bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving restoration success through microsite selection: an example with planting sagebrush seedlings after wildfire
Authors: Davies Kirk W. , Bates Jon D. , Clenet Danielle
Published: February 2020

Post‐fire restoration of foundation plant species, particularly non‐sprouting shrubs, is critically needed in arid and semi‐arid rangeland, but is hampered by low success. Expensive and labor‐intensive methods, including planting seedlings, can improve restoration success. Prioritizing where these more intensive methods are applied may improve restoration efficiency. Shrubs in arid and semi‐arid environments can create resource islands under their canopies that may remain after fire. Seedlings planted post‐fire in former canopy and between canopies (interspace) may have different survival and growth. We compared planting Wyoming big sagebrush (Artemisia tridentata Nutt. ssp. wyomingensis Beetle & Young) seedlings post‐fire in former sagebrush canopy and interspace microsites at five locations. Four growing seasons after planting, seedling survival was 46 and 7% in canopy and interspace microsites, respectively. Sagebrush cover was 5.8 times greater in canopy compared to interspace microsites. Sagebrush survival and cover were likely greater because of less competition from herbaceous vegetation as well as benefiting from resource island effects in canopy microsites. Initially, post‐fire abundance of exotic annual grasses was less in canopy microsites, but by the third year post‐fire it was substantially greater in canopy microsites, indicating that resource availability to seedlings was greater, at least initially, in canopy microsites. These results suggest microsites with greater likelihood of success should be identified and then utilized to improve restoration success and efficiency. This is important as the need for restoration greatly exceeds resources available for restoration.
The UN Convention on the Law of the Sea: A governing framework for ocean acidification?
Authors: Harrould‐Kolieb Ellycia R.
Published: February 2020

Ocean acidification is a major emergent threat to the ocean, its wildlife and the goods and services they provide. While the international community has committed to ‘minimize and address’ ocean acidification as part of the Sustainable Development Goals, it is unclear how this is to be fulfilled, especially as there are no international agreements explicitly designed to tackle this issue. Ocean acidification is of relevance to the work of several global agreements and makes achieving their goals more difficult. Being largely sectoral, these agreements are restricted in their ability to address ocean acidification holistically, often unable to both minimize and address the issue. This has resulted in a very limited response to ocean acidification that is fragmented across a number of regimes. The 1982 United Nations Convention on the Law of the Sea (UNCLOS) has been identified as an agreement that could be used to regulate carbon dioxide emissions and thus mitigate ocean acidification. However, this article argues that a far more pivotal role can be played by UNCLOS, through its creation of a governing framework for ocean acidification. UNCLOS is the one Convention with a mandate broad enough to address ocean acidification in a direct, holistic manner. UNCLOS places a duty on States to both minimize and address ocean acidification through its various provisions that pertain to the protection and preservation of the marine environment and the conservation of marine living resources. The Convention establishes the framework through which ocean governance is to be implemented, which should be understood as extending to ocean acidification. Thus, UNCLOS is uniquely placed to guide a coherent international response.
Identification and definition of asthma–COPD overlap: The CanCOLD study
Authors: Barrecheguren Miriam , Pinto Lancelot , Mostafavi‐Pour‐Manshadi Seyed‐Mohammad‐Yousof , Tan Wan C. , Li Pei Z. , Aaron Shawn D. , Benedetti Andrea , Chapman Kenneth R. , Walker Brandie , Fitzgerald J. Mark , Hernandez Paul , Maltais François , Marciniuk Darcy D. , O'Donnell Denis E. , Sin Don D. , Bourbeau Jean ,   for the CanCOLD Collaborative Research Group and the Canadian Respiratory Research Network
Published: February 2020

Background and objective

Lack of consensus on diagnosis of ACO limits our understanding of the impact, management and outcomes of ACO. The present observational study aims to describe the prevalence, clinical characteristics and course of individuals with ACO based on various definitions used in clinical practice.

Methods

We included individuals with COPD from the prospective, multisite CanCOLD study and defined subjects with ACO using seven definitions commonly used in the literature.

