bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scarless removal of large resistance island AbaR results in antibiotic susceptibility and increased natural transformability inAcinetobacter baumannii
Authors: Godeux Anne-Sophie , Svedholm Elin , Lupo Agnese , Haenni Marisa , Laaberki Maria-Halima , Charpentier Xavier 
Published: April 2020

ABSTRACTWith a great diversity in gene composition including multiple putative antibiotic-resistance genes, AbaR islands are potential contributors to multi-drug resistance inAcinetobacter baumannii. However, the effective contribution of AbaR to antibiotic resistance and bacterial physiology remains elusive. To address this, we sought to accurately remove AbaR islands and restore the integrity of their insertion site. To this end, we devised a versatile scarless genome editing strategy. We performed this genetic modification in two recentA. baumanniiclinical strains: the strain AB5075 and the nosocomial strain AYE which carry AbaR11 and AbaR1 islands of 19.7 kbp and 86.2 kbp, respectively. Antibiotic susceptibilities were then compared between the parental strains and their AbaR-cured derivatives. As anticipated by the predicted function of the ORF of this island, the antibiotic resistance profiles were identical between the wild type and the AbaR11-cured AB5075 strains. In contrast, AbaR1 carries 25 ORFs with a predicted resistance to several classes of antibiotics and the AYE AbaR1-cured derivative showed restored susceptibility to multiple classes of antibiotics. Moreover, curing of AbaRs restored high levels of natural transformability. Indeed, most AbaR islands are inserted into thecomMgene involved in natural transformation. Our data indicate that AbaR insertion effectively inactivatescomMand that the restoredcomMis functional. Curing of AbaR consistently resulted in highly transformable, and therefore, easily genetically tractable strains. Emendation of AbaR provides insight into the functional consequences of AbaR acquisition.
Polyploidy of semi-cloned embryos generated from parthenogenetic haploid embryonic stem cells
Authors: Aizawa Eishi , Dumeau Charles-Etienne , Freimann Remo , Di Minin Giulio , Wutz Anton 
Published: April 2020

AbstractIn mammals, the fusion of two gametes, an oocyte and a spermatozoon, during fertilization forms a totipotent zygote. There has been no reported case of natural parthenogenesis, in which embryos develop from unfertilized oocytes. The genome and epigenetic information of haploid gametes are crucial for the proper development of embryos. Haploid embryonic stem cells (haESCs) are unique stem cells established from uniparental blastocysts and possess only one set of chromosomes. Previous studies have shown that sperm or oocyte genome can be replaced by haESCs with or without manipulation of genomic imprinting for generation of mice. Recently, these remarkable semi-cloning methods have been applied for screening of key factors of mouse embryonic development. While haESCs have been applied as substitute of gametic genome, the fundamental mechanism how haESCs contribute to the genome of totipotent embryos is unclear. Here, we show the generation of fertile semi-cloned mice by injection of parthenogenetic haESCs (phaESCs) into oocytes after deletions of two differentially methylated regions (DMRs), theIG-DMR andH19-DMR. For characterizing the genome of semi-cloned embryos further we establish ESC lines from semi-cloned blastocysts. We report that polyploid karyotypes are observed frequently in semi-cloned ESCs (scESCs). Our results confirm that mitotically arrested phaESCs provide high efficiency for semi-cloning when theIG-DMR andH19-DMR are deleted. In addition, we highlight the occurrence of polyploidy that needs to be considered for further improvement for development of semi-cloned embryos derived by haESC injection.
Hyperiid amphipods from the Gulf of Ulloa and offshore region, Baja California: Intermittent use of the coastal shelf
Authors: Lavaniegos Bertha E. 
Published: April 2020

