bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interdisciplinary Communication
Authors: Watson Anne , Weaver Meaghann , Jacobs Shana , Lyon Maureen E. 
Published: March 2019

Advance care planning is being increasingly recognized as a component of quality in end-of-life care, but standardized documentation in the electronic health record has not yet been achieved, undermining interdisciplinary communication about care needs and limiting research opportunities.
We examined the electronic health records of nine adolescent and young adults with cancer who died after participation in an advance care planning clinical trial (N = 30). In this secondary analysis of this subgroup, disease trajectory and end-of-life information were abstracted from the electronic health record, and treatment preferences from the original study were obtained.
All deceased participants older than 18 years had a surrogate decision maker identified in the electronic health record, and all deceased participants had limitations placed on their care, varying from 1.5 hours up to 2 months before death. However, assessment of relations between treatment preferences and end-of-life care was difficult and revealed the presence of circumstances that advance care planning is designed to avoid, such as family conflict. Lack of an integrated health care record regarding advance care planning and end-of-life care makes both care coordination and examination of the association between planning and goal concordant care more difficult.
Traumatic Falls in the Pediatric Population
Authors: Oleck Nicholas C. , Dobitsch Andrew A. , Liu Farrah C. , Halsey Jordan N. , Le Thuy-My T. , Hoppe Ian C. , Lee Edward S. , Granick Mark S. 
Published: March 2019

Purpose
Falls are a leading cause of nonfatal injury in the pediatric population, resulting in numerous hospitalizations. Children may not have fully developed reflexive and balancing abilities, rendering them more susceptible to traumatic falls. Here the authors present their findings regarding patterns of facial fracture and concomitant injury seen in the pediatric population secondary to falls.

Methods
A retrospective chart review was performed of all facial fractures as a result of falls in the pediatric population in a level 1 trauma center in an urban environment (University Hospital in Newark, NJ). Patient demographics were collected, as well as location of fractures, concomitant injuries, and surgical management strategies.

Results
Fifty-five patients were identified as 18 years or younger and having sustained a facial fracture as the result of a fall. This cohort was compared with 418 pediatric patients with facial fractures due to nonfall etiologies. The mean age was 9.6 years (range, 0–18 years), with a male predominance of 67.3%. There were a total of 70 fractures identified on radiological imaging. The most frequently fractured bones were the orbit (n = 27), nasal bone (n = 15), and mandible (n = 11). Orbital and frontal sinus fractures each occurred more frequently due to falls compared with all other causes of injury. Patients with orbital fractures were significantly more likely to present with an additional facial fracture compared with those without (P < 0.01). The most common concomitant injuries were traumatic brain injury, skull fracture, and intracranial hemorrhage. Patients who suffered a facial fracture due to a fall were significantly more likely to sustain a concomitant skull fracture (P < 0.05) and intra-abdominal injury (P < 0.05) compared with all other etiologies. Fourteen patients required surgical intervention. One patient died.

Conclusions
Pediatric facial fractures are a unique entity. The general plasticity of the pediatric anatomy can predispose patients to significant injury without obvious external signs. A high level of clinical suspicion is required to avoid misdiagnosis and delay of treatment. The authors hope this study can address a preventable issue in child safety, educate caregivers, and provide insight towards fracture management that fosters functional and aesthetic recovery.
Right hospital, right patients: Penetrating injury patients treated at high-volume penetrating trauma centers have lower mortality
Authors: Fu Chih-Yuan , Bajani Francesco , Tatebe Leah , Butler Caroline , Starr Frederic , Dennis Andrew , Kaminsky Matthew , Messer Thomas , Schlanser Victoria , Kramer Kristina , Poulakidas Stathis , Cheng Chi-Tung , Mis Justin , Bokhari Faran 
Published: March 2019

BACKGROUND
The recognition of the relationship between volume and outcomes led to the regionalization of trauma care. The relationship between trauma mechanism-subtype and outcomes has yet to be explored. We hypothesized that trauma centers with a high volume of penetrating trauma patients might be associated with a higher survival rate for penetrating trauma patients.

