bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symptom Trajectories After Military Blast Exposure and the Influence of Mild Traumatic Brain Injury
Authors: Walker William C. , Franke Laura M. , Sima Adam P. , Cifu David X. 
Published: September 2016

Background:
Blast-related mild traumatic brain injury (blast mTBI) is a signature wound of recent US military conflicts in the Middle East, but the relatedness of postconcussive symptoms (PCS) to the blast mTBI is unclear, and longitudinal symptom data are sparse.

Objectives:
To characterize postdeployment symptom levels and trajectories and to determine relationship to blast mTBI.

Methods:
A total of 216 participants within 2 years of blast exposure during deployment underwent structured interviews or algorithmic questionnaires for blast mTBI. Detailed symptom inventories for PCS, pain, posttraumatic stress disorder, and depression were taken serially at enrollment, 6 months, and 12 months later. Repeated-measure analysis of variance models were built.

Results:
Up to 50% of participants had at least 1 high-grade blast mTBI (with posttraumatic amnesia), 31% had low-grade only, and 19% had neither. Within the entire cohort, all 4 composite symptom scores started high and stayed unchanged. Between blast mTBI groups, symptom scores differed at every time point with some evidence of convergence over time. The PCS groups, different by definition to start, diverged further over time with those initially more symptomatic becoming relatively more so.

Conclusions:
History of blast mTBI accompanied by posttraumatic amnesia is associated with greater nonspecific symptoms after deployment, and prognosis for improvement when symptoms are prominent is poor.
Is Hyperbaric Oxygen Therapy Effective for Traumatic Brain Injury? A Rapid Evidence Assessment of the Literature and Recommendations for the Field
Authors: Crawford Cindy , Teo Lynn , Yang EunMee , Isbister Caitlin , Berry Kevin 
Published: September 2016

Objective:
This systematic review examines the efficacy of hyperbaric oxygen (HBO2) for traumatic brain injury (TBI) to make evidence-based recommendations for its application and future research.

Methods:
A comprehensive search was conducted to identify studies through 2014. Methodological quality was assessed and synthesis and interpretation of relevant data was performed.

Results:
Twelve randomized trials were included. All mild TBI studies demonstrated minimal bias and no statistically significant differences between HBO2 and sham arms. Statistically significant improvement occurred over time within both groups. Moderate-to-severe TBI studies were of mixed quality, with majority of results favoring HBO2 compared with “standard care.” The placebo analysis conducted was limited by lack of details.

Conclusions:
For mild TBI, results indicate HBO2 is no better than sham treatment. Improvements within both HBO2 and sham groups cannot be ignored. For acute treatment of moderate-to-severe TBI, although methodology appears flawed across some studies, because of the complexity of brain injury, HBO2 may be beneficial as a relatively safe adjunctive therapy if feasible. Further research should be considered to resolve the controversy surrounding this field, but only if methodological flaws are avoided and bias minimized.
A Retrospective Review of Orbital Decompression for Thyroid Orbitopathy with Endoscopic Preservation of the Inferomedial Orbital Bone Strut
Authors: Finn Avni P. , Bleier Benjamin , Cestari Dean M. , Kazlas Melanie A. , Dagi Linda R. , Lefebvre Daniel R. , Yoon Michael K. , Freitag Suzanne K. 
Published: September 2016

Purpose:
To determine incidence of new-onset diplopia, resolution of preexisting diplopia, and impact on proptosis resulting from endoscopic orbital decompression with and without preservation of the inferomedial orbital strut for thyroid orbitopathy.

Methods:
Retrospective review of all patients undergoing endoscopic 2- or 3-wall decompression with or without preservation of the strut for thyroid orbitopathy from January 2012 to June 2015.

