
r

2

> 0.82;
P
< 0.002), and the relationship was generalizable for biofilms formed by
A. baumannii
and
Escherichia coli
K-12. Augmenting topical antibiotic therapies with a low-mass hypertonic treatment may enhance the efficacy of antibiotics against wound biofilms, particularly when using low-mass hydrophilic antibiotics.

IMPORTANCE
Biofilms form a barrier that protects bacteria from environmental insults, including exposure to antibiotics. We demonstrated that multiple osmotic compounds can enhance antibiotic efficacy against
Acinetobacter baumannii
biofilm communities, but viscosity is a limiting factor, and the most effective compounds have lower molecular mass. The synergism between osmotic compounds and antibiotics is also dependent on the hydrophobicity and mass of the antibiotics. The statistical models presented herein provide a basis for predicting the optimal combination of osmotic compounds and antibiotics against surface biofilms communities.
Models for estimating and projecting global, regional and national prevalence and disease burden of asthma: protocol for a systematic review
Authors: Bhuia Mohammad Romel , Nwaru Bright I , Weir Christopher J , Sheikh Aziz 
Published: July 2017

IntroductionModels that have so far been used to estimate and project the prevalence and disease burden of asthma are in most cases inadequately described and irreproducible. We aim systematically to describe and critique the existing models in relation to their strengths, limitations and reproducibility, and to determine the appropriate models for estimating and projecting the prevalence and disease burden of asthma.MethodsWe will search the following electronic databases to identify relevant literature published from 1980 to 2017: Medline, Embase, WHO Library and Information Services and Web of Science Core Collection. We will identify additional studies by searching the reference list of all the retrieved papers and contacting experts. We will include observational studies that used models for estimating and/or projecting prevalence and disease burden of asthma regarding human population of any age and sex. Two independent reviewers will assess the studies for inclusion and extract data from included papers. Data items will include authors’ names, publication year, study aims, data source and time period, study population, asthma outcomes, study methodology, model type, model settings, study variables, methods of model derivation, methods of parameter estimation and/or projection, model fit information, key findings and identified research gaps. A detailed critical narrative synthesis of the models will be undertaken in relation to their strengths, limitations and reproducibility. A quality assessment checklist and scoring framework will be used to determine the appropriate models for estimating and projecting the prevalence anddiseaseburden of asthma.Ethics and disseminationWe will not collect any primary data for this review, and hence there is no need for formal National Health Services Research Ethics Committee approval. We will present our findings at scientific conferences and publish the findings in the peer-reviewed scientific journal.
Should heart failure be regarded as a terminal illness requiring palliative care? A study of heart failure patients’, carers’ and clinicians’ understanding of heart failure prognosis and its management
Authors: Stocker Rachel , Close Helen , Hancock Helen , Hungin A Pali S 
Published: July 2017

ObjectivesCommunication and planning for heart failure (HF) care near the end of life is known to be complex. Little is known about how the patient experience of palliative assessment and communication needs change over time, and how this might inform management. Our aim was to explore experiences of giving or receiving a prognosis and advanced palliative care planning (ACP) for those with HF.MethodsWe carried out a longitudinal grounded theory study, employing in-depth interviews with 14 clinicians (primary and secondary care) and observations of clinic and home appointments, followed by a series of interviews with 13 patients with HF and 9 carers.ResultsOverall, the majority of participants rejected notions of HF as a terminal illness in favour of a focus on day-to-day management and maintenance, despite obvious deterioration in disease stage and needs over time. Clinicians revealed frustration about the uncertain nature of HF prognosis, leading to difficulties in planning. Others highlighted the need to deliver problem-based, individualised care but felt constrained sometimes by the lack of multidisciplinary ACP. Patients reported an absence of prognostic discussions with clinicians.ConclusionsThis is the first study exploring the experiences of prognostic communication at all stages of HF. Findings raise questions regarding the pragmatic utility of the concept of HF as a terminal illness and have implications for future HF care pathway development. Findings support the incorporation of a problem-based approach to management, which recognises the importance of everyday functioning for patients and carers as well as the opportunity for ACP.
A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers
Authors: Guo Theresa , Sakai Akihiro , Afsari Bahman , Considine Michael , Danilova Ludmila , Favorov Alexander V. , Yegnasubramanian Srinivasan , Kelley Dylan Z. , Flam Emily , Ha Patrick K. , Khan Zubair , Wheelan Sarah J. , Gutkind J. Silvio , Fertig Elana J. , Gaykalova Daria A. , Califano Joseph 
Published: July 2017

