bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-body computed tomography in severely injured patients
Authors: Huber-Wagner Stefan , Kanz Karl-Georg , Hanschen Marc , van Griensven Martijn , Biberthaler Peter , Lefering Rolf 
Published: November 2017

Purpose of review
To provide an update on the relevant and recent studies on whole-body computed tomography (WBCT) imaging of severely injured patients.

Recent findings
The advantages of WBCT in time saving, diagnostic accuracy and even in survival have been proven in numerous studies. WBCT can also be beneficial in haemodynamically unstable major trauma patients. The CT scanner should be located close to the emergency department or even in the trauma room. The issue of radiation is still quite important, however, iterative as well as split-bolus protocols can nowadays reduce radiation significantly. The question: which trauma patient should receive WBCT and which not is not yet solved sufficiently. Postmortem WBCT has a promising potential to promptly define the definitive cause of death of trauma victims comparably to traditional autopsy.

Summary
On account of the recent advances, whole-body CT has become a crucial part of the initial in-hospital assessment of severely injured patients. It is recommended as the standard radiological tool for the emergency diagnostic work-up in major trauma patients.
Carcinoid-syndrome: recent advances, current status and controversies
Authors: Ito Tetsuhide , Lee Lingaku , Jensen Robert T. 
Published: November 2017

Purpose of review
To review recent advances and controversies in all aspects of carcinoid-syndrome.

Recent findings
Over the last few years there have been a number of advances in all aspects of carcinoid syndrome as well as new therapies. These include new studies on its epidemiology which demonstrate it is increasing in frequency; increasing insights into the pathogenesis of its various clinical manifestations and into its natural history: definition of prognostic factors; new methods to verify its presence; the development of new drugs to treat its various manifestations, both initially and in somatostatin-refractory cases; and an increased understanding of the pathogenesis, natural history and management of carcinoid heart disease. These advances have generated several controversies and these are also reviewed.

Summary
There have been numerous advances in all aspects of the carcinoid-syndrome, which is the most common functional syndrome neuroendocrine tumors produce. These advances are leading to new approaches to the management of these patients and in some cases to new controversies.
Verification of the Optimal Chest Compression Depth for Children in the 2015 American Heart Association Guidelines: Computed Tomography Study
Authors: Kim Yong Hwan , Lee Jun Ho , Cho Kwang Won , Lee Dong Woo , Kang Mun Ju , Lee Kyoung Yul , Byun Joung Hun , Lee Young Hwan , Hwang Seong Youn , Lee Na Kyoung 
Published: November 2017

Objective:
The 2015 American Heart Association guidelines recommended pediatric rescue chest compressions of at least one-third the anteroposterior diameter of the chest, which equates to approximately 5 cm. This study evaluated the appropriateness of these two types by comparing their safeties in chest compression depth simulated by CT.

Design:
Retrospective study with data analysis conducted from January 2005 to June 2015

Setting:
Regional emergency center in South Korea.

Patients:
Three hundred forty-nine pediatric patients 1–9 years old who had a chest CT scan.

Interventions:
Simulation of chest compression depths by CT.

Measurements and Main Results:
Internal and external anteroposterior diameter of the chest and residual internal anteroposterior diameter after simulation were measured from CT scans. The safe cutoff levels were differently applied according to age. One-third external anteroposterior diameters were compared with an upper limit of chest compression depth recommended for adults. Primary outcomes were the rates of overcompression to evaluate safety. Overcompression was defined as a negative value of residual internal anteroposterior diameter—age-specific cutoff level. Using a compression of 5-cm depth simulated by chest CT, 16% of all children (55/349) were affected by overcompression. Those 1–3 years old were affected more than those 4–9 years old (p < 0.001). Upon one-third compression of chest anteroposterior depth, only one subject (0.3%) was affected by overcompression. Rate of one-third external anteroposterior diameter greater than 6 cm in children 8 and 9 years old was 16.1% and 33.3%, respectively.

