bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enrich2: a statistical framework for analyzing deep mutational scanning data
Authors: Rubin Alan F. , Lucas Nathan , Bajjalieh Sandra M. , Papenfuss Anthony T. , Speed Terence P. , Fowler Douglas M. 
Published: September 2016

AbstractMeasuring the functional consequences of protein variants can reveal how a protein works or help unlock the meaning of an individual’s genome. Deep mutational scanning is a widely used method for multiplex measurement of the functional consequences of protein variants. A major limitation of this method has been the lack of a common analysis framework. We developed a statistical model for estimating variant scores that can be applied to many experimental designs. Our method generates an error estimate for each score that captures both sampling error and consistency between replicates. We apply our model to one novel and five published datasets comprising 243,732 variants and demonstrate its superiority, particularly for removing noisy variants, detecting variants of small effect, and conducting hypothesis testing. We implemented our model in easy-to-use software, Enrich2, that can empower researchers analyzing deep mutational scanning data.
Fixing the stimulus-as-fixed-effect fallacy in task fMRI
Authors: Westfall Jacob , Nichols Thomas E. , Yarkoni Tal 
Published: September 2016

AbstractMost fMRI experiments record the brain’s responses to samples of stimulus materials (e.g., faces or words). Yet the statistical modeling approaches used in fMRI research universally fail to model stimulus variability in a manner that affords population generalization--meaning that researchers’ conclusions technically apply only to the precise stimuli used in each study, and cannot be generalized to new stimuli. A direct consequence of thisstimulus-as-fixed-effect fallacyis that the majority of published fMRI studies have likely overstated the strength of the statistical evidence they report. Here we develop a Bayesian mixed model (the random stimulus model; RSM) that addresses this problem, and apply it to a range of fMRI datasets. Results demonstrate considerable inflation (50 - 200 % in most of the studied datasets) of test statistics obtained from standard “summary statistics”-based approaches relative to the corresponding RSM models. We demonstrate how RSMs can be used to improve parameter estimates, properly control false positive rates, and test novel research hypotheses about stimulus-level variability in human brain responses.
Identifying Conserved Genomic Elements and Designing Universal Probe Sets To Enrich Them
Authors: Faircloth Brant C. 
Published: September 2016

AbstractTargeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic, and population genetic studies. Yet, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and to design enrichment baits targeting these regions. These shortcomings limit the application of targeted enrichment methods to many organismal groups. Here, I describe a universal workflow for identifying conserved genomic regions in available genomic data and for designing targeted enrichment baits to collect data from these conserved regions. I demonstrate how this computational approach can be applied to diverse organismal groups by identifying sets of conserved loci and designing enrichment baits targeting thousands of these loci in the understudied arthropod groups Arachnida, Coleoptera, Diptera, Hemiptera, or Lepidoptera. I then usein silicoanalyses to demonstrate that these conserved loci reconstruct the accepted relationships among genome sequences from the focal arthropod orders, and we performin vitrovalidation of the Arachnid probe set as part of a separate manuscript (Starrettet al.Submitted). All of the documentation, design steps, software code, and probe sets developed here are available under an open-source license for restriction-free testing and use by any research group, and although the examples in this manuscript focus on understudied and exceptionally diverse arthropod groups, the software workflow is applicable to all organismal groups having some form of pre-existing genomic information.
Availability of sentinel lymph node biopsy for cutaneous squamous cell carcinoma
Authors: Maruyama Hiroshi , Tanaka Ryota , Fujisawa Yasuhiro , Nakamura Yasuhiro , Ito Shusaku , Fujimoto Manabu 
Published: September 2016

