bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Role of Definitive Radiotherapy in Craniopharyngioma
Authors: Zhang Chi , Verma Vivek , Lyden Elizabeth R. , Horowitz David P. , Zacharia Brad E. , Lin Chi , Connolly Eileen P. 
Published: March 2017

Objective:
Assess patterns of care in the management of craniopharyngioma, especially with respect to the use of radiation therapy (RT) alone (which has been understudied to date) as compared with gross total resection (GTR) and subtotal resection (STR) with adjuvant RT.

Materials and Methods:
The epidemiology, treatment modalities, and outcomes of patients with craniopharyngioma were studied using the Surveillance Epidemiology and End Results (SEER) database from 2004 to 2012. Survival was compared between treatment groups using Kaplan-Meier analysis and log-rank tests.

Results:
In total, 1218 patients with craniopharyngioma were identified, with equal distribution across sex. There were bimodal incidence peaks, one 20 years old or below, and the other between 40 and 65 years. The majority of pediatric tumors with known histology were adamantinomatous type, which did not influence outcomes when adjusting for age (P=0.392). Overall survival/cause-specific death for patients that underwent RT, STR+RT, and GTR were not statistically different (P>0.05). There was improved survival between several modalities: RT only versus STR only (P=0.024), RT only versus observation (P=0.006), STR+RT versus observation (P=0.046), and GTR versus observation (P=0.046). Patients above 65 years old were more likely to undergo observation (P=0.002), with highest proportions of surgery (54%)/RT (21%) in the pediatric population. Multivariable analysis demonstrated that though age was associated with overall survival (P<0.001), treatment modality (RT/GTR/STR+RT) was not (P=0.119).

Conclusions:
Although management of craniopharyngioma remains somewhat controversial, there were no observed differences in outcomes between definitive RT, GTR, and STR+RT. Although these data are hypothesis-generating, additional data are needed to validate these findings.
Conjunctival Tattoo With Inadvertent Globe Penetration and Associated Complications
Authors: Cruz Natasha Ferreira Santos da , Santos Kátia Santana , Farah Michelle de Lima , Felberg Sergio 
Published: March 2017

Purpose:
To report a case of conjunctival tattooing for cosmetic purposes with inadvertent globe penetration resulting in severe inflammation, capsular lens opacity, and secondary glaucoma.

Methods:
Case report.

Results:
A 25-year-old woman experienced severe ocular pain and decreased vision in the left eye after conjunctival tattooing for cosmetic purposes on the previous day. Slit-lamp examination revealed black deposits over the conjunctiva, corneal endothelium, anterior chamber angle, iris, and anterior capsular lens due to the tattooing pigment. In addition, severe anterior uveitis triggered by the pigments and, later, secondary glaucoma were diagnosed. The patient underwent clinical and surgical treatments to control ocular inflammation and intraocular pressure. Three months after the injury, the patient was still under follow-up treatment in an effort to control the complications of the eyeball tattooing.

Conclusions:
An unusual case of conjunctival tattooing resulted in severe inflammation, capsular lens opacity, and secondary glaucoma. Because of the increasing popularity of eyeball tattooing, coupled with the procedure being performed by untrained professionals, potentially severe complications of this procedure may become more common.
Enhanced Transitions of Care: Centralizing Discharge Phone Calls Improves Ability to Reach Patients and Reduces Hospital Readmissions
Authors: Schuller Kristin A. , Kash Bita A. , Gamm Larry D. 
Published: March 2017

Background:
The discharge phone call (DPC) is an important initiative aimed at improving transitions of care and reducing readmissions. It is of added importance as financial penalties will be imposed on hospitals with “excessive” Medicare readmissions. This study examines the impact of DPCs on percentages of patients reached through the DPCs and hospital readmission rates based on the centralized or noncentralized mode of DPCs.

Methods:
The health system centralized the Studer Group Discharge Phone Call program into one central call center with the goals of reaching more discharged patients and to ultimately reduce hospital readmissions. The study analyzed hospital visits from 74,754 patient admissions that could result in an unplanned hospital readmission. Hospital discharge data were analyzed from August 2010 to January 2014. Primary outcomes included DPCs reaching discharged patients and effects on hospital readmission rates as a result of centralizing the DPC program.

