bluuebunny/crossref_metadata_2025 huggingface dataset:
Individual Variation in Control Network Topography Supports Executive Function in Youth
Authors: Cui Zaixu , Li Hongming , Xia Cedric H. , Larsen Bart , Adebimpe Azeez , Baum Graham L. , Cieslak Matt , Gur Raquel E. , Gur Ruben C. , Moore Tyler M. , Oathes Desmond J. , Alexander-Bloch Aaron , Raznahan Armin , Roalf David R. , Shinohara Russell T. , Wolf Daniel H. , Davatzikos Christos , Bassett Danielle S. , Fair Damien A. , Fan Yong , Satterthwaite Theodore D.
Published: July 2019

The spatial distribution of large-scale functional networks on the anatomic cortex differs between individuals, and is particularly variable in networks responsible for executive function. However, it remains unknown how this functional topography evolves in development and supports cognition. Capitalizing upon advances in machine learning and a large sample of youth (n=693, ages 8-23y) imaged with 27 minutes of high-quality fMRI data, we delineate how functional topography evolves during youth. We found that the functional topography of association networks is refined with age, allowing accurate prediction of an unseen individual’s brain maturity. Furthermore, the cortical representation of executive networks predicts individual differences in executive function. Finally, variability of functional topography is associated with fundamental properties of brain organization including evolutionary expansion, cortical myelination, and cerebral blood flow. Our results emphasize the importance of considering both the plasticity and diversity of functional neuroanatomy during development, and suggest advances in personalized therapeutics.
Transcriptome assembly from long-read RNA-seq alignments with StringTie2
Authors: Kovaka Sam , Zimin Aleksey V. , Pertea Geo M. , Razaghi Roham , Salzberg Steven L. , Pertea Mihaela
Published: July 2019

RNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of long-read analyses. Here we present StringTie2, a reference-guided transcriptome assembler that works with both short and long reads. StringTie2 includes new computational methods to handle the high error rate of long-read sequencing technology, which previous assemblers could not tolerate. It also offers the ability to work with full-length super-reads assembled from short reads, which further improves the quality of assemblies. On 33 short-read datasets from humans and two plant species, StringTie2 is 47.3% more precise and 3.9% more sensitive than Scallop. On multiple long read datasets, StringTie2 on average correctly assembles 8.3 and 2.6 times as many transcripts as FLAIR and Traphlor, respectively, with substantially higher precision. StringTie2 is also faster and has a smaller memory footprint than all comparable tools.
Monosynaptic projections to excitatory and inhibitory preBötzinger Complex neurons
Authors: Yang Cindy F. , Kim Euiseok J. , Callaway Edward M. , Feldman Jack L.
Published: July 2019

The key driver of breathing rhythm is the preBötzinger Complex (preBötC) whose activity is modulated by various categorical inputs, e.g., volitional, physiological, emotional. While the preBötC is highly interconnected with other regions of the breathing central pattern generator (bCPG) in the brainstem, there is no data about the direct projections to either excitatory and inhibitory preBötC subpopulations from other elements of the bCPG or from suprapontine regions. Using modified rabies tracing, we identified neurons throughout the brain that send monosynaptic projections to identified excitatory and inhibitory preBötC neurons. Within the brainstem, neurons from sites in the bCPG, including the contralateral preBötC, Bötzinger Complex (BötC), the nucleus of the solitary tract (NTS), parafacial region (pFL/pFVor RTN/pFRG), and parabrachial nuclei, send direct projections to both excitatory and inhibitory preBötC neurons. Suprapontine inputs to the excitatory and inhibitory preBötC neurons include the superior colliculus, red nucleus, amygdala, hypothalamus, and cortex; these projections represent potential direct pathways for volitional, emotional, and physiological control of breathing.
Dynamic brain network changes in resting-state reflect neuroplasticity: molecular and cognitive evidence
Authors: Liu Zhaowen , Xiao Xiao , Zhang Kai , Zhao Qi , Cao Xinyi , Li Chunbo , Wang Min , Lin Wei , Qiu Jiang , Sahakian Barbara J. , Feng Jianfeng , Robbins Trevor W. , Zhang Jie
Published: July 2019

Resting-state functional brain networks demonstrate dynamic changes on the scale of seconds. However, their genetic mechanisms and profound cognitive relevance remain less explored. We identified 459 Bonferroni-corrected genes, by associating temporal variability of regional functional connectivity patterns with Allen Brain gene expression profiles across the whole brain. These genes are partially verified in developing human brain gene expression in the BrainSpan Atlas, and are found to be involved in the enrichment of short- and long-term plasticity processes. The former process depends on synaptic plasticity, involving ion transmembrane transport, action potential propagation, and modulation. The latter process depends on structural plasticity, including axonal genesis, development, and guidance. Results from a longitudinal cognitive training study further revealed that baseline variability of the hippocampal network predicted cognitive ability changes after three months of training. Our genetic association results suggest that the short-term plasticity processes may account for the rapid changes of regional functional connectivity, while the underlying long-term plasticity processes explain why temporal variability can predict long-term learning outcomes. To our knowledge, this is the first demonstration that measuring the dynamic brain network can lead to a non-invasive quantification of neuroplasticity in humans.
Alterations of the pro-survival Bcl-2 protein interactome in breast cancer at the transcriptional, mutational and structural level
Authors: Kønig Simon Mathis , Rissler Vendela , Terkelsen Thilde , Lambrughi Matteo , Papaleo Elena
Published: July 2019

