bluuebunny/crossref_metadata_2025 huggingface dataset:
A case of genotype‐3b hepatitis C virus in which the whole genome was successfully analyzed using third‐generation nanopore sequencing
Authors: Uchida Yoshihito , Kouyama Jun‐ichi , Naiki Kayoko , Uemura Hayato , Tsuji Shohei , Sugawara Kayoko , Nakao Masamitsu , Motoya Daisuke , Nakayama Nobuaki , Imai Yukinori , Tomiya Tomoaki , Mochida Satoshi
Published: March 2019

A 42‐year‐old Chinese man with chronic hepatitis C virus (HCV) infection visited our hospital for antiviral therapy. The subgenotype could not be determined using the HCV GENOTYPE Primer Kit (Institute of Immunology, Tokyo, Japan), which can identify genotype 3a HCV exclusively among genotype 3 HCV. Thus, the whole‐genome sequence of HCV was analyzed using the MinION nanopore sequencer (Oxford Nanopore Technologies, Oxford, UK), a third‐generation single‐molecule sequencing platform. Consequently, a total of 9442 bases with a 73.6 mean depth, corresponding to the sequences between nt25 and PolyU/UC were determined (LC414155.2). The similarity analysis revealed that the obtained sequence was classified into genotype 3b HCV and showed nucleotide identities from 87.6% to 93.9% with those of 12 previously reported strains. Furthermore, possible resistance‐associated substitutions in non‐structural protein (NS)3, NS5A, and NS5B based on consensus sequences of 12 genotype 3b HCV strains, including NS5A‐Y93H and NS5B‐S282 T substitutions, were absent. In conclusion, the MinION nanopore sequencer is useful for analyzing the HCV genome, especially the genomes of genotype 3 HCV strains for which standardized real‐ time PCR methods for all subgenotypes have not been established.
Experimental study and optimization of the extraction of Algerian date stones oil (Phoenix dactylifera L.) using supercritical carbon dioxide
Authors: Louaer Mehdi , Zermane Ahmed , Larkeche Ouassila , Meniai Abdeslam‐Hassen
Published: March 2019

An experimental extraction of Algerian date stones oil was carried out using supercritical carbon dioxide. Response surface methodology was used to investigate the effect of pressure (150–250 bar), temperature (313–333 K) and particles diameter (0.3–0.9 mm) on the extraction yield. The comparison of the predicted results with the experimental values confirmed the reliability of this technique. The optimum yield value was determined around 14.26% and was obtained at a pressure of 250 bar, a temperature of 333 K and particles diameter of 0.3 mm. the conventional solvent extraction using Soxhlet apparatus shows that the oil content of the date stones sample was about 16.22%. The fatty acids composition was determined using GC‐FID analysis, showing that the oleic acid was the major compound present in this oil.

Practical applications

Locally date stones are an abundant waste product of date processing industries which are rich in many valuables substances such as carbohydrates, oil, dietary fibers, vitamins, proteins, bioactive polyphenols and natural antioxidants, making them an attractive source for the extraction of bioactive compounds because of their low cost and high nutrient content. They can be used in many applications like the production of caffeine‐free coffee, food products formulation, cosmetics, and functional and medicinal supplements. They are a by‐product that can be easily collected and recycled in an economic and sustainable way. Also date stones oil is a great source of saturated, monounsaturated and polyunsaturated fatty acid acids which have several good human health benefits. The use of supercritical carbon dioxide extraction of date stones oil can be regarded as a great opportunity to develop the production of high quality date stones oil and exploit all the mentioned important properties.
Urban flood risk mapping using an optimised additive weighting methodology based on open data
Authors: Jato‐Espino Daniel , Lobo Amaya , Ascorbe‐Salcedo Agustín
Published: March 2019

Floods are one of the most common and harmful natural disasters worldwide, especially in cities, due to the high concentration of people and goods in these areas. This research aims to provide an accessible and accurate means to model risks associated with floods in urban spaces using open data about a series of susceptibility and impact contributing factors. Hence, a methodology combining geoprocessing tools, additive weighting, dependence measures, and optimisation was designed to generate spatial information, aggregating the factors according to their weights and optimising the modelling of their relationships to flood risk, respectively. The application of the proposed approach to the city of Santander (Spain) yielded a flood risk map providing an accurate assessment of the ranking of flood zones reported by its City Council. The results suggested that flood mitigation might focus on the implementation of permeable pavements, due to their ease of integration in urban environments.
Interoperability: A conceptual framework to bridge the gap between multifunctional and multisystem urban flood management
Authors: Vercruysse Kim , Dawson David A. , Wright Nigel
Published: March 2019

Urban flood management is increasingly expected to be multifunctional to integrate with the existing functioning of cities. Locally, this led to the development of sustainable urban water drainage designs, while at larger scales, blue‐green or water‐sensitive cities are considered as examples for how cities should function. Upscaling local designs to city‐scale flood resilience is not straightforward, however, due to the complexity of physical infrastructure and socio‐economic interactions within urban systems and requires “system‐of‐systems” thinking. To this end, we introduce the concept “interoperability” to guide transition from local multifunctionality to city‐scale multisystem flood management, through actively managing connections between infrastructure systems to convey, divert, and store flood water. While flood management is already based on these connections, interoperability is about explicitly emphasising them to explore and create opportunities to facilitate the integration of systems for flood management. The main research need arising from this conceptualisation is to determine how spatial data on infrastructure, environment, and social characteristics in urban areas can serve as a basis to identify opportunities and barriers for interoperability. By introducing interoperability and the research needs arising from it, a framework is created to facilitate and encourage practical thinking and discussion about system integration in urban flood management.
Atmospheric and human‐induced impacts on temporal variability of water level extremes in the Taihu Basin, China
Authors: Wang Yuefeng , Tabari Hossein , Xu Youpeng , Willems Patrick
Published: March 2019