Results:
Centralized DPCs are significantly associated with increases in the percentage of patients reached by the DPC, which in turn reduces readmissions rates. Patients not reached were 1.32 times more likely to be readmitted than patients reached by centralized DPCs.

Conclusions:
Centralizing the DPC program within a call center helps reach more patients and reduce readmission rates further compared with noncentralized DPCs.
Predictors and Spatial Variation of Radon Testing in Illinois, 2005-2012
Authors: Zahnd Whitney E. , Mueller-Luckey Georgia S. , Ratnapradipa Kendra , Smith Tracey 
Published: March 2017

Context:
Radon is the second leading cause of lung cancer, but exposure can be reduced through testing one's home and mitigating if levels are high.

Objective:
To determine what factors predict radon testing and to identify, through spatial analysis, areas in Illinois with lower or higher than expected testing rates.

Design, Setting, Participants, and Main Outcomes:
An ecological study design was used to evaluate data on radon tests performed in Illinois by a licensed professional or a home radon test kit analyzed by a state-approved laboratory between 2005 and 2012. Zip code–level rates of testing per 1000 occupied residences were calculated for all testing methods combined and for licensed professional testing and home kit testing separately. The following zip code–level factors associated with radon testing were considered: Environmental Protection Agency (EPA) radon zones (ie, categorization of areas by predicted radon risk), socioeconomic characteristics, homeowner occupancy, and rurality. Univariate and multivariable incidence rate ratios were calculated to examine what factors were associated with each testing type. Hotspot analysis was performed to identify zip codes with lower than expected and higher than expected testing rates (ie, “coldspots” and “hotspots,” respectively).

Results:
Radon testing rates varied across EPA zone, socioeconomic characteristics, and level of rurality. In multivariable analysis, EPA zone, education, and median household income positively predicted all testing types combined. Median home value was associated with licensed testing, whereas rurality was negatively associated with licensed testing. Owner occupancy positively predicted home kit testing. Between 19.6% and 31.1% of zip codes were coldspots for radon testing rates, dependent upon testing type. Coldspots of all testing method rates were concentrated in the southern part of the state.

Conclusion:
Public health professionals can benefit from understanding what area-level factors predict radon testing and what geographic areas may under-utilize testing. Such information can aid the development of geographically targeted, cost-effective interventions that increase radon testing and subsequently reduce lung cancer risk.
Financial and Legal Characteristics of Cross-Jurisdictional Shared Service Agreements Between Local Public Health Agencies
Authors: Watts Theresa , Zahner Susan , Mrochek Tracy 
Published: March 2017

Background:
Cross-jurisdictional sharing is a resource management strategy increasingly being used by local health departments to provide essential and mandated public health services. Cross-jurisdictional shared service agreements (CJSSAs) are the legal documents that govern cross-jurisdictional sharing arrangements. Information on the financial and legal characteristics of CJSSAs is limited.

Objective:
This study described the financial and legal elements of a set of formal, written CJSSAs in one state to offer guidance to practitioners on how to structure the financial and legal elements in CJSSAs.

Design:
CJSSAs, which included a written statement about the financial commitment governed by the agreement (n = 63), were analyzed. Data collection occurred through 2 structured data extraction tools and structured telephone interviews conducted with local and tribal health department directors. Descriptive statistics of all variables and a single predictor linear regression were performed.

Results:
The higher population partner to the CJSSA more often provided the public health service and received payment (n = 41; 65%). Financial statements were found to vary by CJSSA characteristic. CJSSAs were more likely to be legally complete when a legal counsel was involved in creating them (odds ratio = 2.74; 95% confidence interval, 2.19-3.29; P ≤ .001). Yet, only 2 (3%) of the CJSSAs described all the legal elements and were considered legally complete.

Conclusion:
Clearly identifying and including necessary fiscal and legal elements when creating and managing CJSSAs may strengthen agreements and reduce local health department legal and fiscal vulnerabilities. Local health department capacity for planning, coordination, budgeting, management, and evaluation is essential when creating CJSSA. Careful consideration of cost-sharing and consulting with legal counsel could strengthen the CJSSA.
Measuring the Cost and Value of Quality Improvement Initiatives for Local Health Departments
Authors: Chen Li-Wu , Wilson Fernando A. , Gregg Abbey , Gupta Niodita , Bekmuratova Sarbinaz , Palm David 
Published: March 2017

Objective:
To demonstrate an approach to measuring the cost and value of quality improvement (QI) implementation in local health departments (LHDs).

