bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasound-Guided Procedures in Rheumatology Daily Practice
Authors: Cipolletta Edoardo , Filippucci Emilio , Incorvaia Antonella , Schettino Martina , Smerilli Gianluca , Di Battista Jacopo , Tesei Giulia , Cosatti Micaela Ana , Di Donato Eleonora , Tardella Marika , Di Matteo Andrea , Di Carlo Marco , Grassi Walter 
Published: January 2020

Background/Objective
The aims of this study were to describe in detail the ultrasound (US)-guided procedures in our daily rheumatology practice, to evaluate the feasibility and accuracy of US-guided procedures, and to test the efficacy of our disinfection protocol in preventing infectious complications.

Methods
This was a cross-sectional and monocentric study. Information regarding patients' age, sex, body mass index, rheumatic disease, US pathological findings, aspirated and/or injected anatomical site, US equipment (ie, probe type and frequency), and needle type was consecutively collected for each US-guided procedure in a third-level rheumatology center.

Results
A total of 643 US-guided procedures were performed, with a mean of 5.2 procedures per working-day. In 94.2% of the patients, only one procedure was carried out, whereas in 5.8%, more than one. The mean time was 7 ± 2.5 minutes. Ultrasound-guided procedures were highly accurate (accuracy rate higher than 95%) and safe (adverse events were reported in 0.8%). Our disinfection protocol was effective in preventing infectious complications. Probes with frequency values between 8 to 13 MHz and 20-, 21-, and 22-gauge needles were the most frequently used at shoulder, knee, wrist, elbow, and ankle level. High-frequency linear probes (ranging between 18 and 22 MHz) and 23- and 25-gauge needles were used for injecting small joints of the hands and feet. Convex low-frequency probe (2–7 MHz) and 18- and 20-gauge needles were the most used for performing hip joint aspirations and/or injections.

Conclusions
This study reports useful information for setting up a service providing US-guided procedures in rheumatology and supports the feasibility, accuracy, and safety of US-guided procedures.
Plasma activated liquids: New decontamination solutions
Authors: Tsoukou Evanthia , Bourke Paula , Boehm Daniela 
Published: January 2020

In the field of new decontaminants, there is an increasing consensus that improved disinfection of environmental surfaces is needed in patient care facilities as an important component in the overall strategy for prevention of HAI. The interaction of cold atmospheric plasma, i.e. an ionized gas, with liquids results in complex physical and chemical processes, which offer a source of short-lived and long-lived reactive chemical species that are critical for microbial inactivation. These solutions may fulfil the urgent need for new decontaminant solutions for special purposes such as disinfection of surfaces, or use as an antiseptic for body surfaces.
In this study, we explored the bactericidal effects of plasma activated liquids (PALs) on E.coli and S. aureus strains and investigated factors which influence PALs stability over time. Liquids of interest were non-complex solutions such as water and saline. An atmospheric cold plasma system using air was employed for the generation of PALs. The solutions were compared with respect to their content of long-lived reactive chemical species and bactericidal effects.
Our results documented that PALs may carry different concentrations of chemical species and maintain diverse antimicrobial properties. The bactericidal activity of these solutions demonstrated high thermal stability and could be preserved over a 6 month period through specific sub-ambient storage conditions. Investigation of the inactivation processes in relation to the PALs’ chemical composition will enhance our knowledge on how prokaryotic and eukaryotic cells respond to these, and demonstrate how PALs could be a promising treatment method for future applications, with chemical and antimicrobial stability.
Salmonella antibiotic persistence and macrophage polarisation
Authors: Majstorovic Andrea , Hill Peter W. S. , Helaine Sophie 
Published: January 2020