Results:
Twenty-six patients (45 orbits) were included and divided into 4 primary categories: 2-wall decompression with strut preservation (4 orbits, 8%), 2-wall decompression with strut removal (7 orbits, 16%), 3-wall decompression with strut preservation (27 orbits, 60%), and 3-wall decompression with strut removal (7 orbits, 16%). The incidence of new-onset diplopia was 20% (2/10 patients without preoperative diplopia) overall and 16% in the strut preservation group (1/6 patients without preoperative diplopia). Resolution of diplopia occurred in 4 of 16 patients (25%) with preoperative diplopia, and all 4 had been treated with a 3-wall decompression with strut preservation. Resolution of diplopia in the group treated with strut preservation was 36% (4/11 patients with preoperative diplopia), and 0% of the 5 diplopic patients treated without strut preservation. Reduction in proptosis was statistically greater in those treated with strut removal (p = 0.003).

Conclusions:
This study demonstrates that endoscopic orbital decompression with preservation of the inferomedial bone strut results in a comparable to lower rate of new-onset diplopia compared with other reported techniques. When combined with 3-wall balanced decompression, this technique demonstrates a high rate of resolution of preexisting diplopia.
Whole blood: back to the future
Authors: Spinella Philip C. , Cap Andrew P. 
Published: September 2016

Purpose of review
We present data comparing whole blood with blood components and summarize the data that support increased availability of whole blood for patients with life-threatening bleeding.

Recent findings
Recent data indicate that whole-blood transfusion is associated with improved or comparable survival compared with resuscitation with blood components. These data complement randomized controlled trials indicating that platelet-containing blood products stored at 4 °C have superior hemostatic function, compared with platelet-containing blood products at 22 °C. Whole blood is rarely available in civilian hospitals and, thus, is rarely transfused into patients with hemorrhagic shock. Misconceptions that whole blood must be ABO specific, that whole blood cannot be leukoreduced and maintain platelets, and that cold storage causes loss of platelet function have limited its availability. Understanding that these barriers are not insurmountable will improve the availability of whole blood and facilitate its use. In addition, there are logistical advantages of whole-blood-based resuscitation, as compared with component therapy, for hemorrhagic shock.

Summary
Low titer Group O whole blood stored for up to 21 days at 4 °C merits further study to compare its efficacy and safety with current resuscitation approaches for patients with life-threatening bleeding.
Congenital Vascular Malformations of the Liver
Authors: Burdall Oliver C. , Grammatikopoulos Tassos , Sellars Maria , Hadzic Nedim , Davenport Mark 
Published: September 2016

ABSTRACTA link between congenital vascular malformation (CVM) of the liver and trisomy 21 has been suggested. We reviewed all children with trisomy 21 referred for investigation to a specialist pediatric hepatobiliary unit (1985–2015). Forty‐five children with trisomy 21 were identified; 7 (15%) had a defined CVMs (4 girls). All such infants were also diagnosed with a range of cardiac defects. CVMs were divided according to the nature of the vascular connection. Group (i) (n = 3): Abnormal venovenous anomaly. This included portocaval shunt and patent ductus venosus (n = 2). Group (ii) (n = 4): Involvement of all 3 vascular systems. Two infants had arterioportal hypertension caused by hepatic arteries feeding into a left portal vein aneurysm within the umbilical fissure. Two infants had more complex hepatic artery to hepatic vein shunts developing early cardiorespiratory failure with progressive jaundice. Our series shows a clear association between cardiac anomalies and CVM in children with trisomy 21.
Repeated therapeutic lumbar punctures in cryptococcal meningitis – necessity and/or opportunity?
Authors: Chang Christina C. , Perfect John R. 
Published: September 2016

Purpose of review
Overall, 50–70% of patients with cryptococcal meningitis have raised intracranial pressure (ICP). Multiple international treatment guidelines recommend repeated therapeutic lumbar punctures as adjunctive management. Here, we review the recent evidence for the role of repeated lumbar punctures on clinical outcome in cryptococcal meningitis and also review the increasing body of data utilizing these repeated cerebrospinal fluid (CSF) samples as a window into understanding immunopathogenesis of cryptococcal meningitis.

Recent findings
Adjunctive dexamethasone led to higher adverse advents and disability and poorer CSF fungal clearance. Performance of a therapeutic lumbar puncture is associated with 69% relative survival protection. An activated innate immune system in the CSF is associated with future cryptococcosis-associated immune reconstitution inflammatory syndrome development. The zebrafish model is being utilized in cryptococcal studies allowing live visualization of central nervous system invasion.

