bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pulmonary levels of biomarkers for inflammation and lung injury in protective versus conventional one-lung ventilation for oesophagectomy
Authors: van der Woude Margaretha C. , Bormans Laura , van der Horst Robrecht P. , Sosef Meindert N. , Belgers Henricus J. , Hemmes Sabrine N. , Tuip-de Boer Anita , Gama de Abreu Marcelo , Pelosi Paolo , Spronk Peter E. , Neto Ary Serpo , Schultz Marcus J. 
Published: January 2020

BACKGROUND
It is uncertain whether protective ventilation reduces ventilation-induced pulmonary inflammation and injury during one-lung ventilation.

OBJECTIVE
To compare intra-operative protective ventilation with conventional during oesophagectomy with respect to pulmonary levels of biomarkers for inflammation and lung injury.

DESIGN
Randomised clinical trial.

SETTING
Tertiary centre for oesophageal diseases.

PATIENTS
Twenty-nine patients scheduled for one-lung ventilation during oesophagectomy.

INTERVENTIONS
Low tidal volume (V

T
) of 6 ml kg−1 predicted body weight (pbw) during two-lung ventilation and 3 ml kgpbw−1 during one-lung ventilation with 5 cmH2O positive end expired pressure versus intermediate V

T
of 10 ml kgpbw−1 during two-lung ventilation and 5 ml kgpbw−1 body weight during one-lung ventilation with no positive end-expiratory pressure.

OUTCOME MEASURES
The primary outcome was the change in bronchoalveolar lavage (BAL) levels of preselected biomarkers for inflammation (TNF-α, IL-6 and IL-8) and lung injury (soluble Receptor for Advanced Glycation End-products, surfactant protein-D, Clara Cell protein 16 and Krebs von den Lungen 6), from start to end of ventilation.

RESULTS
Median [IQR] V

T
in the protective ventilation group (n = 13) was 6.0 [5.7 to 7.8] and 3.1 [3.0 to 3.6] ml kgpbw−1 during two and one-lung ventilation; V

T
in the conventional ventilation group (n = 16) was 9.8 [7.0 to 10.1] and 5.2 [5.0 to 5.5] ml kgpbw−1 during two and one-lung ventilation. BAL levels of biomarkers for inflammation increased from start to end of ventilation in both groups; levels of soluble Receptor for Advanced Glycation End-products, Clara Cell protein 16 and Krebs von den Lungen 6 did not change, while levels of surfactant protein-D decreased. Changes in BAL biomarkers levels were not significantly different between the two ventilation strategies.

CONCLUSION
Intra-operative protective ventilation compared with conventional ventilation does not affect changes in pulmonary levels of biomarkers for inflammation and lung injury in patients undergoing one-lung ventilation for oesophagectomy.

TRIAL REGISTRATION
The ‘Low versus Conventional tidal volumes during one-lung ventilation for minimally invasive oesophagectomy trial’ (LoCo) was registered at the Netherlands Trial Register (study identifier NTR 4391).
Deep neuromuscular blockade during spinal surgery reduces intra-operative blood loss
Authors: Kang Woon-Seok , Oh Chung-Sik , Rhee Ka Y. , Kang Min H. , Kim Tae-Hoon , Lee Suk H. , Kim Seong-Hyop 
Published: January 2020

BACKGROUND
Spinal surgery is usually performed in the prone position using a posterior approach. However, the prone position may cause venous engorgement in the back and thus increase surgical bleeding with interruption of surgery. The prone position also affects cardiac output since large vessels are compressed decreasing venous return to the heart.

OBJECTIVE
We hypothesised that deep neuromuscular blockade would be associated with less surgical bleeding during spinal surgery in the prone position.

DESIGN
Randomised, single blinded trial.

SETTING
University teaching hospital.

PARTICIPANTS
Eighty-eight patients in two groups.

INTERVENTIONS
Patients were randomly assigned to moderate neuromuscular blockade or deep neuromuscular blockade. In the moderate neuromuscular blockade group, administration of rocuronium was adjusted such that the train-of-four count was one to two. In the deep neuromuscular blockade group, rocuronium administration was adjusted such that the train-of-four count was zero with a posttetanic count 2 or less.