AbstractCutaneous squamous cell carcinoma is the second common cutaneous cancer, especially in the elderly. Sentinel lymph node biopsy is generally performed in breast cancers and cutaneous melanomas to detect occult nodal metastases. The benefit of sentinel lymph node biopsy in improving cutaneous squamous cell carcinoma prognosis is doubtful. One hundred and sixty‐nine patients who underwent treatment for cutaneous squamous cell carcinoma between 2004 and 2015, and who were followed up for at least 6 months or developed metastases within the follow‐up period were included. Forty‐nine patients underwent sentinel lymph node biopsy, whereas 120 patients did not, including 13 who exhibited clinical lymph node metastases before treatment. Of these 49 patients, nine (18.4%) presented with sentinel lymph node metastasis, which occurred after treatment in three (6.1%) of them (false‐negative). Among the 107 patients who did not undergo lymph node biopsy, 12 (11.2%) developed post‐treatment metastases. The metastasis‐free and disease‐specific survival rates were not significantly different in those who did or did not undergo sentinel lymph node biopsy. Patients with clinical lymph node metastases had a higher risk compared with those without. Patients with T2–T4 tumors had a higher risk compared with those with T1 tumors. When selecting for those with T2 tumors or greater, the same lack of relationship was observed. In conclusion, in this small retrospective cohort, in patients with cutaneous squamous cell carcinoma, there were no significant differences in metastasis‐free and disease‐specific survival rates between those who did or did not undergo sentinel lymph node biopsy, regardless of T staging.
Do fragment size and edge effects predict carbon stocks in trees and lianas in tropical forests?
Authors: Magnago Luiz Fernando Silva , Magrach Ainhoa , Barlow Jos , Schaefer Carlos Ernesto Goncalves Reynaud , Laurance William F. , Martins Sebastião Venâncio , Edwards David P. 
Published: September 2016

Summary

Tropical forests are critical for protecting global biodiversity and carbon stores. While forest degradation and fragmentation cause negative impacts on trees, many woody lianas benefit, with associated negative effects on carbon storage. Here, we focus on the key question of how abiotic environmental changes resulting from tropical forest fragmentation mediate the allocation of carbon into trees and lianas.

We focus on the globally threatened Brazilian Atlantic Forest, in forest fragments spanning 13–23 442 ha in area and at fragment edges and interiors. Within each fragment, we established two transects: one at the edge and one in the interior. Each transect consisted of ten 10 × 10 m plots spaced at 20 m intervals. Within each plot, we sampled living trees with diameter ≥4·8 cm at 1·3 m above ground, living lianas with diameter ≥1·6 cm at 10 cm above ground, and several microclimatic and soil variables.

Fragmentation changed a broad suite of abiotic environmental conditions recognized as being associated with forest carbon stocks: edges and smaller fragments were hotter, windier, and less humid, with more fertile and less acid soils at edges. Tree carbon stocks were thus higher in forest interiors than at edges, and were positively related to fragment size in interiors, but were not impacted by fragment size at edges.

Trees and lianas showed different responses to fragmentation: in interiors of small fragments, tree carbon stocks declined whereas liana carbon stocks increased; and at edges, tree carbon stocks were not affected by fragment size, whereas liana carbon stocks were highest in smaller fragments. These patterns were strongly related to changes in abiotic environmental conditions.

We conclude that the abiotic changes across the fragmentation gradient, rather than liana proliferation, were more likely to reduce tree carbon stocks. Cutting of lianas is frequently promoted for restoring forest carbon in human‐modified tropical forests. However, this approach may not be effective for restoring forest carbon stocks in fragmented forests.
Parental involvement in neonatal critical care decision‐making
Authors: Shaw Chloe , Stokoe Elizabeth , Gallagher Katie , Aladangady Narendra , Marlow Neil 
Published: September 2016

AbstractThe article analyses the decision‐making process between doctors and parents of babies in neonatal intensive care. In particular, it focuses on cases in which the decision concerns the redirection of care from full intensive care to palliative care at the end of life. Thirty one families were recruited from a neonatal intensive care unit in England and their formal interactions with the doctor recorded. The conversations were transcribed and analysed using conversation analysis. Analysis focused on sequences in which decisions about the redirection of care were initiated and progressed. Two distinct communicative approaches to decision‐making were used by doctors: ‘making recommendations’ and ‘providing options’. Different trajectories for parental involvement in decision‐making were afforded by each design, as well as differences in terms of the alignments, or conflicts, between doctors and parents. ‘Making recommendations’ led to misalignment and reduced opportunities for questions and collaboration; ‘providing options’ led to an aligned approach with opportunities for questions and fuller participation in the decision‐making process. The findings are discussed in the context of clinical uncertainty, moral responsibility and the implications for medical communication training and guidance.A Virtual Abstract of this paper can be accessed at:https://www.youtube.com/watch?v=MyuymxDNupk&feature=youtu.be
Designing a Clean Label Sponge Cake with Reduced Fat Content
Authors: Eslava‐Zomeño Cristina , Quiles Amparo , Hernando Isabel 
Published: September 2016