Summary
Therapeutic lumbar punctures are a critical part of cryptococcal meningitis management and CSF immunological assays are increasingly being performed in research settings. Finer manipulation of CSF removal and safer surgical techniques for intracranial pressure management applicable to resource-limited settings are needed. More precise and validated guidelines in resource-available settings would be an improvement for care. We look forward to identifying a set of biomarkers, easily performed in routine laboratories or at point-of-care, so as to translate these assays into clinical care. Wide-scale ‘–omic’ studies are likely to be required in future cryptococcal meningitis studies to improve our understanding of this deadly fungus.
Prelicensure Simulation-Enhanced Interprofessional Education
Authors: Palaganas Janice C. , Brunette Veronique , Winslow Betty 
Published: September 2016

Summary Statement
This review explores the state of prelicensure interprofessional education (IPE) using simulation-based education (SBE) by examining studies that use SBE for prelicensure IPE through a critical review of the research literature. We focus particularly on studies that included experiential SBE with reported measures and formal IPE with prelicensure participants from at least 2 health care professions. Fifty-four studies met criteria. We explore these studies, providing a compilation of information (e.g., educational, simulation, and research methods used; outcome measures reported; and demographics of learner groups), identifying themes that may affect learning, as well as surfacing challenges and gaps in the field. The quality and rigor of the existing literature is inadequate to confidently determine factors that affect learning through simulation-enhanced IPE. We suggest that more rigorous research criteria be included in future studies and a list of reporting items be provided, where future publications can enhance knowledge to guide best practice in simulation-enhanced IPE.
Behavioral self-management strategies for practice and exercise should be included in neurologic rehabilitation trials and care
Authors: Dobkin Bruce H. 
Published: September 2016

Purpose of review
Rehabilitation trials and postacute care to lessen impairments and disability after stroke, spinal cord injury, and traumatic brain injury almost never include training to promote long-term self-management of skills practice, strengthening and fitness. Without behavioral training to develop self-efficacy, clinical trials, and home-based therapy may fail to show robust results.

Recent findings
Behavioral theories about self-management and self-efficacy for physical activity have been successfully incorporated into interventions for chronic diseases, but rarely for neurologic rehabilitation. The elements of behavioral training include education about the effects of practice and exercise that are relevant to the person, goal setting, identification of possible barriers, problem solving, feedback about performance, tailored instruction, decision making, and ongoing personal or social support. Mobile health and telerehabilitation technologies offer new ways to remotely enable such training by monitoring activity from wearable wireless sensors and instrumented exercise devices to allow real-world feedback, goal setting, and instruction.

Summary
Motivation, sense of responsibility, and confidence to practice and exercise in the home can be trained to increase adherence to skills practice and exercise both during and after formal rehabilitation. To optimize motor learning and improve long-term outcomes, self-management training should be an explicit component of rehabilitation care and clinical trials.
Ethnically relevant consensus Korean reference genome towards personal reference genomes
Authors: Cho Yun Sung , Kim Hyunho , Kim Hak-Min , Jho Sungwoong , Jun JeHoon , Lee Yong Joo , Chae Kyun Shik , Kim Chang Geun , Kim Sangsoo , Eriksson Anders , Edwards Jeremy S. , Lee Semin , Kim Byung Chul , Manica Andrea , Church George M. , Bhak Jong 
Published: September 2016

AbstractHuman genomes are routinely compared against a universal reference. However, this strategy could miss population-specific or personal genomic variations, which may be detected more efficiently using an ethnically-relevant and/or a personal reference. Here we report a hybrid assembly of Korean reference (KOREF) as a pilot case for constructing personal and ethnic references by combining sequencing and mapping methods. KOREF is also the first consensus variome reference, providing information on millions of variants from additional ethnically homogeneous personal genomes. We found that this ethnically-relevant consensus reference was beneficial for efficiently detecting variants. Systematic comparison of KOREF with previously established human assemblies showed the importance of assembly quality, suggesting the necessity of using new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity.
Volumetric Two-photon Imaging of Neurons Using Stereoscopy (vTwINS)
Authors: Song Alexander , Charles Adam S. , Koay Sue Ann , Gauthier Jeff L. , Thiberge Stephan Y. , Pillow Jonathan W. , Tank David W. 
Published: September 2016