AbstractHyperiid amphipod species from the Gulf of Ulloa, Baja California, and the adjacent region (from shelf break to 200 km offshore) were analyzed in order to evaluate diversity and abundances in this productive area that supports small-scale commercial fisheries such as barred sand bass (Paralabrax nebulifer), California spiny lobster (Panulirus interruptus), abalones, clams, and others. Strong coastal upwelling events were observed during summer seasons of the period 2002-2008 between Punta Eugenia and Punta Abreojos. The upwelling plumes at Punta Abreojos are projected southward in slope waters bordering the coastal shelf of the Gulf of Ulloa, contributing to the separation of coastal and oceanic regions, and explain differences in amphipod diversity and abundances. In the offshore region, the most abundant species wereVibilia armata, Lestrigonus schizogeneios, Primno brevidens, andEupronoe minuta, similar to previous findings in northern regions of Baja California and southern California. However, their abundances were lower (between 10 and 30 individuals/1000 m3), only reaching 20-50% of abundance levels reported off northern Baja California. In the coastal shelf of the Gulf of Ulloa, amphipods were virtually absent during 2002, 2003 and 2006. However, during 2004 and 2005, abundances ofP. brevidensincreased (54 and 20 ind/1000 m3, respectively). Moreover, during 2007, abundances ofL. schizogeneios, P. brevidens, Lycaea nasuta, Lycaea pulex, andSimorhynchotus antennariusincreased considerably (261, 39, 31, 68, 416 ind/1000 m3, respectively), indicating occasional utilization of the coastal shelf by pelagic amphipods. Gelatinous organisms paralleled changes in hyperiid populations and were particularly abundant in 2007 in the coastal shelf. Significant correlations of 17 amphipod species with gelatinous taxa, which are often used as host organisms by hyperiid amphipods, suggest that those organisms enhanced hyperiid abundance and promoted the progression onto the coastal shelf during some years of the 2002-2008 period.
Continuous administration of the p38α inhibitor neflamapimod during the subacute phase after transient ischemia-induced stroke in the rat promotes dose-dependent functional recovery accompanied by increase in brain BDNF protein level
Authors: Alam John , Krakovsky Michael , Germann Ursula , Levy Aharon 
Published: April 2020

AbstractThere is unmet need for effective stroke therapies. Numerous neuroprotection attempts for acute cerebral ischemia have failed and there is growing interest in developing therapies that widen the treatment initiation window and promote functional recovery through increasing synaptic plasticity. The p38α mitogen-activated protein kinase is an already proven target for acute experimental stroke intervention and was hypothesized to also contribute to neuroinflammation-mediated impairment of recovery during the subacute phase. Neflamapimod, an orally bioavailable, brain-penetrant, potent and selective small molecule p38α inhibitor was evaluated as a subacute phase stroke treatment to promote recovery in this research study. Neflamapimod administration at two clinically relevant dose levels was initiated outside of the previously characterized neuroprotection window of less than 24 hours after stroke for p38α inhibitors to rats after transient middle cerebral artery occlusion. Continuous administration of neflamapimod, starting at 48 hours after reperfusion, significantly improved behavioral outcomes assessed by the modified neurological severity score at four- and six-weeks post stroke in a dose-dependent manner. Neflamapimod also demonstrated beneficial effects on additional measures of sensory and motor function and resulted in a dose-related increase in the terminal brain-derived neurotrophic factor protein level in both the injured and uninjured brain hemisphere. Variable interleukin-1β levels were detected in the injured brain hemisphere at study termination in a subset of the animals within every test group, implying ongoing, chronic inflammation, however, no clear neflamapimod effect on interleukin-1β production was observable. The dose-relatedin vivoefficacy of neflamapimod offers the possibility of both expanding the window for initiation of therapy after stroke and for improving recovery after a completed stroke. Since neflamapimod is already in mid-stage clinical trials for Alzheimer’s disease and related dementias, the current results make it especially attractive for evaluation in a proof-of- concept clinical trial as therapeutic to promote recovery after ischemic stroke.
OpSeF: Open source Python framework for collaborative instance segmentation of bioimages
Authors: Rasse Tobias M. , Hollandi Réka , Horváth Péter 
Published: April 2020