Abstract
The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased more than 200% in the past 20 years. Recent genetic sequencing efforts have elucidated relevant genes in head and neck cancer, but HPV-related tumors have consistently shown few DNA mutations. In this study, we sought to analyze alternative splicing events (ASE) that could alter gene function independent of mutations. To identify ASE unique to HPV-related tumors, RNA sequencing was performed on 46 HPV-positive OPSCC and 25 normal tissue samples. A novel algorithm using outlier statistics on RNA-sequencing junction expression identified 109 splicing events, which were confirmed in a validation set from The Cancer Genome Atlas. Because the most common type of splicing event identified was an alternative start site (39%), MBD-seq genome-wide CpG methylation data were analyzed for methylation alterations at promoter regions. ASE in six genes showed significant negative correlation between promoter methylation and expression of an alternative transcriptional start site, including AKT3. The novel AKT3 transcriptional variant and methylation changes were confirmed using qRT-PCR and qMSP methods. In vitro silencing of the novel AKT3 variant resulted in significant growth inhibition of multiple head and neck cell lines, an effect not observed with wild-type AKT3 knockdown. Analysis of ASE in HPV-related OPSCC identified multiple alterations likely involved in carcinogenesis, including a novel, functionally active transcriptional variant of AKT3. Our data indicate that ASEs represent a significant mechanism of oncogenesis with untapped potential for understanding complex genetic changes that result in the development of cancer. Cancer Res; 77(19); 5248–58. ©2017 AACR.
89Zr-Lumretuzumab PET Imaging before and during HER3 Antibody Lumretuzumab Treatment in Patients with Solid Tumors
Authors: Bensch Frederike , Lamberts Laetitia E. , Smeenk Michaël M. , Jorritsma-Smit Annelies , Lub-de Hooge Marjolijn N. , Terwisscha van Scheltinga Anton G.T. , de Jong Johan R. , Gietema Jourik A. , Schröder Carolien P. , Thomas Marlene , Jacob Wolfgang , Abiraj Keelara , Adessi Celine , Meneses-Lorente Georgina , James Ian , Weisser Martin , Brouwers Adrienne H. , de Vries Elisabeth G.E. 
Published: July 2017

Abstract
Purpose: We evaluated biodistribution and tumor targeting of 89Zr-lumretuzumab before and during treatment with lumretuzumab, a human epidermal growth factor receptor 3 (HER3)–targeting monoclonal antibody.
Experimental Design: Twenty patients with histologically confirmed HER3-expressing tumors received 89Zr-lumretuzumab and underwent positron emission tomography (PET). In part A, 89Zr-lumretuzumab was given with additional, escalating doses of unlabeled lumretuzumab, and scans were performed 2, 4, and 7 days after injection to determine optimal imaging conditions. In part B, patients were scanned following tracer injection before (baseline) and after a pharmacodynamic (PD)-active lumretuzumab dose for saturation analysis. HER3 expression was determined immunohistochemically in skin biopsies. Tracer uptake was calculated as standardized uptake value (SUV).
Results: Optimal PET conditions were found to be 4 and 7 days after administration of 89Zr-lumretuzumab with 100-mg unlabeled lumretuzumab. At baseline using 100-mg unlabeled lumretuzumab, the tumor SUVmax was 3.4 (±1.9) at 4 days after injection. SUVmean values for normal blood, liver, lung, and brain tissues were 4.9, 6.4, 0.9 and 0.2, respectively. Saturation analysis (n = 7) showed that 4 days after lumretuzumab administration, tumor uptake decreased by 11.9% (±8.2), 10.0% (±16.5), and 24.6% (±20.9) at PD-active doses of 400, 800, and 1,600 mg, respectively, when compared with baseline. Membranous HER3 was completely downregulated in paired skin biopsies already at and above 400-mg lumretuzumab.
Conclusions: PET imaging showed biodistribution and tumor-specific 89Zr-lumretuzumab uptake. Although, PD-active lumretuzumab doses decreased 89Zr-lumretuzumab uptake, there was no clear evidence of tumor saturation by PET imaging as the tumor SUV did not plateau with increasing doses. Clin Cancer Res; 23(20); 6128–37. ©2017 AACR.
Molecular Screening for Cancer Treatment Optimization (MOSCATO-01) in Pediatric Patients: A Single-Institutional Prospective Molecular Stratification Trial
Authors: Harttrampf Anne C. , Lacroix Ludovic , Deloger Marc , Deschamps Frederic , Puget Stephanie , Auger Nathalie , Vielh Philippe , Varlet Pascale , Balogh Zsofia , Abbou Samuel , Allorant Adrien , Valteau-Couanet Dominique , Sarnacki Sabine , Gamiche-Rolland Louise , Meurice Guillaume , Minard-Colin Veronique , Grill Jacques , Brugieres Laurence , Dufour Christelle , Gaspar Nathalie , Michiels Stefan , Vassal Gilles , Soria Jean-Charles , Geoerger Birgit 
Published: July 2017