Design:
We conducted cost estimation for 4 LHD QI projects and return-on-investment (ROI) analysis for 2 selected LHD QI projects.

Setting and Participants:
Four Nebraska LHDs varying in rurality and jurisdiction size.

Main outcome measures:
Total costs, unit costs, incremental cost-effectiveness ratios, and ROI.

Results:
The 4 QI projects vary significantly in their cost estimates. Estimated ROI ratios for 2 QI projects predicted significant savings in health care utilization for respective program participants. A QI project focused on improving breastfeeding rates in WIC (women, infants, and children) clients had a predicted ROI ratio of 3230% and a QI project for improving participation in a Chronic Disease Self-Management Program would need only 34 new participants to have a positive ROI.

Conclusions:
We demonstrated how data can be collected and analyzed for cost estimation and ROI analysis to quantify the economic value of QI for LHDs. Our ROI analysis shows that QI initiatives have great potential to enhance the value of LHDs' public health services. A better understanding of the costs and value of QI will enable LHDs to appropriately allocate and utilize their limited resources for suitable QI initiatives.
First-in-Human Ultrasound Molecular Imaging With a VEGFR2-Specific Ultrasound Molecular Contrast Agent (BR55) in Prostate Cancer
Authors: Smeenge Martijn , Tranquart François , Mannaerts Christophe K. , de Reijke Theo M. , van de Vijver Marc J. , Laguna M. Pilar , Pochon Sibylle , de la Rosette Jean J.M.C.H. , Wijkstra Hessel 
Published: March 2017

Objective
BR55, a vascular endothelial growth factor receptor 2 (VEGFR2)–specific ultrasound molecular contrast agent (MCA), has shown promising results in multiple preclinical models regarding cancer imaging. In this first-in-human, phase 0, exploratory study, we investigated the feasibility and safety of the MCA for the detection of prostate cancer (PCa) in men using clinical standard technology.

Materials and Methods
Imaging with the MCA was performed in 24 patients with biopsy-proven PCa scheduled for radical prostatectomy using a clinical ultrasound scanner at low acoustic power. Safety monitoring was done by physical examination, blood pressure and heart rate measurements, electrocardiogram, and blood sampling. As first-in-human study, MCA dosing and imaging protocol were necessarily fine-tuned along the enrollment to improve visualization. Imaging data were correlated with radical prostatectomy histopathology to analyze the detection rate of ultrasound molecular imaging with the MCA.

Results
Imaging with MCA doses of 0.03 and 0.05 mL/kg was adequate to obtain contrast enhancement images up to 30 minutes after administration. No serious adverse events or clinically meaningful changes in safety monitoring data were identified during or after administration. BR55 dosing and imaging were fine-tuned in the first 12 patients leading to 12 subsequent patients with an improved MCA dosing and imaging protocol. Twenty-three patients underwent radical prostatectomy. A total of 52 lesions were determined to be malignant by histopathology with 26 (50%) of them seen during BR55 imaging. In the 11 patients that were scanned with the improved protocol and underwent radical prostatectomy, a total of 28 malignant lesions were determined: 19 (68%) were seen during BR55 ultrasound molecular imaging, whereas 9 (32%) were not identified.