Understanding the variation of water level extremes with their potential drivers can provide insights for flood risk management. In this study, temporal variability of water level extremes is investigated across the plain river network region of the Taihu Basin. The driving force analysis on water level extremes is mainly conducted for atmospheric (rainfall, climatic index, and tide) and anthropogenic forcing. The quantile perturbation method is employed to examine variability of extreme values and the Spearman correlation analysis to identify potential drivers of extreme water level variability. Considering water level extremes in all seasons, the 1990s have statistically significant positive anomalies, while the late 1960s to the 1970s and the 2000s have significant negative anomalies. The oscillation pattern of anomaly in summer has a higher variability than that in the other three seasons. Significant correlations are detected between the anomalies of water level extremes and rainfall (tide level) during summer and winter. Water level extremes in summer and winter have a strong connection to the Pacific Decadal Oscillation and North Atlantic Oscillation/Arctic Oscillation, respectively. Conversely, no consistent significant correlations between water level extremes and climatic indices are found in spring and autumn, which is mainly related to hydraulic structure construction and operation.
Quality of Life of Caregivers of Older Patients with Advanced Cancer
Authors: Kehoe Lee A. , Xu Huiwen , Duberstein Paul , Loh Kah Poh , Culakova Eva , Canin Beverly , Hurria Arti , Dale William , Wells Megan , Gilmore Nikesha , Kleckner Amber S. , Lund Jennifer , Kamen Charles , Flannery Marie , Hoerger Mike , Hopkins Judith O. , Liu Jane Jijun , Geer Jodi , Epstein Ron , Mohile Supriya G.
Published: March 2019

OBJECTIVES

To evaluate the relationships between aging‐related domains captured by geriatric assessment (GA) for older patients with advanced cancer and caregivers’ emotional health and quality of life (QOL).

DESIGN

In this cross sectional study of baseline data from a nationwide investigation of older patients and their caregivers, patients completed a GA that included validated tests to evaluate eight domains of health (eg, function, cognition).

SETTING

Thirty‐one community oncology practices throughout the United States.

PARTICIPANTS

Enrolled patients were aged 70 and older, had one or more GA domain impaired, and had an incurable solid tumor malignancy or lymphoma. Each could choose one caregiver to enroll.

MEASUREMENTS

Caregivers completed the Generalized Anxiety Disorder‐7, Distress Thermometer, Patient Health Questionnaire‐2 (depression), and Short Form Health Survey‐12 (SF‐12 for QOL). Separate multivariate linear or logistic regression models were used to examine the association of the number and type of patient GA impairments with caregiver outcomes, controlling for patient and caregiver covariates.

RESULTS

A total of 541 patients were enrolled, 414 with a caregiver. Almost half (43.5%) of the caregivers screened positive for distress, 24.4% for anxiety, and 18.9% for depression. Higher numbers of patient GA domain impairments were associated with caregiver depression (adjusted odds ratio [aOR] = 1.29; P < .001], caregiver physical health on SF‐12 (regression coefficient [β] = −1.24; P < .001), and overall caregiver QOL (β = −1.14; P < .01). Impaired patient function was associated with lower caregiver QOL (β = −4.11; P < .001). Impaired patient nutrition was associated with caregiver depression (aOR = 2.08; P < .01). Lower caregiver age, caregiver comorbidity, and patient distress were also associated with worse caregiver outcomes.

CONCLUSION

Patient GA impairments were associated with poorer emotional health and lower QOL of caregivers. J Am Geriatr Soc 67:969–977, 2019.
Who Will Care for the Caregivers? Increased Needs When Caring for Frail Older Adults With Cancer
Authors: Huang Li‐Wen , Smith Alexander K. , Wong Melisa L.
Published: March 2019

This editorial comments on the Clinical Investigation by Kehoe et al. in this issue.
MicroRNA‐135a‐5p reduces P2X7‐dependent rise in intracellular calcium and protects against excitotoxicity
Authors: Reigada David , Calderón‐García Andrés Ángel , Soto‐Catalán Manuel , Nieto‐Díaz Manuel , Muñoz‐Galdeano Teresa , del Águila Ángela , Maza Rodrigo M.
Published: March 2019

