bluuebunny/crossref_metadata_2025_split huggingface dataset:
Representations of Young Cancer Survivorship
Authors: Lewis Peter , Weston Kathryn M. 
Published: March 2018

Background
More young people are surviving treatment for cancer than ever before. Survival can have an adverse impact on their transition to adulthood. Discourses of cancer are applied to cancer survivors of all ages, but they manifest differently for young people.

Objective
The aim of this study was to describe practices of self-representation in an online Web site that supports young Australian cancer survivors.

Method
We conducted a discourse analysis of images and text produced by young cancer survivors (aged 18–35 years) on a public cancer charity Web site.

Results
The dominant subject position of participants published on this web site is one of empowered, beautiful cancer survivor. This applies to young people who have learned to embrace their cancer as providing a positive influence on their lives. However, this discourse can marginalize those whose cancer experience remains a source of distress or shame.

Conclusion
Web based media can provide a valuable forum for some young people to celebrate their cancer survival and to affirm the constructive influence that their cancer experience has had on their lives. However, we ponder the apparent unsuitability of some forums for young cancer survivors who have not yet found cause for celebration.

Implications for Practice
Nurses have the opportunity to contribute to the development of supportive structures that meet the specific needs of different groups of young cancer survivors. This might mean assisting young cancer survivors who are struggling to find meaning in their cancer experience to negotiate the establishment of a new normal that they can embrace.
How Interdisciplinary Teamwork Contributes to Psychosocial Cancer Support
Authors: Daem Michiel , Verbrugghe Mathieu , Schrauwen Wim , Leroux Silvian , Van Hecke Ann , Grypdonck Maria 
Published: March 2018

BackgroundThe organization of psychosocial care is rather complex, and its provision diverse. Access is affected by the acceptance and attitude of patients and professional caregivers toward psychosocial care.ObjectivesThe aims of this study were to examine when patients with cancer experience quality psychosocial care and to identify circumstances in collaboration that contribute to patient-perceived positive psychosocial care.MethodsThis study used a qualitative design in which semistructured interviews were conducted with patients, hospital workers, and primary health professionals.ResultsPsychosocial care is often requested but also refused by patients with cancer. Based on this discrepancy, a distinction is made between psychosocial support and psychosocial interventions. Psychosocial support aims to reduce the chaos in patients' lives caused by cancer and is not shunned by patients. Psychosocial interventions comprise the formal care offered in response to psychosocial problems. Numerous patients are reluctant to use psychosocial interventions, which are often provided by psychologists.ConclusionPsychosocial care aims to assist patients in bearing the difficulties of cancer and its treatment. Patients prefer informal support, given often in conjunction with physical care.Implications for PracticeThis study confirms the important role of nurses in promoting psychosocial care. Patients perceive much support from nurses, although nurses are not considered to be professional psychosocial caregivers. Being perceived as approachable and trustworthy offers nurses a significant opportunity to bring more intense psychosocial interventions within reach of cancer patients.
Predicting Risk Factors for 30-Day Readmissions Following Discharge From Post-Acute Care
Authors: Flanagan Nina M. , Rizzo Victoria M. , James Gary D. , Spegman Adele , Barnawi Najla A. 
Published: March 2018

Purpose of Study:
The specific aims of this descriptive study were to (1) examine the relationships between individual-level determinants of health using standard care admission assessments of residents admitted to a skilled nursing facility (SNF) and those residents readmitted to the hospital within 30 days from discharge from the same SNF; (2) identify and describe the risk factors of the residents readmitted to the hospital within 30 days; and (3) use the findings to inform and refine current practice to target the mutable risk factors correlated with 30-day hospital readmission.

Primary Practice Setting:
A 180-bed skilled nursing center in Northeastern Pennsylvania.

Methodology and Sample:
A retrospective paper medical record review of patients discharged from an SNF to community living was conducted to examine the relationship between individual determinants of health behaviors and 30-day hospital readmissions. The study sample (N = 221) included adults 65 years and older who were admitted to the SNF from January to December 2014 for subacute physical rehabilitation following an acute care hospital stay with a discharge plan to community living.

Results:
The 30-day readmission rate was 11%. The results of the logistic regression including diagnosis at readmission showed that the odds of readmission before 30 days were nearly three times greater in patients who had congestive heart failure (p < .02). Patients who were at “very high risk” on the Braden Scale were 20 times more likely to be readmitted before 30 days compared with those at low risk. Age and gender were not predictors. None of the other standard screening assessments for delirium, depression, functional status, and fall risk were predictive of 30-day readmission.