Apoptosis is an essential defensive mechanism against tumorigenesis. Proteins of the B-cell lymphoma-2 (Bcl-2) family regulates programmed cell death by the mitochondrial apoptosis pathway. In response to intracellular stresses, the apoptotic balance is governed by interactions of three distinct subgroups of proteins; the activator/sensitizer BH3 (Bcl-2 homology 3)-only proteins, the pro-survival, and the pro-apoptotic executioner proteins. Changes in expression levels, stability, and functional impairment of pro-survival proteins can lead to an imbalance in tissue homeostasis. Their overexpression or hyperactivation can result in oncogenic effects. Pro-survival Bcl-2 family members carry out their function by binding the BH3 short linear motif of pro-apoptotic proteins in a modular way, creating a complex network of protein-protein interactions. Their dysfunction enables cancer cells to evade cell death. The critical role in homeostasis and tumorigenesis coupled with progress in their structural elucidation, has led to consider pro-survival Bcl-2 proteins as therapeutic targets.

A better understanding of the transcriptomic level, mutational status and molecular mechanism underlying pro-survival Bcl-2 proteins in different cancer types, could help to clarify their role in cancer development and may guide advancement in drug discovery, targeting these proteins. Here, we shed light on pro-survival Bcl-2 proteins in breast cancer by proposing a ‘multiscale’ bioinformatic approach. We analyzed the changes in expression of the Bcl-2 proteins and their BH3-containing interactors, in breast cancer samples. We then studied, at the structural level, a selection of interactions, also accounting for effects induced by mutations found in the breast cancer samples. We identified the complexes between the up-regulated BCL2A1 and two down-regulated BH3-only candidates (HRK and NR4A1) as targets associated with reduced apoptosis in breast cancer samples, which could deserve future experimental validation. We predicted as damaging mutations altering protein stability L99R, M75R, along with Y120C as a possible allosteric mutation from an exposed surface to the BH3-binding site.
CarboLogR: a Shiny/R application for statistical analysis of bacterial utilisation of carbon sources
Authors: Vervier Kevin , Browne Hilary P. , Lawley Trevor D.
Published: July 2019

The Biolog Phenotype Microarray (PM) and Anaerobic MicroPlates (AN) 96-well plates utilise colorimetric redox reactions to rapidly screen bacteria for the ability to utilise different carbon sources and other metabolites. Measurement of substrate utilisation as bacterial growth curves typically involves extended data normalization, outlier detection, and statistical analysis. The CarboLogR package streamlines this process with a Shiny application, guiding users from raw data generated from Biolog assays to growth profile comparison. We applied chemoinformatics approaches to define clusters of carbon sources, based on molecular similarities, increasing statistical power. Altogether, CarboLogR is a novel integrated tool providing automatic and high-level resolution for bacterial growth patterns and carbon source usage.

Availability and Implementation

CarboLogR application can be downloaded and installed from Github repository https://github.com/kevinVervier/CarboLogR. Tutorial, data, and examples can be downloaded at https://github.com/kevinVervier/CarboLogR/vignettes.

Contact

kv4@sanger.ac.uk

Supplementary Information

Supplementary data are available at Bioinformatics online.
Modulation of tactile detection threshold with rhythmic somatosensory entrainment
Authors: Wälti Michel J. , Bächinger Marc , Wenderoth Nicole
Published: July 2019

Ongoing neural activity in human somatosensory cortex has a strong impact on the detectability of weak tactile stimuli. Recent studies suggest that brain oscillations, which determine the state of excitability of a cortical area, play a crucial role in this process. Mainly two frequency bands have been reported to be involved in conscious sensory perception: alpha (8 – 12 Hz) and beta (15 – 30 Hz). In addition to correlative findings, more recent studies investigated causality by measuring the extent to which directly modulating brain oscillations affects sensory perception. While most of these studies use transcranial alternating current stimulation (tACS), rhythmic sensory stimulation has been suggested as a simple and safe alternative to entrain ongoing neural activity. However, convincing findings demonstrating the modulation of neural signals and related behavioral function are scarce.

Here, we investigated whether rhythmically induced brain oscillations by means of vibrotactile stimulation (i.e. sensory entrainment) modulate tactile detection. In line with previous findings, we show in trials without sensory entrainment that preceding alpha power and phase-angles in beta oscillations predict the detection rate of a weak tactile stimulus. Further, we reveal a masking effect induced by sensory entrainment stimulation resulting in higher perception thresholds. Intriguingly, we find that the masking effect is modulated by the strength of neural entrainment resulting from 20 Hz stimulation. Our data provide evidence for the possibility to modulate sensory processing with rhythmic sensory stimulation. However, in light of the induced masking effects, the feasibility of this entrainment method to modulate human behavior remains questionable.
Isolation of antibiotic Producing Microorganisms from some water bodies within Eastern and Greater Accra Regions of Ghana
Authors: Amiteye Daniel , Dayie Nicholas Tete Kwaku Dzifa , Gbedema Stephen Yao , Boamah Vivian Etsiapa , Adu Francis , Bayor Marcel Tunkumgnen
Published: July 2019

Background

Most antimicrobial agents used today are isolated and extracted from microbial source. The emergence of antimicrobial resistance and need for better, broad spectrum antimicrobial agent is always in high demand. In this study, a total of 112 aquatic microbial isolates from 14 sample sites of water bodies in Ghana were screened by agar-well diffusion method for the ability of antimicrobial metabolites.

