bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating CollaboRATE in a clinical setting: analysis of mode effects on scores, response rates and costs of data collection
Authors: Barr Paul J , Forcino Rachel C , Thompson Rachel , Ozanne Elissa M , Arend Roger , Castaldo Molly Ganger , O'Malley A James , Elwyn Glyn 
Published: March 2017

BackgroundShared decision-making (SDM) has become a policy priority, yet its implementation is not routinely assessed. To address this gap we tested the delivery of CollaboRATE, a 3-item patient reported experience measure of SDM, via multiple survey modes.ObjectiveTo assess CollaboRATE response rates and respondent characteristics across different modes of administration, impact of mode and patient characteristics on SDM performance and cost of administration per response in a real-world primary care practice.DesignObservational study design, with repeated assessment of SDM performance using CollaboRATE in a primary care clinic over 15 months of data collection. Different modes of administration were introduced sequentially including paper, patient portal, interactive voice response (IVR) call, text message and tablet computer.ParticipantsConsecutive patients ≥18 years, or parents/guardians of patients <18 years, visiting participating primary care clinicians.Main measuresCollaboRATE assesses three core SDM tasks: (1) explanation about health issues, (2) elicitation of patient preferences and (3) integration of patient preferences into decisions. Responses to each item range from 0 (no effort was made) to 9 (every effort was made). CollaboRATE scores are calculated as the proportion of participants who report a score of nine on each of the three CollaboRATE questions.Key resultsScores were sensitive to mode effects: the paper mode had the highest average score (81%) and IVR had the lowest (61%). However, relative clinician performance rankings were stable across the different data collection modes used. Tablet computers administered by research staff had the highest response rate (41%), although this approach was costly. Clinic staff giving paper surveys to patients as they left the clinic had the lowest response rate (12%).ConclusionsCollaboRATE can be introduced using multiple modes of survey delivery while producing consistent clinician rankings. This may allow routine assessment and benchmarking of clinician and clinic SDM performance.
‘We both just wanted to be normal parents’: a qualitative study of the experience of maternity care for women with learning disability
Authors: Malouf Reem , McLeish Jenny , Ryan Sara , Gray Ron , Redshaw Maggie 
Published: March 2017

BackgroundMore women with learning disability (LD) are becoming mothers. Women with LD have rights to equal access to maternity care that meets their needs, however, many have poor pregnancy and birth outcomes compared to other women in the UK. Research is limited in this area.ObjectivesThe aim of the study was to explore the lived experiences of pregnancy, childbirth, prenatal and postnatal care and services received by this group of women in the UK, including their expressed information and support needs relating to maternity care.MethodsA qualitative study in which data were generated using in-depth semistructured interviews with learning disabled women who were pregnant or had given birth within the last 3 years in the UK; data were analysed using interpretative phenomenological analysis.Results9 women with varying levels of cognitive impairment took part. 4 super-ordinate themes were identified: ‘I hate being treated differently’, ‘I find it harder to understand than other people’, ‘We've had to prove ourselves’ and ‘Make sure you've got very good support around you’. Subthemes included: ‘Negative attitudes and denial of choice’, ‘Understanding of normal care’, ‘Written information’ and ‘Being judged by professionals’.ConclusionsWith support from family and services, learning disabled women can become confident and successful parents. Maternity services should make reasonable adjustments when providing care to this group, including adapting to their individual communication and learning needs: allowing sufficient time in appointments, offering clear explanations of each aspect of care and sensitive support for autonomy and fully informed choice. Mothers who will be subject to a social care assessment of their parenting skills need clear information about the process, their choices and the level of skill they must demonstrate, as well as access to sufficient antenatal and postnatal support to give them the best possible chance of passing the assessment.
The Royal College of Emergency Medicine composite pain scale for children: level of inter-rater agreement
Authors: James Ffion , Edwards Rosie , James Nirmal , Dyer Rhian , Goodwin Victoria 
Published: March 2017