METHODS
A retrospective cohort analysis of penetrating trauma patients presenting between 2011 and 2015 was conducted using the National Trauma Database and the trauma registry at the Stroger Cook County Hospital. Linear regression was used to determine the relationship between mortality and the annual volume of penetrating trauma seen by the treating hospital.

RESULTS
Nationally, penetrating injuries account for 9.5% of the trauma cases treated. Patients treated within the top quartile penetrating-volume hospitals (≥167 penetrating cases per annum) are more severely injured (Injury Severity Score: 8.9 vs. 7.7) than those treated at the lowest quartile penetrating volume centers (<36.6 patients per annum). There was a lower mortality rate at institutions that treated high numbers of penetrating trauma patients per annum. A penetrating trauma mortality risk adjustment model showed that the volume of penetrating trauma patients was an independent factor associated with survival rate.

CONCLUSION
Trauma centers with high penetrating trauma patient volumes are associated with improved survival of these patients. This association with improved survival does not hold true for the total trauma volume at a center but is specific to the volume of the penetrating trauma subtype.

LEVEL OF EVIDENCE
Prognostic/Epidemiology Study, Level-III; Therapeutic/Care Management, Level IV.
Computed tomography correlation of skeletal landmarks and vascular anatomy in civilian adult trauma patients: Implications for resuscitative endovascular balloon occlusion of the aorta
Authors: Eliason Jonathan L. , Derstine Brian A. , Horbal Steven R. , Wang Nicholas C. , Holcombe Sven A. , Chiu Chien-Hung , Ross Brian E. , Bromwell Brenna , Morrison Jonathan , Wang Stewart C. 
Published: March 2019

BACKGROUND
Resuscitative endovascular balloon occlusion of the aorta (REBOA) is a valuable resuscitative adjunct in a variety of clinical settings. In resource-limited or emergency environments, REBOA may be required with delayed or absent image-guidance or verification. Catheter insertion lengths may be informed by making computed tomography (CT) correlations of skeletal landmarks with vascular lengths.

METHODS
Between 2000 and 2015 at a single civilian tertiary care center, 2,247 trauma patients with CT imaging were identified, yielding 1,789 patients with adequate contrast opacification of the arterial system in the chest, abdomen, and pelvis. Individual scans were analyzed using MATLAB software, with custom high-throughput image processing algorithms applied to correlate centerline vascular anatomy with musculoskeletal landmarks. Data were analyzed using R version 3.3.

RESULTS
The median centerline distance from the skin access to the aortic bifurcation was longer by 0.3 cm on the right than on the left side. Median aortic zone I length was 21.6 (interquartile range, 20.3–22.9) cm, while zone III was 8.7 (7.8–9.5) cm. Torso extent (TE) correlation to zone I was much higher than that for zone III (R2, 0.58 vs. 0.26 (right) and 0.58 vs. 0.27 (left); p < 0.001). Assuming a 4-cm balloon length, optimal fixed insertion length would be 48 cm and 28 cm for zones I and III (error, 0.4% vs. 33.3%), respectively, although out of zone placements can be reduced if adjusted for TE (error, 0% vs. 26.4%).

CONCLUSION
Computed tomography morphometry suggests that a fixed REBOA catheter insertion length of 48 cm for zone I and 28 cm for zone III is optimal (on average, for average-height individuals), with improved accuracy by formulaic adjustments for TE. High residual error for zone III placement may require redesign of existing catheter balloon lengths or consideration of the relative risk associated with placing the balloon catheter too low or too high.

LEVEL OF EVIDENCE
Prognostic/epidemiological, level III.
Should they stay or should they go? Who benefits from interfacility transfer to a higher-level trauma center following initial presentation at a lower-level trauma center
Authors: Adzemovic Tessa , Murray Thomas , Jenkins Peter , Ottosen Julie , Iyegha Uroghupatei , Raghavendran Krishnan , Napolitano Lena M. , Hemmila Mark R. , Gipson Jonathan , Park Pauline , Tignanelli Christopher J. 
Published: March 2019

BACKGROUND
Interfacility transfer of patients from Level III/IV to Level I/II (tertiary) trauma centers has been associated with improved outcomes. However, little data are available classifying the specific subsets of patients that derive maximal benefit from transfer to a tertiary trauma center. Drawbacks to transfer include increased secondary overtriage. Here, we ask which injury patterns are associated with improved survival following interfacility transfer.