Implications for Case Management Practice:
(1) Care coordination and communication with residents, caregivers, and home health can have an impact on 30-day readmissions post-SNF discharge. (2) Chronic respiratory diseases continue to be a challenge in prevention of hospital readmissions.
Pediatric Forefoot Fractures
Authors: Lim Rodrick K. , Gerson Bridgette , Seabrook Jamie A. , Reardon Jaime , Poonai Naveen 
Published: March 2018

Background
Forefoot fractures account for 6% to 10% of fractures in children, and although the majority heals with supportive treatment, complications may lead to pain and disability. No previous study in children has evaluated complication risk in the emergency department based on initial assessment characteristics.

Study Objectives
The study aim was to identify the radiological and clinical variables that increase the complication rate of pediatric forefoot fractures. This may help emergency physicians refer patients who require more thorough follow-up or surgical intervention.

Methods
We evaluated 497 forefoot fractures on initial presentation to a pediatric emergency department at the Children’s Hospital at London Health Science Centre over a 6-year period. We collected variables such as degree of angulation, displacement, number of concurrent fractures, and demographic data such as age and sex. We then determined the variables associated with complications by reviewing each patient's chart.

Results
Overall, there was a 6.4% complication rate. Analysis identified sex as an important predictor of complications. Females, although representing approximately one third of the sample, represented nearly two thirds of the cases with complicated outcomes (P = 0.001; odds ratio [OR], 4.67). Increased number of fractures was also significant (P = 0.01; OR, 2.41) as was increasing age (P = 0.01; OR, 1.17) and patients who chose to return to the emergency department (P < 0.05; OR, 5.282). Lateral angulation/displacement and anteroposterior angulation/displacement were not associated with increased complications.

Conclusion
Identifying features, such as female sex, increasing age, multiple fractures, and return to emergency departments for repeat visits, may help guide the emergency physician on whom to refer for specialized care.
Optimal Use of Surgical Drains: Evidence-Based Strategies
Authors: Khansa Ibrahim , Khansa Lara , Meyerson Joseph , Janis Jeffrey E. 
Published: March 2018

Background:
Closed-suction drains are widely used to reduce the incidence of seroma whenever potential spaces are surgically created. However, few studies have examined the parameters that affect drain efficacy.

Methods:
An in vitro model was created to assess the effects of tubing length, tubing size, tubing type, fluid viscosity, fluid clotting, evacuator type, evacuator squeeze method, evacuator fill, and evacuator pressure on the performance of closed-suction drains.

Results:
Fluid flow rate through the drain increases with increasing intracavitary tubing length, decreasing extracavitary tubing length, increasing tubing diameter, increasing negative pressure, decreasing fluid viscosity, and the use of perforated rather than fluted drains. Bulbs generate more effective suction when squeezed “side-to-side” than when squeezed “bottom-up,” and evacuators were only able to generate half the maximal negative pressure when 25 percent full or greater. Stripping the drain tubing helped relieve obstruction caused by clotting.

Conclusions:
The authors’ findings have practical clinical implications for surgeons hoping to maximize the efficacy of closed-suction drains. Through this comprehensive review of the literature and in vitro analysis of relevant variables that affect drain function, the performance of closed-suction drains can be optimized by increasing intracavitary tubing length, decreasing extracavitary tubing length, increasing tubing diameter, increasing the pressure differential, using perforated drains, squeezing bulbs side-to-side, stripping drain tubing frequently, and evacuating containers whenever they are 25 percent full.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, V.
A deep learning approach for uncovering lung cancer immunome patterns
Authors: Hess Moritz , Lenz Stefan , Binder Harald 
Published: March 2018

AbstractTumor immune cell infiltration is a well known factor related to survival of cancer patients. This has led to deconvolution approaches that can quantify immune cell proportions for each individual. What is missing, is an approach for modeling joint patterns of different immune cell types. We adapt a deep learning approach, deep Boltzmann machines (DBMs), for modeling immune cell gene expression patterns in lung adenocarcinoma. Specifically, a partially partitioned training approach for dealing with a relatively large number of genes. We also propose a sampling-based approach that smooths the original data according to a trained DBM and can be used for visualization and clustering. The identified clusters can subsequently be judged with respect to association with clinical characteristics, such as tumor stage, providing an external criterion for selecting DBM network architecture and tuning parameters for training. We show that the hidden nodes of the trained networks cannot only be linked to clinical characteristics but also to specific genes, which are the visible nodes of the network. We find that hidden nodes that are linked to tumor stage and survival represent expression of T-cell and mast cell genes among others, probably reflecting specific immune cell infiltration patterns. Thus, DBMs, trained and selected by the proposed approach, might provide a useful tool for extracting immune cell gene expression patterns. In the case of lung adenocarcinomas, these patterns are linked to survival as well as other patient characteristics, which could be useful for uncovering the underlying biology.
Simultaneous detection of invasive signal crayfish, endangered white-clawed crayfish and the crayfish plague pathogen using environmental DNA
Authors: Robinson Chloe Victoria , Webster Tamsyn M. Uren , Cable Joanne , James Joanna , Consuegra Sofia 
Published: March 2018