ObjectiveTo assess the inter-rater agreement of the Royal College of Emergency Medicine (RCEM) Composite Pain Scale.MethodsA prospective, observational study of 117 children who presented to the ED with pain due to a limb injury. Pain severity was assessed by the triage nurse, doctor and child (depending on their age) using indicators of the RCEM Composite Pain Scale. This pain scale comprises a modified Wong-Baker FACES Pain Rating Scale (FACES Scale), a Behaviour scale and a numerical rating scale (Ladder). Comparisons were made between scores from individual scales and raters.Results117 children (26 aged 0–8 years (group 1) and 91 aged >8–16 years (group 2)) were enrolled in the study. Pain in group 1 was assessed by the nurse and doctor using the FACES Scale and the Behaviour scale. The FACES Scale demonstrated greater inter-rater agreement than the Behaviour scale. Pain in group 2 was assessed by the nurse and doctor using the Behaviour scale and by the child using the FACES Scale and Ladder. The Ladder demonstrated poor inter-rater agreement in comparison with the Behaviour Score.ConclusionThe Ladder score could be omitted from this composite tool as it has poor inter-rater agreement in comparison with the other indicators.
Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer
Authors: Shah Manasi S , DeSantis Todd Z , Weinmaier Thomas , McMurdie Paul J , Cope Julia L , Altrichter Adam , Yamal Jose-Miguel , Hollister Emily B 
Published: March 2017

ObjectiveColorectal cancer (CRC) is the second leading cause of cancer-associated mortality in the USA. The faecal microbiome may provide non-invasive biomarkers of CRC and indicate transition in the adenoma–carcinoma sequence. Re-analysing raw sequence and metadata from several studies uniformly, we sought to identify a composite and generalisable microbial marker for CRC.DesignRaw 16S rRNA gene sequence data sets from nine studies were processed with two pipelines, (1) QIIME closed reference (QIIME-CR) or (2) a strain-specific method herein termed SS-UP (Strain Select, UPARSE bioinformatics pipeline). A total of 509 samples (79 colorectal adenoma, 195 CRC and 235 controls) were analysed. Differential abundance, meta-analysis random effects regression and machine learning analyses were carried out to determine the consistency and diagnostic capabilities of potential microbial biomarkers.ResultsDefinitive taxa, including Parvimonas micra ATCC 33270, Streptococcus anginosus and yet-to-be-cultured members of Proteobacteria, were frequently and significantly increased in stools from patients with CRC compared with controls across studies and had high discriminatory capacity in diagnostic classification. Microbiome-based CRC versus control classification produced an area under receiver operator characteristic (AUROC) curve of 76.6% in QIIME-CR and 80.3% in SS-UP. Combining clinical and microbiome markers gave a diagnostic AUROC of 83.3% for QIIME-CR and 91.3% for SS-UP.ConclusionsDespite technological differences across studies and methods, key microbial markers emerged as important in classifying CRC cases and such could be used in a universal diagnostic for the disease. The choice of bioinformatics pipeline influenced accuracy of classification. Strain-resolved microbial markers might prove crucial in providing a microbial diagnostic for CRC.
Gut symbiotic microbes imprint intestinal immune cells with the innate receptor SLAMF4 which contributes to gut immune protection against enteric pathogens
Authors: Cabinian Allison , Sinsimer Daniel , Tang May , Jang Youngsoon , Choi Bongkum , Laouar Yasmina , Laouar Amale 
Published: March 2017