MAIN OUTCOME MEASURES
The primary outcome was the volume of intra-operative surgical bleeding. The surgeon's satisfaction with operating conditions, haemodynamic and respiratory status, and postoperative pain scores were evaluated.

RESULTS
The median [IQR] volume of intra-operative surgical bleeding was significantly less in the deep neuromuscular blockade group than in the moderate neuromuscular blockade group; 300 ml [200 to 494] vs. 415 ml [240 to 601]; difference: 117 ml (95% CI, 9 to 244; P = 0.044). The mean ± SD surgeon's satisfaction with the intra-operative surgical conditions was greater in the deep neuromuscular blockade group than in the moderate neuromuscular blockade group; 3.5 ± 1.0 vs. 2.9 ± 0.9 (P = 0.004). In intergroup comparisons of respiratory variables, peak inspiratory pressure was lower in the deep neuromuscular blockade group overall (P < 0.001). The median [IQR] postoperative pain score was lower in the deep neuromuscular blockade group than the moderate neuromuscular blockade group; 50 [36 to 60] vs. 60 [50 to 70], (P = 0.023).

CONCLUSION
Deep neuromuscular blockade reduced intra-operative surgical bleeding in patients undergoing spinal surgery. This may be related to greater relaxation in the back muscles and lower intra-operative peak inspiratory pressure when compared with moderate neuromuscular blockade.

TRIAL REGISTRATION
KCT0001264 (http://cris.nih.go.kr).
Nonadherence to antibiotic guidelines in patients admitted to ICU with sepsis is associated with increased mortality
Authors: Lindberg Oscar , De Geer Lina , Chew Michelle S. 
Published: January 2020

BACKGROUND
Early appropriate antibiotic therapy is an important component of the Surviving Sepsis Guidelines bundles that are associated with decreased in-hospital mortality. National antibiotic guidelines for the treatment of sepsis in Sweden have been available since 2008. Compliance with these guidelines is largely unknown, and whether it translates to improved patient outcome has not been studied.

OBJECTIVE
To assess mortality and its relationship to compliance with Swedish antibiotic guidelines. A secondary aim was to assess the effect of timing of antibiotic administration and mortality.

DESIGN
A registry-based, retrospective cohort study. Registry data were supplemented by manual extraction of data on antibiotic treatment from patient charts. The association between guideline compliance and mortality was evaluated using multivariable analysis. Three levels of compliance were predefined: full compliance – correct antibiotics and dose; partial compliance – correct antibiotic but wrong dose and/or wrong initial antibiotic but corrected within 24 h and/or wrong combination in a combined regime that is at least one antibiotic not in line with the national antibiotic guideline; no compliance – incorrect antibiotic.

SETTING
Two general ICUs in Sweden between 1 January 2011 and 31 December 2015.

PATIENTS
Seven hundred and thirteen patients over the age of 18 with severe sepsis or septic shock identified through the Swedish ICU Registry.

MAIN OUTCOME MEASURES
The primary outcome was 30-day mortality.

RESULTS
Full compliance was observed in 47.0% of patients, partial compliance in 36.0%, and no compliance in 17.0%. Lack of compliance was independently associated with increased risk of 30-day mortality: the adjusted hazard ratio was 1.86 (95% CI 1.34 to 2.58 P < 0.001) for partial compliance and 2.18 (95% CI 1.34 to 3.40 P < 0.001) for no compliance. The time to first antibiotic administration was not associated with mortality.

