bluuebunny/crossref_metadata_2025_split huggingface dataset:
Safety of Venipuncture Sites at the Cubital Fossa as Assessed by Ultrasonography
Authors: Mukai Kanae , Nakajima Yukari , Nakano Tomotaka , Okuhira Manami , Kasashima Aya , Hayashi Rina , Yamashita Misaki , Urai Tamae , Nakatani Toshio 
Published: November 2017

Objective
The aim of the present observational study was to identify safe and suitable venipuncture sites for nursing in the clinical setting using ultrasonography to measure the depth and cross-sectional area of each superficial vein before and after tourniquet application as well as the distance between each superficial vein and the median nerve or brachial artery.

Methods and Results
Twenty healthy volunteers (21.8 [0.6] y) were recruited. The visible rate of each superficial vein before and after tourniquet application was 65% for the basilic vein, 90% to 95% for the median cubital vein, and 65% to 80% for the cephalic vein. The cross-sectional area of the median cubital vein after tourniquet application was significantly larger than that of the basilic vein and cephalic vein. The distance between the basilic vein or median cubital vein and median nerve was significantly smaller than that between the cephalic vein and median nerve. The distance between the basilic vein or median cubital vein and brachial artery was significantly smaller than that between the cephalic vein and brachial artery.

Conclusions
These results demonstrated that the cephalic vein at the cubital fossa is a relatively safe venipuncture site because of its distance from the median nerve and brachial artery. When puncturing the cephalic vein is difficult because it is not visible, the median cubital vein at the cubital fossa may be selected for venipuncture due to its cross-sectional area and visibility; however, care is needed to avoid penetrating the vein because the median nerve and brachial artery are located underneath.
Relationship Between Postoperative Pain and Overall 30-Day Complications in a Broad Surgical Population
Authors: van Boekel Regina L. M. , Warlé Michiel C. , Nielen Renske G. C. , Vissers Kris C. P. , van der Sande Rob , Bronkhorst Ewald M. , Lerou Jos G. C. , Steegers Monique A. H. 
Published: November 2017

Objective:
The aim of this study was to establish the relationship between postoperative pain and 30-day postoperative complications.

Background:
Only scarce data are available on the association between postoperative pain and a broad range of postoperative complications in a large heterogeneous surgical population.

Methods:
Having postoperative pain was assessed in 2 ways: the movement-evoked pain score on the Numerical Rating Scale (NRS-MEP) and the patients’ opinion whether the pain was acceptable or not. Outcome was the presence of a complication within 30 days after surgery. We used binary logistic regression for the total population and homogeneous subgroups to control for case complexity. Results for homogeneous subgroups were summarized in a meta-analysis using inverse variance weighting.

Results:
In 1014 patients, 55% experienced moderate-to-severe pain on the first postoperative day. The overall complication rate was 34%. The proportion of patients experiencing postoperative complications increased from 0.25 [95% confidence interval (CI) = 0.21–0.31] for NRS-MEP = 0 to 0.45 (95% CI = 0.36–0.55) for NRS-MEP = 10. Patients who found their pain unacceptable had more complications (adjusted odds ratio = 2.17 (95% CI = 1.51–3.10; P < 0.001)). Summary effect sizes obtained with homogeneous groups were similar to those obtained from the total population who underwent very different types of surgery.

Conclusions:
Higher actual postoperative pain scores and unacceptable pain, even on the first postoperative day, are associated with more postoperative complications. Our findings provide important support for the centrality of personalized analgesia in modern perioperative care.
Hypertonic saline resuscitation after emergent laparotomy and temporary abdominal closure
Authors: Loftus Tyler J. , Efron Philip A. , Bala Trina M. , Rosenthal Martin D. , Croft Chasen A. , Smith R. Stephen , Moore Frederick A. , Mohr Alicia M. , Brakenridge Scott C. 
Published: November 2017

BACKGROUND
Our objective was to establish the safety of 3% hypertonic saline (HTS) resuscitation for trauma and acute care surgery patients undergoing emergent laparotomy and temporary abdominal closure (TAC) with the hypothesis that HTS administration would be associated with hyperosmolar hypercholoremic acidosis, lower resuscitation volumes, and higher fascial closure rates, without adversely affecting renal function.

