bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intraoperative Computed Tomography and Finite Element Modelling for Multimodal Image Fusion in Brain Surgery
Authors: Riva Marco , Hiepe Patrick , Frommert Mona , Divenuto Ignazio , Gay Lorenzo G , Sciortino Tommaso , Nibali Marco Conti , Rossi Marco , Pessina Federico , Bello Lorenzo 
Published: July 2019

Abstract

BACKGROUND
intraoperative computer tomography (iCT) and advanced image fusion algorithms could improve the management of brainshift and the navigation accuracy.

OBJECTIVE
To evaluate the performance of an iCT-based fusion algorithm using clinical data.

METHODS
Ten patients with brain tumors were enrolled; preoperative MRI was acquired. The iCT was applied at the end of microsurgical resection. Elastic image fusion of the preoperative MRI to iCT data was performed by deformable fusion employing a biomechanical simulation based on a finite element model. Fusion accuracy was evaluated: the target registration error (TRE, mm) was measured for rigid and elastic fusion (Rf and Ef) and anatomical landmark pairs were divided into test and control structures according to distinct involvement by the brainshift. Intraoperative points describing the stereotactic position of the brain were also acquired and a qualitative evaluation of the adaptive morphing of the preoperative MRI was performed by 5 observers.

RESULTS
The mean TRE for control and test structures with Rf was 1.81 ± 1.52 and 5.53 ± 2.46 mm, respectively. No significant change was observed applying Ef to control structures; the test structures showed reduced TRE values of 3.34 ± 2.10 mm after Ef (P < .001). A 32% average gain (range 9%-54%) in accuracy of image registration was recorded. The morphed MRI showed robust matching with iCT scans and intraoperative stereotactic points.

CONCLUSIONS
The evaluated method increased the registration accuracy of preoperative MRI and iCT data. The iCT-based non-linear morphing of the preoperative MRI can potentially enhance the consistency of neuronavigation intraoperatively.
Development of a Heat-Inducible Gene Expression System Using Female Gametophytes of Arabidopsis thaliana
Authors: Hwang Dukhyun , Wada Satomi , Takahashi Azusa , Urawa Hiroko , Kamei Yasuhiro , Nishikawa Shuh-ichi 
Published: July 2019

AbstractFemale gametophyte (FG) is crucial for reproduction in flowering plants. Arabidopsis thaliana produces Polygonum-type FGs, which consist of an egg cell, two synergid cells, three antipodal cells and a central cell. Egg cell and central cell are the two female gametes that give rise to the embryo and surrounding endosperm, respectively, after fertilization. During the development of a FG, a single megaspore produced by meiosis undergoes three rounds of mitosis to produce an eight-nucleate cell. A seven-celled FG is formed after cellularization. The central cell initially contains two polar nuclei that fuse during female gametogenesis to form the secondary nucleus. In this study, we developed a gene induction system for analyzing the functions of various genes in developing Arabidopsis FGs. This system allows transgene expression in developing FGs using the heat-inducible Cre-loxP recombination system and FG-specific embryo sac 2 (ES2) promoter. Efficient gene induction was achieved in FGs by incubating flower buds and isolated pistils at 35ï¿½C for short periods of time (1–5 min). Gene induction was also induced in developing FGs by heat treatment of isolated ovules using the infrared laser-evoked gene operator (IR-LEGO) system. Expression of a dominant-negative mutant of Sad1/UNC84 (SUN) proteins in developing FGs using the gene induction system developed in this study caused defects in polar nuclear fusion, indicating the roles of SUN proteins in this process. This strategy represents a new tool for analyzing the functions of genes in FG development and FG functions.
Successful treatment of anti-MDA5 antibody-positive refractory interstitial lung disease with plasma exchange therapy
Authors: Abe Yoshiyuki , Kusaoi Makio , Tada Kurisu , Yamaji Ken , Tamura Naoto 
Published: July 2019

Abstract

Objectives
We examined the effectiveness of plasma exchange (PE) therapy to reduce the mortality of rapidly progressive interstitial lung disease (RP-ILD) in patients positive for anti-melanoma differentiation-associated gene 5 (MDA5) antibodies.