Salmonella enterica infections have a high incidence of relapse due in part to the high levels of antibiotic persistence. It is known that growing and non-growing (e.g. persister) Salmonella utilise the Salmonella Pathogenicity Island 2 (SPI-2) Type 3 Secretion System (T3SS) to dampen the pro-inflammatory M1 state of macrophages and push the immune cells towards an anti-inflammatory M2 state. This allows Salmonella prolonged survival in the host and facilitates relapse. However, this interplay between Salmonella survival and macrophage activation states remains incompletely understood.
Here, I present a study on the influence of the initial phenotypic state of untreated (M0), IFN-γ (M1) and IL-4/IL-10 (M2) prepolarised differentiated murine bone marrow-derived macrophages (MΦs) on the survival and proliferation of Salmonella enterica Serovar Typhimurium (S. Typhimurium). As expected, pro-inflammatory M1 MΦs kill S. Typhimurium more efficiently than M0 cells. Surprisingly, S. Typhimurium shows decreased survival within anti-inflammatory M2 MΦs compared to M0 MΦs, which appears to be SPI-2 dependent. Further investigation revealed that even though S. Typhimurium induces SPI-2 T3SS within M1 and M2 prepolarised MΦs, the timing of SPI-2 activation is affected during infection of M2 MΦs, thereby reducing the ability of bacteria to proliferate. This leads to many more antibiotic tolerant non-growing S. Typhimurium surviving to combined antibiotic and macrophage challenges in prepolarised MΦs.
Together, these results suggest that infection of M0 MΦs followed by reprogramming to M2 MΦs appears to promote the optimal conditions for S. Typhimurium proliferation; nevertheless, non-growing cells may immediately persist and survive better in prepolarised MΦs.
Ferrovibrio terrae sp. nov., isolated from soil
Authors: Ryu Dajung , Kim Minji , Han Bit , Lee Ki-Eun , Lee Byoung-Hee , Lee Eun-Young , Jung Gi-Yong , Kim So-Jeong , Park Soo-Je 
Published: January 2020

Designated strain K5T was isolated from soil on Jeju Island. The bacterium was aerobic, Gram-stain-negative, oxidase-positive, catalase-low activity, motile, short-rod shaped, opaque and formed white colonies that were circular, raised and had entire margins. Strain K5T was able to grow at 15–40 °C, pH 4–9 and at 0–2 % (w/v) NaCl concentration. Phylogenetic analysis based on its 16S rRNA gene sequences indicated that strain K5T is closely related to

Ferrovibrio soli

A15T (98.9 % sequence similarity),

Ferrovibrio denitrificans

Sp-1T (98.7 %) and

Ferrovibrio xuzhouensis

LM-6T (97.4 %). The sole respiratory quinone was determined to be ubiquinone-10. The dominant fatty acids of strain K5T were summed feature 8 (C18 : 1
ω7c / C18 : 1ω6c, 29.8 %), C19 : 0 cyclo ω8c (20.2 %) and C16 : 0 (24.4 %). DNA G+C content was 63.6 % and DNA–DNA relatedness between strain K5T and other three members of the genus

Ferrovibrio

ranged from 24 to 28 %. The major polar lipids were identified as phosphatidylglycerol, phosphatidylethanolamine and aminolipids. Moreover, polyphasic characterization revealed that strain K5T represents a novel species in the genus Ferrovibrio, for which the name Ferrovibrio terrae sp. nov. is proposed. The type strain is K5T (=KCCM 43295T=LMG 30611T).
Ultrafiltration Segregates Tissue Regenerative Stimuli Harboured Within and Independent of Extracellular Vesicles
Authors: Cooper TT , Sherman SE , Dayarathna T , Bell GI , Ma Jun , McRae DM , Lagugné-Labarthet F , Pasternak SH , Lajoie GA , Hess DA 
Published: January 2020