Excitotoxic cell death because of the massive release of glutamate and ATP contributes to the secondary extension of cellular and tissue loss following traumatic spinal cord injury (SCI). Evidence from blockage experiments suggests that over‐expression and activation of purinergic receptors, especially P2X7, produces excitotoxicity in neurodegenerative diseases and trauma of the central nervous system. We hypothesize that the down‐regulation of specific miRNAs after the SCI contributes to the over‐expression of P2X7 and that restorative strategies can be used to reduce the excitotoxic response. In the present study, we have employed bioinformatic analyses to identify microRNAs whose down‐regulation following SCI can be responsible for P2X7 over‐expression and excitotoxic activity. Additional luciferase assays validated microRNA‐135a‐5p (miR‐135a) as a posttranscriptional modulator of P2X7. Moreover, gene expression analysis in spinal cord samples from a rat SCI model confirmed that the decrease in miR‐135a expression correlated with P2X7 over‐expression after injury. Transfection of cultures of Neuro‐2a neuronal cell line with a miR‐135a inhibitory sequences (antagomiR‐135a), simulating the reduction of miR‐135a observed after SCI, resulted in the increase of P2X7 expression and the subsequent ATP‐dependent rise in intracellular calcium concentration. Conversely, a restorative strategy employing miR‐135a mimicked reduced P2X7 expression, attenuating the increase in intracellular calcium concentration that depends on this receptor and protecting cells from excitotoxic death. Therefore, we conclude that miR‐135a is a potential therapeutic target for SCI and that restoration of its expression may reduce the deleterious effects of ATP‐dependent excitotoxicity induced after a traumatic spinal cord injury.

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Investigation of the presence and variation of the ascending mental artery: Conventional dissections and ultrasonographic study
Authors: Tansatit Tanvaa , Phumyoo Thirawass , Jitaree Benrita , Sawatwong Worapat , Sahraoui Yasmina M. E.
Published: March 2019

Background

Tongue and mouth floor infarction following filler injections for chin augmentation is a rare complication that has the increase in incidence been reported.

Objective

This study investigated the arterial anastomosis between the submental and sublingual arteries that can lead to the emboli and subsequent tongue infarction during chin augmentation.

Methods

Forty‐two formaldehyde‐embalmed cadavers and four soft‐embalmed cadavers were dissected to verify the incidence and source of the ascending mental artery. Ultrasonographic study of the artery was performed in 10 healthy volunteers. Attention was paid to discriminate whether the ascending mental artery arose from the submental artery or the sublingual artery using the arch of the mylohyoid muscle as the discriminating landmark.

Results

Incidence of ascending mental artery from the sublingual artery was 7.1% in the studied population. All ascending mental arteries were 0.7 ± 0.2 mm in diameter at the mental protuberance and were branches of the submental artery that arose from the facial artery, except for two arteries that arose from the sublingual artery. Ultrasonographic study revealed that one left and one right sublingual artery from the lingual arteries penetrated the mylohyoid muscle near the midline to become the ascending mental artery in two volunteers. The ascending mental artery from the other side continued from the submental artery.

Conclusion

Findings from the cadaveric dissections and ultrasonographic study revealed that the ascending mental artery may be a branch that continues from the lingual artery, or communicates with the sublingual artery through the mouth floor.
Management of status epilepticus in children prior to medical retrieval: Deviations from the guidelines
Authors: Uppal Preena , Cardamone Michael , Webber Christopher , Briggs Nancy , Lawson John A
Published: March 2019

Aim

To evaluate the influence of adherence to treatment guidelines on outcomes in children presenting with status epilepticus (SE) using the Newborn and Paediatric Emergency Transport Service, New South Wales prospective registry.

Methods

We reviewed the treatment of children with SE, transported by the Newborn And Paediatric Emergency Transport Service to a tertiary paediatric hospital, over 1 year. We evaluated variation in management from the New South Wales clinical practice guideline.

Results

There was excessive administration of benzodiazepines (BZD) and a delay in administration of appropriate second‐line treatment of status (median 45 min). There was excessive use of BZD, with five or more doses of BZD associated with significantly higher odds for intubation.

Conclusion

There is considerable scope to improve clinician compliance with the SE clinical practice guidelines.
Are cortisol and melatonin involved in the immune modulation by the light environment in pike perch Sander lucioperca?
Authors: Baekelandt Sébastien , Mandiki Syaghalirwa N. M. , Kestemont Patrick
Published: March 2019

The pineal gland is the main organ involved in the transduction process converting environmental light information into a melatonin response. Since light environment was described as an important factor that could affect physiology of teleosts, and because melatonin is a crucial hormone regulating numerous physiological processes, we hypothesized that environmental light may act on both stress and circadian axes which in turn could influence the immune status of pike perch. Therefore, we investigated the effects of two light spectra (red and white) and two light intensities (10 and 100 lx) with a constant photoperiod 12L(8:00‐20:00)/12D on pike perch physiological and immune responses. Samples were collected at 04:00 and 16:00 at days 1 and 30 of the experiment. Stress markers, plasma melatonin levels, humoral innate immune markers, and expression of key immune genes in the head kidney were assessed. Light intensity clearly affected pike perch physiology. This included negative growth performances, increase in stress status, decrease in plasma melatonin levels, and immune depression. Light spectrum had only little influences. These results demonstrate that high stress status may have impacted melatonin production and secretion by the pineal organ. The drop in circulating melatonin and the increase in stress status may both be involved in the immune suppression.
IRMSas a tool to obtain the carbon turnover (δ13C) in organs of weaned piglets fed glutamic acid and nucleotides
Authors: Anton Dib Saleh Mayra , Sousa dos Santos Luan , Antonio Berto Dirlei , Borges Amorim Alessandro , Lívio Panhoza Tse Marcos , Eliodoro Costa Vladimir
Published: March 2019