AbstractTwo-photon laser scanning microscopy of calcium dynamics using fluorescent indicators is a widely used imaging method for large scale recording of neural activity in vivo. Here we introduce volumetric Two-photon Imaging of Neurons using Stereoscopy (vTwINS), a volumetric calcium imaging method that employs an elongated, V-shaped point spread function to image a 3D brain volume. Single neurons project to spatially displaced image pairs in the resulting 2D image, and the separation distance between images is proportional to depth in the volume. To demix the fluorescence time series of individual neurons, we introduce a novel orthogonal matching pursuit algorithm that also infers source locations within the 3D volume. We illustrate vTwINS by imaging neural population activity in mouse primary visual cortex and hippocampus. Our results demonstrate that vTwINS provides an effective method for volumetric two-photon calcium imaging that increases the number of neurons recorded while maintaining a high frame-rate.
High-throughput detection of RNA processing in bacteria
Authors: Gill Erin E. , Chan Luisa S. , Winsor Geoffrey L. , Dobson Neil , Lo Raymond , Ho Sui Shannan J. , Dhillon Bhavjinder K. , Taylor Patrick K. , Shrestha Raunak , Spencer Cory , Hancock Robert E. W. , Unrau Peter J. , Brinkman Fiona S L 
Published: September 2016

ABSTRACTBackgroundUnderstanding the RNA processing of an organism's transcriptome is an essential but challenging step in understanding its biology. Here we investigate with unprecedented detail the transcriptome ofPseudomonas aeruginosaPAO1, a medically important and innately multi-drug resistant bacterium. We systematically mapped RNA cleavage and dephosphorylation sites that result in 5'-monophosphate terminated RNA using a new high-throughput methodology called monophosphate RNA-Seq (pRNA-Seq). Transcriptional start sites (TSS) were also mapped using differential RNA-Seq (dRNA-Seq) and both datasets were compared to conventional RNA-Seq performed in a variety of growth conditions.ResultsThe pRNA-Seq transcript library revealed known tRNA, rRNA and tmRNA processing sites, together with previously uncharacterized RNA cleavage events that were found disproportionately near the 5' ends of transcripts associated with basic bacterial functions such as oxidative phosphorylation and purine metabolism. The majority (97%) of the processed mRNAs were cleaved at precise codon positions within defined sequence motifs indicative of distinct endonucleolytic activities. The most abundant of these motifs corresponded closely to anE. coliRNase E site previously establishedin vitro. Using the dRNA-Seq library, we performed an operon analysis and predicted 3,159 potential TSS. A correlation analysis uncovered 105 antiparallel pairs of TSS that were separated by 18 bp from each other and that were centered on a palindromic TAT(A/T)ATA motif, suggesting that such sites may provide a novel form of transcriptional regulation. TSS and RNA-Seq analysis allowed us to confirm expression of small non-coding RNAs (ncRNAs), many of which are differentially expressed in swarming and biofilm formation conditions.ConclusionsThis study introduces pRNA-Seq methodology, which provides the first comprehensive, genome-wide survey of RNA processing in any organism. As a proof of concept, we have employed this technique to study the bacteriumPseudomonas aeruginosaand have discovered extensive transcript processing not previously appreciated. We have also gained novel insight into RNA maturation and turnover as well as a potential novel form of transcription regulation.NOTE: All sequence data has been submitted to the NCBI short read archive. Accession numbers are as follows: [NCBI short read archive: SRX156386, SRX157659, SRX157660, SRX157661, SRX157683 and SRX158075]. The sequence data is viewable using Jbrowse onwww.pseudomonas.com(example:http://tinyurl.com/pao1-prna-seq).(An example of certain tracks is shown for convenience, but other tracks of data can be displayed using the “select tracks” option, and tracks may be clicked on and dragged to re-order them.)
Cell-free translation is more variable than transcription
Authors: Chizzolini Fabio , Forlin Michele , Yeh Martín Noël , Berloffa Giuliano , Cecchi Dario , Mansy Sheref S. 
Published: September 2016