METHODS
We performed a retrospective cohort analysis of 189 trauma and acute care surgery patients who underwent emergent laparotomy and TAC, comparing patients with normal baseline renal function who received 3% HTS at 30 mL/h (n = 36) to patients with standard resuscitation (n = 153) by baseline characteristics, resuscitation parameters, and outcomes including primary fascial closure and Kidney Disease: Improving Global Outcomes stages of acute kidney injury.

RESULTS
The HTS and standard resuscitation groups had similar baseline illness severity and organ dysfunction, though HTS patients had lower serum creatinine at initial laparotomy (1.2 mg/dL vs. 1.4 mg/dL; p = 0.078). Forty-eight hours after TAC, HTS patients had significantly higher serum sodium (145.8 mEq/L vs. 142.2 mEq/L, p < 0.001), chloride (111.8 mEq/L vs. 106.6 mEq/L, p < 0.001), and osmolarity (305.8 mOsm/kg vs. 299.4 mOsm/kg; p = 0.006), and significantly lower arterial pH (7.34 vs. 7.38; p = 0.011). The HTS patients had lower intravenous fluid (IVF) volumes within 48 hours of TAC (8.5 L vs. 11.8 L; p = 0.004). Serum creatinine, urine output, and kidney injury were similar between groups. Fascial closure was achieved for 92% of all HTS patients and 77% of all standard resuscitation patients (p = 0.063). Considering all 189 patients, higher IVF resuscitation volumes within 48 hours of TAC were associated with decreased odds of fascial closure (odds ratio, 0.90; 95% confidence interval, 0.83–0.97; p = 0.003).

CONCLUSION
Hypertonic saline resuscitation was associated with the development of a hypernatremic, hyperchloremic, hyperosmolar acidosis, and lower total IVF resuscitation volumes, without adversely affecting renal function. These findings may not be generalizable to patients with baseline renal dysfunction and susceptibility to hyperchloremic acidosis-induced kidney injury.

Level of Evidence
Prognostic study, level II.
Development of clinical process measures for pediatric burn care: Understanding variation in practice patterns
Authors: Kazis Lewis E. , Sheridan Robert L. , Shapiro Gabriel D. , Lee Austin F. , Liang Matthew H. , Ryan Colleen M. , Schneider Jeffrey C. , Lydon Martha , Soley-Bori Marina , Sonis Lily A. , Dore Emily C. , Palmieri Tina , Herndon David , Meyer Walter , Warner Petra , Kagan Richard , Stoddard Frederick J. , Murphy Michael , Tompkins Ronald G. 
Published: November 2017

BACKGROUND
There has been little systematic examination of variation in pediatric burn care clinical practices and its effect on outcomes. As a first step, current clinical care processes need to be operationally defined. The highly specialized burn care units of the Shriners Hospitals for Children system present an opportunity to describe the processes of care. The aim of this study was to develop a set of process-based measures for pediatric burn care and examine adherence to them by providers in a cohort of pediatric burn patients.

METHODS
We conducted a systematic literature review to compile a set of process-based indicators. These measures were refined by an expert panel of burn care providers, yielding 36 process-based indicators in four clinical areas: initial evaluation and resuscitation, acute excisional surgery and critical care, psychosocial and pain control, and reconstruction and aftercare. We assessed variability in adherence to the indicators in a cohort of 1,076 children with burns at four regional pediatric burn programs in the Shriners Hospital system. The percentages of the cohort at each of the four sites were as follows: Boston, 20.8%; Cincinnati, 21.1%; Galveston, 36.0%; and Sacramento, 22.1%. The cohort included children who received care between 2006 and 2010.