ABSTRACTAquatic Invasive Species (AIS) are important vectors for the introduction of novel pathogens which can, in turn, become drivers of rapid ecological and evolutionary change, compromising the persistence of native species. Conservation strategies rely on accurate information regarding presence and distribution of AIS and their associated pathogens to prevent or mitigate negative impacts, such as predation, displacement or competition with native species for food, space or breeding sites. Environmental DNA is increasingly used as a conservation tool for early detection and monitoring of AIS. We used a novel eDNA high-resolution melt curve (HRM) approach to simultaneously detect the UK endangered native crayfish (Austropotamobius pallipes), the highly invasive signal crayfish (Pacifastacus leniusculus) and their dominant pathogen, Aphanomyces astaci, (causative agent of crayfish plague). We validated the approach with laboratory and field samples in areas with known presence or absence of both crayfish species as well as the pathogen, prior to the monitoring of areas where their presence was unknown. We identified the presence of infected signal crayfish further upstream than previously detected in an area where previous intensive eradication attempts had taken place, and the coexistence of both species in plague free catchments. We also detected the endangered native crayfish in an area where trapping had failed. With this method, we could estimate the distribution of native and invasive crayfish and their infection status in a rapid, cost effective and highly sensitive way, providing essential information for the development of conservation strategies in catchments with populations of endangered native crayfish.
Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children
Authors: Zinter MS , Dvorak CC , Mayday MY , Iwanaga K , Ly NP , McGarry ME , Church GD , Faricy LE , Rowan CM , Hume JR , Steiner ME , Crawford ED , Langelier C , Kalantar K , Chow ED , Miller S , Shimano K , Melton A , Yanik GA , Sapru A , DeRisi JL 
Published: March 2018

ABSTRACTRATIONALEDespite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant morbidity and mortality.OBJECTIVESTo develop a highly sensitive metagenomic next generation sequencing (mNGS) assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children.METHODSWe collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at 3 children’s hospitals from 2014-2016. Samples underwent mechanical homogenization, paired RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the NCBI nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort.MEASUREMENTS & MAIN RESULTSWe identified a rich cross-domain pulmonary microbiome containing bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median 0.58, IQR 0.33-0.62 vs. median 0.94, IQR 0.93-0.95, p<0.001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (p<0.001).CONCLUSIONSAn optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease.
Structural disruption of exonic stem-loops immediately upstream of the intron regulates mammalian splicing
Authors: Saha Kaushik , England Whitney , Fernandez Mike Minh , Biswas Tapan , Spitale Robert C. , Ghosh Gourisankar 
Published: March 2018

ABSTRACTRecognition of highly degenerate mammalian splice sites by the core spliceosomal machinery is regulated by several protein factors that predominantly bind exonic splicing motifs. These are postulated to be single-stranded in order to be functional, yet knowledge of secondary structural features that regulate the exposure of exonic splicing motifs across the transcriptome is not currently available. Using transcriptome-wide RNA structural information we show that retained introns in mouse are commonly flanked by a short (≲70 nucleotide), highly base-paired segment upstream and a predominantly single-stranded exonic segment downstream. Splicing assays with select pre-mRNA substrates demonstrate that loops immediately upstream of the introns contain pre-mRNA-specific splicing enhancers, the substitution or hybridization of which impedes splicing. Additionally, the exonic segments flanking the retained introns appeared to be more enriched in a previously identified set of hexameric exonic splicing enhancer (ESE) sequences compared to their spliced counterparts, suggesting that base-pairing in the exonic segments upstream of retained introns could be a means for occlusion of ESEs. The upstream exonic loops of the test substrate promoted recruitment of splicing factors and consequent pre-mRNA structural remodeling, leading up to assembly of the early spliceosome. These results suggest that disruption of exonic stem-loop structures immediately upstream (but not downstream) of the introns regulate alternative splicing events, likely through modulating accessibility of splicing factors.
Non-parametric and semi-parametric support estimation using SEquential RESampling random walks on biomolecular sequences
Authors: Wang Wei , Smith Jack , Hejase Hussein A. , Liu Kevin J. 
Published: March 2018