AbstractVarious pre-trained deep learning models for the segmentation of bioimages have been made available as ‘developer-to-end-user’ solutions. They usually require neither knowledge of machine learning nor coding skills, are optimized for ease of use, and deployability on laptops. However, testing these tools individually is tedious and success is uncertain.Here, we present the ‘Op’en ‘Se’gmentation ‘F’ramework (OpSeF), a Python framework for deep learning-based instance segmentation. OpSeF aims at facilitating the collaboration of biomedical users with experienced image analysts. It builds on the analysts’ knowledge in Python, machine learning, and workflow design to solve complex analysis tasks at any scale in a reproducible, well-documented way. OpSeF defines standard inputs and outputs, thereby facilitating modular workflow design and interoperability with other software. Users play an important role in problem definition, quality control, and manual refinement of results. All analyst tasks are optimized for deployment on Linux workstations or GPU clusters, all user tasks may be performed on any laptop in ImageJ.OpSeF semi-automates preprocessing, convolutional neural network (CNN)-based segmentation in 2D or 3D, and post-processing. It facilitates benchmarking of multiple models in parallel. OpSeF streamlines the optimization of parameters for pre- and post-processing such, that an available model may frequently be used without retraining. Even if sufficiently good results are not achievable with this approach, intermediate results can inform the analysts in the selection of the most promising CNN-architecture in which the biomedical user might invest the effort of manually labeling training data.We provide Jupyter notebooks that document sample workflows based on various image collections. Analysts may find these notebooks useful to illustrate common segmentation challenges, as they prepare the advanced user for gradually taking over some of their tasks and completing their projects independently. The notebooks may also be used to explore the analysis options available within OpSeF in an interactive way and to document and share final workflows.Currently, three mechanistically distinct CNN-based segmentation methods, the U-Net implementation used in Cellprofiler 3.0, StarDist, and Cellpose have been integrated within OpSeF. The addition of new networks requires little, the addition of new models requires no coding skills. Thus, OpSeF might soon become both an interactive model repository, in which pre-trained models might be shared, evaluated, and reused with ease.
Dynamics of theBacillus subtilisMin system
Authors: Feddersen Helge , Würthner Laeschkir , Frey Erwin , Bramkamp Marc 
Published: April 2020

SummaryDivision site selection is a vital process to ensure generation of viable offspring. In many rod-shaped bacteria a dynamic protein system, termed the Min system, acts as a central regulator of division site placement. The Min system is best studied inEscherichia coliwhere it shows a remarkable oscillation from pole to pole with a time-averaged density minimum at midcell. Several components of the Min system are conserved in the Gram-positive model organismBacillus subtilis. However, inB. subtilisit is believed that the system forms a stationary bipolar gradient from the cell poles to midcell. Here, we show that the Min system ofB. subtilislocalizes dynamically to active sites of division, often organized in clusters. We provide physical modelling using measured diffusion constants that describe the observed enrichment of the Min system at the septum. Modelling suggests that the observed localization pattern of Min proteins corresponds to a dynamic equilibrium state. Our data provide evidence for the importance of ongoing septation for the Min dynamics, consistent with a major role of the Min system to control active division sites, but not cell pole areas.
The Function Annotations of ST3GAL4 in Human LAMP1 and Lassa virus GP-C Interaction from the Perspective of Systems Virology
Authors: Chukwudozie Onyeka S. 
Published: April 2020