Results

Data including questionnaires, lung function and CT scans were analysed from 522 individuals with COPD who were randomly recruited from the population. Among them, 264 fulfilled at least one of the seven definitions of ACO. Prevalence of ACO varied from 3.8% to 31%. Regardless of the definition, individuals with ACO had worse outcomes (lung function and higher percentage of fast decliners, symptoms and exacerbations, health‐related quality of life and comorbidities) than the remaining patients with COPD. Conversely, patients with non‐ACO had higher emphysema and bronchiolitis scores. The three definitions that included atopy and/or physician diagnosis of asthma identified subjects who differed significantly from patients with COPD. The two ACO definitions with post‐bronchodilator reversibility were concordant with COPD and were the least stable, with less than 50% of the patients from each group maintaining reversibility over visits.

Conclusion

Atopy and physician‐diagnosed asthma are more distinguishing characteristics to identify ACO. This finding needs to be validated using measures of airway inflammation and other specific biomarkers.
Improving Probability Judgment in Intelligence Analysis: From Structured Analysis to Statistical Aggregation
Authors: Karvetski Christopher W. , Mandel David R. , Irwin Daniel
Published: February 2020

As in other areas of expert judgment, intelligence analysis often requires judging the probability that hypotheses are true. Intelligence organizations promote the use of structured methods such as “Analysis of Competing Hypotheses” (ACH) to improve judgment accuracy and analytic rigor, but these methods have received little empirical testing. In this experiment, we pitted ACH against a factorized Bayes's theorem (FBT) method, and we examined the value of recalibration (coherentization) and aggregation methods for improving the accuracy of probability judgment. Analytic techniques such as ACH and FBT were ineffective in improving accuracy and handling correlated evidence, and ACH in fact decreased the coherence of probability judgments. In contrast, statistical postanalytic methods (i.e., coherentization and aggregation) yielded large accuracy gains. A wide range of methods for instantiating these techniques were tested. The interactions among the factors considered suggest that prescriptive theorists and interventionists should examine the value of ensembles of judgment‐support methods.
Export revenue and quality: Firm‐level evidence from developing countries
Authors: Minondo Asier
Published: February 2020

I combine firm‐level export data from eight low‐income and middle‐income countries to test the relation between export price and export revenue. Across‐firm estimations show a strong positive association between export price and export revenue. Within‐firm estimations show that firms generate larger export revenue from their high‐price products. The positive correlation between export price and export revenue is strong for manufactures, weak for primary commodities, and nonexistent for extractables. Results are robust to using an alternative quality measure and controlling for exporters’ market power.
Voters’ Knowledge of Their Representatives: The Direct and Conditioned Effects of Parliamentary Work
Authors: François Abel , Navarro Julien
Published: February 2020

This article examines factors that influence voters’ knowledge of their representatives, a key element in securing the responsiveness and accountability of parliamentarians. We argue that the parliamentary work of MPs (Members of Parliament) benefits incumbents through increased name recall, and that this relationship is conditional on: the incumbents’ candidacy; the voters’ political competence; and their ideological proximity with their representatives. Combining data on French MPs’ activities with a 2007 CSES post‐election survey enables us to test our hypotheses, while controlling for confounding factors. The empirical analysis demonstrates that some parliamentary activities increase the voters’ capacity to recall the name of their MPs. The latter are therefore incentivised to be responsive to and serve their constituents. However, we also find that voters’ political competence and ideological proximity with their MP alter the relationship between parliamentary work and name recall. This may potentially introduce some biases in the democratic process of accountability.
Recognition of the Trachypetidae stat.n. as a new extant family of Ichneumonoidea (Hymenoptera), based on molecular and morphological evidence
Authors: Quicke Donald L. J. , Austin Andrew D. , Fagan‐Jeffries Erinn P. , Hebert Paul D.N. , Butcher Buntika A.
Published: February 2020