Conclusions
Ultrasound molecular imaging with BR55 is feasible with clinical standard technology and demonstrated a good safety profile. Detectable levels of the MCA can be reached in patients with PCa opening the way for further clinical trials.
Heterogeneous chromatin mobility derived from chromatin states is a determinant of genome organisation inS. cerevisiae
Authors: Sewitz Sven A. , Fahmi Zahra , Aljebali Latifa , Bancroft Jeremy , Brustolini Otávio J. B. , Saad Hicham , Goiffon Isabelle , Várnai Csilla , Wingett Steven , Wong Hua , Javierre Biola-Maria , Schoenfelder Stefan , Andrews Simon R. , Oliver Stephen G. , Fraser Peter , Bystricky Kerstin , Lipkow Karen 
Published: March 2017

AbstractSpatial organisation of the genome is essential for regulating gene activity, yet the mechanisms that shape this three-dimensional organisation in eukaryotes are far from understood. Here, we combine bioinformatic determination of chromatin states during normal growth and heat shock, and computational polymer modelling of genome structure, with quantitative microscopy and Hi-C to demonstrate that differential mobility of yeast chromosome segments leads to spatial self-organisation of the genome. We observe that more than forty percent of chromatin-associated proteins display a poised and heterogeneous distribution along the chromosome, creating a heteropolymer. This distribution changes upon heat shock in a concerted, state-specific manner. Simulating yeast chromosomes as heteropolymers, in which the mobility of each segment depends on its cumulative protein occupancy, results in functionally relevant structures, which match our experimental data. This thermodynamically driven self-organisation achieves spatial clustering of poised genes and mechanistically contributes to the directed relocalisation of active genes to the nuclear periphery upon heat shock.One Sentence SummaryUnequal protein occupancy and chromosome segment mobility drive 3D organisation of the genome.
A flexible ontology for inference of emergent whole cell function from relationships between subcellular processes
Authors: Hansen Jens , Meretzky David , Woldesenbet Simeneh , Stolovitzky Gustavo , Iyengar Ravi 
Published: March 2017

AbstractWhole cell responses arise from coordinated interactions between diverse human gene products functioning within various pathways underlying sub-cellular processes (SCP). Lower level SCPs interact to form higher level SCPs, often in a context specific manner to give rise to whole cell function. We sought to determine if capturing such relationships enables us to describe the emergence of whole cell functions from interacting SCPs. We developed the “Molecular Biology of the Cell” ontology based on standard cell biology and biochemistry textbooks and review articles. Currently, our ontology contains 5,385 genes, 753 SCPs and 19,180 expertly curated gene-SCP associations. Our algorithm to populate the SCPs with genes enables extension of the ontology on demand and the adaption of the ontology to the continuously growing cell biological knowledge. Since whole cell responses most often arise from the coordinated activity of multiple SCPs, we developed a dynamic enrichment algorithm that flexibly predicts SCP-SCP relationships beyond the current taxonomy. This algorithm enables us to identify interactions between SCPs as a basis for higher order function in a context dependent manner, allowing us to provide a detailed description of how SCPs together can give rise to whole cell functions. We conclude that this ontology can, from omics data sets, enable the development of detailed multidimensional SCP networks for predictive modeling of emergent whole cell functions.
Extensive farming in Estonia started through a sex-biased migration from the Steppe
Authors: Saag Lehti , Varul Liivi , Scheib Christiana Lyn , Stenderup Jesper , Allentoft Morten E. , Saag Lauri , Pagani Luca , Reidla Maere , Tambets Kristiina , Metspalu Ene , Kriiska Aivar , Willerslev Eske , Kivisild Toomas , Metspalu Mait 
Published: March 2017

AbstractFarming-based economies appear relatively late in Northeast Europe and the extent to which they involve genetic ancestry change is still poorly understood. Here we present the analyses of low coverage whole genome sequence data from five hunter-gatherers and five farmers of Estonia dated to 4,500 to 6,300 years before present. We find evidence of significant differences between the two groups in the composition of autosomal as well as mtDNA, X and Y chromosome ancestries. We find that Estonian hunter-gatherers of Comb Ceramic Culture are closest to Eastern hunter-gatherers. The Estonian first farmers of Corded Ware Culture show high similarity in their autosomes with Steppe Belt Late Neolithic/Bronze Age individuals, Caucasus hunter-gatherers and Iranian farmers while their X chromosomes are most closely related with the European Early Farmers of Anatolian descent. These findings suggest that the shift to intensive cultivation and animal husbandry in Estonia was triggered by the arrival of new people with predominantly Steppe ancestry, but whose ancestors had undergone sex-specific admixture with early farmers with Anatolian ancestry.
Zika viruses encode multiple upstream open reading frames in the 5′ viral region with a role in neurotropism
Authors: Lefèvre Charlotte , Cook Georgia M. , Dinan Adam M. , Torii Shiho , Stewart Hazel , Gibbons George , Nicholson Alex S. , Echavarría-Consuegra Liliana , Meredith Luke W. , Lulla Valeria , Kenyon Julia C. , Goodfellow Ian , Deane Janet E. , Graham Stephen C. , Lakatos Andras , Lambrechts Louis , Brierley Ian , Irigoyen Nerea 
Published: March 2017