Early weaning of piglets causes stress characterized by a decrease in feed intake followed by a decline in growth rates; thus, a fast recovery represents an essential step for proper growth of these animals. Considering thatIRMSis a potential tool for non‐destructive sampling and the fact that it provides time‐integrated estimate of assimilated and not just ingested nutrients turned possible its application to evaluate the effects of dietary nucleotides and glutamate on carbon turnover (δ13C) in organs of weanling piglets. At day 0, three piglets were slaughtered (prior to diet switch), the remaining eighty‐four piglets weaned at 21‐day‐old were randomly assigned in a complete block design with a 2 × 2 factorial arrangement of treatments (two Nu levels: 0 and 0.1% and two Glu levels: 0 and 1%), being three piglets per treatment slaughtered on trial days 3, 6, 9, 14, 21, 35 and 49. The samples were analysed byIRMSand adjusted to first‐order equation by a non‐linear regression analysis usingNLINofSAS, in order to establish exponential graphics. After that, the turnover data were submitted to analysis of variance usingGLMofSAS. The turnover value (t95%) verified for spleen was faster (p < 0.05) when glutamate was supplemented in diets. For pancreas and liver, the turnover rates were faster (p < 0.05) for the mixture of additives. However, for renal tissue, the turnover rate (t95%) was greater (p < 0.05) for the free additive diet. The results obtained suggest that the mixture of additives was more efficient to develop the digestive tract at post‐weaning phase, taking into account the functional importance of pancreas and liver for nutrients’ digestion and processing.
An E3 ubiquitin ligase fromNicotiana benthamianatargets the replicase ofBamboo mosaic virusand restricts its replication
Authors: Chen I‐Hsuan , Chang Jui‐En , Wu Chen‐Yu , Huang Ying‐Ping , Hsu Yau‐Huei , Tsai Ching‐Hsiu
Published: March 2019

One up‐regulated host gene identified previously was found involved in the infection process ofBamboo mosaic virus(BaMV), a single‐stranded positive‐sense RNA virus. The full length cDNA of this gene was cloned by 5′ and 3′‐rapid amplification of cDNA ends and found to encode a polypeptide containing a conserved really interesting new gene (RING) domain and a transmembrane domain. The gene might function as an ubiquitin E3 ligase. We designated this protein inNicotiana benthamianaas ubiquitin E3 ligase containing RING domain 1 (NbUbE3R1). Further characterization by usingTobacco rattle virus‐based virus‐induced gene silencing (loss‐of‐function) revealed that increased BaMV accumulation was in both knockdown plants and protoplasts. The gene might have a defensive role in the replication step of BaMV infection. To further inspect the functional role of NbUbE3R1 in BaMV accumulation, NbUbE3R1 was expressed inN. benthamianaplants. The wild‐type NbUbE3R1‐orange fluorescent protein (NbUbE3R1‐OFP), NbUbE3R1/△TM‐OFP (removal of the transmembrane domain) and NbUbE3R1/mRING‐OFP (mutation at the RING domain, the E2 interaction site) were transiently expressed in plants. NbUbE3R1 and its derivatives all functioned in restricting the accumulation of BaMV. The common feature of these constructs was the intact substrate‐interacting domain. Yeast two‐hybrid and co‐immunoprecipitation experiments used to determine the possible viral‐encoded substrate of NbUbE3R1 revealed the replicase of BaMV as the possible substrate. In conclusion, we identified an up‐regulated gene, NbUbE3R1 that plays a role in BaMV replication.
Giant viruses: spore‐like missing links between Rickettsia and mitochondria?
Authors: Seligmann Hervé
Published: March 2019

Phyloproteomics indicate common viral origin from ancient cells before archaea, bacteria, and eukaryota split and subsequent size and complexity reductions occurred. Further independent evidence for the cellular origin of viruses is reviewed for the virus order Megavirales, focusing on the family Poxviridae. Megavirales comprises giant viruses, double‐stranded DNA viruses whose genomes exceed some bacterial ones and large enough to parasitize large‐celled protists (amoeba). Giant viruses, virophages, and mitochondria have homologous DNA and RNA polymerases and share RNA splicing punctuation by stem–loop hairpins. Giant virus factories and amoeban mitochondria colocate, with viral proteins homologous to mitochondrial proteins specifically targeting mitochondrial inner membranes. Mitochondria share asexual budding with many bacterial endospores and membrane‐enveloped viruses. These megavirus−mitochondrion similarities are not coincidental: systematic alignment analyses have detected candidate megaviral homologs of each amoeban mitogene (including ribosomal RNAs) distributed across megaviral genomes. These candidate megaviral homologs overall follow mitogene order, and megaviral−mitogenome synteny increases with viral genome reduction. This analysis is repeated within Poxviridae, whose organellar‐like morphogenesis is reminiscent of mitochondria. More generally, the results confirm the patterns observed in Megavirales: synteny with amoeban mitogenomes increases with genome reduction. Parsimoniously interpreting this suggests Megavirales and mitochondria have a rickettsia‐like common ancestor. Megavirales could be the missing links between bacterial‐like cells and mitochondria, implying cellular‐to‐viral‐to‐subcellular macroevolution.
From farm management to bacteriophage therapy: strategies to reduce antibiotic use in animal agriculture
Authors: Kahn Laura H. , Bergeron Gilles , Bourassa Megan W. , De Vegt Bert , Gill Jason , Gomes Filomena , Malouin François , Opengart Ken , Ritter G. Donald , Singer Randall S. , Storrs Carina , Topp Edward
Published: March 2019