Results

Out of these antibacterial activities, 10 inhibited the growth of at least one test microorganism with zones of growth inhibitions ranged between 2.5±0.5 - 35.5±0.5 mm againstStaphylococcus aureus(ATCC25923),Streptococcus pyogenes(clinical isolates), Escherichia coli(NCTC9002),Pseudomonas aeruginosa(ATCC27853),Neisseria gonorrhoeae(clinical isolate),Klebsiella pneumoniae (Clinical isolate),Bacillus subtilis(NCTC10073) andSalmonella typhi(NCTC 6017). The extracts of the isolates showed minimum inhibitory concentrations of which extract NKSEW3againstEscherichia coli, Klebsiella pneumoniaeandPseudomonas aeruginosawere 25.00, 12.50 and 25.00 mg/mL respectively while that of NKLS6were 12.50, 6.25 and 25.00 mg/mL. The isolates NKSEW3and NKLS6were identified to bePseudomonas speciesusing chromagar and biochemical tests. The GC-MS result for NKLS62 (a fraction obtained from NKLS6) revealed five compounds including; Tridecanal, 17-octadecanal, ethanol, 2-(9-octadecenyloxy)-, (Z), 2-pentadecanone, 6, 10, 14-trimethyl diisooctyl phthalate and 17-octadecanal (C18H34O) as good pharmacological agents.

Conclusion

Microorganisms isolated from water bodies in Ghana have the potential of producing antimicrobial agents.

Author Summary

In this study we use the agar well-diffusion to screen the isolates of water and soil samples collected within Greater Accra and Eastern Regions in Ghana against the test organisms.
Structural basis for recognition of RALF peptides by LRX proteins during pollen tube growth
Authors: Moussu Steven , Broyart Caroline , Santos-Fernandez Gorka , Augustin Sebastian , Wehrle Sarah , Grossniklaus Ueli , Santiago Julia
Published: July 2019

Plant reproduction relies on the highly regulated growth of the pollen tube for proper sperm delivery. This process is controlled by secreted RALF signaling peptides, which have been previously shown to be perceived by CrRLK1Ls membrane receptor-kinases and leucine-rich (LRR) extensin proteins (LRXs). Here we demonstrate that RALF peptides are active as folded, disulfide bond-stabilized proteins, which can bind to the LRR domain of LRX proteins with nanomolar affinity. Crystal structures of the LRX-RALF signaling complexes reveal LRX proteins as constitutive dimers. The N-terminal LRR domain containing the RALF binding site is tightly linked to the extensin domain via a cysteine-rich tail. Our biochemical and structural work reveals a complex signaling network by which RALF ligands may instruct different signaling proteins – here CrRLK1Ls and LRXs – through structurally different binding modes to orchestrate cell wall remodeling in rapidly growing pollen tubes.

Significance

Plant reproduction relies on proper pollen tube growth to reach the female tissue and release the sperm cells. This process is highly regulated by a family of secreted signaling peptides that are recognized by cell-wall monitoring proteins to enable plant fertilization. Here, we report the crystal structure of the LRX-RALF cell-wall complex and we demonstrate that RALF peptides are active as folded proteins. RALFs are autocrine signaling proteins able to instruct LRX cell-wall modules and CrRKL1L receptors, through structurally different binding modes to coordinate pollen tube integrity.
Between preservation and change: performing arts heritage development in South Korea
Authors: Creutzenberg Jan
Published: July 2019

Purpose

As intangible cultural heritage, traditional performing arts depend on transmission by individuals and collectives. The purpose of this paper is to explore how traditional performers practice their arts in South Korea. The analysis focuses on the transformations of performance conventions and contexts, as well as on new genres that developed in response to heritage legislation and social change during the last 200 years.

Design/methodology/approach

Drawing on a wide array of existing ethnographic research, the paper compares processes of transmission and transformation of three different genres: the solo singing-storytelling genre pansori, the ensemble percussion-dance genre pungmul and the various regional forms of mask dance drama subsumed under the label talnori. The paper argues that the artists, who perform these genres, while not unaffected by the expectations of their audiences, have the power to transcend traditional boundaries.

Findings

Due to early professionalization in the nineteenth century, pansori performers could adapt to the changing contexts of market-oriented modernity and survive until governmental intervention in 1962. Pre-modern pungmul and talnori was performed primarily by and for rural communities, resulting in an interruption of transmission when these contexts disappeared and partial re-invention in the wake of official preservation legislation.

Originality/value

The need for repeated performance in historically varying contexts makes the analysis of performing arts particular fruitful for understanding how practitioners of tradition (have to) adapt to change. A historical-comparative perspective provides concise insights into the dynamics of development that informs tradition today. The inclusion of offspring genres (changgeuk, madang-geuk, samulnori) furthermore shows the potential of heritage development beyond the official system of preservation.
The effect of rounding radius in bump foil structure on the static performance of foil journal bearings
Authors: Hu Hongyang , Feng Ming
Published: July 2019

Purpose

The purpose of this paper is to investigate the effect of the rounding in bump foil on the static performance of air foil journal bearings.

