bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypoxia, hypercarbia, and mortality reporting in studies of anaesthesia-related neonatal neurodevelopmental delay in rodent models
Authors: Floyd Thomas F. , Khmara Kseniya , Lamm Ryan , Seidman Peggy 
Published: January 2020

BACKGROUNDThe concept of anaesthesia-related neonatal neurotoxicity originated in neonatal rodent models, yet prospective clinical studies have largely not supported this concern.OBJECTIVESTo determine the frequency and magnitude of hypercarbia, hypoxia and death in rodent models of neonatal anaesthetic toxicity and neurodevelopmental delay.DESIGNSystematic review of published rodent studies of neonatal anaesthesia neurotoxicity. We documented anaesthetic, route, dose, frequency and duration of exposures. We further report ventilation method, documentation of adequacy of ventilation [arterial blood gas (ABG), other], mortality and the reporting of mortality.DATA SOURCESA PubMed literature search from 2003 to 2017 was conducted to identify studies on neurotoxicity in neonatal rodent models.ELIGIBILITYStudies were included when at least one group of animals fell within the postnatal age range of 3 to 15 days. Only English language original studies published as full-length articles in peer reviewed journals were included in the final analysis.RESULTSOne hundred and three manuscripts were included. Ninety-eight percent of studies were conducted using spontaneous ventilation (101/103), with ABG monitoring used in only 33% of studies and visual monitoring alone for respiratory distress or cyanosis was employed in 60%. Of the 33% who reported ABG results, there were widely divergent values, with most reporting modest-to-severe hypercarbia. Mortality (median 11%, range of 0 to 40%), which infers severe hypoxia, was documented in only 36/103 (35%) reports.CONCLUSIONHypoxia and hypercarbia have known apoptotic effects on developing brains. Hence, the inadequate control of hypercarbia and hypoxia in neonatal rodent models of anaesthetic exposure during spontaneous ventilation suggests that the evidence for developmental delay and neurotoxicity attributed to anaesthesia may not be valid in humans.
A single-dose of stellate ganglion block for the prevention of postoperative dysrhythmias in patients undergoing thoracoscopic surgery for cancer
Authors: Wu Cai-Neng , Wu Xin-Hai , Yu Dong-Nan , Ma Wu-Hua , Shen Chun-Hui , Cao Ying 
Published: January 2020

BACKGROUND
New-onset arrhythmias and sleep disturbances are frequently observed during the postoperative period in patients undergoing thoracic surgery.

OBJECTIVE
We evaluated the effectiveness of a single-dose stellate ganglion block (SGB) to prevent the occurrence of arrhythmias in patients undergoing thoracic surgery for cancer.

DESIGN
Randomised controlled double-blind study.

SETTING
Single university hospital.

PATIENTS
Ninety patients with lung cancer or oesophagal cancer scheduled for elective video-assisted thoracoscopic surgery were randomly randomised into one of two equal groups (the SGB group and control group, n = 40 each).

INTERVENTIONS
Patients received a single dose of 5 ml of 0.5% ropivacaine during ultrasound-guided SGB before induction of general anaesthesia in the SGB group.

MAIN OUTCOME MEASURES
Holter ECG was continuously monitored during the first 48 postoperative hours, and sleep state was monitored during the first two postoperative nights.

RESULTS
The incidences of postoperative supraventricular tachycardias were lower in the SGB group compared with the control group during the first 48 postoperative hours; 11.6 (5/43) vs. 31.8% (14/44), respectively, P = 0.023 (odds ratio 0.28, 95% confidence interval 0.09 to 0.87). The SGB also prolonged the total sleep time and increased the sleep efficiency during the first two postoperative nights. The duration of stage N2 sleep was longer in the SGB group compared with the control group [28 (interquartile range, 14 to 58) to 94 (interquartile range, 69 to 113) min, P = 0.016] on the first postoperative night. There were no differences in the duration of stage N1 and N3 sleep (P = 0.180, 0.086, respectively) on the first postoperative night, and the duration of stage N1, N2 and N3 sleep (P = 0.194, 0.057, 0.405, respectively) on the second postoperative night between the groups.

CONCLUSION
A pre-operative SGB effectively prevented the occurrence of postoperative supraventricular tachycardias and improves the objective sleep quality in patients undergoing thoracic surgery for cancer.