METHODS
Data from the National Trauma Data Bank was utilized. Inclusion criteria were adults (≥16 years). Patients with Injury Severity Score of 10 or less or those who arrived with no signs of life were excluded. Patients were divided into two cohorts: those admitted to a Level III/IV trauma center versus those transferred into a tertiary trauma center. Multiple imputation was performed for missing values, and propensity scores were generated based on demographics, injury patterns, and disease severity. Using propensity score–stratified Cox proportional hazards regression, the hazard ratio for time to death was estimated.

RESULTS
Twelve thousand five hundred thirty-four (5.2%) were admitted to Level III/IV trauma centers, and 227,315 (94.8%) were transferred to a tertiary trauma center. Patients transferred to a tertiary trauma center had reduced mortality (hazard ratio, 0.69; p < 0.001). We identified that patients with traumatic brain injury with Glasgow Coma Scale score less than 13, pelvic fracture, penetrating mechanism, solid organ injury, great vessel injury, respiratory distress, and tachycardia benefited from interfacility transfer to a tertiary trauma center. In this sample, 56.8% of the patients benefitted from transfer. Among those not transferred, 49.5% would have benefited from being transferred.

CONCLUSION
Interfacility transfer is associated with a survival benefit for specific patients. These data support implementation of minimum evidence-based criteria for interfacility transfer.

LEVEL OF EVIDENCE
Therapeutic/Care Management, Level IV.
Robust Hierarchical Density Estimation and Regression for Re-stained Histological Whole Slide Image Co-registration
Authors: Jiang Jun , Larson Nicholas B. , Prodduturi Naresh , Flotte Thomas J. , Hart Steven N. 
Published: March 2019

AbstractFor many disease conditions, tissue samples are colored with multiple dyes and stains to add contrast and location information for specific proteins to accurately identify and diagnose disease. This presents a computational challenge for digital pathology, as whole-slide images (WSIs) need to be properly overlaid (i.e. registered) to identify co-localized features. Traditional image registration methods sometimes fail due to the high variation of cell density and insufficient texture information in WSIs – particularly at high magnifications. In this paper, we proposed a robust image registration strategy to align re-stained WSIs precisely and efficiently. This method is applied to 30 pairs of immunohistochemical (IHC) stains and their hematoxylin and eosin (H&E) counterparts. Our approach advances the existing methods in three key ways. First, we introduce refinements to existing image registration methods. Second, we present an effective weighting strategy using kernel density estimation to mitigate registration errors. Third, we account for the linear relationship across WSI levels to improve accuracy. Our experiments show significant decreases in registration errors when on matching IHC and H&E pairs, enabling subcellular-level analysis on stained and re-stained histological images. We also provide a tool to allow users to develop their own registration benchmarking experiments.
Methods for Analyzing Imaging Mass Cytometry Data with Tellurium Probes
Authors: Bassan Jay , Nitz Mark 
Published: March 2019

AbstractImaging mass cytometry (IMC) is a technique allowing visualization and quantification of over 40 biological parameters in a single experiment with subcellular spatial resolution, however most IMC experiments are limited to endpoint analysis with antibodies and DNA stains. Small molecules containing tellurium are promising probes for IMC due to their cell permeability, synthetic versatility, and most importantly their application to sequential labelling with isotopologous probes (SLIP) experiments. SLIP experiments with tellurium-containing probes allow quantification of intracellular biology at multiple timepoints with IMC. Despite the promise of tellurium in IMC, there are unique challenges in image processing associated with tellurium IMC data. Here, we address some of these issues by demonstrating the removal of xenon background signal, combining channels to improve signal-to-noise ratio, and calculating isotope transmission efficiency biases. These developments add accuracy to the unique temporal resolution afforded by tellurium IMC probes.
A comparison of DNA stains and staining methods for Agarose Gel Electrophoresis
Authors: Hall Andie C. 
Published: March 2019