Design/methodology/approach

During the study, the bending moment of the new foil structure with rounding is proposed, and the bump foil stiffness is obtained from the elastic deformation energy theory. The validity of the presented foil model is verified through comparison with previous models. The static characteristics of foil bearings such as film thickness and attitude angle are obtained using a fully coupled elastic-gas algorithm and are compared to models with various rounding radius and friction coefficients.

Findings

There is an optimal rounding radius that makes the stiffness of bump foil maximum. As the static load increases, the minimum film thickness is proportional to the rounding radius but the attitude angle is inversely proportional. The effect of rounding with a large friction coefficient becomes negligible.

Originality/value

The rounding brings fundamental difference in the structural stiffness and static performance of foil bearings. The results are expected to be helpful to bearing designers, researchers and academicians concerned.
Incorporating the environmental dimension into the balanced scorecard
Authors: Khalid Salim , Beattie Claire , Sands John , Hampson Veronica
Published: July 2019

Purpose

This study aims to explore the ways that the balanced scorecard (BSC) can be adapted to incorporate environmental performance in a health care context.

Design/methodology/approach

This research adopts a qualitative approach that uses an in-depth case study including semi-structured interviews and document review. Interviews are conducted with individuals working within a regional public hospital and health service organisation in Australia. The research is informed by stakeholder theory.

Findings

The participants identified a number of approaches to incorporating environmental dimensions within the BSC: fully integrated, partially integrated, a separate additional perspective and differentiation based on the origin of the environmental activities and events. These findings confirm the contingent nature of the selected model and reinforce the importance of organisational vision and environmental strategy as formative factors.

Research limitations/implications

This research provides a starting point for future research to refine the proposed models and evaluate their viability and relevance in other contexts.

Practical implications

This study provides motivations for managers to engage with the BSC as an effective performance measurement system, which can be developed and adapted to incorporate important environmental elements of organisational performance.

Social implications

This study reveals the importance of difference between endogenous and exogenous environmental activities. As concerns around the environmental consequences of organisational activities continue to grow, opportunities for institutions to reassure stakeholders of their sustainable practices are increasingly critical.

Originality/value

This study presents preliminary evidence on the suitability of various models for integrating environmental dimensions within the BSC. The findings provide a valuable contribution to literature on performance measurement systems in the healthcare sector.
Supporting ex-service personnel moving to social care work with older people: a systematic rapid review of the role of education
Authors: Manthorpe Jill , Bramley Stephanie
Published: July 2019

Purpose

The purpose of this paper is to review evidence about the role of education in supporting ex-service personnel to move to social care work with older people. Social care has long-standing, well-recognised problems of staff recruitment and retention in many jurisdictions. Within ageing societies, the need for more social care staff is predicted to rise. Therefore, policy makers and employers are exploring if there are untapped sources of potential employees. Some ex-service personnel may be interested in exploring a move to social care work with older people but may need to gain additional qualifications.

Design/methodology/approach

Databases and grey literature were searched systematically to provide an overview of the evidence on this topic. Six articles were included in the review.

Findings

A narrative analysis revealed two themes: preparing ex-service personnel for enrolment onto health and social care programmes, and supporting ex-service personnel during health and social care programmes.

Research limitations/implications

This review was confined to English language studies published between 2008 and 2018. Few mentioned specific user or client groups.

Originality/value

This review identified evidence gaps relating to whether the skills, education, training and experience gained in the armed services are transferable to civilian social care work with older people; the types of support which are offered to ex-service personnel who are interested in completing qualifications necessary for social care roles and the views of ex-service personnel about their experiences of completing educational courses to facilitate a transition into social care work with older people.
The economic recession and civic participation: the curious case of Rotterdam's civil society, 2008–2013
Authors: Custers Gijs , Engbersen Godfried , Snel Erik
Published: July 2019

This paper investigates how the 2008–9 recession affected civic participation in disadvantaged and affluent neighbourhoods in the city of Rotterdam. We hypothesize that levels of civic participation may either diverge or converge across neighbourhoods with a different socioeconomic status. We build upon a recent wave of studies examining how civil society has been affected by the 2008–9 recession. Using five waves from the Rotterdam Neighbourhood Profile survey (N = 63,134; 71 neighbourhoods), we find converging trends in civic participation. Between 2008 and 2013, civic participation declined in affluent neighbourhoods but increased slightly in disadvantaged neighbourhoods. This convergence is partly due to the level of perceived problems in the neighbourhood and differences in the types of volunteering found in disadvantaged and affluent neighbourhoods. In addition, we argue that these converging trends can be better understood by considering the neighbourhood organizational infrastructure and local policy configurations. Next to examining the impact of the 2008–9 recession on civic participation, we contribute to research on civil society by comparing the UK and Dutch context.
Do chorionic villus samplings (CVS) or amniocenteses (AC) induce RhD immunisation? An evaluation of a large Danish cohort with no routine administration of anti‐D after invasive prenatal testing
Authors: Kristensen SS , Nørgaard LN , Tabor A , Sundberg K , Dziegiel MH , Hedegaard M , Ekelund CK
Published: July 2019

Objective

To evaluate the risk of inducing RhD immunisation in pregnancies of RhD‐negative mothers with an RhD‐positive fetus undergoing chorionic villus samplings (CVS) or amniocenteses (AC).

Design, setting and population

Registry‐based study in a Danish cohort which has not been given rhesus prophylaxis.