TRIAL REGISTRATION NUMBER
ChiCTR-1900023064.
Simulated patient-based teaching of medical students improves pre-anaesthetic assessment
Authors: Berger-Estilita Joana M. , Greif Robert , Berendonk Christoph , Stricker Daniel , Schnabel Kai P. 
Published: January 2020

BACKGROUND
Pre-anaesthetic assessment of patients is a complex competency that needs to be taught during anaesthesia clerkships.

OBJECTIVES
We aimed to improve student teaching and investigated the effectiveness of trained ‘simulated patients’ (lay persons or actors trained to portray specific roles or symptoms) in the teaching of medical students to perform routine pre-anaesthetic assessments. We hypothesised that the intervention of one 30-min teaching sequence with a simulated patient will improve the performance of year 4 medical students in pre-anaesthesia assessment of elective surgical patients, compared with the control of standard apprentice-based teaching.

DESIGN
Randomised controlled trial.

SETTING/PARTICIPANTS
One hundred and forty-four year 4 medical students at the University of Bern.

INTERVENTION
These students were randomised to either the standard clinician-supervised learning in the operating theatre (n=71; control group) or a single teaching session with a simulated patient (nonhealthcare provider, as a trained layperson) (n=73; intervention group). Both groups of students then performed pre-anaesthetic patient visits. The student performances during these visits were assessed according to the mini-Clinical Evaluation Exercise tool by trained anaesthesiologists blinded to randomisation. The 71 students in the standard clinical supervision group also underwent the simulated patient teaching session on the day following the assessments.

RESULTS
The students in the intervention group of simulated patient teaching scored significantly higher in both their mini-Clinical Evaluation Exercise overall impression scores (8.8 ± 0.8 vs. 8.3 ± 0.9; P = 0.004) and mean domain scores (8.7 ± 0.8 vs. 8.3 ± 0.9; P = 0.01), compared with those of the control group with the standard clinical supervision.

CONCLUSION
The current single teaching encounter with a trained layperson acting as a simulated patient improved medical student performances in their pre-anaesthetic clinical assessment of surgical patients. This might be a suitable alternative to reduce the teaching burden for busy and costly clinicians.
Extracorporeal cardiopulmonary resuscitation at the emergency department
Authors: Poppe Michael , Schriefl Christoph , Steinacher Anna , Clodi Christian , Warenits Alexandra-Maria , Nürnberger Alexander , Hubner Pia , Holzer Michael , Horvat Johann , Wiedemann Dominik , Weiser Christoph 
Published: January 2020

BACKGROUND
There is an increasing use of extracorporeal life support in refractory cardiac arrest. Recent studies highlighted the importance of an early and accurate patient selection for this invasive procedure.

OBJECTIVES
The aim of this study was to retrospectively validate a six-criteria-screening-checklist (witnessed collapse, bystander-cardiopulmonary resuscitation/first medical contact <5 min, shockable, age <70 years, end tidal carbon dioxide >14 mmHg and pupils not anisocoric/distorted/mydriatic) as an early screening tool in patients treated with extracorporeal cardiopulmonary resuscitation (eCPR) at the emergency department.

DESIGN
Retrospective observational study.

SETTING/PATIENTS
All patients at least 18 years of age with nontraumatic cardiac arrest and without return of spontaneous circulation before eCPR treatment at our department between January 2013 and December 2018 were included in this retrospective observational study.

INTERVENTION
No specific intervention was set in this observational study.

MAIN OUTCOME MEASURES
Primary outcome was the rate of patients who fulfilled all criteria, secondary outcome was 30-day and 6-month survival in accordance with the criteria.

RESULTS
Overall, data from a total of 92 patients were eligible for analyses. Out of these, 27 patients (29%) met all criteria. Patients, who fulfilled all criteria, showed significantly higher odds for 30-day survival [OR 6.0 (95% CI 1.78 to 20.19)] P
= 0.004. Patients, who did not fulfil all criteria, showed significantly higher rates of early mortality after eCPR initiation [OR 4.57 (95% CI 1.69 to 12.37)] P
= 0.003.