To reduce the use of antibiotics in animal agriculture, a number of effective or commercially viable alternatives have been implemented by food animal producers or are under development. Perhaps the most well‐established strategies are flock and herd management practices to mitigate disease introduction and spread, and, subsequently, reduce the need for antibiotic use. While vaccines in food animal production have been used to prevent both bacterial and viral diseases, but historically, most vaccines have targeted viral diseases. Though vaccines against viral diseases can help reduce the need for antibiotic use by controlling the spread of secondary bacterial infections, more recent vaccines under development specifically target bacteria. New developments in selecting and potentially tailoring bacteriophages provide a promising avenue for controlling pathogenic bacteria without the need for traditional small‐molecule antibiotics. In this article we discuss these established and emerging strategies, which are anticipated to reduce the reliance on antibiotics in food animal production and should reduce the prevalence and transmission to humans of antimicrobial resistant bacteria from these systems.
Complexities in understanding antimicrobial resistance across domesticated animal, human, and environmental systems
Authors: Graham David W. , Bergeron Gilles , Bourassa Megan W. , Dickson James , Gomes Filomena , Howe Adina , Kahn Laura H. , Morley Paul S. , Scott H. Morgan , Simjee Shabbir , Singer Randall S. , Smith Tara C. , Storrs Carina , Wittum Thomas E.
Published: March 2019

Antimicrobial resistance (AMR) is a significant threat to both human and animal health. The spread of AMR bacteria and genes across systems can occur through a myriad of pathways, both related and unrelated to agriculture, including via wastewater, soils, manure applications, direct exchange between humans and animals, and food exposure. Tracing origins and drivers of AMR bacteria and genes is challenging due to the array of contexts and the complexity of interactions overlapping health practice, microbiology, genetics, applied science and engineering, as well as social and human factors. Critically assessing the diverse and sometimes contradictory AMR literature is a valuable step in identifying tractable mitigation options to stem AMR spread. In this article we review research on the nonfoodborne spread of AMR, with a focus on domesticated animals and the environment and possible exposures to humans. Attention is especially placed on delineating possible sources and causes of AMR bacterial phenotypes, including underpinning the genetics important to human and animal health.
Antimicrobial resistance in a One Health context: exploring complexities, seeking solutions, and communicating risks
Authors: Scott H. Morgan , Acuff Gary , Bergeron Gilles , Bourassa Megan W. , Simjee Shabbir , Singer Randall S.
Published: March 2019

Four articles presented in this special issue of Annals of the New York Academy of Sciences stem from a meeting of experts on antimicrobial resistance (AMR) in food animal production hosted by the New York Academy of Sciences on May 8 and 9, 2018. The articles discuss (1) competing considerations of the criticality of different classes of antimicrobials used for human and animal health and how guidelines and regulations might result in more prudent patterns of use; (2) the increasingly recognized importance of the environment (i.e., soil, water, and air) as a reservoir of resistant bacteria and resistance genes as well as a pathway for the dissemination of AMR between human and animal host populations; (3) established and novel solutions for measuring and containing the AMR problem; and (4) effective strategies for communicating to consumers the risks of AMR spreading from food production and other nonhuman sources. The authors of this commentary served as the scientific advisory committee to the meeting.
Integration, functional differentiation and problem‐solving in multilevel governance
Authors: Trein Philipp , Thomann Eva , Maggetti Martino
Published: March 2019

The European Union (EU) is currently facing unprecedented challenges to its problem‐solving capacity, such as those represented by pressing transnational crises and by bottom‐up criticisms towards the European integration process. Moreover, the EU is said to compensate its weak input legitimacy with an enhanced problem‐solving capacity. However, the notion of problem‐solving itself has remained remarkably vague in the multilevel governance (MLG) literature. This symposium analyses problem‐solving in different MLG settings. In this introduction, we identify procedural and operational notions of problem‐solving in MLG, and present a structural framework to guide the comparative analyses of multilevel systems along the dimensions of political integration, functional differentiation and decentralization. The contributions to the symposium illustrate how structural elements of different multilevel systems shape both the policy‐making process and the politics of problem‐solving within these systems. In doing so, they pave the way for further comparative research.
Convergence and functional evolution of longirostry in crocodylomorphs
Authors: Ballell Antonio , Moon Benjamin C. , Porro Laura B. , Benton Michael J. , Rayfield Emily J.
Published: March 2019

During the Mesozoic, Crocodylomorpha had a much higher taxonomic and morphological diversity than today. Members of one particularly successful clade, Thalattosuchia, are well‐known for being longirostrine: having long, slender snouts. It has generally been assumed that Thalattosuchia owed their success in part to the evolution of longirostry, leading to a feeding ecology similar to that of the living Indian gharial, Gavialis. Here, we compare form and function of the skulls of the thalattosuchian Pelagosaurus and Gavialis using digital reconstructions of the skull musculoskeletal anatomy and finite element models to show that they had different jaw muscle arrangements and biomechanical behaviour. Additionally, the relevance of feeding‐related mandibular traits linked to longirostry in the radiation of crocodylomorph clades was investigated by conducting an evolutionary rates analysis under the variable rates model. We find that, even though Pelagosaurus and Gavialis share similar patterns of stress distribution in their skulls, the former had lower mechanical resistance. This suggests that compared to Gavialis, Pelagosaurus was unable to process large, mechanically less tractable prey, instead operating as a specialized piscivore that fed on softer and smaller prey. Secondly, innovation of feeding strategies was achieved by rate acceleration of functional characters of the mandible, a key mechanism for the diversification of certain clades like thalattosuchians and eusuchians. Different rates of functional evolution suggest divergent diversification dynamics between teleosaurids and metriorhynchids in the Jurassic.
Pathways to Paraptosis After ER Photodamage in OVCAR‐5 Cells
Authors: Kessel David
Published: March 2019