Conclusions:
A chest compression depth of one-third anteroposterior might be more appropriate than the 5-cm depth chest compression for younger Korean children. But, one-third anteroposterior depth chest compression might induce deep compressions greater than an upper limit of compression depth for adults in older Korean children.
Risk Factors for Ventilator-Associated Events in a PICU*
Authors: Guess Raeley , Vaewpanich Jarin , Coss-Bu Jorge A. , Phongjitsiri Siriporn , Kennedy Curtis , Starke Jeffrey , Thammasitboon Satid 
Published: November 2017

Objective:
The term ventilator-associated events includes ventilator-associated condition, infection-related ventilator-associated complication, and ventilator-associated pneumonia. We sought to identify potential new risk factors for ventilator-associated condition and infection-related ventilator-associated complication in the PICU population.

Design:
Matched case control study.

Setting:
Children’s hospital at a tertiary care academic medical center.

Patients:
During the study period, 606 patients were admitted to PICU and ventilated more than 48 hours; 70 children met ventilator-associated condition criteria.

Interventions:
None.

Measurements and Main Results:
We applied the definition for ventilator-associated condition (i.e., a sustained increase in ventilator settings after a period of stable or decreasing support) to our database. Within ventilator-associated condition cases, 40 cases were infection-related ventilator-associated complication and 30 cases were noninfectious-related ventilator-associated condition. We identified 140 controls and matched to ventilator-associated condition cases with regard to age, immunocompromised status, and ventilator days to event. Patients with ventilator-associated condition had longer ICU stay versus controls; 24 days median (12–43 interquartile range) versus 7 days (4–14); (p < 0.01), respectively, and longer duration of ventilatory support 17 days (10–32) versus 6 days (3–10); p < 0.01, respectively. Mortality was 22.8% in the ventilator-associated condition versus 9% in the control group (p < 0.01). A multivariate regression analysis adjusted for Pediatric Index of Mortality 2 identified mean peak inspiratory pressure and acute kidney injury to be associated with ventilator-associated condition (odds ratio, 1.12 [95% CI, 1.02–1.22] and odds ratio, 2.85 [1.43–5.66], respectively). Acute kidney injury and neuromuscular blockade in a multivariate regression analysis adjusted for Pediatric Index of Mortality 2 were associated with infection-related ventilator-associated complication (odds ratio, 2.36 [1.03–5.40] and 3.19 [1.17–8.68], respectively).

Conclusions:
There is an association between ventilator-associated condition and infection-related ventilator-associated complication in critically ill children with acute kidney injury, ventilatory support, and neuromuscular blockade. Attention should be given by clinical practitioners to recognize these modifiable risk factors and to implement strategies to decrease the prevalence of ventilator-associated events.
Quantitative Computed Tomography Metrics From the Transplanted Lung can Predict Forced Expiratory Volume in the First Second After Lung Transplantation
Authors: Mortani Barbosa Eduardo J. , Shou Haochang , Simpsom Scott , Gee James , Tustison Nicholas , Lee James C. 
Published: November 2017

Purpose:
Bronchiolitis obliterans syndrome after lung transplantation (LTx) manifests as a sustained decline in forced expiratory volume in the first second (FEV1). Quantitative computed tomography (QCT) metrics may predict FEV1 better than semiquantitative scores (SQSs), and the transplanted lung may provide better information than the native lung in unilateral LTx.

Materials and Methods:
Paired inspiratory-expiratory CT scans and pulmonary function testing of 178 LTx patients were analyzed retrospectively. SQS were graded (absent, mild, moderate, severe) for features including mosaic attenuation and bronchiectasis. QCT included lung volumes and air-trapping volumes, by lobe. Multivariate Pearson correlation and multivariate linear least squares regression analyses were performed.

Results:
Multivariate linear least squares regression models using FEV1 as the outcome variable and SQS or QCT metrics as predictor variables demonstrated SQS to be a weak predictor of FEV1 (adjusted R
2, 0.114). QCT metrics were much stronger predictors of FEV1 (adjusted R
2, 0.654). QCT metrics demonstrated stronger correlation (r) with FEV1 than SQS. In bilateral LTx, whole lung volume difference (r=0.69), left lung volume difference (r=0.69), and right lung volume difference (r=0.65) were better than the sum of SQS (r=−0.54). Interestingly, in left LTx we obtained r=0.81, 0.86, 0.25, and −0.39, respectively. In right LTx, we obtained r=0.69, 0.49, 0.68, and −0.31, respectively.