Abstract
Purpose: This single-institutional feasibility study prospectively characterized genomic alterations in recurrent or refractory solid tumors of pediatric patients to select a targeted therapy.
Experimental Design: Following treatment failure, patients with signed consent and ages above 6 months, underwent tumor biopsy or surgical resection of primary or metastatic tumor site. These newly acquired samples were analyzed by comparative genomic hybridization array, next-generation sequencing for 75 target genes, whole-exome and RNA sequencing. Biological significance of the alterations and suggestion of most relevant targeted therapies available were discussed in a multidisciplinary tumor board.
Results: From December 2012 to January 2016, 75 patients were included, 73 patients underwent 79 interventions, 56 of which were research biopsies with a low complication rate. All patients were pretreated, 37.0% had a brain tumor, and 63.0% had an extra-cranial solid tumor. Median tumor cell content was 70% (range, 0%–100%). Successful molecular analysis in 69 patients detected in 60.9% of patients an actionable alteration in various oncogenic pathways (42.4% with copy-number change, 33.3% with mutation, 2.1% with fusion), and change in diagnosis in three patients. Fourteen patients received 17 targeted therapies; two had received a matched treatment before inclusion.
Conclusions: Research biopsies are feasible in advanced pediatric malignancies that exhibit a considerable amount of potentially actionable alterations. Genetic events affecting different cancer hallmarks and limited access to targeted agents within pediatric clinical trials remain the main obstacles that are addressed in our two subsequent precision medicine studies MAPPYACTS and AcSé-ESMART. Clin Cancer Res; 23(20); 6101–12. ©2017 AACR.
Dose Transition Pathways: The Missing Link Between Complex Dose-Finding Designs and Simple Decision-Making
Authors: Yap Christina , Billingham Lucinda J. , Cheung Ying Kuen , Craddock Charlie , O'Quigley John 
Published: July 2017

Abstract
The ever-increasing pace of development of novel therapies mandates efficient methodologies for assessment of their tolerability and activity. Evidence increasingly support the merits of model-based dose-finding designs in identifying the recommended phase II dose compared with conventional rule-based designs such as the 3 + 3 but despite this, their use remains limited. Here, we propose a useful tool, dose transition pathways (DTP), which helps overcome several commonly faced practical and methodologic challenges in the implementation of model-based designs. DTP projects in advance the doses recommended by a model-based design for subsequent patients (stay, escalate, de-escalate, or stop early), using all the accumulated information. After specifying a model with favorable statistical properties, we utilize the DTP to fine-tune the model to tailor it to the trial's specific requirements that reflect important clinical judgments. In particular, it can help to determine how stringent the stopping rules should be if the investigated therapy is too toxic. Its use to design and implement a modified continual reassessment method is illustrated in an acute myeloid leukemia trial. DTP removes the fears of model-based designs as unknown, complex systems and can serve as a handbook, guiding decision-making for each dose update. In the illustrated trial, the seamless, clear transition for each dose recommendation aided the investigators' understanding of the design and facilitated decision-making to enable finer calibration of a tailored model. We advocate the use of the DTP as an integral procedure in the co-development and successful implementation of practical model-based designs by statisticians and investigators. Clin Cancer Res; 23(24); 7440–7. ©2017 AACR.
Implementation of a Model-Based Design in a Phase Ib Study of Combined Targeted Agents
Authors: Wages Nolan A. , Portell Craig A. , Williams Michael E. , Conaway Mark R. , Petroni Gina R. 
Published: July 2017

Abstract
In recent years, investigators have recognized the rigidity of single-agent, safety-only, traditional designs, rendering them ineffective for conducting contemporary early-phase clinical trials, such as those involving combinations and/or biological agents. Novel approaches are required to address these research questions, such as those posed in trials involving targeted therapies. We describe the implementation of a model-based design for identifying an optimal treatment combination, defined by low toxicity and high efficacy, in an early-phase trial evaluating a combination of two oral targeted inhibitors in relapsed/refractory mantle cell lymphoma. Operating characteristics demonstrate the ability of the method to effectively recommend optimal combinations in a high percentage of trials with reasonable sample sizes. The proposed design is a practical, early-phase, adaptive method for use with combined targeted therapies. This design can be applied more broadly to early-phase combination studies, as it was used in an ongoing study of a melanoma helper peptide vaccine plus novel adjuvant combinations. Clin Cancer Res; 23(23); 7158–64. ©2017 AACR.
Direct Metabolic Interrogation of Dihydrotestosterone Biosynthesis from Adrenal Precursors in Primary Prostatectomy Tissues
Authors: Dai Charles , Chung Yoon-Mi , Kovac Evan , Zhu Ziqi , Li Jianneng , Magi-Galluzzi Cristina , Stephenson Andrew J. , Klein Eric A. , Sharifi Nima 
Published: July 2017