Methods
Among 142 patients newly diagnosed with PM/DM or clinically amyopathic DM from 2008 to 2019 at our hospital, 10 were diagnosed with refractory RP-ILD and were positive for anti-MDA5 antibodies. PE was used as an adjunct to standard therapy and consisted of fresh frozen plasma as replacement solution. The primary outcome was non-disease-specific mortality.

Results
Anti-MDA5 antibodies were detected in 28 patients, of whom 21 were diagnosed with RP-ILD and 10 were refractory to intensive immunosuppressive therapy. Six patients received PE (PE group) and four did not (non-PE group). The 1-year survival rate of the PE group was higher than that of the non-PE group (100% and 25%, respectively, P = 0.033). Regarding adverse events associated with PE, two patients had anaphylactic shock, one had high fever due to fresh frozen plasma allergy and one had a catheter infection. All adverse events resolved with appropriate treatment.

Conclusion
We evaluated the association between 1-year survival rate and PE for refractory RP-ILD in patients positive for anti-MDA5 antibodies. Intensive immunosuppressive therapy improved the survival rate in RP-ILD patients with anti-MDA5 antibodies, but 20–30% of cases were still fatal. PE could be administered to patients with active infectious disease who were immunocompromised by intensive immunosuppressive therapy. PE may be considered in refractory RP-ILD patients positive for anti-MDA5 antibodies.
Experimental investigations on the partner-finding behaviour of Isohypsibius dastychi (Isohypsibiidae: Tardigrada)
Authors: Bartel Sandra , Hohberg Karin 
Published: July 2019

Abstract
The present study gives the first detailed results on the partner-finding behaviour of tardigrades. We investigated whether the finding of mating partners by Isohypsibius dastychi followed certain criteria that are expected if pheromone signals are involved. For this purpose, tardigrade pairs were positioned in an arena, at a range of distances from each other. Only those females that were ready for mating attracted the male. The smaller the initial distance between them, the more directly the male headed for the female. The route travelled and time taken increased exponentially with increasing initial distance between partners, which means that the male lost orientation with respect to the female the larger the distance between the pair became. The findings indirectly suggest a yet undetermined female pheromone, which produces a concentration gradient in the water and loses strength quickly in terms of distance. Our assumption is supported by rare observations of sperm release without direct contact between partners that nevertheless resulted in fertile offspring. The observation that the female partners in this no-contact mating behaviour then deposited their eggs (a behaviour that was never seen when males were absent) suggests that they, likewise, can sense a fresh ejaculate of spermatozoa in their direct vicinity.
Quantification of Optical Coherence Tomography Angiography in Age and Age-related Macular Degeneration using Vessel Density analysis
Authors: Vaghefi Ehsan , Hill Sophie , Kersten Hannah M , Squirrell David 
Published: July 2019

AbstractPurposeTo determine whether vessel density (VD) as measured by optical coherence tomography angiography (OCT-A) provide insights into retinal and choriocapillaris vascular changes with ageing and intermediate dry age related macular degeneration (AMD).MethodsSeventy-five participants were recruited into three cohorts; young healthy (YH) group, old healthy (OH) and those at high-risk for exudative AMD. Raw OCT and OCT-A data from TOPCON DRI OCT Triton were exported using Topcon IMAGENET 6.0 software, and 3D datasets were analysed to determine retinal thickness and vessel density.ResultsCentral macular thickness measurements revealed a trend of overall retinal thinning with increasing age. VD through the full thickness of the retina was highest in ETDRS sector 4 (the inferior macula) in all the cohorts. Mean VD was significantly higher in the deep capillary plexus than the superficial capillary plexus in all ETDRS sectors in all cohorts but there was no significant difference noted between groups. Choriocapillaris VD was significantly lower in all ETDRS sectors in the in the AMD group compared with the YH and the OH groups.ConclusionsRetinal vessel density maps, derived from the retinal plexi are not reliable biomarkers for assessing the ageing macular. Our non-proprietary analysis of the vascular density of the choriocapillaris revealed a significant drop off of VD with age and disease but further work is required to corroborate this finding. If repeatable, choriocapillaris VD may provide a non-invasive biomarker of healthy ageing and disease.Brief SummaryIn this manuscript, we have studied the potential of retinal vessel density as measured by optical coherence tomography angiography (OCT-A), as a biomarker for detection of high-risk of developing exudative age-related macular degeneration (AMD).
Genome Complexity Browser: estimation and visualization of prokaryote genome variability
Authors: Manolov Alexander I , Konanov Dmitry N , Fedorov Dmitry E , Osmolovsky Ivan S , Ilina Elena N 
Published: July 2019