Conclusions:
QCT metrics demonstrate stronger correlations with FEV1 and are better predictors of pulmonary function than SQS. SQS performs moderately well in bilateral LTx, but poorly on unilateral LTx. In unilateral LTx, QCT metrics from the transplanted lung are better predictors of FEV1 than QCT metrics from the nontransplanted lung.
Visual snow syndrome: what we know so far
Authors: Puledda Francesca , Schankin Christoph , Digre Kathleen , Goadsby Peter J. 
Published: November 2017

Purpose of review
We provide an overview of the neurological condition known as visual snow syndrome. Patients affected by this chronic disorder suffer with a pan-field visual disturbance described as tiny flickering dots, which resemble the static noise of an untuned television.

Recent findings
The term ‘visual snow’ has only appeared in the medical literature very recently. The clinical features of the syndrome have now been reasonably described and the pathophysiology has begun to be explored. This review focuses on what is currently known about visual snow.

Summary
Recent evidence suggests visual snow is a complex neurological syndrome characterized by debilitating visual symptoms. It is becoming better understood as it is systematically studied. Perhaps the most important unmet need for the condition is a sufficient understanding of it to generate and test hypotheses about treatment.
Coarse-graining as a downward causation mechanism
Authors: Flack Jessica C. 
Published: November 2017

Downward causation is the controversial idea that ‘higher’ levels of organization can causally influence behaviour at ‘lower’ levels of organization. Here I propose that we can gain traction on downward causation by being operational and examining how adaptive systems identify regularities in evolutionary or learning time and use these regularities to guide behaviour. I suggest that in many adaptive systems components collectively compute their macroscopic worlds through coarse-graining. I further suggest we move from simple feedback to downward causation when components tune behaviour in response to estimates of collectively computed macroscopic properties. I introduce a weak and strong notion of downward causation and discuss the role the strong form plays in the origins of new organizational levels. I illustrate these points with examples from the study of biological and social systems and deep neural networks.
This article is part of the themed issue ‘Reconceptualizing the origins of life’.
Subsumed complexity: abiogenesis as a by-product of complex energy transduction
Authors: Adam Z. R. , Zubarev D. , Aono M. , Cleaves H. James 
Published: November 2017

The origins of life bring into stark relief the inadequacy of our current synthesis of thermodynamic, chemical, physical and information theory to predict the conditions under which complex, living states of organic matter can arise. Origins research has traditionally proceeded under an array of implicit or explicit guiding principles in lieu of a universal formalism for abiogenesis. Within the framework of a new guiding principle for prebiotic chemistry calledsubsumed complexity, organic compounds are viewed as by-products of energy transduction phenomena at different scales (subatomic, atomic, molecular and polymeric) that retain energy in the form of bonds that inhibit energy from reaching the ground state. There is evidence for an emergent level of complexity that is overlooked in most conceptualizations of abiogenesis that arises from populations of compounds formed from atomic energy input. We posit that different forms of energy input can exhibit different degrees of dissipation complexity within an identical chemical medium. By extension, the maximum capacity for organic chemical complexification across molecular and macromolecular scales subsumes, rather than emerges from, the underlying complexity of energy transduction processes that drive their production and modification.This article is part of the themed issue ‘Reconceptualizing the origins of life’.
Differential and defective expression of Koala Retrovirus indicate complexity of host and virus evolution
Authors: Tarlinton R.E , Legione A.R. , Sarker N. , Fabijan J. , Meers J. , McMichael L. , Simmons G. , Owen H. , Seddon J.M. , Dick G. , Ryder J.S. , Hemmatzedah F. , Trott D.J. , Speight N. , Holmes N. , Loose M. , Emes R.D. 
Published: November 2017