AbstractZika virus (ZIKV) is an emerging mosquito-borne flavivirus recently associated with congenital diseases and neurological complications. As for all flaviviruses, the ZIKV RNA genome is expected to encode a single polyprotein with all the enzymatic activities required for viral replication. Here, we report the discovery of multiple non-canonical open reading frames (ORFs) identified by ribosome profiling. In both mammalian and insect cells infected with Asian/American and African ZIKV strains, we observed translation of previously unrecognised upstream ORFs (uORFs) in the 5′ region. In the Asian/American ZIKV lineage, ribosomes translated uORF1 and uORF2 that initiated from non-AUG start codons, whereas in the African ZIKV lineage, these two uORFs were fused into a single uORF (African uORF). Using a reverse genetics system, we examined the impact on ZIKV fitness of the expression of single or dual uORFs by analysing a panel of mutant viruses. We found that expression of the African uORF, and more significantly, the Asian/American uORF1, modulated virus growth and tropism in human cortical neurons and 3D organoid tissue, indicating that these novel uORFs contribute to ZIKV neurotropism. Although ZIKV uORFs are expressed in mosquito cells, they did not have a detectable effect on transmission by the mosquito vectorin vivo. Our discovery of ZIKV uORFs sheds new light on ZIKV-induced neuropathogenesis and raises the question of their existence in other neurotropic flaviviruses.
Genome-wide analysis of cell-gene interactions
Authors: Cardinale S. 
Published: March 2017

AbstractThe study presents an analysis of how different cellular functions link cell size to the expression of synthetic genes inE. coli. The Size-Expression interaction was mapped with a two-gene genetic probe across 3800 single-gene deletion strains. Through regression analysis, expression-specific effects and gene-specific effects were derived from size effects and generic expression effects, respectively. The entire compendium of cell functions broadly mapped to four systems of distinct primary influence on the Size-Expression map. Specifically, membrane structural components primarily affected size, whereas protein and RNA stability primarily affected gene expression. In addition, major Size-Expression shifts showed no substantial gene-specific effects unless they were mediated by key components of the protein synthesis apparatus.Subject Category:Synthetic Biology
Seasonal influenza circulation patterns and projections for 2017-2018
Authors: Bedford Trevor , Neher Richard A. 
Published: March 2017

AbstractThis is not meant as a comprehensive report of recent influenza evolution, but is instead intended as particular observations that may be of relevance. Please also note that observed patterns reflect the GISAID database and may not be entirely representative of underlying dynamics. All analyses are based on the nextflu pipeline [1] with continual updates posted tonextflu.org. We arrive at the following results:H3N2In H3N2, clade 3c2.a has continued to diversify genetically with complicated and rapid dynamics of different subclades. This diversification is not reflected in serological data that shows only minor to moderate antigenic evolution. Nevertheless, the highly parallel mutation patterns and the rapid rise and fall of clades suggests competitive dynamics of phenotypically distinct viruses.H1N1pdmVery few H1N1pdm viruses have been observed in recent months. The dominant clade continues to be 6b.1 and there is little amino acid sequence variation within HA. The only notable subclade that has been growing recently is the clade bearing HA1:R205K/S183P. This clade is dominated by North American viruses and we see no evidence that this clade has a particular competitive advantage.B/VicClade 1A has continued to dominate and mutation 117V has all but taken over the global population. The rise of this mutation was fairly gradual and we have no evidence that it is associated with antigenic change or other benefit to the virus.B/YamClade 3 has continued to dominate. Within clade 3, a clade with mutation HA1:251V is globally at frequency of about 80% throughout 2016. Within this clade, mutation 211R is at 25% frequency. In addition, a clade without prominent amino acid mutations has been rising throughout 2016.