Abstract
Purpose: A major mechanism of castration-resistant prostate cancer (CRPC) involves intratumoral biosynthesis of dihydrotestosterone (DHT) from adrenal precursors. We have previously shown that adrenal-derived androstenedione (AD) is the preferred substrate over testosterone (T) for 5α-reductase expressed in metastatic CRPC, bypassing T as an obligate precursor to DHT. However, the metabolic pathway of adrenal-derived DHT biosynthesis has not been rigorously investigated in the setting of primary disease in the prostate.
Experimental Design: Seventeen patients with clinically localized prostate cancer were consented for fresh tissues after radical prostatectomy. Prostate tissues were cultured ex vivo in media spiked with an equimolar mixture of AD and T, and stable isotopic tracing was employed to simultaneously follow the enzymatic conversion of both precursor steroids into nascent metabolites, detected by liquid chromatography-tandem mass spectrometry. CRPC cell line models and xenograft tissues were similarly assayed for comparative analysis. A tritium-labeled steroid radiotracing approach was used to validate our findings.
Results: Prostatectomy tissues readily 5α-reduced both T and AD. Furthermore, 5α-reduction of AD was the major directionality of metabolic flux to DHT. However, AD and T were comparably metabolized by 5α-reductase in primary prostate tissues, contrasting the preference exhibited by CRPC in which AD was favored over T. 5α-reductase inhibitors effectively blocked the conversion of AD to DHT.
Conclusions: Both AD and T are substrates of 5α-reductase in prostatectomy tissues, resulting in two distinctly nonredundant metabolic pathways to DHT. Furthermore, the transition to CRPC may coincide with a metabolic switch toward AD as the favored substrate. Clin Cancer Res; 23(20); 6351–62. ©2017 AACR.
TCR Repertoire Intratumor Heterogeneity in Localized Lung Adenocarcinomas: An Association with Predicted Neoantigen Heterogeneity and Postsurgical Recurrence
Authors: Reuben Alexandre , Gittelman Rachel , Gao Jianjun , Zhang Jiexin , Yusko Erik C. , Wu Chang-Jiun , Emerson Ryan , Zhang Jianhua , Tipton Christopher , Li Jun , Quek Kelly , Gopalakrishnan Vancheswaran , Chen Runzhe , Vence Luis M. , Cascone Tina , Vignali Marissa , Fujimoto Junya , Rodriguez-Canales Jaime , Parra Edwin R. , Little Latasha D. , Gumbs Curtis , Forget Marie-Andrée , Federico Lorenzo , Haymaker Cara , Behrens Carmen , Benzeno Sharon , Bernatchez Chantale , Sepesi Boris , Gibbons Don L. , Wargo Jennifer A. , William William N. , Swisher Stephen , Heymach John V. , Robins Harlan , Lee J. Jack , Sharma Padmanee , Allison James P. , Futreal P. Andrew , Wistuba Ignacio I. , Zhang Jianjun 
Published: July 2017

Abstract
Genomic intratumor heterogeneity (ITH) may be associated with postsurgical relapse of localized lung adenocarcinomas. Recently, mutations, through generation of neoantigens, were shown to alter tumor immunogenicity through T-cell responses. Here, we performed sequencing of the T-cell receptor (TCR) in 45 tumor regions from 11 localized lung adenocarcinomas and observed substantial intratumor differences in T-cell density and clonality with the majority of T-cell clones restricted to individual tumor regions. TCR ITH positively correlated with predicted neoantigen ITH, suggesting that spatial differences in the T-cell repertoire may be driven by distinct neoantigens in different tumor regions. Finally, a higher degree of TCR ITH was associated with an increased risk of postsurgical relapse and shorter disease-free survival, suggesting a potential clinical significance of T-cell repertoire heterogeneity.
Significance: The present study provides insights into the ITH of the T-cell repertoire in localized lung adenocarcinomas and its potential biological and clinical impact. The results suggest that T-cell repertoire ITH may be tightly associated to genomic ITH and disease relapse. Cancer Discov; 7(10); 1088–97. ©2017 AACR.
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