BackgroundInteractions between host immune cells and gut microbiota are crucial for the integrity and function of the intestine. How these interactions regulate immune cell responses in the intestine remains a major gap in the field.AimWe have identified the signalling lymphocyte activation molecule family member 4 (SLAMF4) as an immunomodulator of the intestinal immunity. The aim is to determine how SLAMF4 is acquired in the gut and what its contribution to intestinal immunity is.MethodsExpression of SLAMF4 was assessed in mice and humans. The mechanism of induction was studied using GFPtgbone marrow chimaera mice, lymphotoxin α and TNLG8A-deficient mice, as well as gnotobiotic mice. Role in immune protection was revealed using oral infection withListeria monocytogenesandCytobacter rodentium.ResultsSLAMF4 is a selective marker of intestinal immune cells of mice and humans. SLAMF4 induction occurs directly in the intestinal mucosa without the involvement of the gut-associated lymphoid tissue. Gut bacterial products, particularly those of gut anaerobes, and gut-resident antigen-presenting cell (APC)TNLG8Aare key contributors of SLAMF4 induction in the intestine. Importantly, lack of SLAMF4 expression leads the increased susceptibility of mice to infection by oral pathogens culminating in their premature death.ConclusionsSLAMF4 is a marker of intestinal immune cells which contributes to the protection against enteric pathogens and whose expression is dependent on the presence of the gut microbiota. This discovery provides a possible mechanism for answering the long-standing question of how the intertwining of the host and gut microbial biology regulates immune cell responses in the gut.
Effect of fixation time on breast biomarker expression: a controlled study using cell line-derived xenografted (CDX) tumours
Authors: Kao K R , Hasan T , Baptista A , Truong T , Gai L , Smith A C , Li S , Gonzales P , Voisey K , Eriwvo P , Power J , Denic N 
Published: March 2017

AimsAltering the length of time specimens are placed in fixative without compromising analytical testing accuracy is a continuous challenge in the anatomical pathology lab. The aim of this study was to determine under controlled conditions the effects of variable fixation time on breast biomarker expression in human breast cancer cell line-derived xenografted (CDX) tumours.MethodsCDX tumours using strong oestrogen receptor (ER)-positive, Her2-negative (MCF7) and weak ER-positive, Her2 equivocal (T47D) breast cancer cell lines were fixed for various times ranging from 1 to 336 hours in 10% neutral buffered formalin. CDX tumours were processed according to routine biomarker testing protocols and stained for ER and Her2 immunohistochemistry (IHC) and processed forHER2 fluorescence in situ hybridisation (FISH). The tumours were evaluated using Allred scoring for ER and current ASCO/CAP guidelines for Her2, and by objective cell counting methodology.ResultsNo differences were found in expression of ER in either MCF7 or T47D CDX tumours under variable fixation. T47D tumours displayed equivocal Her2 staining when fixed for 24 hours, but fixation for ≤8 hours resulted in consistently negative staining while tumours fixed for >72 hours demonstrated consistent equivocal staining (p<0.01). Cell counting assays revealed only a significant increase in sensitivity in tumours fixed for >72 hours (p<0.01). As expected, FISH results were unaffected by variable fixation.ConclusionsNeither shortened nor prolonged fixation affects ER expression, consistent with previous findings. In equivocal Her2-expressing tumours, however, increasing fixation increased the sensitivity of Her2 IHC reporting while not affecting FISH.
Twenty miles per hour speed limits: a sustainable solution to public health problems in Wales
Authors: Jones Sarah J , Brunt Huw 
Published: March 2017

BackgroundPrevention, rather than treatment, is the key to longer healthier lives. Identifying interventions that will impact positively on road traffic injuries, air quality and encourage active travel is a significant public health challenge. This paper aimed to explore whether 20 mph limits could be useful in achieving this.MethodsResearch evidence was reviewed to identify the effect of 20 mph zones and limits on health and well-being. The evidence was then used to estimate the effect of a change to a 20 mph limit on road traffic casualties and air pollution. It was then mapped against the seven goals of the Well-being of Future Generations Act (2015).ResultsIf all current 30 mph limit roads in Wales became 20 mph limits, it is estimated that 6–10 lives would be saved and 1200–2000 casualties avoided each year, at a value of prevention of £58M–£94M. In terms of air pollution, deaths attributed to nitrogen dioxide (NO2) may increase by 63, and years of life lost by 753. However, deaths attributed to particulates (PM2.5) may decrease by 117 and years of life lost by 1400. Evidence review suggests benefits in terms of road traffic casualties, air quality, active travel, noise pollution, greater social inclusion, greater community cohesion and local business viability.ConclusionsRoad traffic injuries, air pollution and obesity are an inter-related, interdependent triad. The challenge facing public health today is identifying robust interventions that will have positive effects on all three as a minimum; default 20 mph limits is the solution to increasing public health problems in Wales.
Low Recombination Proficiency Score (RPS) Predicts Heightened Sensitivity to DNA-Damaging Chemotherapy in Breast Cancer
Authors: Pitroda Sean P. , Bao Riyue , Andrade Jorge , Weichselbaum Ralph R. , Connell Philip P. 
Published: March 2017