ABSTRACTLassa virus (LASV) is a single-stranded RNA virus that has plagued the Sub-Saharan part of Africa, precisely Nigeria where various pathogenic strains with varied genomic isoforms have been identified. The human lysosomal-associated membrane protein 1 (LAMP1) is alternately required for the micropinocytosis of LASV. Therefore, it is of interest to understand the mechanism of action of the host LAMP1 with LASV protein during infection. The role of ST3 beta-galactoside alpha-2, 3-sialyltransferase 4 (ST3GAL4) in the interaction between LASV (glycoprotein) GP-C and the human LAMP1 is relevant in this context. Deposited curated protein sequences of both LAMP1 and LASV GP-C were retrieved for the study. The ST3GAL4 associated data was constructed and analyzed from weighted network analysis to infer the function annotations and molecular mediators that characterize the LASV infection. The gene network shows that glycoprotein sialylation, sialyltransferase enzymatic activities and glycosphingolipid biosynthesis are linked with the ST3GAL4 function. However, the physical interaction of FAM 213A, CD8B molecule and proprotein convertase subtilisin/kexin type 1 inhibitor (PCSK1N) with ST3GAL4 is intriguing in this perspective. There are eleven glycosylated asparagine sequons of the human LAMP1 but only nine were assigned a sialylated glycan cap to mediate the LASV GP-C and LAMP1 interaction having exceeded a recommended glycosylation threshold of 0.5. Therefore, the sialylated glycans of the human LAMP1 are a total of 9 and these sialylated glycans mediates the molecular recognition between LASV and LAMP1. This study therefore, predicts that there is a cellular interchange betweenN-linkedglycosylation properties of the human LAMP1 and LASV glycoprotein, and sialylation functions of ST3GAL4 in LASV infectivity. Further studies and the clinical trial of this predictive model on the sialylated glycans of LAMP1 will facilitate the understanding of LASV micropinocytosis process in host cell.
Suspended multiwalled, acid-functionalized carbon nanotubes promote aggregation of the opportunistic pathogenPseudomonas aeruginosa
Authors: Kovach Kristin , Sabaraya Indu Venu , Patel Parth , Kirisits Mary Jo , Saleh Navid B. , Gordon Vernita D. 
Published: April 2020

AbstractThe increasing prevalence of carbon nanotubes (CNTs) as components of new functional materials has the unintended consequence of causing increases in CNT concentrations in aqueous environments. Aqueous systems are reservoirs for bacteria, including human and animal pathogens, that can form biofilms. At high concentrations, CNTs have been shown to display biocidal effects; however, at low concentrations, the interaction between CNTs and bacteria is more complicated, and antimicrobial action is highly dependent upon the properties of the CNTs in suspension. Here, impact of low concentrations of multiwalled CNTs (MWCNTs) on the biofilm-forming opportunistic human pathogenPseudomonas aeruginosais studied. Using phase contrast and confocal microscopy, flow cytometry, and antibiotic tolerance assays, it is found that sub-lethal concentrations (2 mg/L) of MWCNTs promote aggregation ofP. aeruginosainto multicellular clusters. However, the antibiotic tolerance of these “young” bacterial-CNT aggregates is similar to that of CNT-free cultures. Overall, our results indicate that the co-occurrence of MWCNTs andP. aeruginosain aqueous systems, which promotes the increased number and size of bacterial aggregates, could increase the dose to which humans or animals are exposed.
A model explaining mRNA level fluctuations based on activity demands and RNA age
Authors: Xu Zhongneng , Asakawa Shuichi 
Published: April 2020

ABSTRACTCellular RNA levels are usually fluctuated and are affected by many factors. However, knowledge on the fundamental relationships between RNA abundance, environmental stimuli, and RNA activities is lacking, and the effects of RNA age on RNA levels remain unknown. A model based on activity demands and RNA age was developed to explore the mechanisms of RNA level fluctuations. With single cell time-series gene expression experimental data, we could assess transcription rates, RNA degradation rates, RNA life spans, RNA demands, accumulated transcription amounts, and accumulated RNA degradation amounts by this model. The model could also predict RNA levels under simulation backgrounds, such as stimuli leading to regular oscillations in RNA abundance, stable RNA levels over time being resulted from the long shortage of total RNA activity or uncontrollable transcription, and relationship between RNA levels and protein levels. Given explaining partly mechanisms of some RNA level fluctuations by the present model, further proves and suitable applications are expected.
Effects of external hydrogen on hydrogen-assisted crack initiation in type 304 stainless steel
Authors: Chen Xingyang , Ma Linlin , Xie Haoping , Zhao Fengting , Ye Yufeng , Zhang Lin 
Published: April 2020

Purpose
The purpose of this paper is to present a crack initiation mechanism of the external hydrogen effect on type 304 stainless steel, as well as on fatigue crack propagation in the presence of hydrogen gas.