AbstractThe fat in a sponge cake formulation was partially replaced (0%, 30%, 50%, and 70%) with OptiSol™5300.This natural functional ingredient derived from flax seeds, rich in fiber and alpha‐linoleic acid, provides a natural substitute for guar and xanthan gums, avoiding E‐numbers on labels. The structure and some physicochemical properties of the formulations were examined, sensory analysis was conducted and changes in starch digestibility due to adding this ingredient were determined. Increasing quantities of OptiSol™5300 gave harder cakes, with less weight loss during baking, without affecting the final cake height. There were no significant differences (P > 0.05) in texture, flavor and overall acceptance between the control and the 30% substitution cake, nor in the rapidly digestible starch values. Consequently, replacing up to 30% of the fat with OptiSol™5300 gives a new product with health benefits and a clean label that resembles the full‐fat sponge cake.
Use of Multi‐Intake Temporal Dominance of Sensations (TDS) to Evaluate the Influence of Cheese on Wine Perception
Authors: Galmarini Mara V. , Loiseau Anne‐Laure , Visalli Michel , Schlich Pascal 
Published: September 2016

AbstractThough the gastronomic sector recommends certain wine–cheese associations, there is little sensory evidence on how cheese influences the perception of wine. It was the aim of this study to dynamically characterize 4 wines as they would be perceived when consumed with and without cheese. The tasting protocol was based on multi‐intake temporal dominance of sensations (TDS) coupled with hedonic rating. In the 1st session, 31 French wine and cheese consumers evaluated the wines (Pacherenc, Sancerre, Bourgogne, and Madiran) over 3 consecutive sips. In the following sessions, they performed the same task, but eating small portions of cheese (Epoisses, Comté, Roquefort, Crottin de Chavignol) between sips. All cheeses were tasted with all wines over 4 sessions. TDS data were mainly analyzed in terms of each attribute's duration of dominance by analysis of variance, multivariate analysis of variance, and canonical variate analysis. Results showed that cheese consumption had an impact (P < 0.1) on dominance duration of attributes and on preference for most wines. For example, in Madiran, all cheeses reduced dominance duration (P < 0.01) of astringency and sourness and increased duration of red fruit aroma. Although the number of consumers was small to make extended general conclusions on wine's preference, significant changes were observed before and after cheese intake.
Characterizing Runoff and Water Yield for Headwater Catchments in the Southern Sierra Nevada
Authors: Safeeq Mohammad , Hunsaker Carolyn T. 
Published: September 2016

AbstractIn a Mediterranean climate where much of the precipitation falls during winter, snowpacks serve as the primary source of dry season runoff. Increased warming has led to significant changes in hydrology of the western United States. An important question in this context is how to best manage forested catchments for water and other ecosystem services? Answering this basic question requires detailed understanding of hydrologic functioning of these catchments. Here, we depict the differences in hydrologic response of 10 catchments. Size of the study catchments ranges from 50 to 475 ha, and they span between 1,782 and 2,373 m elevation in the rain‐snow transitional zone. Mean annual streamflow ranged from 281 to 408 mm in the low elevation Providence and 436 to 656 mm in the high elevation Bull catchments, resulting in a 49 mm streamflow increase per 100 m (R2 = 0.79) elevation gain, despite similar precipitation across the 10 catchments. Although high elevation Bull catchments received significantly more precipitation as snow and thus experienced a delayed melt, this increase in streamflow with elevation was mainly due to a reduction in evapotranspiration (ET) with elevation (45 mm/100 m, R2 = 0.65). The reduction in ET was attributed to decline in vegetation density, growing season, and atmospheric demand with increasing elevation. These findings suggest changes in streamflow in response to climate warming may likely depend on how vegetation responds to those changes in climate.
Clinical review of treatment outcomes and patterns of failure with adjuvant radiotherapy in node‐positive malignant melanoma
Authors: Keenan Lorna G , O'Sullivan Siobhra , Glynn Aisling , Higgins Martin , Flavin Aileen , Brennan Sinead 
Published: September 2016