ABSTRACTAlthough RNA synthesis can be reliably controlled with different T7 transcriptional promoters during cell-free gene expression with the PURE system, protein synthesis remains largely unaffected. To better control protein levels, a series of ribosome binding sites (RBS) was investigated. While RBS strength did strongly affect protein synthesis, the RBS sequence could explain less than half of the variability of the data. Protein expression was found to depend on other factors besides the strength of the RBS, including GC content. The complexity of protein synthesis in comparison to RNA synthesis was observed by the higher degree of variability associated with protein expression. This variability was also observed in anE.colicell extract-based system. However, the coefficient of variation was larger withE.coliRNA polymerase than with T7 RNA polymerase, consistent with the increased complexity ofE.coliRNA polymerase.
Validation of Reference Genes for RT-qPCR in Marine Bivalve Ecotoxicology: Systematic Review and Case Study
Authors: Volland Moritz , Blasco Julián , Hampel Miriam 
Published: September 2016

AbstractReverse transcription real-time quantitative PCR (RT-qPCR) is the predominant method of choice for the quantification of mRNA transcripts of a selected gene of interest. Here reference genes are commonly used to normalize non-biological variation in mRNA levels and their appropriate selection is therefore essential for the accurate interpretation the collected data. In recent years the use of multiple validated references genes has been shown to substantially increase the robustness of the normalization. It is therefore considered good practice to experimentally validate putative reference genes under specific experimental conditions, determine the optimal number of reference genes to be employed, and report the method or methods used.Under this premise, we assessed the current state of reference gene base normalization in RT-qPCR bivalve ecotoxicology studies (post 2011), employing a systematic quantitative literature review. A total of 52 papers published met our criteria and were analysed for the gene or genes used, whether they employed multiple reference genes, as well as the validation method employed. In addition we performed a case study using primary hemocytes from the marine bivalveRuditapes philippinarumafterin vitrocopper exposure. Herein we further critically discuss methods for reference gene validation, including the established algorithms geNorm, NormFinder and BestKeeper, as well as the popular online tool RefFinder.We identified that RT-qPCR normalization in bivalve ecotoxicology studies is largely performed using single reference genes, while less than 40% of the studies attempted to experimentally validate the expression stability of the reference genes used. 18s rRNA and β-Actin were the most popular genes, yet their un-validated use did introduce artefactual variance that altered the interpretation of the resulting data, while the use of appropriately validated reference genes did substantially improve normalization. Our findings further suggest that combining the results from multiple individual algorithms and calculating the overall best-ranked gene, as e.g. computed by the RefFinder tool, does not by default lead to the identification of the most suitable reference gene or combination of reference genes.
Critical literature review: effectiveness of individual psychodynamic psychotherapy for adults with intellectual disabilities
Authors: McInnis Erica E. 
Published: September 2016

PurposeThe purpose of this paper is to report the evidence base for the practice of individual psychodynamic psychotherapy with adults with intellectual disabilities (IDs).Design/methodology/approachLiterature review.FindingsIn total, 14 papers were reviewed. From these, one existing review and seven individual papers provided enough evidence to support effectiveness of individual psychodynamic psychotherapy for people with IDs.Research limitations/implicationsThis research indicates individual psychodynamic psychotherapy to be of benefit. Indeed, all studies reviewed supported individual psychodynamic psychotherapy, but methodological shortcomings weakened the confidence placed in findings for some studies. Limitations of this review include methodological shortcomings of studies reviewed, a small number of existing studies and reliance on case studies.Practical implicationsTherapists and commissioners of services should routinely make individual psychodynamic psychotherapy available as part of a spectrum of therapies available to people with IDs who experience emotional and behavioural problems. This is because it is needed for some clients and they benefit.Social implicationsIndividual psychodynamic psychotherapy for people with IDs adds to the range of therapies available to alleviate emotional distress and enhance well-being. These are necessary to provide a foundation for meaningful contribution to society, particularly for those who have experienced psychological trauma (Frankish, 2016).Originality/valueThis review includes more relevant studies than previous reviews and adds to a limited number of reviews in this area.