AbstractThe release of extracellular vesicles (EVs) from human multipotent stromal cells (MSC) has been proposed as a mechanism by which MSC mediate regenerative functionsin vivo. Our recent work has characterized MSC derived from human pancreatic tissues (Panc-MSC) that generated a tissue regenerative secretome. Despite these advancements, it remains unknown whether regenerative stimuli are released independent or within extracellular vesicles. Herein, this study demonstrates ultrafiltration is a simple method to enrich for EVs which can be injected in murine models of tissue regeneration. The enrichment of EVs from Panc-MSC conditioned media (CM) was validated using nanoscale flow cytometry and atomic force microscopy; in addition to the exclusive detection of classical EV-markers CD9, CD81, CD63 using label-free mass spectrometry. Additionally, we identified several pro-regenerative stimuli, such as WNT5A or ANGPT1, exclusive to EV-enriched CM. Endothelial cell tubule formation was enhanced in response to both Panc-MSC CM fractionsin vitroyet only intramuscular injection of EV-enriched CM demonstrated vascular regenerative functions in NOD/SCID mice with unilateral hind-limb ischemia (*<p<0.05). Furthermore, both EV-depleted and EV-enriched CM reduced hyperglycemia following intrapancreatic injection in hyperglycemic mice (**p<0.01). Collectively, understanding the functional synergy between compartments of the secretome is required to advance cell-free biotherapeutics into applications of regenerative medicine.
Can constraint closure provide a generalized understanding of community dynamics in ecosystems?
Authors: Peck Steven L. , Heiss Andrew 
Published: January 2020

AbstractSince the inception of the discipline, understanding causal complexity in ecological communities has been a challenge. Here we draw insights from recent work on constraint closure that suggests ways of grappling with ecological complexity that yield generalizable theoretical insights. Using a set of evolutionary constraints on species flow through ecological communities, which include: selection, species drift, dispersal, and speciation, combined with multispecies interactions such as mutualistic interactions, and abiotic constraints, we demonstrate how constraint closure allows communities to emerge as semi-autonomous structures. Here we develop an agent-based model to explore how evolutionary constraints provide stability to ecological communities. The model is written in Netlogo, an agent based-modeling system, with advanced tools for manipulating spatially structured models and tools for tracking pattern formation. We articulate ways that ecological pattern formation, viewed through the lens of constraint closure, informs questions about stability and turnover in community ecology. The role of the chosen constraints was clear from the simulation results. It took the shape of both inducing stability and creating conditions for a more dynamic community with increases in species turnover through time. Key ecological and evolutionary variables showed overall stability in the landscape structure when plotted against the number of constraints, suggesting that these evolutionary forces act as constraints to the flow of species in such a way that constraint closure is achieved effecting semi-autonomy.Author SummaryEcosystems are among the most complex structures studied. They comprise elements that seem both stable and contingent. The stability of these systems depends on interactions among their evolutionary history, including the accidents of organisms moving through the landscape and microhabitats of the earth, and the biotic and abiotic conditions in which they occur. When ecosystems are stable, how is that achieved? Here we look at ecosystem stability through a computer simulation model that suggests that it may depend on what constrains the system and how those constraints are structured. Specifically, if the constraints found in an ecological community form a closed loop, that allows particular kinds of feedback may give structure to the ecosystem processes for a period of time. In this simulation model, we look at how evolutionary forces act in such a way these closed constraint loops may form. This may explain some kinds of ecosystem stability. This work will also be valuable to ecological theorists in understanding general ideas of stability in such systems.
Multiscale modelling of motility wave propagation in cell migration
Authors: Khatee Hamid , Czirok Andras , Neufeld Zoltan 
Published: January 2020

AbstractThe collective motion of cell monolayers within a tissue is a fundamental biological process that occurs during tissue formation, wound healing, cancerous invasion, and viral infection. Experiments have shown that at the onset of migration, the motility is self-generated as a polarization wave starting from the leading edge of the monolayer and progressively propagates into the bulk. However, it is unclear how the propagation of this motility wave is influenced by cellular properties. Here, we investigate this using a computational model based on the Potts model coupled to the dynamics of intracellular polarization. The model captures the propagation of the polarization wave initiated at the leading edge and suggests that the cells cortex can regulate the migration modes: strongly contractile cells may depolarize the monolayer, whereas less contractile cells can form swirling movement. Cortical contractility is further found to limit the cells motility, which (i) decelerates the wave speed and the leading edge progression, and (ii) destabilises the leading edge into migration fingers. Together, our model describes how different cellular properties can contribute to the regulation of collective cell migration.
Genetic regulation of the bacterial omega-3 polyunsaturated fatty acid biosynthesis pathway
Authors: Allemann Marco N. , Allen Eric E. 
Published: January 2020