The Trachypetinae (type genus Trachypetus Guérin de Méneville) comprise seven species of large‐bodied wasps in three genera (Cercobarcon Tobias, Megalohelcon Turner and Trachypetus) endemic to continental Australia. Historically they have been variously treated, as members of the Helconinae in the case of Megalohelcon, or as separate subfamilies (Cercobarconinae and Trachypetinae). Some 25 years ago they were united in a single subfamily, the Trachypetinae, based on a number of characters. Although there has been conflicting evidence from morphological and molecular phylogenetic studies as to how best to treat the group, there has been a growing consensus that they fall outside the rest of the Braconidae, although taxon sampling has been a limiting factor for molecular studies. We generated a molecular dataset comprising five gene fragments (nuclear 28S ribosomal rDNA, nuclear 18S, elongation factor 1‐alpha, mitochondrial 16S rDNA, and mitochondrial cytochrome oxidase subunit 1) for a taxonomically broad range of Braconidae, Ichneumonidae, trachypetines and outgroup hymenopterans including the first molecular data for the trachypetines Cercobarcon and Trachypetus obtained using specially designed internal primers. Molecular and combined molecular and morphological analyses confirm the monophyly of the Trachypetinae and robustly place them as sister to the Braconidae. Detailed morphological analysis including newly recognized characters shows that trachypetines lack several synapomorphies that define the Braconidae, and that they possess a number of symplesiomorphies absent from this family but found in some ichneumonids. We conclude that family‐level status is warranted for the group based on both molecular and morphological criteria, and hence we propose the new family, Trachypetidae Schulz stat.n. (type genus Trachypetus Guérin de Méneville), for it. As a result, the remaining extant Braconidae become clearly defined based on synapomorphies not present in Trachypetidae stat.n.

This published work has been registered on ZooBank,
http://zoobank.org/urn:lsid:urn:lsid:zoobank.org:pub:5418F709‐D724‐4F14‐89D8‐1E054D1D27D0.
Functional analysis of phospholipase Dδ family in tobacco pollen tubes
Authors: Pejchar Přemysl , Sekereš Juraj , Novotný Ondřej , Žárský Viktor , Potocký Martin
Published: February 2020

Phosphatidic acid (PA), an important signalling and metabolic phospholipid, is predominantly localized in the subapical plasma membrane (PM) of growing pollen tubes. PA can be produced from structural phospholipids by phospholipase D (PLD), but the isoforms responsible for production of PM PA were not identified yet and their functional roles remain unknown. Following genome‐wide bioinformatic analysis of the PLD family in tobacco, we focused on the pollen‐overrepresented PLDδ class. Combining live‐cell imaging, gene overexpression, lipid‐binding and structural bioinformatics, we characterized five NtPLDδ isoforms. Distinct PLDδ isoforms preferentially localize to the cytoplasm or subapical PM. Using fluorescence recovery after photobleaching, domain deletion and swapping analyses we show that membrane‐bound PLDδs are tightly bound to PM, primarily via the central catalytic domain. Overexpression analyses suggested isoform PLDδ3 as the most important member of the PLDδ subfamily active in pollen tubes. Moreover, only PLDδ3 shows significant constitutive PLD activity in vivo and, in turn, PA promotes binding of PLDδ3 to the PM. This forms a positive feedback loop leading to PA accumulation and the formation of massive PM invaginations. Tightly controlled production of PA generated by PLDδ3 at the PM is important for maintaining the balance between various membrane trafficking processes that are crucial for plant cell tip growth.
Music Theory Pedagogy: What Paul Taught Nadia
Authors: Gjerdingen Robert O.
Published: February 2020

The teaching of harmony in the United States, if judged objectively, has been a massive failure, even though a dedicated corps of fine musician-scholars labors to impart the curriculum to eager if not always adequately prepared students. These students are taught "about" harmony, as
if the topic were really about tonality or the imaginary desires of chords. The only students who can perform and create harmony at a professional level are those who learned such skills outside the academy. The situation was not always so bleak. Nadia Boulanger, for example, learned the art
of harmony from her teacher at the Paris Conservatory, Paul Vidal. Even though she was not taught roman numerals or chord functions, she learned harmony as a performative art, as something to express what was implicit in a given melody or bass. The article describes what Paul taught Nadia,
and how the incredibly high standards for crafting harmonic-contrapuntal musical fabrics at the Paris Conservatory could be mastered by students willing to memorize the intricacies of a centuries-old art.
Deformation spaces and normal forms around transversals
Authors: Bischoff Francis , Bursztyn Henrique , Lima Hudson , Meinrenken Eckhard
Published: February 2020