CONCLUSION
Patients fulfilling all inclusion criteria showed higher rates of survival after eCPR. Our results affirm that there is a possibility and even an obvious necessity for early patient selection based on standardised criteria before eCPR treatment. Large randomised trials are urgently needed to answer this question accurately.
Mariana serpentinite mud volcanism exhumes subducted seamount materials: implications for the origin of life
Authors: Fryer Patricia , Wheat C. Geoffrey , Williams Trevor , Kelley Christopher , Johnson Kevin , Ryan Jeffrey , Kurz Walter , Shervais John , Albers Elmar , Bekins Barbara , Debret Baptiste , Deng Jianghong , Dong Yanhui , Eickenbusch Philip , Frery Emanuelle , Ichiyama Yuji , Johnston Raymond , Kevorkian Richard , Magalhaes Vitor , Mantovanelli Simone , Menapace Walter , Menzies Catriona , Michibayashi Katsuyoshi , Moyer Craig , Mullane Kelli , Park Jung-Woo , Price Roy , Sissmann Olivier , Suzuki Shino , Takai Ken , Walter Bastien , Zhang Rui , Amon Diva , Glickson Deborah , Pomponi Shirley 
Published: January 2020

The subduction of seamounts and ridge features at convergent plate boundaries plays an important role in the deformation of the overriding plate and influences geochemical cycling and associated biological processes. Active serpentinization of forearc mantle and serpentinite mud volcanism on the Mariana forearc (between the trench and active volcanic arc) provides windows on subduction processes.  Here, we present (1) the first observation of an extensive exposure of an undeformed Cretaceous seamount currently being subducted at the Mariana Trench inner slope; (2) vertical deformation of the forearc region related to subduction of Pacific Plate seamounts and thickened crust; (3) recovered Ocean Drilling Program and International Ocean Discovery Program cores of serpentinite mudflows that confirm exhumation of various Pacific Plate lithologies, including subducted reef limestone; (4) petrologic, geochemical and paleontological data from the cores that show that Pacific Plate seamount exhumation covers greater spatial and temporal extents; (5) the inference that microbial communities associated with serpentinite mud volcanism may also be exhumed from the subducted plate seafloor and/or seamounts; and (6) the implications for effects of these processes with regard to evolution of life.
This article is part of a discussion meeting issue ‘Serpentine in the Earth system’.
NetCombin: An algorithm for optimal level-k network construction from triplets
Authors: Poormohammadi Hadi , Zarchi Mohsen Sardari 
Published: January 2020

AbstractPhylogenetic networks construction is one the most important challenge in phylogenetics. These networks can present complex non-treelike events such as gene flow, horizontal gene transfers, recombination or hybridizations. Among phylogenetic networks, rooted structures are commonly used to represent the evolutionary history of a species set, explicitly. Triplets are well known input for constructing the rooted networks. Obtaining an optimal rooted network that contains all given triplets is main problem in network construction. The optimality criteria include minimizing the level and the number of reticulation nodes. The complexity of this problem is known to be NP-hard. In this research, a new algorithm called Netcombin is introduced to construct an optimal network which is consistent with input triplets. The innovation of this algorithm is based on binarization and expanding processes. The binarization process innovatively uses a measure to construct a binary rooted treeTconsistent with the maximum number of input triplets. ThenTis expanded in an intellectual process by adding minimum number of edges to obtain final network with the minimum number of reticulation nodes. In order to evaluate the proposed algorithm, NetCombin is compared with four state of the art algorithms, RPNCH, NCHB, TripNet, and SIMPLISTIC. The experimental results on real data indicate that by considering the trade-off between speed and precision, the NetCombin outperforms the others.Author summaryHadi Poormohammadi got his PhD in Mathematics, Applied combinatorics from Shahid Beheshti University, Tehran, Iran in 2013. He is now working as an assistant professor at the Faculty of Computer Engineering, Meybod University. His research interests include Combinatorics, Graph theory and Bioinformatics.Mohsen Sardari Zarchi got his PhD in computer engineering, Artificial Intelligence from University of Isfahan in 2015. He is now working as an assistant professor at the Faculty of Computer Engineering, Meybod University. His research interests include Deep learning, Image processing, Artificial intelligence and Bioinformatics.
An unorthodox mechanism underlying voltage sensitivity of TRPV1 ion channel
Authors: Yang Fan , Xu Lizhen , Lee Bo Hyun , Xiao Xian , Yarov-Yarovoy Vladimir , Zheng Jie 
Published: January 2020