AbstractKoala retrovirus (KoRV) is unique amongst endogenous (inherited) retroviruses in that its incorporation to the host genome is still active, providing an opportunity to study what drives this fundamental process in vertebrate genome evolution. Animals in the southern part of the natural range of koalas were previously thought to be either virus free or to have only exogenous variants of KoRV with low rates of KoRV induced disease. In contrast, animals in the northern part of their range universally have both endogenous and exogenous KoRV with very high rates of KoRV induced disease such as lymphoma. This paper uses a combination of sequencing technologies, Illumina RNA sequencing of “southern” (south Australian) and “northern” (SE QLD) koalas and CRISPR enrichment and nanopore sequencing of DNA of “southern” (South Australian and Victorian animals) to retrieve full length loci and intregration sites of KoRV variants. We demonstrate that koalas that tested negative to the KoRV pol gene qPCR, used to detect replication competent KoRV, are not in fact KoRV free but harbour defective, presumably endogenous, “RecKoRV” variants that are not fixed between animals. This indicates that these populations have historically been exposed to KoRV and raises questions as to whether these variants have arisen by chance or whether they provide a protective effect from the infectious forms of KoRV. This latter explanation would offer the intriguing prospect of being able to monitor and selectively breed for disease resistance to protect the wild koala population from KoRV induced disease.
Diallel analysis revealsMx1-dependent andMx1-independent effects on response to influenza A virus in mice
Authors: Maurizio Paul L. , Ferris Martin T. , Keele Gregory R. , Miller Darla R. , Shaw Ginger D. , Whitmore Alan C. , West Ande , Morrison Clayton R. , Noll Kelsey E. , Plante Kenneth S. , Cockrell Adam S. , Threadgill David W. , Pardo-Manuel de Villena Fernando , Baric Ralph S. , Heise Mark T. , Valdar William 
Published: November 2017

1.ABSTRACTInfluenza A virus (IAV) is a respiratory pathogen that causes substantial morbidity and mortality during both seasonal and pandemic outbreaks. Infection outcomes in unexposed populations are affected by host genetics, but this host genetic architecture is not well understood. Here we obtain a broad view of how heritable factors affect a mouse model of response to IAV infection using an 8×8 diallel of the eight inbred founder strains of the Collaborative Cross (CC). Expanding on a prior statistical framework for modeling treatment response in diallels, we explore how a range of heritable effects modify acute host response to IAV through 4 days post-infection. Heritable effects in aggregate explained about 57% of the variance in IAV-induced weight loss. Much of this was attributable to a pattern of additive effects that became more prominent through day 4 post-infection and was consistent with previous reports of anti-influenza myxovirus resistance 1 (Mx1) polymorphisms segregating between these strains; the additive effects largely recapitulated haplotype effects observed at theMx1locus in a previous study of the incipient CC (pre-CC), and are also replicated here in a CC recombinant intercross (CC-RIX) population. Genetic dominance of protectiveMx1haplotypes was observed to differ by subspecies origin: relative to thedomesticusnullMx1allele,musculusacts dominantly whereascastaneusacts additively. After controlling forMx1, heritable effects, though less distinct, accounted for about 34% of the phenotypic variance. Implications for future mapping studies are discussed.
The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea
Authors: Deeg Christoph M. , Chow Cheryl-Emiliane T. , Suttle Curtis A. 
Published: November 2017

AbstractGiant viruses are ecologically important players in aquatic ecosystems that have challenged concepts of what constitutes a virus. Herein, we present the giant Bodo saltans virus (BsV), the first characterized representative of the most abundant giant viruses in the oceans, and the first klosneuvirus isolate, a subgroup of theMimiviridaeproposed from metagenomic data. BsV infects an ecologically important microzooplankton, the kinetoplastidBodo saltans. Its 1.39 Mb genome is the largest described for theMimiviridaeand encodes 1227 predicted ORFs, including pathways for host-independent replication. Yet, much of its translational machinery has been lost, including all tRNAs. Essential genes are invaded by homing endonuclease-encoding self-splicing introns that may defend against competing viruses. Putative anti-host factors show extensive gene duplication via a genomic accordion indicating an ongoing evolutionary arms race and highlighting the rapid evolution and genomic plasticity that has led to genome gigantism and the enigma that is giant viruses.
Butterflyfishes as a System for Investigating Pair Bonding
Authors: Nowicki Jessica P. , O’Connell Lauren A. , Cowman Peter F. , Walker Stefan P. W. , Coker Darren J. , Pratchett Morgan S. 
Published: November 2017