CONCLUSION
Less than half of the patients with severe sepsis and septic shock received antibiotics according to Swedish national guidelines. Full compliance with the guidelines was associated with decreased mortality. The results of this study show that a strict approach to guideline compliance seems to be beneficial: half measures and inadequate doses should be avoided.
A highly contiguous genome for the Golden-fronted Woodpecker (Melanerpes aurifrons) via a hybrid Oxford Nanopore and short read assembly
Authors: Wiley Graham , Miller Matthew J. 
Published: January 2020

AbstractBackgroundWoodpeckers are found in nearly every part of the world, absent only from Antarctica, Australasia, and Madagascar. Woodpeckers have been important for studies of biogeography, phylogeography, and macroecology. Woodpeckers hybrid zones are often studied to understand the dynamics of introgression between bird species. Notably, woodpeckers are gaining attention for their enriched levels of transposable elements (TEs) relative to most other birds. This enrichment of TEs may have substantial effects on woodpecker molecular evolution. The Golden-fronted Woodpecker (Melanerpes aurifrons) is a member of the largest radiation of New World woodpeckers. However, comparative studies of woodpecker genomes are hindered by the fact that no high-contiguity genome exists for any woodpecker species.FindingsUsing hybrid assembly methods that combine long-read Oxford Nanopore and short-read Illumina sequencing data, we generated a highly contiguous genome assembly for the Golden-fronted Woodpecker. The final assembly is 1.31 Gb and comprises 441 contigs plus a full mitochondrial genome. Half of the assembly is represented by 28 contigs (contig N50), each of these contigs is at least 16 Mb in size (contig L50). High recovery (92.6%) of bird-specific BUSCO genes suggests our assembly is both relatively complete and relatively accurate. Accuracy is also demonstrated by the recovery of a putatively error-free mitochondrial genome. Over a quarter (25.8%) of the genome consists of repetitive elements, with 287 Mb (21.9%) of those elements assignable to the CR1 superfamily of transposable elements, the highest proportion of CR1 repeats reported for any bird genome to date.ConclusionOur assembly provides a useful tool for comparative studies of molecular evolution and genomics in woodpeckers and allies, a group emerging as important for studies on the role that TEs may play in avian evolution. Additionally, the sequencing and bioinformatic resources used to generate this assembly were relatively low-cost and should provide a direction for the development of high-quality genomes for future studies of animal biodiversity.
Congruent population genetic structures and divergence histories in anther-smut fungi and their host plantsSilene italicaand theS. nutansspecies complex
Authors: Hartmann Fanny E. , Snirc Alodie , Cornille Amandine , Godé Cécile , Touzet Pascal , Van Rossum Fabienne , Fournier Elisabeth , Prieur Stéphanie Le , Shykoff Jacqui , Giraud Tatiana 
Published: January 2020

AbstractThe study of population genetic structure congruence between hosts and pathogens gives important insights into their shared phylogeographic and coevolutionary histories. We studied the population genetic structure of castrating anther-smut fungi (Microbotryumgenus) and of their host plants, theSilene nutansspecies complex, and the morphologically and genetically closeS. italica,which can be found in sympatry. Phylogeographic population genetic structure related to persistence in separate glacial refugia has been recently revealed in theS. nutansplant species complex across Western Europe, identifying several distinct lineages. We genotyped 171 associated plant-pathogen pairs of anther-smut fungi and their host plant individuals using microsatellite markers and plant chloroplastic SNPs. We found clear differentiation between fungal populations parasitizingS. nutansandS. italicaplants. The population genetic structure of fungal strains parasitizing theS. nutansplant species complex mirrored the host plant genetic structure, suggesting that the pathogen was isolated in glacial refugia together with its host and/or that it has specialized on the plant genetic lineages. Using random forest approximate Bayesian computation (ABC-RF), we found that the divergence history of the fungal lineages onS. nutanswas congruent with the one previously inferred for the host plant and likely occurred with ancient but no recent gene flow. Genome sequences confirmed the genetic structure and the absence of recent gene flow between fungal genetic lineages. Our analyses of host-pathogen individual pairs contribute to a better understanding of co-evolutionary histories between hosts and pathogens in natural ecosystems, in which such studies are still scarce.
Robotic Stereotaxic System based on 3D skull reconstruction to improve surgical accuracy and speed
Authors: Ly Phuong T. , Lucas Alexandra , Pun Sio Hang , Dondzillo Anna , Liu Chao , Klug Achim , Lei Tim C. 
Published: January 2020