RESULTS
Adherence to the process indicators varied both across sites and by clinical area. Adherence was lowest for the clinical areas of acute excisional surgery and critical care, with a range of 35% to 48% across sites, followed by initial evaluation and resuscitation (range, 34%–60%). In contrast, the clinical areas of psychosocial and pain control and reconstruction and aftercare had relatively high adherence across sites, with ranges of 62% to 93% and 71% to 87%, respectively. Of the 36 process indicators, 89% differed significantly in adherence between clinical sites (p < 0.05). Acute excisional surgery and critical care exhibited the most variability.

CONCLUSION
The development of this set of process-based measures represents an important step in the assessment of clinical practice in pediatric burn care. Substantial variation was observed in practices of pediatric burn care. However, further research is needed to link these process-based measures to clinical outcomes.

LEVEL OF EVIDENCE
Therapeutic/care management, level IV.
A probabilistic framework for identifying biosignatures using Pathway Complexity
Authors: Marshall Stuart M. , Murray Alastair R. G. , Cronin Leroy 
Published: November 2017

One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random structures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can easily be distinguished from non-living material assemblies. Many complex artefacts, from ordinary bioproducts to human tools, though they are not living things, are ultimately produced by biological processes—whether those processes occur at the scale of cells or societies, they are the consequences of living systems. While these objects are not living, they cannot randomly form, as they are the product of a biological organism and hence are either technological or cultural biosignatures. A generalized approach that aims to evaluate complex objects as possible biosignatures could be useful to explore the cosmos for new life forms. However, it is not obvious how it might be possible to create such a self-contained approach. This would require us to prove rigorously that a given artefact is too complex to have formed by chance. In this paper, we present a new type of complexity measure, which we call ‘Pathway Complexity’, that allows us not only to threshold the abiotic–biotic divide, but also to demonstrate a probabilistic approach based on object abundance and complexity which can be used to unambiguously assign complex objects as biosignatures. We hope that this approach will not only open up the search for biosignatures beyond the Earth, but also allow us to explore the Earth for new types of biology, and to determine when a complex chemical system discovered in the laboratory could be considered alive.
This article is part of the themed issue ‘Reconceptualizing the origins of life’.
Life as an emergent phenomenon: studies from a large-scale boid simulation and web data
Authors: Ikegami Takashi , Mototake Yoh-ichi , Kobori Shintaro , Oka Mizuki , Hashimoto Yasuhiro 
Published: November 2017

A large group with a special structure can become the mother of emergence. We discuss this hypothesis in relation to large-scale boid simulations and web data. In the boid swarm simulations, the nucleation, organization and collapse dynamics were found to be more diverse in larger flocks than in smaller flocks. In the second analysis, large web data, consisting of shared photos with descriptive tags, tended to group together users with similar tendencies, allowing the network to develop a core–periphery structure. We show that the generation rate of novel tags and their usage frequencies are high in the higher-order cliques. In this case, novelty is not considered to arise randomly; rather, it is generated as a result of a large and structured network. We contextualize these results in terms of adjacent possible theory and as a new way to understand collective intelligence. We argue that excessive information and material flow can become a source of innovation.This article is part of the themed issue ‘Reconceptualizing the origins of life’.
Resurrecting ancestral genes in bacteria to interpret ancient biosignatures
Authors: Kacar Betul , Guy Lionel , Smith Eric , Baross John 
Published: November 2017