AbstractNon-parametric and semi-parametric resampling procedures are widely used to perform support estimation in computational biology and bioinformatics. Among the most widely used methods in this class is the standard bootstrap method, which consists of random sampling with replacement. While not requiring assumptions about any particular parametric model for resampling purposes, the bootstrap and related techniques assume that sites are independent and identically distributed (i.i.d.). The i.i.d. assumption can be an over-simplification for many problems in computational biology and bioinformatics. In particular, sequential dependence within biomolecular sequences is often an essential biological feature due to biochemical function, evolutionary processes such as recombination, and other factors.To relax the simplifying i.i.d. assumption, we propose a new non-parametric/semi-parametric sequential resampling technique that generalizes “Heads-or-Tails” mirrored inputs, a simple but clever technique due to Landan and Graur. The generalized procedure takes the form of random walks along either aligned or unaligned biomolecular sequences. We refer to our new method as the SERES (or “SEquential RESampling”) method.To demonstrate the flexibility of the new technique, we apply SERES to two different applications – one involving aligned inputs and the other involving unaligned inputs. Using simulated and empirical data, we show that SERES-based support estimation yields comparable or typically better performance compared to state-of-the-art methods for both applications.
Discovery of a pre-mRNA structural scaffold as a contributor to the mammalian splicing code
Authors: Saha Kaushik , Fernandez Mike Minh , Biswas Tapan , Joseph Simpson , Ghosh Gourisankar 
Published: March 2018

ABSTRACTThe specific recognition of splice signals at or near exon-intron junctions is not explained by their weak conservation and instead is postulated to require a multitude of features embedded in the pre-mRNA strand. We explored the possibility of three-dimensional structural scaffold of AdML – a model pre-mRNA substrate – guiding early spliceosomal components to the splice signal sequences. We find that mutations in the non-cognate splice signal sequences impede recruitment of early spliceosomal components due to disruption of the global structure of the pre-mRNA. We further find that the pre-mRNA segments potentially interacting with the early spliceosomal component U1 snRNP are distributed across the intron, that there is a spatial proximity of 5′ and 3′ splice sites within the pre-mRNA scaffold, and that an interplay exists between the structural scaffold and splicing regulatory elements in recruiting early spliceosomal components. These results suggest that early spliceosomal components can recognize a three-dimensional structural scaffold beyond the short splice signal sequences, and that in our model pre-mRNA, this scaffold is formed across the intron involving the major splice signals. This provides a conceptual basis to analyze the contribution of recognizable three-dimensional structural scaffolds to the splicing code across the mammalian transcriptome.
A Preliminary Analysis of the Age of Full Expression of Sexually Dimorphic Cranial Traits
Authors: Stock Michala K. 
Published: March 2018

AbstractAlthough high accuracy rates have been achieved for adult skeletal sex estimation, it is unclear at what age sexually dimorphic traits of the skull become fully developed and useful in subadults. Four linear distances that capture sexual dimorphism—the nuchal crest, mastoid process, glabella, and mental eminence—were measured in a longitudinal sample of lateral cranial radiographs from 10 males and 10 females in the Denver Growth Study (total n = 190). The age full trait expression was attained was compared to that of dental maturity (i.e., third molar eruption). The mental eminence reached full expression significantly earlier than dental maturity (p < 0.001), although a high degree of variability was observed. Ages of expression of the other traits did not differ significantly from dental maturity. These results suggest that in forensic cases, where misclassification can have substantial impacts, cranial traits cannot yet be used reliably for sex estimation prior to third molar eruption.
Long‐term survival in locally advanced non‐small cell lung cancer invading the great vessels and heart
Authors: Park Byungjoon , Cho Jong Ho , Kim Hong Kwan , Choi Yong Soo , Zo Jae Il , Shim Young Mog , Kim Jhingook 
Published: March 2018

BackgroundThe aim of this study was to analyze the surgical outcomes of locally advanced lung cancer invading the great vessels or heart, according to the extension of cancer invasion.MethodsFrom 1995 to 2015, 59 patients who were surgically treated and pathologically diagnosed with T4N0–1 non‐small cell lung cancer with invasion to the great vessels or heart were enrolled. Surgical outcomes were compared between patient groups with and without intrapericardial invasion.ResultsThe median age was 64 years (interquartile range [IQR] 57–68) and 56 patients (95%) were male. In‐hospital mortality was 9% and median overall survival was 30 months (IQR 12–83). One and five‐year overall survival rates were 75% and 44%, respectively. The median overall survival in patients with lung cancer invasion to the intrapericardial space (n = 45) was 27 months (IQR 10–63), while it was 42 months (IQR 18–104) in patients without intrapericardial invasion (n = 14). Median disease‐free survival was significantly poorer in patients with intrapericardial invasion (12 months; IQR 6–55), especially in patients with heart invasion (n = 11, 7 months, IQR 5–27), than in patients without intrapericardial invasion (30 months, IQR 13–103).ConclusionPatients with lung cancer invading the intrapericardial space showed worse surgical outcomes in both overall and disease‐free survival. Therefore, surgical management should be carefully considered in patients with intrapericardial invasion.