A death mode termed paraptosis is initiated by photodamage to the endoplasmic reticulum (ER). This is characterized by an extensive pattern of cytoplasmic vacuole formation and leads to a gradual loss of cytoplasm and of viability. Many photosensitizers in clinical use target sub‐cellular organelles that include the ER and can, therefore, invoke paraptosis as well as apoptosis. In this study, we explore pathways to paraptosis in OVCAR‐5, an ovarian cancer cell line of human origin. At low PDT doses, the route to paraptosis follows the pattern that occurs after chemotherapy, that is, a pattern of vacuole formation that can be suppressed by MAPK antagonists or inhibition of new protein synthesis. At PDT doses clinically pertinent for tumor eradication, the pathway to paraptosis appears to be independent of these factors. In addition to morphologic changes, translocation of the nuclear protein HMGB1(high mobility group protein B1) to the cell periphery has been described as a potential marker for drug‐induced paraptosis. This occurs to only a very minor extent after a lethal PDT dose that targets the ER. It appears that a lethal level of ER photodamage can initiate a different pathway to paraptosis, perhaps associated with ER protein cross‐linking.
Xanthene Dyes and Green LED for the Inactivation of Foodborne Pathogens in Planktonic and Biofilm States
Authors: Silva Alex Fiori , dos Santos Adriele Rodrigues , Trevisan Daliah Alves Coelho , Bonin Edineia , Freitas Camila Fabiano , Batista Andreia Farias Pereira , Hioka Noboru , Simões Manuel , Graton Mikcha Jane Martha
Published: March 2019

This study evaluated the rose bengal‐ and erythrosine‐mediated photoinactivation against Salmonella Typhimurium and Staphylococcus aureus planktonic and sessile cells using green LED as a light source. The free‐living or 2‐day‐old biofilm cells were treated with different concentrations of the photosensitizing agents and subjected to irradiation. Only 5 min photosensitization with rose bengal at 25 nmol L−1 and 75 μmol L−1 completely eliminated S. aureus and S. Typhimurium planktonic cells, respectively. Erythrosine at 500 nmol L−1 and 5 min of light exposure also reduced S. aureus planktonic cells to undetectable levels. Eradication of S. aureus biofilms was achieved when 500 μmol L−1 of erythrosine or 250 μmol L−1 of rose bengal was combined with 30 min of irradiation. Scanning electron microscopy allowed the observation of morphological changes in planktonic cells and disruption of the biofilm architecture after photodynamic treatment. The overall data demonstrate that rose bengal and erythrosine activated by green LED may be a targeted strategy for controlling foodborne pathogens in both planktonic and sessile states.
A Multicompartment SIS Stochastic Model with Zonal Ventilation for the Spread of Nosocomial Infections: Detection, Outbreak Management, and Infection Control
Authors: López‐García Martín , King Marco‐Felipe , Noakes Catherine J.
Published: March 2019

In this work, we study the environmental and operational factors that influence airborne transmission of nosocomial infections. We link a deterministic zonal ventilation model for the airborne distribution of infectious material in a hospital ward, with a Markovian multicompartment SIS model for the infection of individuals within this ward, in order to conduct a parametric study on ventilation rates and their effect on the epidemic dynamics. Our stochastic model includes arrival and discharge of patients, as well as the detection of the outbreak by screening events or due to symptoms being shown by infective patients. For each ventilation setting, we measure the infectious potential of a nosocomial outbreak in the hospital ward by means of a summary statistic: the number of infections occurred within the hospital ward until end or declaration of the outbreak. We analytically compute the distribution of this summary statistic, and carry out local and global sensitivity analysis in order to identify the particular characteristics of each ventilation regime with the largest impact on the epidemic spread. Our results show that ward ventilation can have a significant impact on the infection spread, especially under slow detection scenarios or in overoccupied wards, and that decreasing the infection risk for the whole hospital ward might increase the risk in specific areas of the health‐care facility. Moreover, the location of the initial infective individual and the protocol in place for outbreak declaration both form an interplay with ventilation of the ward.
Bayesian Modelling for Binary Outcomes in the Regression Discontinuity Design
Authors: Geneletti Sara , Ricciardi Federico , O’Keeffe Aidan G. , Baio Gianluca
Published: March 2019

The regression discontinuity (RD) design is a quasi-experimental design which emulates a randomized study by exploiting situations where treatment is assigned according to a continuous variable as is common in many drug treatment guidelines. The RD design literature focuses principally on continuous outcomes. We exploit the link between the RD design and instrumental variables to obtain an estimate for the causal risk ratio for the treated when the outcome is binary. Occasionally this risk ratio for the treated estimator can give negative lower confidence bounds. In the Bayesian framework we impose prior constraints that prevent this from happening. This is novel and cannot be easily reproduced in a frequentist framework. We compare our estimators with those based on estimating equation and generalized methods-of-moments methods. On the basis of extensive simulations our methods compare favourably with both methods and we apply our method to a real example to estimate the effect of statins on the probability of low density lipoprotein cholesterol levels reaching recommended levels.
Epidemiology of invasive fungal infections in lung transplant recipients in Western Australia
Authors: Chang Andrew , Musk Michael , Lavender Melanie , Wrobel Jeremy , Yaw Meow‐Chong , Lawrence Sharon , Chirayath Shiji , Boan Peter
Published: March 2019

Background

Invasive fungal infections (IFI) are common after lung transplantation with reported incidence of 8.1% to 16% at 12 months post‐transplant, and 3‐month all‐cause mortality after IFI of 21.7%.