AbstractFor many animals, affiliative relationships such as pair bonds form the foundation of society, and are highly adaptive. Animal systems amenable for comparatively studying pair bonding are important for identifying underlying biological mechanisms, but mostly exist in mammals. Better establishing fish systems will enable comparison of pair bonding mechanisms across taxonomically distant lineages that may reveal general underlying principles. We examined the utility of wild butterflyfishes (f: Chaetodontidae; g:Chaetodon) for comparatively studying pair bonding. Stochastic character mapping inferred that within the family, pairing is ancestral, with at least seven independent transitions to group formation and seven transition to solitary behavior from the late Miocene to recent. In six sympatric and wide-spread species representing a clade with one ancestrally reconstructed transition from paired to solitary grouping, we then verified social systems at Lizard Island, Australia.In situobservations confirmed thatChaetodon baronessa, C. lunulatus, andC. vagabundusare predominantly pair bonding, whereasC. rainfordi, C. plebeius, andC. trifascialisare predominantly solitary. Even in the predominantly pair bonding species,C. lunulatus, a proportion of adults (15 %) are solitary. Importantly, inter- and intra-specific differences in social systems do not co-vary with other previously established attributes (geographic occurrence, parental care, diet, or territoriality). Hence, the proposed butterflyfish populations are promising for comparative analyses of pair bonding and its mechanistic underpinnings. Avenues for further developing the system are proposed, including determining whether the utility of these species applies across their geographic disruptions.
Uncovering cell-free protein expression dynamics by a promoter library with diverse strengths
Authors: Galiñanes Reyes Sabrina , Kuruma Yutetsu , Tsuda Soichiro 
Published: November 2017

AbstractCell-free protein expression systems have been widely used for synthetic biology and metabolic engineering applications in recent years. Yet little is known about protein expression in the cell-free systems. Here we take a systems approach to uncover underlying dynamics of cell-free protein expression. We construct a set of T7 promoter variants to express proteins at different transcription rates in a reconstituted andE. coliextract-based cell-free systems. We find that the maximum expression level and the rate of protein synthesis as responses to the transcription rate change are different in the two cell-free systems, suggesting they are driven by different expression dynamics. We confirm this by constructing a simple mathematical model for each cell-free system, which well reproduce the experimental results and also identify different limiting factors for better protein expression in the two cell-free systems. In particular, they revealed there is a negative feedback effect in the mRNA-protein translation by the PURE system and also identified different limiting factors for better protein expression in the two cell-free systems.
Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos
Authors: Trivedi Vikas , Choi Harry M.T. , Fraser Scott E. , Pierce Niles A. 
Published: November 2017

ABSTRACTFor decades, in situ hybridization methods have been essential tools for studies of vertebrate development and disease, as they enable qualitative analyses of mRNA expression in an anatomical context. Quantitative mRNA analyses typically sacrifice the anatomy, relying on embryo microdissection, dissociation, cell sorting, and/or homogenization. Here, we eliminate the tradeoff between quantitation and anatomical context, using multiplexed in situ hybridization chain reaction (HCR) to perform accurate and precise relative quantitation of mRNA expression with subcellular resolution within whole-mount vertebrate embryos. Gene expression can be queried in two directions: read-out from anatomical space to expression space reveals co-expression relationships in selected regions of the specimen; conversely, read-in from multidimensional expression space to anatomical space reveals those anatomical locations in which selected gene co-expression relationships occur. As we demonstrate by examining gene circuits underlying somitogenesis, quantitative read-out and read-in analyses provide the strengths of flow cytometry expression analyses, but by preserving subcellular anatomical context, they enable iterative bi-directional queries that open a new era for in situ hybridization.SUMMARYMultiplexed in situ hybridization chain reaction (HCR) enables quantitative multidimensional analyses of developmental gene expression with subcellular resolution in an anatomical context.