Abstract
Purpose: Molecular-based cancer tests have been developed to augment the standard clinical and pathologic features used to tailor treatments to individual breast cancer patients. Homologous recombination (HR) repairs double-stranded DNA breaks and promotes tolerance to lesions that disrupt DNA replication. Recombination Proficiency Score (RPS) quantifies HR efficiency based on the expression of four genes involved in DNA damage repair. We hypothesized low RPS values can identify HR-deficient breast cancers most sensitive to DNA-damaging chemotherapy.
Experimental Design: We collected pathologic tumor responses and tumor gene expression values for breast cancer patients that were prospectively enrolled on clinical trials involving preoperative chemotherapy followed by surgery (N = 513). We developed an algorithm to calculate breast cancer–specific RPS (RPSb) values on an individual sample basis.
Results: Low RPSb tumors are approximately twice as likely to exhibit a complete pathologic response or minimal residual disease to preoperative anthracycline-based chemotherapy as compared with high RPSb tumors. Basal, HER2-enriched, and luminal B breast cancer subtypes exhibit low RPSb values. In addition, RPSb predicts treatment responsiveness after controlling for clinical and pathologic features, as well as intrinsic breast subtype.
Conclusions: Overall, our findings indicate that low RPS breast cancers exhibit aggressive features at baseline, but they have heightened sensitivity to DNA-damaging chemotherapy. Low RPSb values in basal, HER2-enriched, and luminal B subtypes provide a mechanistic explanation for their clinical behaviors and genomic instability. RPSb augments standard clinical and pathologic features used to tailor treatments, thereby enabling more personalized treatment strategies for individual breast cancer patients. Clin Cancer Res; 23(15); 4493–500. ©2017 AACR.
MET Tyrosine Kinase Inhibition Enhances the Antitumor Efficacy of an HGF Antibody
Authors: Farrell Pamela J. , Matuszkiewicz Jennifer , Balakrishna Deepika , Pandya Shweta , Hixon Mark S. , Kamran Ruhi , Chu Shaosong , Lawson J. David , Okada Kengo , Hori Akira , Mizutani Akio , Iwata Hidehisa , de Jong Ron , Hibner Barbara , Vincent Patrick 
Published: March 2017

Abstract
Receptor tyrosine kinase therapies have proven to be efficacious in specific cancer patient populations; however, a significant limitation of tyrosine kinase inhibitor (TKI) treatment is the emergence of resistance mechanisms leading to a transient, partial, or complete lack of response. Combination therapies using agents with synergistic activity have potential to improve response and reduce acquired resistance. Chemoreagent or TKI treatment can lead to increased expression of hepatocyte growth factor (HGF) and/or MET, and this effect correlates with increased metastasis and poor prognosis. Despite MET's role in resistance and cancer biology, MET TKI monotherapy has yielded disappointing clinical responses. In this study, we describe the biological activity of a selective, oral MET TKI with slow off-rate and its synergistic antitumor effects when combined with an anti-HGF antibody. We evaluated the combined action of simultaneously neutralizing HGF ligand and inhibiting MET kinase activity in two cancer xenograft models that exhibit autocrine HGF/MET activation. The combination therapy results in additive antitumor activity in KP4 pancreatic tumors and synergistic activity in U-87MG glioblastoma tumors. Pharmacodynamic characterization of biomarkers that correlate with combination synergy reveal that monotherapies induce an increase in the total MET protein, whereas combination therapy significantly reduces total MET protein levels and phosphorylation of 4E-BP1. These results hold promise that dual targeting of HGF and MET by combining extracellular ligand inhibitors with intracellular MET TKIs could be an effective intervention strategy for cancer patients who have acquired resistance that is dependent on total MET protein. Mol Cancer Ther; 16(7); 1269–78. ©2017 AACR.
Aspirin and Risk of Subarachnoid Hemorrhage
Authors: Phan Kevin , Moore Justin M. , Griessenauer Christoph J. , Ogilvy Christopher S. , Thomas Ajith J. 
Published: March 2017

Background and Purpose—
Recent studies have suggested that the use of low-dose aspirin may reduce the risk of aneurysmal subarachnoid hemorrhage (aSAH). We aimed to evaluate any association between aspirin use and risk of aSAH based on the literature, and whether this is influenced by duration or frequency of aspirin use.