AbstractA characteristic among many marine Gammaproteobacteria is the biosynthesis and incorporation of omega-3 polyunsaturated fatty acids into membrane phospholipids. Biosynthesis of eicosapentaenoic (EPA) and/or docosahexaenoic (DHA) acids is accomplished using a polyketide/fatty acid synthase mechanism encoded by a set of five genespfaABCDE.This unique fatty acid synthesis (FAS) pathway co-exists with the canonical Type II dissociated fatty acid synthesis pathway, which is responsible for the biosynthesis of saturated, monounsaturated, and hydroxylated fatty acids used in phospholipid and lipid A biosynthesis. In this work, a genetic approach was undertaken to elucidate genetic regulation of thepfagenes in the model marine bacteriumPhotobacterium profundumSS9. Using a reporter gene fusion, we showed that expression of thepfaoperon is down regulated in response to exogenous fatty acids, particularly long chain monounsaturated fatty acids. This regulation occurs independently of the canonical fatty acid regulators, FabR and FadR, present inP. profundumSS9. Transposon mutagenesis and screening of a library of mutants identified a novel transcriptional regulator, which we have designatedpfaF, to be responsible for the observed regulation of thepfaoperon inP. profundumSS9. Gel mobility shift and DNase I footprinting assays confirmed that PfaF binds thepfaApromoter and identified the PfaF binding site.ImportanceThe production of polyunsaturated fatty acids (PUFA) by marine Gammaproteobacteria, particularly those from deep-sea environments, has been known for decades. These unique fatty acids are produced by a polyketide-type mechanism and subsequently incorporated into the phospholipid membrane. While much research has focused on the biosynthesis genes, their products and the phylogenetic distribution of these gene clusters, no prior studies have detailed the genetic regulation of this pathway. This study describes how this pathway is regulated under various culture conditions and has identified and characterized a fatty acid responsive transcriptional regulator specific to the PUFA biosynthesis pathway.
Developing an Individualized Clinical Prediction Rules of Antihypertensive Drugs: A Study Protocol Based on Real-world Practice
Authors: Hong Dongsheng , Shi Wendan , Lu Xiaoyang , Jiaying Wu , Lou Yan , Li Lu 
Published: January 2020

AbstractBackgroundHypertension is one of the most urgent public health challenges, and drug therapy is the primary method to control blood pressure for patients. However, blood pressure control rate is still poor with antihypertensive drugs use. Although Clinical Prediction Rules (CPR) is useful to help clinicians make more appropriate decisions at the point of medication, the evidence is still limited in china. The objective of this study is to develop an CPR of antihypertensive drugs in individualized application of patients based on real-world practice.MethodsA two-way cohort study has been conducted in one China’s large tertiary hospital using clinical information on patient characteristics, drug use and clinical outcome. Data extraction is through ICD-10 disease codes of hypertension from Electronic Medical Record System. Eligible patients admitted from September 2016 to August 2018 who have received at least one antihypertensive drug therapy is included. Patients were grouped into several exposure groups according to medications. COX regression model and clinical specialty survey is applied to identify Influencing Factors (IF) in different study groups, and the discriminant model was used to construct a CPR according IF. The accuracy of the CPR is analyzed by sensitivity, specificity, Youden’s index and Receiver Operating Characteristic (ROC) curve.DiscussionResult is expected to provide valuable CPR for physicians and policymakers with respect to treating hypertension according characteristic of individual patients. By developing a predictive method for clinical outcomes and treatment costs of antihypertensive medication, we expect to discriminate those patients who would profit from specific scheme of antihypertensive drugs to minimal incidence probability of costs and complications in region of china.Trial registrationThis study was registered at www.chictr.org as a primary register of the WHO International Clinical Trials Registry Platform (ICTRP), and the registered number is ChiCTR1900026339.HighlightsAlthough Clinical Prediction Rules (CPR) could recognize individual patient risk and help clinicians to make more appropriate decision at the point of medication as part of clinical decision support systems, the evidence in this respect is still limited in China.This study is first going to construct the CPR of multiple antihypertensive drugs in real world practice of China.The highlights of this study is aimed to provide a pragmatic method to support clinical decisions for patients who has received antihypertensive drugs before long-term diagnosis of hypertension in real world practice according to their characteristics that are accessible to clinicians.
Biofilms deform soft surfaces and disrupt epithelia
Authors: Cont Alice , Rossy Tamara , Al-Mayyah Zainebe , Persat Alexandre 
Published: January 2020