Two datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physico-chemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its approximately 3.8 billion years of history on the Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions. The geologic record provides an array of biologically independent indicators of macroscale atmospheric and oceanic composition, but provides little in the way of the exact behaviour of the molecular components that influenced the compositions of these reservoirs. By reconstructing sequences of proteins that might have been present in ancient organisms, we can downselect to a subset of possible sequences that may have been optimized to these ancient environmental conditions. How can one use modern life to reconstruct ancestral behaviours? Configurations of ancient sequences can be inferred from the diversity of extant sequences, and then resurrected in the laboratory to ascertain their biochemical attributes. One way to augment sequence-based, single-gene methods to obtain a richer and more reliable picture of the deep past, is to resurrect inferred ancestral protein sequences in living organisms, where their phenotypes can be exposed in a complex molecular-systems context, and then to link consequences of those phenotypes to biosignatures that were preserved in the independent historical repository of the geological record. As a first step beyond single-molecule reconstruction to the study of functional molecular systems, we present here the ancestral sequence reconstruction of the beta-carbonic anhydrase protein. We assess how carbonic anhydrase proteins meet our selection criteria for reconstructing ancient biosignatures in the laboratory, which we term palaeophenotype reconstruction.This article is part of the themed issue ‘Reconceptualizing the origins of life’.
Protoenzymes: the case of hyperbranched polyesters
Authors: Mamajanov Irena , Cody George D. 
Published: November 2017

Enzymes are biopolymeric complexes that catalyse biochemical reactions and shape metabolic pathways. Enzymes usually work with small molecule cofactors that actively participate in reaction mechanisms and complex, usually globular, polymeric structures capable of specific substrate binding, encapsulation and orientation. Moreover, the globular structures of enzymes possess cavities with modulated microenvironments, facilitating the progression of reaction(s). The globular structure is ensured by long folded protein or RNA strands. Synthesis of such elaborate complexes has proven difficult under prebiotically plausible conditions. We explore here that catalysis may have been performed by alternative polymeric structures, namely hyperbranched polymers. Hyperbranched polymers are relatively complex structures that can be synthesized under prebiotically plausible conditions; their globular structure is ensured by virtue of their architecture rather than folding. In this study, we probe the ability of tertiary amine-bearing hyperbranched polyesters to form hydrophobic pockets as a reaction-promoting medium for the Kemp elimination reaction. Our results show that polyesters formed upon reaction between glycerol, triethanolamine and organic acid containing hydrophobic groups, i.e. adipic and methylsuccinic acid, are capable of increasing the rate of Kemp elimination by a factor of up to 3 over monomeric triethanolamine.This article is part of the themed issue ‘Reconceptualizing the origins of life’.
FLIM-based pH measurements reveal incretin-induced rejuvenation of aged insulin secretory granules
Authors: Neukam Martin , Sönmez Anke , Solimena Michele 
Published: November 2017

AbstractInsulin is stored in dense-core secretory granules (SGs) and is released from beta cells in two distinct phases upon glucose stimulation. Newly synthesized insulin SGs are secreted preferentially, but the underlying mechanism of this phenomenon remains elusive. The relationship of SG age with their intraluminal pH is of particular interest: proinsulin conversion by prohormone convertases follows the acidification of immature SGs by the vacuolar proton-translocating ATPase (v-ATPase). v-ATPases may also participate in the formation of the fusion pore for SG exocytosis, with intraluminal alkalinization inhibiting membrane fusion. Previous studies examined the luminal pH of SGs on a population level only. Here we measured the pH-dependent lifetime changes of eCFP fused to the ICA512-RESP18 homology domain to assess for the first time the luminal pH of individual age-defined SGs in insulinoma INS-1 cells by fluorescence-lifetime imaging microscopy. We show that 2-4-hour-old young SGs have a pH of ~5.5, while 26-28-hour-old SGs have a pH of ~6.2. Remarkably, the GLP-1 receptor agonist Exendin-4 prompted the re-acidification of old SGs in a glutamate-dependent fashion, while it did not affect the pH of young SGs. This study demonstrates that insulin SGs change their pH over time - a change that is reversible by insulin secretagogues. Hence, it provides novel insight into the mechanisms accounting for aging and exocytosis of SGs and suggests that their ‘rejuvenation’ may be exploited to enhance insulin secretion in diabetes.
PAIRUP-MS: Pathway Analysis and Imputation to Relate Unknowns in Profiles from Mass Spectrometry-based metabolite data
Authors: Hsu Yu-Han H. , Churchhouse Claire , Pers Tune H. , Mercader Josep M. , Metspalu Andres , Fischer Krista , Fortney Kristen , Morgen Eric K. , Gonzalez Clicerio , Gonzalez Maria E. , Esko Tonu , Hirschhorn Joel N. 
Published: November 2017