ABSTRACTNucleic acid stains are necessary for Agarose Gel Electrophoresis (AGE). The commonly used but mutagenic Ethidium Bromide is being usurped by a range of safer but more expensive alternatives. These safe stains vary in cost, sensitivity and the impedance of DNA as it migrates through the gel. Modified protocols developed to reduce cost increase this variability. In this study, five Gel stains (GelRed™, GelGreen™, SYBR™ safe, SafeView and EZ-Vision®In-Gel Solution) two premixed loading dyes (SafeWhite, EZ-Vision®One) and four methods (pre-loading at 100x, pre-loading at 10x, precasting and post-staining) are evaluated for sensitivity and effect on DNA migration. GelRed™ was found to be the most sensitive while the EZ-Vision® dyes and SafeWhite had no discernible effect on DNA migration. Homemade loading dyes were as effective as readymade ones at less than 4% of the price. This method used less than 1% of the dye needed for the manufacturer recommended protocols. Thus, with careful consideration of stain and method, Gel stain expenditure can be reduced by over 99%.
A hierarchical approach to model decision making: a study in chemotactic behavior ofEscherichia coli
Authors: Vafadar Safar , Kavousi Kaveh , Safdari Hadiseh , Kalirad Ata , Sadeghi Mehdi 
Published: March 2019

AbstractReducing the complex behavior of living entities to its underlying physical and chemical processes is a formidable task in biology. Complex behaviors can be characterized as decision making: the ability to process the incoming information via an intracellular network and act upon this information to choose appropriate strategies. Motility is one such behavior that has been the focus many modeling efforts in the past. Our aim is to reduce the chemotactic behavior in E. coli to its molecular constituents in order to paint a comprehensive and end-to-end picture of this intricate behavior. We utilize a hierarchical approach, consisting of three layers, to achieve this goal: at the first level, chemical reactions involved in chemotaxis are simulated. In the second level, the chemical reactions give rise to the mechanical movement of six independent flagella. At the last layer, the two lower layers are combined to allow a digital bacterium to receive information from its environment and swim through it with verve. Our results are in concert with the experimental studies concerning the motility of E. coli cells. In addition, we show that our detailed model of chemotaxis is reducible to a non-homogeneous Markov process.
Differential requirements of cyclase associated protein (CAP) for actin turnover during the lytic cycle of Toxoplasma gondii
Authors: Hunt Alex , Wagener Jeanette , Kent Robyn , Carmeille Romain , Russell Matt , Peddie Christopher , Collinson Lucy , Heaslip Aoife , Ward Gary E. , Treeck Moritz 
Published: March 2019

AbstractToxoplasma gondii contains a limited subset of actin binding proteins. Here we show that ablation of the putative actin regulator cyclase-associated protein (TgCAP) leads to significant defects in some but not all actin dependent processes, including a defect in cell-cell communication, but surprisingly not synchronicity of division. Two CAP isoforms originate from alternative translational start sites and are beneficial for parasite fitness while a single isoform is sufficient for virulence in mice. Examination of the mutant parasites by 3D electron microscopy reveals that loss of CAP results in a defect to form a normal residual body, but all parasites remain connected within the vacuole. This dissociates synchronicity of division and parasite rosetting and reveals that establishment and maintenance of the residual body may be more complex than previously thought. These results highlight the different spatial requirements for actin turnover in Toxoplasma, controlled by a reduced subset of actin binding proteins.
Towards next generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics
Authors: Goig Galo A. , Torres-Puente Manuela , Mariner-Llicer Carla , Villamayor Luis M. , Chiner-Oms Álvaro , Gil-Brusola Ana , Borrás Rafa , Comas Iñaki 
Published: March 2019

AbstractTuberculosis remains one of the main causes of death worldwide. The long and cumbersome process of culturingMycobacterium tuberculosiscomplex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel tuberculosis diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study had been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers. In this work, we use large-scale comparative genomics to provide a catalog of 30 characterized loci that are unique to the MTBC. Some of these genes could be targeted to assess the physiological status of the bacilli. Remarkably, none of the conventional MTBC markers is in our catalog. In addition, we develop a qPCR assay to accurately quantify MTBC DNA in clinical samples.
Distinct defense strategies allow different grassland species to cope with root herbivore attack
Authors: Hervé Maxime R , Erb Matthias 
Published: March 2019