AbstractDuring chronic infections and in microbiota, bacteria predominantly colonize their hosts as multicellular structures called biofilms. Despite their ubiquityin vivo, we still lack a basic understanding of how they interact with biological tissues, and ultimately how they influence host physiology. A common assumption is that biofilms interact with their hosts biochemically. However, the contributions of mechanics, while being central to the process of biofilm formation, have been vastly overlooked as a factor influencing host physiology. Specifically, how biofilms form on soft, tissue-like materials remains unknown. Here we show that biofilms can deform soft substrates by transmission of internally-generated mechanical stresses. We found that biofilms from bothVibrio choleraeandPseudomonas aeruginosacan induce large deformations of soft synthetic hydrogels. Using a combination of mechanical measurements and mutants in matrix components, we found that biofilms deform their substrates by simultaneous buckling and adhesion. Specifically, mechanical constraints opposing growth causes biofilm buckling, while matrix components maintaining surface adhesion transmit buckling forces to the substrate. Finally, we demonstrate that biofilms can generate sufficient mechanical stress to deform and disrupt soft epithelial cell monolayers, suggesting that these forces can damage a host independently of typical virulence factors. Altogether, our results illustrate that forces generated by bacterial communities play an important role not only in biofilm morphogenesis but also in host physiology, suggesting a mechanical mode of infection.
Implicit Learning of Temporal Behavior in Complex Dynamic Environments
Authors: Salet Josh M. , Kruijne Wouter , van Rijn Hedderik 
Published: January 2020

AbstractHumans can automatically detect and learn to exploit repeated aspects (regularities) of the environment. Timing research suggests that such learning is not only used to anticipate what will happen, but also when. However, in timing experiments, the intervals to be timed are presented in isolation from other stimuli and explicitly cued, contrasting with naturalistic environments in which intervals are embedded in a constant stream of events and individuals are hardly aware of them. It is unclear whether laboratory findings from timing research translate to a more ecologically valid, implicit environment. Here we show in a game-like experiment, specifically designed to measure naturalistic behavior, that participants implicitly use regular intervals to anticipate future events, even when these intervals are constantly interrupted by irregular yet behaviorally relevant events. This finding extends previous research by showing that individuals not only detect such regularities but can also use this knowledge to decide when to act in a complex environment. Furthermore, this finding demonstrates that this type of learning can occur independently from the ordinal sequence of motor actions, which contrasts this work with earlier motor learning studies. Taken together, our results demonstrate that regularities in the time between events are implicitly monitored and used to predict and act on what happens when, thereby showing that laboratory findings from timing research can generalize to naturalistic environments. Additionally, with the development of our game-like experiment we demonstrate an approach to test cognitive theories in less controlled, ecologically more valid environments.
Adaptive Circuit Dynamics Across Human Cortex During Evidence Accumulation in Changing Environments
Authors: Murphy Peter R , Wilming Niklas , Hernandez-Bocanegra Diana C , Ortega Genis Prat , Donner Tobias H 
Published: January 2020

AbstractMany decisions under uncertainty entail the temporal accumulation of evidence that informs about the state of the environment. When environments are subject to hidden changes in their state, maximizing accuracy and reward requires non-linear accumulation of the evidence. How this adaptive, non-linear computation is realized in the brain is unknown. We analyzed human behavior and cortical population activity (measured with magnetoencephalography) recorded during visual evidence accumulation in a changing environment. Behavior and decision-related activity in cortical regions involved in action planning exhibited hallmarks of adaptive evidence accumulation, which could also be implemented by a recurrent cortical microcircuit. Decision dynamics in action-encoding parietal and frontal regions were mirrored in a frequency-specific modulation of the state of visual cortex that depended on pupil-linked arousal and the expected probability of change. These findings link normative decision computations to recurrent cortical circuit dynamics and highlight the adaptive nature of decision-related feedback to sensory cortex.