Given a manifold$M$with a submanifold$N$, the deformation space${\mathcal{D}}(M,N)$is a manifold with a submersion to$\mathbb{R}$whose zero fiber is the normal bundle$\unicode[STIX]{x1D708}(M,N)$, and all other fibers are equal to$M$. This article uses deformation spaces to study the local behavior of various geometric structures associated with singular foliations, with$N$a submanifold transverse to the foliation. New examples include$L_{\infty }$-algebroids, Courant algebroids, and Lie bialgebroids. In each case, we obtain a normal form theorem around$N$, in terms of a model structure over$\unicode[STIX]{x1D708}(M,N)$.
Whole-Cell Phenotypic Screening of Medicines for Malaria Venture Pathogen Box Identifies Specific Inhibitors of
Plasmodium falciparum
Late-Stage Development and Egress
Authors: Patra Alok Tanala , Hingamire Tejashri , Belekar Meenakshi A. , Xiong Aoli , Subramanian Gowtham , Bozdech Zbynek , Preiser Peter , Shanmugam Dhanasekaran , Chandramohanadas Rajesh
Published: February 2020

We report a systematic, cellular phenotype-based antimalarial screening of the Medicines for Malaria Venture Pathogen Box collection, which facilitated the identification of specific blockers of late-stage intraerythrocytic development of
Plasmodium falciparum
. First, from standard growth inhibition assays, we identified 173 molecules with antimalarial activity (50% effective concentration [EC
50
] ≤ 10 μM), which included 62 additional molecules over previously known antimalarial candidates from the Pathogen Box.
Hydrogen Peroxide-Mediated Oxygen Enrichment Eradicates Helicobacter pylori
In Vitro
and
In Vivo
Authors: Di Jia , Zhang Jun , Cao Lei , Huang Ting-ting , Zhang Jun-xia , Mi Yan-ni , Xiao Xue , Yan Ping-ping , Wu Man-li , Yao Tong , Liu Dong-zheng , Liu Jing , Cao Yong-xiao
Published: February 2020

Helicobacter pylori
is an important risk factor for gastric ulcers. However, antibacterial therapies increase the resistance rate and decrease the eradication rate of
H. pylori
. Inspired by the microaerophilic characteristics of
H. pylori
, we aimed at effectively establishing an oxygen-enriched environment to eradicate and prevent the recurrence of
H. pylori
. The effect and the mechanism of an oxygen-enriched environment in eradicating
H. pylori
and preventing the recurrence were explored
in vitro
and
in vivo
.
Assessment of Drug Resistance during Phase 2b Clinical Trials of Presatovir in Adults Naturally Infected with Respiratory Syncytial Virus
Authors: Porter Danielle P. , Guo Ying , Perry Jason , Gossage David L. , Watkins Timothy R. , Chien Jason W. , Jordan Robert
Published: February 2020

This study summarizes drug resistance analyses in 4 recent phase 2b trials of the respiratory syncytial virus (RSV) fusion inhibitor presatovir in naturally infected adults. Adult hematopoietic cell transplant (HCT) recipients, lung transplant recipients, or hospitalized patients with naturally acquired, laboratory-confirmed RSV infection were enrolled in 4 randomized, double-blind, placebo-controlled studies with study-specific presatovir dosing. Full-length RSV
F
sequences amplified from nasal swabs obtained at baseline and postbaseline were analyzed by population sequencing.
In Vitro
Activity of Ceftazidime-Avibactam against Isolates from Respiratory and Blood Specimens from Patients with Nosocomial Pneumonia, Including Ventilator-Associated Pneumonia, in a Phase 3 Clinical Trial
Authors: Stone Gregory G. , Bradford Patricia A. , Tawadrous Margaret , Taylor Dianna , Cadatal Mary Jane , Chen Zhangjing , Chow Joseph W.
Published: February 2020