Methods

We performed a retrospective study of IFI and fungal colonization in lung transplants (LTs) from November 2004 to February 2017.

Results

137 LTs were followed for a median 4.1 years (IQR 2.1‐6.2 years). In addition to nebulized amphotericin for the transplant admission to all LTs, systemic mold‐active azole was given to 80/130 (61.5%) LTs in the first 6 months post‐transplant, 57/121 (47.1%) in the period 6‐12 months after transplant, and 93/124 (75%) in the period more than 12 months post‐transplant. Mold airways colonization was found in 81 (59.1%) LTs before and 110 (80.3%) LTs after transplantation. There were 13 IFIs for an overall incidence of 2.1 per 100 person‐years, occurring at a median 583 days (IQR 182‐1110 days) post‐transplant, a cumulative incidence of 3.8% at 1 year, 7.6% at 3 years and 10.1% at 5 years post‐transplant. All‐cause 3‐month mortality after IFI was 7.7%. Aspergillus species followed by Scedosporium apiospermum and Cryptococcus species were the commonest fungi causing IFI.

Conclusions

In our cohort the rate of IFI was comparatively low, likely because of comprehensive early antifungal use and preemptive therapy at any time after transplant. Prospective studies of fungal colonization late after LT are required to determine the risks and benefits of watchful waiting compared to preemptive therapy.
Membraneless organelles: P granules in Caenorhabditis elegans
Authors: Marnik Elisabeth A. , Updike Dustin L.
Published: March 2019

Membraneless organelles are distinct compartments within a cell that are not enclosed by a traditional lipid membrane and instead form through a process called liquid‐liquid phase separation. Examples of these non‐membrane‐bound organelles include nucleoli, stress granules, P bodies, pericentriolar material and germ granules. Many recent studies have used Caenorhabditis elegans germ granules, known as P granules, to expand our understanding of the formation of these unique cellular compartments. From this work, we know that proteins with intrinsically disordered regions (IDRs) play a critical role in the process of phase separation. IDR phase separation is further tuned through their interactions with RNA and through protein modifications such as phosphorylation and methylation. These findings from C elegans, combined with work done in other model organisms, continue to provide insight into the formation of membraneless organelles and the important role they play in compartmentalizing cellular processes.
Thromboelastographic platelet mapping in dogs with complicated Babesia rossi infection
Authors: van Rooyen Liesl J. , Hooijberg Emma H. , Schoeman Johan P. , Goddard Amelia
Published: March 2019

Background

Dogs with Babesia rossi infection display a normocoagulable thromboelastogram, despite being markedly thrombocytopenic, which is purportedly due to large‐scale platelet activation. Thromboelastographic platelet mapping (TEG‐PM) evaluates individual contributions of thrombin, fibrinogen, and platelets to clot formation, and may elucidate some of the pathomechanisms of thrombocytopenia‐associated hemostatic alterations.

Objective

This study investigated potential differences in TEG‐PM variables in dogs with complicated B rossi infection compared with healthy controls, and whether these variables correlated with platelet activation indices.

Methods

The maximum amplitude (MA) following thrombin generation (MAThrombin) was determined using kaolin‐activated TEG. The TEG‐PM variables included MA following the addition of platelet agonists arachidonic acid (MAAA) and adenosine diphosphate (MAADP), and MA due to fibrin alone (MAFibrin). In addition, platelet indices and fibrinogen concentrations were determined.

Results

Thirteen dogs with complicated B rossi infection and five healthy controls were included. The median MAFibrin and fibrinogen concentrations were significantly higher (P < 0.01 for both) and median platelet count was significantly lower (P < 0.01) in the babesiosis group vs the control group. No significant differences were found for MAThrombin and MAAA/ADP. maximum amplitude due to fibrin alone was positively correlated with fibrinogen concentration (r = 0.735), mean platelet volume (r = 0.517), and mean platelet mass (r = 0.498), and negatively correlated with hematocrit (r = −0.685), platelet count (r = −0.476), and plateletcrit (r = −0.479) (P < 0.05 for all).

Conclusions

This study suggests that the presence of hyperfibrinogenemia offsets the severe thrombocytopenia associated with B rossi to result in normal thromboelastograms and lack of overt clinical bleeding.
Robust Functional Interval Observer for Multivariable Linear Systems
Authors: Meyer Luc
Published: March 2019

The study of a continuous-time multivariable linear system may not need the knowledge of the entire internal state vector, but only of a linear function of it. In this case, instead of designing a complete observer, only a functional (also called reduced order) observer is used. In this field of research, this paper focuses on robust functional cooperative interval observers. Such an observer is proposed and its properties (in particular, its convergence) are established. Then, a design procedure is given for practical use. Finally, the theoretical contributions are illustrated in examples.
System Identification Based on Output-Only Decomposition and Subspace Appropriation
Authors: Sadeqi Amirali , Moradi Shapour , Shirazi Kourosh Heidari
Published: March 2019