AbstractMotivationComparative genomics studies may be used to acquire new knowledge about chromosomal architecture - the rules to combine a set of genes in a genome of a living organism. Hundreds of thousands of prokaryote genomes were sequenced and assembled. Still, there is a lack of computational tools able to compare hundreds of genomes simultaneously, i.e. to find hotspots of genome rearrangements and horizontal gene transfer or to analyze which part of an operon is conservative and which is variable.ResultsWe developed Genomic Complexity Browser (GCB), a tool that allows to visualize gene contexts in a graph form and evaluate genome variability of different parts of a prokaryotic chromosome. We introduce a measure called complexity, which is an indirect measure of genome variability. Intraspecies and interspecies comparisons reveal that regions with high complexity tend to be located in a similar context in different strains and species. While many of such hot spots are associated with prophages and pathogenicity islands, some of them lack these determinants and mechanisms that govern their dynamics are to be elucidated.AvailabilityGCB is freely available as a web server athttp://gcb.rcpcm.organd as a stand-alone application athttps://github.com/DNKonanov/GCBContactparaslonic@gmail.com
Emergence of B2-ST131-C2 and A-ST617 Escherichia coli clones producing both CTX-M-15- and CTX-M-27 and ST147 NDM-1 positive Klebsiella pneumoniae in the Tunisian community
Authors: Mhaya Amel , Trabelsi Rahma , Begu Dominique , Aillerie Sabine , M’zali Fatima , Tounsi Slim , Gdoura Radhouane , Arpin Corinne 
Published: July 2019

ABSTRACTCTX-M ESBLs have been increasingly reported from human enterobacteria isolates in Tunisia. NDM-1 carbapenemase was recently reported in isolates from Tunisian Hospitals. During a 2-month period (December 2017 to January 2018), we have collected 23 ESBL-producing Enterobacteriaceae (ESBL-E) from urines of patients hospitalized in three health care facilities and from community, situated in two distinct Tunisian geographical regions. They were divided into 15 Escherichia coli and eight Klebsiella pneumoniae. The aim of this study was to characterize ESBL-E with regard to their β-lactamase content and their epidemiological relationship. The results indicated a high rate (47%) of E. coli producing both CTX-M group-1 and −9. For the first time, we demonstrated the presence of E. coli having concomitantly CTX-M-15 and CTX-M-27 which belong to two sequences types (ST), ie. A-ST617 (2 isolates) and B2-ST131 subclade C2 (2 isolates). All four E. coli isolates carried a multireplicon IncF with an identical allelic combination, F31:A4:B1. This study reports also the first description of K. pneumoniae belonging to the clone ST147 carrying the carbapenemase NDM-1 in the Tunisian community. In conclusion, our data confirms the need for monitoring the resistance to extended-spectrum cephalosporins and to carbapenems among enterobacteria in Tunisia.
ThX – A next-generation probe for the early detection of amyloid aggregates
Authors: Needham Lisa-Maria , Weber Judith , Varela Juan A. , Fyfe James W. B. , Do Dung T. , Xu Catherine K , Keenlyside Benjamin , Cliffe Rachel , Klenerman David , Dobson Christopher M. , Hunter Christopher A. , Bohndiek Sarah E. , Snaddon Thomas N. , Lee Steven F. 
Published: July 2019