Methods

Data were retrieved from the Department of Clinical Immunology at Rigshospitalet. All RhD‐negative women carrying an RhD‐positive fetus with screen test results from weeks 8–12 and weeks 25–29 were linked to data from the Danish Fetal Medicine Database. Data were divided into cases where no invasive prenatal diagnostic procedure was performed, cases that had AC performed, and cases that had CVS performed.

Main outcome measures

A comparison of the proportion of women who developed RhD immunisation between the two screen tests.

Results

The cohort consisted of 10 085 women: 9353 had no invasive procedures performed, 189 had AC and 543 had CVS performed. No women were immunised spontaneously or due to the procedure between the first and second screen test in the group with no procedure performed, or in the AC group. One woman was immunised in the CVS group. When comparing the proportion of women who was immunised in the CVS group with the no invasive test group a non‐significant difference was found (P = 0.055).

Conclusion

The RhD immunisation rate before gestational weeks 25–29 in RhD‐negative women carrying an RhD‐positive fetus is very low, even in women undergoing prenatal invasive testing without rhesus prophylaxis.

Tweetable abstract

The RhD immunisation rate during pregnancy is very low even in women undergoing prenatal invasive testing.
Effect of couple‐based cognitive behavioural intervention on prevention of postnatal depression: multisite randomised controlled trial
Authors: Ngai F‐W , Wong PW‐C , Chung K‐F , Chau P‐H , Hui P‐W
Published: July 2019

Objective

To compare a couple‐based cognitive behavioural intervention (CBI) for postnatal depression with CBI delivered to women alone and control (standard perinatal care).

Design

Multisite randomised controlled trial.

Setting

Antenatal clinics at three regional public hospitals in Hong Kong.

Sample

388 low‐risk childbearing couples.

Methods

Childbearing couples were randomly allocated to couple‐based CBI (n = 134), women‐alone CBI (n = 124) or control (n = 130). The CBI consists of a 3‐hour antenatal group session and two 30‐minute postnatal telephone follow‐up sessions.

Main outcome measures

The primary outcome was depressive symptoms, measured on the Edinburgh Postnatal Depression Scale (EPDS). Assessments were collected at baseline (during pregnancy), 6 weeks, 6 months, and 12 months postpartum.

Results

Depressive symptoms were significantly more improved at 6 weeks postpartum for mothers in couple‐based CBI than in women‐alone CBI (difference 1.46, 95% CI 0.11–2.81) or control groups (difference 1.71, 95% CI 0.29–3.13). The proportion of mothers with postnatal depression (EPDS score ≥ 10) was significantly lower at 6 weeks postpartum in couple‐based CBI than in control (difference 17.8%, 95% CI 3.6–32.0). However, the treatment effect was not maintained at 6 and 12 months. There was no significant intervention effect among fathers.

Conclusions

Couple‐based CBI is more effective than CBI delivered to mothers alone and standard perinatal care in reducing the incidence of postnatal depression among Chinese mothers in the early postpartum period.

Tweetable abstract

Couple‐based cognitive behavioural intervention is effective in reducing postnatal depression among Chinese mothers in the early postpartum period.
Thermal stress modifies the marine sponge virome
Authors: Laffy Patrick W. , Botté Emmanuelle S. , Wood‐Charlson Elisha M. , Weynberg Karen D. , Rattei Thomas , Webster Nicole S.
Published: July 2019

Marine sponges can form stable partnerships with a wide diversity of microbes and viruses, and this high intraspecies symbiont specificity makes them ideal models for exploring how host‐associated viromes respond to changing environmental conditions. Here we exposed the abundant Great Barrier Reef sponge Rhopaloiedes odorabile to elevated seawater temperature for 48 h and utilised a metaviromic approach to assess the response of the associated viral community. An increase in endogenous retro‐transcribing viruses within the Caulimorviridae and Retroviridae families was detected within the first 12 h of exposure to 32 °C, and a 30‐fold increase in retro‐transcribing viruses was evident after 48 h at 32 °C. Thermally stressed sponges also exhibited a complete loss of ssDNA viruses which were prevalent in field samples and sponges from the control temperature treatment. Despite these viromic changes, functional analysis failed to detect any loss or gain of auxiliary metabolic genes, indicating that viral communities are not providing a direct competitive advantage to their host under thermal stress. In contrast, endogenous sponge retro‐transcribing viruses appear to be replicating under thermal stress, and consistent with retroviral infections in other organisms, may be contributing to the previously described rapid decline in host health evident at elevated temperature.
Competition for alfalfa nodulation under metal stress by the metal‐tolerant strain Ochrobactrum cytisi Azn6.2
Authors: Navarro‐Torre Salvadora , Rodríguez‐Llorente Ignacio D. , Doukkali Bouchra , Caviedes Miguel A. , Pajuelo Eloísa
Published: July 2019