AbstractSome experimental approaches in neuroscience research require the precise placement of a recording electrode, pipette or other tool into a specific brain area that can be quite small and/or located deep beneath the surface. This process is typically aided with stereotaxic methods but remains challenging due to a lack of advanced technology to aid the experimenter. Currently, procedures require a significant amount of skill, have a high failure rate, and take up a significant amount of time.We developed a next generation robotic stereotaxic platform for small rodents by combining a three-dimensional (3D) skull profiler sub-system and a full six degree-of-freedom (6DOF) robotic platform. The 3D skull profiler is based on structured illumination in which a series of horizontal and vertical line patterns are projected onto an animal skull. These patterns are captured by two two-dimensional (2D) CCD cameras which reconstruct an accurate 3D skull surface based on structured illumination and geometrical triangulation. Using the reconstructed 3D profile, the skull can repositioned using a 6DOF robotic platform to accurately align a surgical tool. The system was evaluated using mechanical measurement techniques, and the accuracy of the platform was demonstrated using brain phantoms. Additionally, small and deep brain nuclei were targeted in rodents for additional testing. The results indicate that this new stereotaxic system can improve the accuracy and speed of small-animal brain surgeries and reduce the failure rate of experiments.
Fine Sieving of Collected Atmospheric Particles using Oil Electrophoresis (iSCAPE)
Authors: Li Xinyue , Xu Siyu , Yao Maosheng 
Published: January 2020

AbstractIt is rather challenging to separate atmospheric particles from nano-to micro-metre mixed in a sample. Here, a system named iSCAPE was invented to efficiently sieve particles out from a mixture by employing an electrostatic field and a non-conductive mineral oil. Tests with atmospheric particles of different cities as well as soil and road dust samples demonstrated that the iSCAPEd particles under different operating conditions moved rapidly with different velocities and both directions. Particles of different sources such as ambient air, soil or road were shown to have different polarity-charged particle fractions, and exhibited clearly different particle electrical mobility graphs after the iSCAPE sieving from seconds to minutes. Data also revealed that after the sieving some particles were enriched at specific mobility ranges. Bacterial ATP measurements implied that the iSCAPE can be also used to efficiently separate bacteria of different sizes and charge polarity. Experimental data here suggest that the iSCAPE sieving strongly replies on the electrostatic field strength, mineral oil viscosity and the run time. In theory, the iSCAPE system can be used to extract any desired targets from a complex sample, thus opening up many outstanding opportunities for environmental, biomedical and life science fields.TOC
Contrasting adaptations to synaptic physiology of prefrontal cortex interneuron subtypes in a mouse model of binge drinking
Authors: Joffe Max E. , Winder Danny G. , Jeffrey Conn P. 
Published: January 2020

AbstractAlcohol use disorder (AUD) affects all sexes, however women who develop AUD may be particularly susceptible to cravings and other components of the disease. While many brain regions are involved in AUD etiology, proper function of the prefrontal cortex (PFC) is particularly important for top-down craving management and the moderation of drinking behaviors. Essential regulation of PFC output is provided by local inhibitory interneurons, yet the effects of chronic drinking on interneuron physiology remain poorly understood, particularly in female individuals. To address this gap, we generated fluorescent reporter transgenic mice to label the two major classes of interneuron in deep layer prelimbic PFC, based on expression of parvalbumin (PV-IN) or somatostatin (SST-IN). We then interrogated PV-IN and SST-IN membrane and synaptic physiology in a rodent model of binge drinking. Beginning in late adolescence, mice received 3-4 weeks of intermittent access (IA) ethanol. One day after the last drinking session, adaptations to PV-IN and SST-IN intrinsic physiology were observed in male mice but not in female mice. Furthermore, IA ethanol precipitated diametrically opposing changes to PV-IN synaptic physiology based on sex. IA ethanol decreased excitatory synaptic strength onto PV-INs from female mice and potentiated excitatory transmission onto PV-INs male mice. In contrast, decreased synaptic strength onto SST-INs was observed following IA ethanol in all groups of mice. Together, these findings illustrate novel sex differences in drinking-related PFC pathophysiology. Discovering means to restore PV-IN and SST-IN dysfunction following extended drinking provides opportunities for developing new treatments for all AUD patients.
Cryo-EM structures of the ATP release channel pannexin 1
Authors: Deng Zengqin , He Zhihui , Maksaev Grigory , Bitter Ryan M. , Rau Michael , Fitzpatrick James A.J. , Yuan Peng 
Published: January 2020