Methods—
A search of electronic databases was done from inception to September 2016. For each study, data on risk of aSAH in aspirin versus nonaspirin users were used to generate odds ratios and 95% confidence intervals, and combined using inverse variance–weighted averages of logarithmic odds ratios in a random-effects models.

Results—

From 7 included studies, no significant difference was noted between aspirin use of any duration or frequency and nonaspirin users (odds ratio, 1.00; 95% confidence interval, 0.81–1.24;
P
=0.99). We found a significant association between short-term use of aspirin (<3 months) and the risk of aSAH (odds ratio, 1.61; 95% confidence interval, 1.20–2.18;
P
=0.002). No significant difference was found in terms of risk of aSAH for 3 to 12 months, 1 to 3 years, and >3 years of durations of use. No significant association was found between infrequent aspirin use (≤2× per week) or frequent use (≥3× per week) with risk of aSAH.

Conclusions—
Current evidence suggests that short-term (<3 months) use of aspirin is associated with increased risk of aSAH. Limitations include substantial heterogenity of the included studies. The role of long-term aspirin in reducing risk of aSAH remains unclear and ideally should be addressed by an appropriately designed randomized controlled trial.
Energetics of Deep Alpine Valleys in Pooling and Draining Configurations
Authors: Arduini Gabriele , Chemel Charles , Staquet Chantal 
Published: March 2017

Abstract
The Weather Research and Forecasting Model is used to investigate the nocturnal atmospheric boundary layer in a valley that opens either on a wider valley (draining configuration) or on a narrower valley (pooling configuration). One draining case and three weak to strong pooling cases are considered. Results show that the structure of the nocturnal boundary layer is substantially different for the draining and pooling configurations. Greater pooling corresponds with a deeper and colder boundary layer. Down-valley winds are weaker for pooling and draining configurations than in an equivalent valley opening directly on a plain. For the strong pooling case, an up-valley flow develops from the narrower to the wider valley during the evening transition, affecting the mass budget of the wider valley during that period. Considering the heat budget of the valley system, the contribution of the diabatic processes, when appropriately weighted, hardly varies along the valley axis. Conversely, the contribution of advection varies along the valley axis: it decreases for a pooling configuration and increases for a draining configuration. Consequently, for a pooling configuration, the heat transfer between the valley and the plain is reduced, thereby increasing the temperature difference between them. For the strong pooling case, this temperature difference can be explained by the valley-volume effect once the down-valley flow has developed. This occurs in a valley when the “extra” heat loss within the valley due to the surface sensible heat flux balances the heat input due to advection.
Resurfacing of South Pacific Tropical Water in the Equatorial Pacific and Its Variability Associated with ENSO
Authors: Qu Tangdong , Gao Shan 
Published: March 2017

AbstractAnalysis of results from a simulated passive tracer confirms the resurfacing of South Pacific Tropical Water in the equatorial Pacific. Over the period of integration (1993–2011), both the volume and barycenter of the South Pacific Tropical Water that resurfaces in the equatorial Pacific are tightly linked to El Niño–Southern Oscillation (ENSO), with their correlation with the Niño-3.4 index reaching −0.79 and 0.84, respectively. Their correlation (−0.75 and 0.85) with the sea surface salinity index, Niño-S34.8, is also high. Of particular interest is that both the volume and barycenter of the resurfacing South Pacific Tropical Water peak earlier than the ENSO indices by about 3 months. On the interannual time scale, the resurfacing of South Pacific Tropical Water may modulate the sea surface salinity in the equatorial Pacific at a rate equivalent to as much as 25% of the surface freshwater flux. The results suggest that the resurfacing of South Pacific Tropical Water directly contributes to the sea surface salinity variability in the equatorial Pacific and potentially plays a role in ENSO evolution.