Legume plants, in association with rhizobia, are gaining increasing interest for heavy metal rhizoremediation. This symbiotic interaction combines the advantages of rhizoremediation and soil nitrogen enrichment. In metal polluted soils, Ochrobactrum cytisi can elicit non‐fixing nodules on legumes, including Medicago sativa. Nodulation kinetics was much slower when M. sativa plants were inoculated with O. cytisi Azn6.2 compared with the natural symbiont Ensifer meliloti 1021 and nodules were ineffective in nitrogen fixation. A competition experiment was performed using alfalfa grown on heavy metals, and co‐inoculated with equal amounts of the metal‐sensitive E. meliloti 1021 and the metal‐resistant O. cytisi Azn6.2. When plants were inoculated in non‐polluted substrates, all nodules were formed by E. meliloti 1021. Nevertheless, under increasing metal concentrations, the number of nodules occupied by O. cytisi grew. At the highest metal concentration, all nodules were elicited by O. cytisi, suggesting that the resistant species can take the place of the natural symbiont. This fact has important ecological and environmental implications when proposing legume–rhizobia symbioses for rhizoremediation and highlights the need of selecting highly resistant rhizobia in order to be competitive in polluted soils.
Pantoprazole in ICU patients at risk for gastrointestinal bleeding—1‐year mortality in the SUP‐ICU trial
Authors: Marker Søren , Krag Mette , Perner Anders , Wetterslev Jørn , Lange Theis , Wise Matt P. , Borthwick Mark , Bendel Stepani , Keus Frederik , Guttormsen Anne Berit , Schefold Joerg C. , Rasmussen Bodil S. , Elkmann Thomas , Bestle Morten , Arenkiel Bjørn , Laake Jon H. , Kamper Maj K. , Lång Maarit , Pawlowicz‐Dworzanska Malgorzata B. , Karlsson Sari , Liisanantti Janne , Dey Nilanjan , Knudsen Heidi , Granholm Anders , Møller Morten Hylander ,   the SUP-ICU trial investigators
Published: July 2019

Background

The long‐term effects of stress ulcer prophylaxis with pantoprazole are unknown in ICU patients. We report 1‐year mortality outcome in the Stress Ulcer Prophylaxis in the Intensive Care Unit (SUP‐ICU) trial.

Methods

In the SUP‐ICU trial, acutely admitted adult ICU patients at risk of gastrointestinal bleeding were randomised to intravenous pantoprazole 40 mg vs placebo (saline) once daily during their ICU stay. We assessed mortality at 1 year and did sensitivity analyses according to the trial protocol and statistical analysis plan.

Results

A total of 3261 of the 3291 patients with available data (99.1%) were followed up at 1 year after randomisation; 1635 were allocated to pantoprazole and 1626 to placebo. At 1 year after randomisation, 610 of 1635 patients (37.3%) had died in the pantoprazole group as compared with 601 of 1626 (37.0%) in the placebo group (relative risk, 1.01; 95% confidence interval 0.92‐1.10). The results were consistent in the sensitivity analysis adjusted for baseline risk factors and in those of the per‐protocol population. We did not observe heterogeneity in the effect of pantoprazole vs placebo on 1‐year mortality in the predefined subgroups, that is, patients with and without shock, mechanical ventilation, liver disease, coagulopathy, high disease severity (SAPS II > 53) or in medical vs surgical ICU patients.

Conclusion

We did not observe a difference in 1‐year mortality among acutely admitted adult ICU patients with risk factors for gastrointestinal bleeding allocated to stress ulcer prophylaxis with pantoprazole or placebo during the ICU stay. (The SUP‐ICU trial was funded by Innovation Fund Denmark and others; ClinicalTrials.gov number, NCT02467621).
Combination of perineural and wound infusion after above knee amputation: A randomized, controlled multicenter study
Authors: von Plato Hanna , Peltoniemi Marko , Kauhanen Petteri , Löyttyniemi Eliisa , Hamunen Katri , Kontinen Vesa ,   The FinAPain‐1 study group
Published: July 2019

Background

Post‐operative pain after an above‐knee amputation is often severe, and in the elderly patients the adverse effects of post‐operative opioids are evident. We hypothesized that continuous perineural local anesthetic infusion (CPI) combined to a wound infusion will reduce acute pain and opioid consumption compared to placebo after above knee amputation.

Methods

Ninety‐three patients going through an above knee amputation were recruited for this randomized, controlled trial. Two catheters were placed, one to the sciatic nerve sheath and one under the fasciae during the amputation. After two 10 mL boluses of ropivacaine 0.75% a post‐operative infusion of ropivacaine 0.2% or placebo (NaCl 0.9%) at 2 mL/h was administered for 72 hours to both catheters. The primary outcome was average stump pain during the first 5 days.

Results

The mean intensity of stump pain during the first five post‐operative days was 1.4 (0.8) in the CPI group and 1.9 (0.9) in the placebo group on VRS, mean (SD), P = .006. The opioid consumption on first five post‐operative days did not differ between the groups.

Conclusion

A combination of continuous perineural and wound local anesthetic infusion seems to diminish the intensity of stump pain after above knee amputation.
N‐Acetylcysteine treatment during acute stress prevents stress‐induced augmentation of addictive drug use and relapse
Authors: Garcia‐Keller Constanza , Smiley Cora , Monforton Cara , Melton Samantha , Kalivas Peter W. , Gass Justin
Published: July 2019