Nosocomial pneumonia (NP), including ventilator-associated pneumonia (VAP), is increasingly associated with multidrug-resistant Gram-negative pathogens. This study describes the
in vitro
activity of ceftazidime-avibactam, ceftazidime, and relevant comparator agents against bacterial pathogens isolated from patients with NP, including VAP, enrolled in a ceftazidime-avibactam phase 3 trial. Gram-positive pathogens were included if coisolated with a Gram-negative pathogen.
In vitro
susceptibility was determined at a central laboratory using Clinical and Laboratory Standards Institute broth microdilution methods.
Genomic Characterization of Neisseria gonorrhoeae Strains from 2016 U.S. Sentinel Surveillance Displaying Reduced Susceptibility to Azithromycin
Authors: Schmerer Matthew W. , Abrams A. Jeanine , Seby Sandra , Thomas Jesse C. , Cartee John , Lucking Sean , Vidyaprakash Eshaw , Pham Cau D. , Sharpe Samera , Pettus Kevin , St. Cyr Sancta B. , Torrone Elizabeth A. , Kersh Ellen N. ,   Antimicrobial-Resistant Neisseria gonorrhoeae Working Group, Gernert Kim M. ,   Antimicrobial-Resistant Neisseria gonorrhoeae Working Group, Dominguez Catherine , Dominguez Catherine , Hun Sopheay , Soge Olusegun O. , Whelen A. Christian , O'Brien Pamela , Harvey Alesia , Henning Tara
Published: February 2020

In 2016, the proportion of
Neisseria gonorrhoeae
isolates with reduced susceptibility to azithromycin rose to 3.6%. A phylogenetic analysis of 334
N. gonorrhoeae
isolates collected in 2016 revealed a single, geographically diverse lineage of isolates with MICs of 2 to 16 μg/ml that carried a mosaic-like
mtr
locus, whereas the majority of isolates with MICs of ≥16 μg/ml appeared sporadically and carried 23S rRNA mutations.
Suppression of Cytotoxic T Cell Functions and Decreased Levels of Tissue-Resident Memory T Cells during H5N1 Infection
Authors: Kandasamy Matheswaran , Furlong Kevin , Perez Jasmine T. , Manicassamy Santhakumar , Manicassamy Balaji
Published: February 2020

Influenza viruses cause upper respiratory tract infections in humans. In healthy adults, seasonal influenza virus infections result in mild disease. Occasionally, influenza viruses endemic in domestic birds can cause severe and fatal disease even in healthy individuals. In avian influenza virus-infected patients, the host immune system is activated in an uncontrolled manner and is unable to control infection in a timely fashion. In this study, we investigated why the immune system fails to effectively control a modified form of avian influenza virus. Our studies show that T cell functions important for clearing virally infected cells are impaired by higher negative regulatory signals during modified avian influenza virus infection. In addition, memory T cell numbers were decreased in modified avian influenza virus-infected mice. Our studies provide a possible mechanism for the severe and prolonged disease associated with avian influenza virus infections in humans.
The African Swine Fever Virus Transcriptome
Authors: Cackett Gwenny , Matelska Dorota , Sýkora Michal , Portugal Raquel , Malecki Michal , Bähler Jürg , Dixon Linda , Werner Finn
Published: February 2020

African swine fever virus (ASFV) causes incurable and often lethal hemorrhagic fever in domestic pigs. In 2020, ASF presents an acute and global animal health emergency that has the potential to devastate entire national economies as effective vaccines or antiviral drugs are not currently available (according to the Food and Agriculture Organization of the United Nations). With major outbreaks ongoing in Eastern Europe and Asia, urgent action is needed to advance our knowledge about the fundamental biology of ASFV, including the mechanisms and temporal control of gene expression. A thorough understanding of RNAP and transcription factor function, and of the sequence context of their promoter motifs, as well as accurate knowledge of which genes are expressed when and the amino acid sequence of the encoded proteins, is direly needed for the development of antiviral drugs and vaccines.
The HLA A03 Supertype and SeveralPanSpecies Major Histocompatibility Complex Class I A Allotypes Share a Preference for Binding Positively Charged Residues in the F Pocket: Implications for Controlling Retroviral Infections
Authors: de Groot Natasja G. , Heijmans Corrine M. C. , de Ru Arnoud H. , Otting Nel , Koning Frits , van Veelen Peter A. , Bontrop Ronald E.
Published: February 2020