AbstractThe plasma membrane ATP release channel pannexin 1 has been implicated in numerous physiological and pathophysiological processes associated with purinergic signaling, including cancer progression, apoptotic cell clearance, inflammation, blood pressure regulation, oocyte development, epilepsy and neuropathic pain. Here, we present near-atomic resolution structures ofXenopus tropicalisandHomo sapiensPANX1 determined by cryo-electron microscopy that reveal a heptameric channel architecture. Compatible with ATP permeation, the transmembrane pore and cytoplasmic vestibule are exceptionally wide. An extracellular tryptophan ring located at the outer pore creates a constriction site, potentially functioning as a molecular sieve that restricts the size of permeable substrates. In combination with functional characterization, this work elucidates the previously unknown architecture of pannexin channels and establishes a foundation for understanding their unique channel properties as well as for developing rational therapies.
Identification of NLR-associated amyloid signaling motifs in filamentous bacteria
Authors: Dyrka Witold , Coustou Virginie , Daskalov Asen , Lends Alons , Bardin Thierry , Berbon Mélanie , Kauffmann Brice , Blancard Corinne , Salin Bénédicte , Loquet Antoine , Saupe Sven J. 
Published: January 2020

AbstractNLRs (Nod-like receptors) are intracellular receptors regulating immunity, symbiosis, non-self recognition and programmed cell death in animals, plants and fungi. Several fungal NLRs employ amyloid signaling motifs to activate downstream cell-death inducing proteins. Herein, we identify in Archaea and Bacteria, short sequence motifs that occur in the same genomic context as fungal amyloid signaling motifs. We identify 10 families of bacterial amyloid signaling sequences (we term BASS), one of which (BASS3) is related to mammalian RHIM and fungal PP amyloid motifs. We find that BASS motifs occur specifically in bacteria forming multicellular structures (mainly inActinobacteriaandCyanobacteria). We analyze experimentally a subset of these motifs and find that they behave as prion forming domains when expressed in a fungal model. All tested bacterial motifs also formed fibrilsin vitro.We analyze by solid-state NMR and X-ray diffraction, the amyloid state of a protein fromStreptomyces coelicolorbearing the most common BASS1 motif and find that it forms highly ordered non-polymorphic amyloid fibrils. This work expands the paradigm of amyloid signaling to prokaryotes and underlies its relation to multicellularity.
Economic evaluation of a prospective Farm Animal Welfare program in Turkey
Authors: Turan Özlem , Gurluk Serkan , Madiyoh Abdulhakim 
Published: January 2020

PurposeThe purpose of this paper is to examine producer preferences for changing Farm Animal Welfare (FAW) levels in regards to sheep and goat husbandry in Bursa-Turkey.Design/methodology/approachThe paper tests “panel estimators” in a stated preference data by using the payment card question format. Probit panels are employed to measure individual effects on FAW levels by considering producers’ willingness to accept. Three different FAW levels were identified for valuation as “base” level, “better” level, and the “best” level. The current study suggests a protocol with WTA(P) nomenclature to resolve complexity issues in FAW studies by investigating producers rather than consumers because the scenarios regarding FAW levels include quite technical and difficult topics which are vague to consumers.FindingsIf half of the total number of the sheep and goats in Turkey are assumed to be in bad animal welfare conditions, which are worse than base level, the non-use benefits of bringing them to at least the base level would be about US$130.3m. Figures would be 166.2m US$/year and 175m US$/year for “better” and “best” FAW conditions, respectively.Originality/valueThis paper provides a contribution to the existing literature by examining the producers’ responses to new FAW schemes. Also it helps policy makers to understand producers’ environmental behavior as well as their sensitivity to FAW schemes.