Converging epidemiological studies show that a life‐threatening event increases the incidence of posttraumatic stress disorder (PTSD), which carries 30% to 50% comorbidity with substance use disorders (SUDs). Such comorbidity results in greater drug use and poorer treatment outcomes. There is overlap between the enduring synaptic neuroadaptations produced in nucleus accumbens core (NAcore) by acute restraint stress and cocaine self‐administration. Because of these coincident neuroadaptations, we hypothesized that an odor paired with acute restraint stress would reinstate drug seeking and chose two mechanistically distinct drugs of abuse to test this hypothesis: alcohol and cocaine. Rats were trained to self‐administer either drug beginning 3 weeks after odor pairing with acute stress or sham, and acute restraint stress increased alcohol consumption. Following context extinction training, the stress‐paired odor reinstated both alcohol and cocaine seeking, while an unpaired odor had no effect. N‐Acetylcysteine (NAC) restores drug and stress‐induced reductions in glial glutamate transporter‐1 and has proven effective at reducing cue‐induced reinstatement of drug seeking. We administered NAC for 5 days prior to reinstatement testing and abolished the capacity of the stress‐paired odor to increase alcohol and cocaine seeking. Importantly, daily NAC given during or just following experiencing acute restraint stress also prevented the capacity of stress‐paired odors to reinstate alcohol and cocaine seeking and prevented stress‐induced deficits in behavioral flexibility. These data support using daily NAC treatment during or immediately after experiencing a strong acute stress to prevent subsequent conditioned stress responding, in particular relapse and cognitive deficits induced by stress‐conditioned stimuli.
Predictive value of thromboelastography parameters combined with antithrombin III and D‐Dimer in patients with recurrent spontaneous abortion
Authors: Wang Ping , Yang Hongjun , Wang Guoying , Tian Jun
Published: July 2019

Problem

To investigate the value of thromboelastography (TEG) combined with antithrombin III (AT‐III) and D‐Dimer in predicting the occurrence of recurrent spontaneous abortion (RSA).

Method of study

One hundred and five RSA patients and 40 fertile women were enrolled. The subjects were subjected into four groups: group 1 (40 fertile women), group 2 (58 women with 2 abortions), group 3 (30 women with 3 abortions), and group 4 (17 women with four abortions). TEG was conducted on all subjects. Clotting time, reaction time, angle degree, coagulation index, and maximum amplitude were measured. The levels AT‐III, D‐Dimer, platelet counts, and fibrinogen concentration were determined. The ROC curve analysis was done using MedCalc software to analyse the diagnosis accuracy of the parameters of interest and the combined approach.

Results

The AT‐III level in all group 4 was significantly lower than in fertile women. The D‐Dimer concentration, platelet count, and MA in patients with four prior abortions were significantly higher than the other three groups. CI and fibrinogen concentration in patients with four prior pregnancy losses were significantly higher than group 1. The ROC curves suggested that combined use of CI, MA, AT‐III, and D‐Dimer was with the highest accuracy 92.8%, thus predicting the most accurate diagnosis for RSA.

Conclusion

Recurrent spontaneous abortion is associated with abnormal coagulation and anticoagulation. TEG combined with detection of AT‐III and D‐Dimer levels can distinguish patient with RSA from those with normal fertility and highly possibly predict the occurrence of RSA.
A comparison of four risk models for the prediction of cardiovascular complications in patients with a history of atrial fibrillation undergoing non‐cardiac surgery
Authors: McAlister F. A. , Youngson E. , Jacka M. , Graham M. , Conen D. , Chan M. , Szczeklik W. , Alonso‐Coello P. , Devereaux P. J. ,   the vascular events in non‐cardiac surgery patIents cohort evaluation (VISION) investigators
Published: July 2019

It is unclear how best to predict peri‐operative cardiovascular risk in patients with atrial fibrillation undergoing non‐cardiac surgery. This study examined the accuracy of the revised cardiac risk index and three atrial fibrillation thrombo‐embolic risk models for predicting 30‐day cardiovascular events after non‐cardiac surgery in patients with a pre‐operative history of atrial fibrillation. We conducted a prospective cohort study in 28 centres from 2007 to 2013 of 40,004 patients ≥ 45 years of age undergoing inpatient non‐cardiac surgery who were followed until 30 days after surgery for cardiovascular events (defined as myocardial injury, heart failure, stroke, resuscitated cardiac arrest or cardiovascular death). The 2088 patients with a pre‐operative history of atrial fibrillation were at higher risk of peri‐operative cardiovascular events compared with the 34,830 patients without a history of atrial fibrillation (29% vs. 13%, respectively, adjusted odds ratio 1.30 (95%CI 1.17–1.45). Compared with the revised cardiac risk index (c‐index 0.60), all atrial fibrillation thrombo‐embolic risk scores were significantly better at predicting peri‐operative cardiovascular events: CHADS2 (c‐index 0.62); CHA2DS2‐VASc (c‐index 0.63); and R2CHADS2 (c‐index 0.65), respectively. Although the three thrombo‐embolic risk prediction models were significantly better than the revised cardiac risk index for prediction of peri‐operative cardiovascular events, none of the four models exhibited strong discrimination metrics. There remains a need to develop a better peri‐operative risk prediction model.
Real‐world 10‐year experiences with intravitreal treatment with ranibizumab and aflibercept for neovascular age‐related macular degeneration
Authors: Brynskov Troels , Munch Inger Christine , Larsen Tobias Malte , Erngaard Liv , Sørensen Torben Lykke
Published: July 2019

Purpose

To report 10‐year, real‐world experiences with intravitreal therapy (IVT) using vascular endothelial growth factor inhibitors for neovascular age‐related macular degeneration (nAMD).

Methods

Retrospective single‐centre review of IVT‐log 2007–2019 with a treatment‐as‐needed regimen and ETDRS visual acuity charts.