Output-only identification methods have been developed on a stochastic framework, but for the first time, a subspace-based approach is proposed without using geometric and statistical tools. This aids the computational efforts to be significantly reduced and the range of input sources to be extended in a much realistic manner for future output-only analyses. The approach encompasses any input type and can properly work for systems excited by inputs with finite periods. It is demonstrated that the row space of the output sequences spanned by column vectors of the decomposed orthonormal matrix is sufficient to reconstruct the observations. The transient and steady-state portions of the output row space, afterward, can be captured to reconstruct an integrated innovation model. The advantages of the algorithm are highlighted through several numerical and experimental examples comparing with the traditional subspace identification algorithms.
Predation, prey preference and reproduction of predatory mites Amblydromalus limonicus (Garman), Amblyseius herbicolus (Chant) and Neoseiulus cucumeris (Oudemans) (Mesostigmata: Phytoseiidae) on immature Sericothrips staphylinus Haliday (Thysanoptera: Thripidae), a biocontrol agent of gorse
Authors: Lam Wendy , Paynter Quentin , Zhang Zhi-Qiang
Published: March 2019

Gorse, Ulex europaeus, is an invasive weed that has serious agricultural, economic and ecological impacts. Although various biological control agents have been released in New Zealand, these have showed no noticeable impact on gorse populations. One such agent, Sericothrips staphylinus, was introduced to New Zealand in 1990 and although laboratory impact studies indicated it was a highly promising gorse biological control agent, it has not been as effective as was hoped. We hypothesized this was due to predation by natural enemies. This study investigated the predation and oviposition rates of three phytoseiid mites (Amblydromalus limonicus, Amblyseius herbicolus, and Neoseiulus cucumeris) that have been found on gorse plants in New Zealand on three S. staphylinus stages (1st instar larvae, 2nd instar larvae, and prepupa) in both choice and non-choice conditions. In non-choice conditions, A. limonicus had the highest predation and oviposition rate across all three immature stages, and N. cucumeris had the lowest. Amblydromalus  limonicus, A. herbicolus, and N. cucumeris all had their highest predation rate when consuming 1st instar larvae, and their lowest predation rate when consuming prepupa. In the choice experiment, all three predatory mite species consumed their highest proportion of 1st instar larvae, and their lowest proportion of prepupae.  The oviposition rate of all three mite species in the choice experiment was similar to the oviposition rate when presented with 1st instar larvae only. The results from this study confirm that A. limonicus, A. herbicolus, and N. cucumeris can predate and reproduce on S. staphylinus 1st instar larvae, 2nd instar larvae, and prepupa. This indicates that predation may be the reason why S. staphylinus is an ineffective biocontrol agent in New Zealand.
Experimental learning of quantum states
Authors: Rocchetto Andrea , Aaronson Scott , Severini Simone , Carvacho Gonzalo , Poderini Davide , Agresti Iris , Bentivegna Marco , Sciarrino Fabio
Published: March 2019

A photonic system is used to demonstrate that quantum states can be approximately learned using a linear number of measurements.
Labyrinth ice pattern formation induced by near-infrared irradiation
Authors: Guy Preis Shlomit , Chayet Haim , Katz Adam , Yashunsky Victor , Kaner Avigail , Ullman Shimon , Braslavsky Ido
Published: March 2019

High-power illumination of thin ice crystals drives the formation of dynamic holes and water microchannel labyrinths.
Nanoscale ferroelastic twins formed in strained LaCoO
3
films
Authors: Guo Er-Jia , Desautels Ryan , Keavney David , Roldan Manuel A. , Kirby Brian J. , Lee Dongkyu , Liao Zhaoliang , Charlton Timothy , Herklotz Andreas , Zac Ward T. , Fitzsimmons Michael R. , Lee Ho Nyung
Published: March 2019

We propose a convenient means to effectively control the physical ground state of a ferroelastic film through domain engineering.
Label-free surface-sensitive photonic microscopy with high spatial resolution using azimuthal rotation illumination
Authors: Kuai Yan , Chen Junxue , Tang Xi , Xiang Yifeng , Lu Fengya , Kuang Cuifang , Xu Liang , Shen Weidong , Cheng Junjie , Gui Huaqiao , Zou Gang , Wang Pei , Ming Hai , Liu Jianguo , Liu Xu , Lakowicz Joseph R. , Zhang Douguo
Published: March 2019

Extending SPs and BSWs for microscopy leads to imaging artifacts, which are removed by using azimuthal rotation illumination.
Clever-1 contributes to lymphocyte entry into the spleen via the red pulp
Authors: Tadayon Sina , Dunkel Johannes , Takeda Akira , Halle Olga , Karikoski Marika , Gerke Heidi , Rantakari Pia , Virtakoivu Reetta , Pabst Oliver , Salmi Marko , Hollmén Maija , Jalkanen Sirpa
Published: March 2019

Lymphocyte entry into the spleen is initiated by their binding to Clever-1–expressing vessels in the red pulp.
Geographic Mapping of Escherichia coli Susceptibility To Develop a Novel Clinical Decision Support Tool
Authors: Legenza Laurel , Barnett Susanne , Lacy James P. , See Codie , Desotell Natalee , Eibergen Andrea , Piccirillo Jeffrey F. , Rose Warren E.
Published: March 2019

Antimicrobial resistance (AMR) varies regionally. This study longitudinally maps
Escherichia coli
susceptibility leveraging Wisconsin antibiograms (
n
 = 202) collected from 2009, 2013, and 2015 to inform the development of a novel clinical decision support tool.