Design/methodology/approach
The effects of external hydrogen on hydrogen-assisted crack initiation in type 304 stainless steel were discussed by performing fatigue crack growth rate and fatigue life tests in 5 MPa argon and hydrogen.

Findings
Hydrogen can reduce the incubation period of fatigue crack initiation of smooth fatigue specimens and greatly promote the fatigue crack growth rate during the subsequent fatigue cycle. During the fatigue cycle, hydrogen invades into matrix through the intrusion and extrusion and segregates at the boundaries of α′ martensite and austenite. As the fatigue cycle increased, hydrogen-induced cracks would initiate along the slip bands. The crack initiation progress would greatly accelerate in the presence of hydrogen.

Originality/value
To the best of the authors’ knowledge, this paper is an original work carried out by the authors on the hydrogen environment embrittlement of type 304 stainless steel. The effects of external hydrogen and argon were compared to provide understanding on the hydrogen-assisted crack initiation behaviors during cycle loading.
Flight reconfiguration system – an emergency system of the future
Authors: Grzybowski Piotr , Szpakowska-Peas Ewelina 
Published: April 2020

Purpose
This paper aims to describe the idea and partial result of research on flight reconfiguration system (FRS) which is to be used in case of pilot incapacitation while performing the single-pilot operations for defining and guiding an aircraft to a safe destination.

Design/methodology/approach
Multiple problems with the development of emergency systems which could deal with crisis on-board occurs, e.g. definition of emergency destination which is dealing with the thread, ensuring that route to an emergency destination is safe, avoiding of air traffic and making sure that aircraft performance limitations would not be exceeded. FRS is a sophisticated hardware design, gathering data from aircraft on-board systems, commanding autopilot where to go and informing air traffic on crisis on-board. Developed algorithm analyzes data from onboard systems, internal database to calculate potential safe places and best routes to them. Multi-criteria decision-making is used to choose the best of them and execute it when needed.

Findings
Algorithms and hardware were tested in a simulated environment. An exemplary research experiment oriented on finding emergency destination and flying to it in the Software-In-The-Loop environment was presented.

Research limitations/implications
Currently, the use of the system is limited to use on-board of well-equipped CS-23 class aircraft and is limited to use in good weather conditions.

Practical implications
The use of FRS will in case of emergency constitute a new category of emergency maneuver, used for dealing with no-human pilot available on-board situations – autonomous emergency destination finding and route execution.

Originality/value
This study helps in the introduction of multi-stage decision-making to autonomously reconfigure route.
Food and cultural norms: rural mothers' selection of nutrition intake for their young children
Authors: Baloch Fozia Ahmed , Jogezai Nazir Ahmed , Mohamed Ismail Shaik Abul Malik 
Published: April 2020

PurposeThis study aimed at exploring food related cultural norms that influence rural mothers' food selection for their primary school aged children (aged 4–7 years).Design/methodology/approachThis is a qualitative study conducted in northern parts of Balochistan province of Pakistan. The Theory of Planned Behaviour (TPB) was applied as the theoretical framework of the study. Within a qualitative research method four focused group interviews with 30 rural mothers were employed to generate data.FindingsThe study found that mothers’ food selection for their children was heavily influenced by certain cultural norms that have become taboos with the passage of time. It is evident through findings that subjective norms have a greater influence on mothers' behaviour than their attitude and perceived behavioural control (PBC).Originality/valueWe ensure originality of this research paper as fewer researches have been conducted to further elaborate the link between socio-cultural norms and food selection. In particular, the influence of this close relationship on child health has been of limited consideration in a developing context. This paper has neither been published elsewhere, nor it is currently under consideration for publication in any other journal.