ABSTRACTMetabolomics is a powerful approach for discovering biomarkers and metabolic quantitative trait loci. While untargeted profiling methods can measure up to thousands of metabolite signals in a single experiment, many signals cannot be readily identified as known metabolites or compared across datasets, making it difficult to infer biology and to conduct well-powered meta-analyses across studies. To deal with these challenges, we developed a suite of computational methods, PAIRUP-MS, to match metabolite signals across mass spectrometry-based profiling datasets using an imputation-based approach and to generate pathway annotations for these signals. We performed meta and pathway analyses for both known and unknown signals in multiple datasets and then validated the results using genetic associations. Finally, we applied the methods to detect metabolite signals and pathways associated with body mass index, demonstrating that our framework is useful for analyzing unknown signals in a robust and biologically meaningful manner and for improving the power of untargeted metabolomics studies.
PRS-on-Spark (PRSoS): a novel, efficient and flexible approach for generating polygenic risk scores
Authors: Chen Lawrence M. , Yao Nelson , Garg Elika , Zhu Yuecai , Nguyen Thao T. T. , Pokhvisneva Irina , Dass Shantala A. Hari , Forest Marie , McEwen Lisa M. , MacIsaac Julia L. , Kobor Michael S. , Greenwood Celia , Silveira Patricia P. , Meaney Michael J. , O’Donnell Kieran J. 
Published: November 2017

AbstractMotivationPolygenic risk scores describe the genomic contribution to complex phenotypes and consistently account for a larger proportion of the variance than single nucleotide polymorphisms alone. However, there is little consensus on the optimal data input for generating polygenic risk scores and existing approaches largely preclude the use of imputed posterior probabilities and strand-ambiguous SNPs.ResultsWe developed PRS-on-Spark (PRSoS) a polygenic risk score software implemented in Apache Spark and Python that accommodates a variety of data input (e.g., observed genotypes, imputed genotypes, or imputed posterior probabilities) and strand-ambiguous SNPs. We show that PRSoS is flexible and efficient and computes polygenic risk scores at a range of p-value thresholds more quickly than existing software (PRSice). We also show that the use of imputed posterior probabilities and the inclusion of strand-ambiguous SNPs increases the proportion of variance explained by polygenic risk scores for major depression.Availability and ImplementationPRSoS is written in Apache Spark and Python and is freely available (see https://github.com/MeaneyLab/PRSoS).
An analytical framework for understanding regulatory novelty accompanying allopolyploidization
Authors: Hu Guanjing , Wendel Jonathan F. 
Published: November 2017

AbstractAllopolyploidy is a prevalent process in plants, having important physiological, ecological, and evolutionary consequences. Massive, genome-wide transcriptomic rewiring in response to genomic merger and doubling has been demonstrated in many allopolyploid systems, encompassing a diversity of phenomena, including homoeolog expression bias, genome dominance, expression-level dominance, and revamping of co-expression networks. Here we present an analytical framework to reconcile these patterns of regulatory novelty as governed by distinct sets of intra- and inter-subgenome cis-trans relationships. This approach is a novel extension of classic allele-specific expression analysis to incorporate and distinguish the separate effects of parental regulatory interactions as well as further complications at the allopolyploid level. We demonstrated that the cis-trans framework devised not only offers new perspective on disentangling genetic from epigenetic and higher-order effects that impact gene expression, but also provides the conceptual basis and tools to unify recently presented models for both genome-wide expression dominance and biased fractionation in allopolyploids.