AbstractNeurodegenerative diseases such as Alzheimer’s and Parkinson’s are associated with protein misfolding and aggregation. Recent studies suggest that the small, rare and heterogeneous oligomeric species, formed early on in the aggregation process, may be a source of cytotoxicity. Thioflavin T (ThT) is currently the gold-standard fluorescent probe for the study of amyloid proteins and aggregation processes. However, the poor photophysical and binding properties of ThT impairs the study of oligomers. To overcome this challenge, we have designed Thioflavin X, (ThX), a next-generation fluorescent probe which displays superior properties; including a 5-fold increase in brightness and 7-fold increase in binding affinity to amyloidogenic proteins. As an extrinsic dye, this can be used to study unique structural amyloid features both in bulk and on a single-aggregate level. Furthermore, ThX can be used as a super-resolution imaging probe in single-molecule localisation microscopy. Finally, we demonstrate that ThX can be used to detect a distinct oligomeric species, not observed via traditional ThT imaging.
Phage composition of a fermented milk and colostrum product assessed by microbiome array; putative role of open reading frames in reference to cell signaling and neurological development
Authors: Pacini Stefania , Ruggiero Marco 
Published: July 2019

AbstractBacteriophages (phages), Earth’s most numerous biological entities, are natural constituents of alimentary matrices; in this study we describe the characterization of phage populations in a product obtained by fermentation of bovine milk and colostrum. Such characterizations were achieved using a microarray consisting of a chip covered in short DNA sequences that are specific to certain target organisms for a total of approximately 12,000 species. The only viruses evidenced by the array belonged to Siphoviridae, the largest phage family that targets bacteria and archea. The array yielded 27 iterations corresponding to a unique target. We discuss the putative role of some open reading frames of these phages in conferring health-supporting properties with particular reference to cells signaling and neurological development. We also describe the in vitro interaction of this fermented product with alpha-N-acetylgalactosaminidase, an enzyme whose activity in serum is elevated in neurodevelopmental disorders.
Sellimonas caecigallum sp. nov., description and genome sequence of a new member of the Sellimonas genus isolated from the cecum of feral chicken
Authors: Wongkuna Supapit , Ghimire Sudeep , Antony Linto , Chankhamhaengdecha Surang , Janvilisri Tavan , Scaria Joy 
Published: July 2019

AbstractAn obligately anaerobic, non-motile, Gram-positive coccobacillus strain SW451 was isolated from pooled cecum contents of feral chickens. Comparative analysis based on 16s rRNA sequence showed that strain SW451 had 95.24% nucleotide sequence similarity to Sellimonas intestinalis BR31T, the closest species with a valid taxonomy. The genome of SW451 is 2.67 Mbp with 45.23 mol% of G+C content. The major cellular fatty acids were C16: 0, C14: 0 and C16: 0 DMA. Based on taxonogenomic, physiological, and biochemical analysis, the strain SW451 represents a new species of the genus Sellimonas, for which the name Sellimonas caecigallum sp. nov. is proposed. The type strain of Sellimonas caecigallum is SW451 (=DSM 109473T)
An automated data processing and analysis pipeline for transmembrane proteins in detergent solutions
Authors: Molodenskiy D. , Mertens H. , Svergun D. 
Published: July 2019

AbstractThe application of small angle X-ray scattering (SAXS) to the structural characterization of transmembrane proteins (MPs) in detergent solutions has become a routine procedure at the most synchrotron BioSAXS beamlines around the world. SAXS provides overall parameters and low resolution shapes of solubilized MPs, but is also meaningfully employed in hybrid modeling procedures that combine scattering data with information provided by high-resolution techniques (eg.macromolecular crystallography, nuclear magnetic resonance and cryo-electron microscopy). Structural modeling of MPs from SAXS data is non-trivial, and the necessary computational procedures require further formalization and facilitation. We propose an automated pipeline integrated with the laboratory-information management system ISPyB, aimed at preliminary SAXS analysis and the first-step reconstruction of MPs in detergent solutions, in order to streamline high-throughput studies, especially at synchrotron beamlines. The pipeline queries an ISPyB database for availablea prioriinformationviadedicated services, estimates model-free SAXS parameters and generates preliminary models utilizing eitherab initio, high-resolution-based, or mixed/hybrid methods. The results of the automated analysis can be inspected online using the standard ISPyB interface and the estimated modeling parameters may be utilized for further in-depth modeling beyond the pipeline. Examples of the pipeline results for the modelling of the tetrameric alpha-helical membrane channel Aquaporin0 and mechanosensitive channel T2, solubilized by n-Dodecyl β-D-maltoside are presented. We demonstrate how the increasing amounta prioriinformation improves the model resolution and enables deeper insights into the molecular structure of protein-detergent complexes.STATEMENT OF SIGNIFICANCESmall angle X-ray scattering (SAXS) using synchrotron radiation is a powerful technique for the structural characterization of transmembrane proteins (MPs) in detergent solutions Overall structural characterization and modeling of MPs from SAXS data is non-trivial, and the necessary computational procedures require further formalization and facilitation. We propose an automated pipeline integrated with the laboratory-information management system ISPyB, aimed at preliminary SAXS analysis and modelling of MPs in detergent solutions, in order to streamline high-throughput studies, especially at synchrotron beamlines.
Microglia depletion disrupts normal functional development of adult-born neurons in the olfactory bulb
Authors: Wallace Jenelle , Lord Julia , Dissing-Olesen Lasse , Stevens Beth , Murthy Venkatesh 
Published: July 2019