AbstractWhile the capsaicin receptor TRPV1 channel is a polymodal nociceptor for heat, capsaicin, and proton, the channel’s responses to each of these stimuli are profoundly regulated by membrane potential, damping or even prohibiting its response at negative voltages and amplifying its response at positive voltages. Though voltage sensitivity plays an important role is shaping pain responses, how voltage regulates TRPV1 activation remains unknown. Here we showed that the voltage sensitivity of TRPV1 does not originate from the S4 segment like classic voltage-gated ion channels; instead, outer pore acidic residues directly partake in voltage-sensitive activation, with their negative charges collectively constituting the observed gating charges. Voltage-sensitive outer pore movement is titratable by extracellular pH and is allosterically coupled to channel activation, likely by influencing the upper gate in the ion selectivity filter. Elucidating this unorthodox voltage-gating process provides a mechanistic foundation for understanding polymodal gating and opens the door to novel approaches regulating channel activity for pain managements.
A deep dive into the ancestral chromosome number and genome size of flowering plants
Authors: Carta Angelino , Bedini Gianni , Peruzzi Lorenzo 
Published: January 2020

SummaryChromosome number and genome variation in flowering plants has stimulated a blossoming number of speculations about the ancestral chromosome number of angiosperms, but estimates so far remain equivocal.We used a probabilistic approach to model haploid chromosome number (n) changes along a phylogeny embracing more than 10 thousands taxa, to reconstruct the ancestral chromosome number of the common ancestor of extant angiosperms and the most recent common ancestor for single angiosperm families. Independently, we carried out an analysis of 1C genome size evolution, including over 5 thousands taxa.Our inferences revealed an ancestral haploid chromosome number for angiospermsn= 7, a diploid status, and an ancestral 1C = 1.73 pg. For 160 families, inferred ancestralnare provided for the first time.Both descending dysploidy and polyploidy played crucial roles in chromosome number evolution. While descending dysploidy is equally distributed early and late across the phylogeny, polyploidy is detected mainly towards the tips. Similarly, also 1C genome size significantly increases (or decreases) in late-branching lineages. Therefore, no evidence exists for a clear link between ancestral chromosome numbers and ancient polyploidization events, suggesting that further insights are needed to elucidate the organization of genome packaging into chromosomes.
Module analysis using single-patient differential expression signatures improve the power of association study for Alzheimer’s disease
Authors: Huang Jialan , Lu Dong , Meng Guofeng 
Published: January 2020

AbstractThe causal mechanism of Alzheimer’s disease is extremely complex. It usually requires a huge number of samples to achieve a good statistical power in association studies. In this work, we illustrated a different strategy to identify AD risk genes by clustering AD patients into modules based on their single-patient differential expression signatures. Evaluation suggested that our method could enrich AD patients with common clinical manifestations. Applying it to a cohort of only 310 AD patients, we identified 175 AD risk loci at a strict threshold of empiricalp< 0.05 while only two loci were identified using all the AD patients. As an evaluation, we collected 23 AD risk genes reported in a recent large-scale meta-analysis and found that 18 of them were re-discovered by association studies using clustered AD patients, while only three of them were re-discovered using all AD patients. Functional annotation suggested that AD associated genetic variants mainly disturbed neuronal/synaptic function. Our results suggested module analysis, even randomly clustering, helped to enrich AD patients affected by the common risk variants.
An ExbD Disordered Domain Peptide Inhibits TonB System Activity
Authors: Kopp Dale R. , Postle Kathleen 
Published: January 2020