AbstractIntroductionAdjuvant radiotherapy is proven to prevent lymph node field relapse after therapeutic lymphadenectomy for melanoma, but does not improve overall survival based on current data. There remains a high rate of distant relapse. This study reports patterns of failure in patients treated with adjuvant radiotherapy, looking at factors associated with distant metastasis and comparing this to recent literature.MethodsThis retrospective study included patients treated with adjuvant nodal irradiation after lymphadenectomy between June 2012 and March 2015.ResultsTwenty‐one patients were treated during this period. Median follow‐up was 13.5 months. There were no lymph node field recurrences. Distant metastasis (DM) rate was 48%. DM rate was significantly higher (P = 0.027) in patients with extracapsular extension (ECE) (71%) than those without ECE (0%). DM rate was higher in those with a maximum tumour size of >3 cm (71%) than those with tumour size <3 cm (30%) (P = 0.160). Number of nodes, BRAF status or nodal site did not correlate with rate of DM. The median time to DM was 16 weeks after completion of radiotherapy.ConclusionRadiotherapy is well tolerated and effective in regional control. However, patients are at risk of early distant relapse, particularly those with ECE or large tumour size. There are currently no useful prognostic markers to differentiate the risk of regional versus distant recurrence, and the optimal treatment paradigm remains undefined. Research on adjuvant systemic therapies and abscopal effects of radiotherapy have shown improved management of distant metastasis; creating an even greater need for effective regional control strategies.
Habitat fragmentation, EFN‐bearing trees and ant communities: Ecological cascades in Atlantic Forest of northeastern Brazil
Authors: Câmara Talita , Almeida Walkiria R. , Tabarelli Marcelo , Andersen Alan N. , Leal Inara R. 
Published: September 2016

AbstractHabitat fragmentation has a marked impact on the functional composition of tropical forest tree assemblages, and such change is likely to cascade through other trophic levels. Here, we investigate how habitat fragmentation affects extrafloral nectary (EFN)‐bearing plants and ant functional groups known to attend EFNs in a fragmented landscape of the Atlantic Forest. Extrafloral nectary‐bearing trees were identified in 50 0.1‐ha plots located in forest fragments, edge and interior patches. Ants were surveyed in 30 1‐m2litter samples in each of 17 forest fragments and in forest interior. Extrafloral nectary‐bearing plants accounted for 19.9% of individuals and 10.5% of species and included both pioneer and shade‐tolerant species similarly rich in the three habitat types. However, shade‐tolerant individuals accounted for >80% of EFN‐bearing plants in forest interior, compared with 2% in forest edge and 29% in fragments. Forest edge and fragment plots had a third fewer EFN‐bearing individuals and species compared with forest interior. This appeared to have important implications for local ant communities as the density of EFN‐bearing trees was the most important variable explaining the species richness of arboreal dominant ants. Our results show that plant loser–winner replacements promoted by forest fragmentation can cascade through higher trophic levels, with implications for forest dynamics and biodiversity conservation.
Comparison of Feline Brain Anatomy in 0.25 and 3 Tesla Magnetic Resonance Images
Authors: Przyborowska P. , Adamiak Z. , Holak P. , Zhalniarovich Y. 
Published: September 2016