Results

The 4,678 treatment‐naïve eyes of 3,668 patients received a mean of 5.4 IVT in the first year and 4.0–4.3 IVT yearly thereafter. Baseline mean best corrected visual acuity (BCVA) was 57.9 (±16.4) letters (6/18) that improved a mean +2.1 (±0.2) letters at the first follow‐up visit and gradually declined to −5.0 (±2.2) letters after 10 years. At baseline, there were 29% with BCVA ≥6/12. This proportion increased to 31–37% until year 9. There were 8% with BCVA loss of ≥3 lines at the first follow‐up visit increasing to 34% after 10 years. Poorer baseline BCVA was associated with larger increase in BCVA (p < 0.0001, multiple linear regression). The 2,566 (55%) discontinued eyes had a mean baseline BCVA of 56.9 (±16.4) letters compared with 61.5 (±15.9) letters for eyes remaining in treatment. In year 0–7, the discontinued eyes lost an additional mean 2–4 letters (last observation carried forward) but were similar thereafter. There were 12.6% (74 of 585 eligible eyes) that were still in treatment after 10 years. At baseline, 10% had bilateral nAMD. Of patients with unilateral presentation, 17% had received fellow‐eye IVT after 5 years.

Conclusion

A treatment‐as‐needed regimen stabilized BCVA in active nAMD up to 10 years in most eyes. Baseline BCVA was the most important prognostic factor.
Evaluation of high nutrient diets and additional dextrose on reproductive performance and litter performance of heat‐stressed lactating sows
Authors: Kim KwangYeol , Choi YoHan , Hosseindoust Abdolreza , Kim MinJu , Hwang SungJun , Bu MinSu , Lee JunHyung , Kim YoungHwa , Chae Byung‐Jo
Published: July 2019

This study investigated the litter performance of lactating sows fed nutrient‐dense diets with or without dextrose at farrowing to weaning, during the summer with an average room temperature of 28.4°C. A total of 60 (13 first parity, 13 second parity, 19 third parity, and 15 forth parity) cross‐bred sows were assigned to three treatments. The three treatments were: standard diet (ST), high nutrient diet (HN; ST + 3% higher energy and 18.0% protein), and high nutrient diet plus dextrose (HND; 3% higher energy, 18.0% protein, and 5% dextrose). BW loss was reduced in the HND sows compared with the ST sows during lactation. The HN and HND sows had a higher piglet and litter weight at weaning. Also, the HND sows had the highest post‐prandial insulin levels at weaning and the shortest weaning‐to‐service interval (WSI). Serum LH was higher in the HND sows than the ST sows. The milk fat level was higher in the HND sows compared with the ST sows, but similar to the HN sows. In conclusion, these results suggest that it is possible to increase the blood insulin response by supplementing dextrose to a high nutrient diet, thus, improving WSI interval and litter growth during heat stress.
Efficient Path Generation with Reduced Coordinates
Authors: Chen Renjie , Gotsman Craig , Hormann Kai
Published: July 2019

Path generation is an important problem in many fields, especially robotics. One way to create a path between a source point z and a target point y inside a complex planar domain Ω is to define a non‐negative distance function d(y, z), such that following the negative gradient of d (by z) traces out such a path. This presents two challenges: (1) The mathematical challenge of defining d, such that d(y, z) has a single minimum at z = y for any fixed y, because the gradient‐descent path may otherwise terminate at a local minimum before reaching y; (2) The computational challenge of defining d, such that it can be computed efficiently. Using the concepts of harmonic measure and f‐divergence, we show how to assign a set of reduced coordinates to each point in Ω and to define a family of distance functions based on these coordinates, such that both the mathematical and the computational challenge are met. Since in practice, especially in robotics applications, the path is often restricted to follow the edges of a discrete network defined on a finite set of sites sampled from Ω, any method that works well in the continuous setting must be discretized appropriately to preserve the important properties of the continuous case. We show how to define a network connecting a finite set of sites, such that a greedy routing algorithm, which is the discrete equivalent of continuous gradient descent, based on our reduced coordinates is guaranteed to generate a path in the network between any two sites. In many cases, this network is close to a planar graph, especially if the set of sites is dense. Guaranteeing the existence of a greedy route between any two points in the graph is a significant advantage in practical applications, avoiding the complexity of other path‐planning methods, such as the shortest‐path and A* algorithms. While the paths generated by our algorithm are not the shortest possible, in practice we found that they are close to that.
Principal Geodesic Analysis in the Space of Discrete Shells
Authors: Heeren B. , Zhang C. , Rumpf M. , Smith W.
Published: July 2019

Important sources of shape variability, such as articulated motion of body models or soft tissue dynamics, are highly nonlinear and are usually superposed on top of rigid body motion which must be factored out. We propose a novel, nonlinear, rigid body motion invariant Principal Geodesic Analysis (PGA) that allows us to analyse this variability, compress large variations based on statistical shape analysis and fit a model to measurements. For given input shape data sets we show how to compute a low dimensional approximating submanifold on the space of discrete shells, making our approach a hybrid between a physical and statistical model. General discrete shells can be projected onto the submanifold and sparsely represented by a small set of coefficients. We demonstrate two specific applications: model‐constrained mesh editing and reconstruction of a dense animated mesh from sparse motion capture markers using the statistical knowledge as a prior.