ABSTRACTThe TonB system energizes transport of essential nutrients, such as iron siderophores, across unenergized outer membranes of Gram-negative bacteria. The integral cytoplasmic membrane proteins of the TonB system--ExbB, ExbD, and TonB--transduce the protonmotive force of the cytoplasmic membrane to TonB-dependent outer membrane transporters for active transport. ExbD protein is anchored in the cytoplasmic membrane, with the majority of it occupying the periplasm. We previously identified a conserved motif within a periplasmic disordered domain that is essential for TonB system function. Here we demonstrated that export of a peptide derived from that motif into the periplasm prevented TonB system function and inhibited all known ExbD interactions in vivo. Formaldehyde crosslinking captured the ExbD peptide in multiple ExbD and TonB complexes. Furthermore, peptides with mutations in the conserved motif not only had significantly reduced ability to inhibit TonB system activity, but they also altered interactions with ExbD and TonB, indicating the specificity of the interaction. Conserved motif peptide interactions with ExbD and TonB mostly occurred between Stage II and Stage III of the TonB energy transduction cycle, a transition that is characterized by the use of protonmotive force. Taken together, the data suggest that the ExbD disordered domain motif has multiple interactions with TonB and ExbD during between Stage II and III of the TonB energization cycle. Because of the essentiality of the motif, it may be a potential template for design of novel antibiotics that target the TonB system.IMPORTANCEGram-negative bacteria are intrinsically antibiotic-resistant due to the diffusion barrier posed by their outer membranes. The TonB system allows them to circumvent this barrier for their own nutritional needs, including iron. The ability of bacteria to acquire iron is a virulence factor for many Gram-negative pathogens. However, no antibiotics currently target the TonB system. Because TonB and ExbD must interact productively in the periplasm for transport across the outer membrane, they constitute attractive targets for potential antibiotic development where chemical characteristics need not accommodate the need to cross the hydrophobic cytoplasmic membrane. Here we show that a small ExbD-derived peptide can interfere with the TonB-ExbD interaction to inhibit the TonB system in vivo.
Prediction of synonymous corrections by the BE-FF computational tool expands the targeting scope of base editing
Authors: Roy Rabinowitz , Shiran Abadi , Shiri Almog , Daniel Offen 
Published: January 2020

ABSTRACTBase editing is a genome-editing approach that employs the CRISPR/Cas system to precisely install point mutations within the genome. A cytidine or adenosine deaminase enzyme is fused to a deactivated Cas and converts C to T or A to G, respectively. The diversified repertoire of base editors, varied in their Cas and deaminase proteins, provides a wide range of functionality. However, existing base-editors can only induce transition substitutions in a specified region determined by the base editor, thus, they are incompatible for many point mutations. Here, we present BE-FF (Base Editors Functional Finder), a novel computational tool that identifies suitable base editors to correct the translated sequence erred by a given single nucleotide variation. Even if a perfect correction of the single nucleotide variation is not possible, BE-FF detects synonymous corrections to produce the reference protein. To assess the potential of BE-FF, we analysed a database of human pathogenic point mutations and found suitable base editors for 60.9% of the transition mutations. Importantly, 19.4% of them were made possible only by synonymous corrections. Moreover, we detected 298 cases in which pathogenic mutations caused by transversions were potentially repairable by base editing via synonymous corrections, although it had been thought impractical. The BE-FF tool and the database are available athttps://www.danioffenlab.com/be-ff.GRAPHICAL ABSTRACT
Rapid contextualization of fragmented scene information in the human visual system
Authors: Kaiser Daniel , Inciuraite Gabriele , Cichy Radoslaw M. 
Published: January 2020

AbstractReal-world environments are extremely rich in visual information. At any given moment in time, only a fraction of this information is available to the eyes and the brain, rendering naturalistic vision a collection of incomplete snapshots. Previous research suggests that in order to successfully contextualize this fragmented information, the visual system sorts inputs according to spatial schemata, that is knowledge about the typical composition of the visual world. Here, we used a large set of 840 different natural scene fragments to investigate whether this sorting mechanism can operate across the diverse visual environments encountered during real-world vision. We recorded brain activity using electroencephalography (EEG) while participants viewed incomplete scene fragments at fixation. Using representational similarity analysis on the EEG data, we tracked the fragments’ cortical representations across time. We found that the fragments’ typical vertical location within the environment (top or bottom) predicted their cortical representations, indexing a sorting of information according to spatial schemata. The fragments’ cortical representations were most strongly organized by their vertical location at around 200ms after image onset, suggesting rapid perceptual sorting of information according to spatial schemata. In control analyses, we show that this sorting is flexible with respect to visual features: it is neither explained by commonalities between visually similar indoor and outdoor scenes, nor by the feature organization emerging from a deep neural network trained on scene categorization. Demonstrating such a flexible sorting across a wide range of visually diverse scenes suggests a contextualization mechanism suitable for complex and variable real-world environments.