SummaryThe intention of the comparison of both low and high field was to examine which anatomical brain structures of cats were visible on low field images, as in clinical veterinary practice, 3 Tesla (T) magnets were of limited availability. The research was performed on 20 European short‐haired male and female cats, aged 1–3 years, with body weight of 2–4 kg. 0.25 T magnetic resonance images of neurocranium were acquired in all using T2‐weighted fast spin echo sequences with repetition time (TR) of 4010 ms and echo time (TE) of 90 ms in dorsal and transverse plane, and T2‐weighted fast spine echo sequences with TR of 4290 ms and TE of 120 ms in sagittal plane. Based on a detailed catalogue of feline brain structures visible at 3 T in previously published studies, it was examined which structures were visible on low field images. Anatomic structures were identified and compared to assess the reliability of diagnoses made based on low‐field magnetic resonance imaging. In low‐field scans, 92 structures were identified. Elements of auditory, visual, motor pathways, hippocampus and cerebral ventricular system were distinguished. Low‐field as well as high‐field magnetic resonance imaging support the identification of local tissue lesions, metastasis, focal ischaemia and haemorrhage, disorders associated with ventricular system dilation and hydrocephalus. It also produced accurate images of the hippocampus, which contributes to reliable diagnoses of various forms of epilepsy in cats. Due to technical limitations, a low‐field scanner is unlikely to visualize microtraumas, local inflammations, small haematomas or metastatic tumours.
Estimated costs before, during and after the introduction of the emergency laparotomy pathway quality improvement care (ELPQuIC) bundle
Authors: Eveleigh M. O. , Howes T. E. , Peden C. J. , Cook T. M. 
Published: September 2016

SummaryImplementation of a quality improvement bundle for peri‐operative management of emergency laparotomy (ELPQuIC) improved mortality in a previous study. We used data from one site that participated in that study to examine whether it was associated with the cost of care. We collected data from 396 patients: 144 before, 144 during and 108 after implementation of the bundle. We estimated costs incurred using previously published methodology based on the time the patient spent in hospital, in the operating theatre and in critical care. Duration of stay in hospital and critical care did not differ between time periods, p = 0.14 and p = 0.28, respectively. The costs per patient and per survivor did not differ between the time periods, p = 0.87 and p = 0.17, respectively. Costs were similar for patients aged < 80 years vs. ≥ 80 years. Implementation of a quality improvement bundle for emergency laparotomy has the capacity to save lives without increasing hospital costs.
Implementation of a ‘care bundle’ improves the management of patients admitted to hospital with decompensated cirrhosis
Authors: Dyson J. K. , Rajasekhar P. , Wetten A. , Hamad A. H. , Ng S. , Paremal S. , Baqai M. F. , Lamb C. A. , Masson S. , Hudson M. , Dipper C. , Cowlam S. , Hussaini H. , McPherson S. 
Published: September 2016

SummaryBackgroundSince 1970, there has been a 400% increase in liver‐related deaths due to the increasing prevalence of chronic liver disease in the United Kingdom (UK). The 2013 UK National Confidential Enquiry into Patient Outcome and Death report found that only 47% of patients who died from alcohol‐related liver disease received ‘good care’ during their hospital stay.AimTo develop a ‘care bundle’ for patients with decompensated cirrhosis, aiming to ensure that evidence‐based treatments are delivered within the first 24 h of hospital admission.MethodsThis work gives practical advice about how to implement the bundle and examines its effects on patient care at three National Health Service Hospital Trusts in the UK by collecting data on patient care before and after introduction of the bundle.ResultsData were collected on 228 patients across three centres (59% male, median age 53 years). Alcohol‐related liver disease was the aetiology of chronic liver disease in 85% of patients. The overall mortality rate during hospital admission was 15%. The audits demonstrated improvements in patient care for patients with a completed care bundle who were significantly more likely to have a diagnostic ascitic performed within the first 24 h (P = 0.020), have an accurate alcohol history documented (P < 0.0001) and be given antibiotics as prophylaxis against infection following a variceal haemorrhage (P = 0.0096). In Newcastle, the bundle completion rate increased from 25% to 90% during the review periods.ConclusionsThe introduction of a care bundle was associated with increased rates of diagnostic paracentesis and antibiotic prophylaxis with variceal haemorrhage in patients with decompensated cirrhosis.