AbstractMicroglia play key roles in regulating synapse development and refinement in the developing brain, but it is unknown whether they are similarly involved during adult neurogenesis. By transiently ablating microglia from the healthy adult mouse brain, we show that microglia are necessary for the normal functional development of adult-born granule cells (abGCs) in the olfactory bulb. Microglia ablation reduces the odor responses of developing, but not preexisting GCs in vivo in both awake and anesthetized mice. Microglia preferentially target their motile processes to interact with mushroom spines on abGCs, and when microglia are absent, abGCs develop smaller spines and receive weaker excitatory synaptic inputs. These results suggest that microglia promote the development of excitatory synapses onto developing abGCs, which may impact the function of these cells in the olfactory circuit.
TSG-6 in extracellular vesicles from canine mesenchymal stem/stromal is a major factor in relieving DSS-induced colitis
Authors: An Ju-Hyun , Song Woo-Jin , Li Qiang , Ryu Min-Ok , Nam A-Ryung , Bhang Dong-Ha , Jung Yun-Chan , Youn Hwa-Young 
Published: July 2019

AbstractMesenchymal stem/stromal cell (MSC)-derived extracellular vesicles (EV) have been reported to be beneficial against dextran sulfate sodium (DSS)-induced colitis in mice. However, the underlying mechanisms have not been fully elucidated. We hypothesize that the tumor necrosis factor-α-stimulated gene/protein 6 (TSG-6) in EVs is a key factor influencing the alleviation of colitis symptoms. DSS-induced colitis mice (C57BL/6, male, n = 6-8/group) were intraperitoneally administered EVs (100 ug/mice) on day 1, 3, and 5; colon tissues were collected on day 10 for histopathological, qRT-PCR, western blot, and immunofluorescence analyses. In mice injected with EV, inflammation was alleviated. Indeed, EVs regulated the levels of pro- and anti-inflammatory cytokines, such as TNF-α, IL-1β, IFN-γ, IL-6, and IL-10 in inflamed colons. However, when injected with TSG-6 depleted EV, the degree of inflammatory relief was reduced. Furthermore, TSG-6 in EVs plays a key role in increasing regulatory T cells (Tregs) in the colon. In conclusion, this study shows that TSG-6 in EVs is a major factor in the relief of DSS-induced colitis, by increasing the number of Tregs in the colon.
Effect of index-based livestock insurance on loan uptake
Authors: Gebrekidan Tnsue , Kaiyu Lyu 
Published: July 2019

Purpose
The purpose of this paper is to weigh up the effect of index-based livestock insurance (IBLI) on loan take up behavior of the pastoral households in the Borena zone of Southern Ethiopia. Although the insurance was introduced over the last decade and it appears to have promising welfare benefit, there is a lack of pragmatic evidence on its effect in leveraging the household’s future wealth for the hope of better productivity in the present.

Design/methodology/approach
The authors analyze household-level unique panel data collected in three rounds using descriptive statistics and the fixed effect model estimated by least squares dummy variable analysis.

Findings
The authors found that the IBLI appears to have a positive and significant effect on the loan uptake behavior of the herding households.

Social implications
This increased likelihood of loan uptake suggests that the insurance can reduce the cognitive cost of loan default that would occur due to weather shocks and build-up of the household’s confidence to uptake loan. Consequently, this likelihood can promote the creditworthiness of the insured and reduce his/her fear and worry regarding the possibility of loan delinquency.

Originality/value
The paper is, except where otherwise stated, entirely new work.