AbstractRoot-feeding insect herbivores are of substantial evolutionary, ecological and economical importance. Plants can resist insect herbivores through a variety of tolerance and resistance strategies. To date, few studies have systematically assessed the prevalence and importance of these strategies for root-herbivore interactions across different plant species.Here, we characterize the defense strategies used by three different grassland species to cope with a generalist root herbivore, the larvae of the European cockchafer Melolontha melolontha.Our results reveal that the different plant species rely on distinct sets of defense strategies. The spotted knapweed (Centaurea stoebe) resists attack by dissuading the larvae through the release of repellent chemicals. White clover (Trifolium repens) does not repel the herbivore, but reduces feeding, most likely through structural defenses and low nutritional quality. Finally, the common dandelion (Taraxacum officinale) allows M. melolontha to feed abundantly but compensates for tissue loss through induced regrowth.Synthesis: Three co-occurring plant species have evolved different solutions to defend themselves against attack by a generalist root herbivore. The different root defense strategies may reflect distinct defense syndromes.
Human motor fatigability as evoked by repetitive movements results from a gradual breakdown of surround inhibition
Authors: Bächinger Marc , Lehner Rea , Thomas Felix , Hanimann Samira , Balsters Joshua Henk , Wenderoth Nicole 
Published: March 2019

SummaryMotor fatigability emerges when demanding tasks are executed over an extended period of time. Here, we used repetitive low-force movements that cause a gradual reduction in movement speed (or “motor slowing”) to study the central component of fatigability in healthy adults. We show that motor slowing is associated with a gradual increase of net excitability in the motor network and, specifically, in primary motor cortex (M1), which results from overall disinhibition. Importantly, we link performance decrements to a breakdown of surround inhibition in M1, which is associated with high coactivation of antagonistic muscle groups. This is consistent with the model that a loss of inhibitory control might broaden the tuning of population vectors such that movement patterns become more variable, ill-timed and effortful. We propose that the release of inhibition in M1 is an important mechanism underpinning motor fatigability and, potentially, also pathological fatigue as frequently observed in patients with brain disorders.
Genome-wide association analysis for resistance to infectious pancreatic necrosis virus identifies candidate genes involved in viral replication and immune response in rainbow trout (Oncorhynchus mykiss)
Authors: Rodríguez Francisco H. , Flores-Mara Raúl , Yoshida Grazyella M. , Barría Agustín , Jedlicki Ana M. , Lhorente Jean P. , Reyes-López Felipe , Yáñez José M. 
Published: March 2019

ABSTRACTInfectious pancreatic necrosis (IPN) is a viral disease with considerable negative impact on the rainbow trout (Oncorhynchus mykiss) aquaculture industry. The aim of the present work was to detect genomic regions that explain resistance to infectious pancreatic necrosis virus (IPNV) in rainbow trout. A total of 2,278 fish from 58 full-sib families were challenged with IPNV. Of the challenged fish, 768 individuals were genotyped (488 resistant and 280 susceptible), using a 57K single nucleotide polymorphisms (SNPs) panel Axiom®, Affymetrix®. A genome-wide association study (GWAS) was performed using the phenotypes time to death (TD) and binary survival (BS), along with the genotypes of the challenged fish using a Bayesian model (Bayes C). Heritabilities for resistance to IPNV estimated using pedigree information, were 0.39 and 0.32 for TD and BS, respectively. Heritabilities for resistance to IPNV estimated using genomic information, were 0.50 and 0.54 for TD and BS, respectively. The Bayesian GWAS detected a SNP located on chromosome 5 explaining 18% of the genetic variance for TD. A SNP located on chromosome 23 was detected explaining 9% of the genetic variance for BS. The proximity of Sentrin-specific protease 5 (SENP5) to a significant SNP makes it a candidate gene for resistance against IPNV. However, the moderate-low proportion of variance explained by the detected marker leads to the conclusion that the incorporation of all genomic information, through genomic selection, would be the most appropriate approach to accelerate genetic progress for the improvement of resistance against IPNV in rainbow trout.