Most experimentally infected chimpanzees seem to control an HIV-1 infection and are therefore considered to be relatively resistant to developing AIDS. Contemporary free-ranging chimpanzees may carry SIVcpz, and there is evidence for AIDS-like symptoms in these free-ranging animals, whereas SIV infections in bonobos appear to be absent. In humans, the natural control of an HIV-1 infection is strongly associated with the presence of particular HLA class I allotypes. The ancestor of the contemporary living chimpanzees and bonobos survived a selective sweep targeting the MHC class I repertoire. We have put forward a hypothesis that this may have been caused by an ancestral retroviral infection similar to SIVcpz. Characterization of the relevant MHC allotypes may contribute to understanding the shaping of their immune repertoire. The abundant presence of MHC-A allotypes that prefer peptides with basic amino acids at the C termini suggests that these molecules may contribute to the control of retroviral infections in humans, chimpanzees, and bonobos.
Extensive Genetic Diversity of Polyomaviruses in Sympatric Bat Communities: Host Switching versus Coevolution
Authors: Tan Zhizhou , Gonzalez Gabriel , Sheng Jinliang , Wu Jianmin , Zhang Fuqiang , Xu Lin , Zhang Peisheng , Zhu Aiwei , Qu Yonggang , Tu Changchun , Carr Michael J. , He Biao
Published: February 2020

Since the discovery of murine polyomavirus in the 1950s, polyomaviruses (PyVs) have been considered highly host restricted in mammals. Sympatric bat communities commonly contain several different bat species in an ecological niche facilitating viral transmission, and they therefore represent a model to identify host-switching events of PyVs. In this study, we screened PyVs in a large number of bats in sympatric communities from diverse habitats across China. We provide evidence that cross-species bat-borne PyV transmission exists, though is limited, and that host-switching events appear relatively rare during the evolutionary history of these viruses. PyVs with close genomic identities were also identified in different bat species without host-switching events. Based on these findings, we propose an evolutionary scheme for bat-borne PyVs in which limited host-switching events occur on the background of codivergence and lineage duplication, generating the viral genetic diversity in bats.
New View on Dietary Fiber Selection for Predictable Shifts in Gut Microbiota
Authors: Cantu-Jungles T. M. , Hamaker B. R.
Published: February 2020

Dietary fibers can be utilized to shape the human gut microbiota. However, the outcomes from most dietary fibers currently used as prebiotics are a result of competition between microbes with overlapping abilities to utilize these fibers. Thus, divergent fiber responses are observed across individuals harboring distinct microbial communities. Here, we propose that dietary fibers can be classified hierarchically according to their specificity toward gut microbes. Highly specific fibers harbor chemical and physical characteristics that allow them to be utilized by only a narrow group of bacteria within the gut, reducing competition for that substrate.
Modulation of Symbiotic Compatibility by Rhizobial Zinc Starvation Machinery
Authors: Zhang Pan , Zhang Biliang , Jiao Jian , Dai Shi-Qi , Chen Wen-Xin , Tian Chang-Fu
Published: February 2020

The rhizobium-legume symbiosis contributes around 65% of biological nitrogen fixation in agriculture systems and is critical for sustainable agriculture by reducing the amount of chemical nitrogen fertilizer being used. Rhizobial inocula have been commercialized for more than 100 years, but the efficiency of inoculation can vary among legume cultivars, field sites, and years. These long-lasting challenging problems impede the establishment of a sustainable agriculture, particularly in developing countries. Here, we report that rhizobial zinc starvation machinery containing a conserved high-affinity zinc transporter and accessory components makes cumulative contributions to modulating rhizobial symbiotic compatibility. This work highlights a critical role of largely unexplored nutritional immunity in the rhizobium-legume symbiosis, which makes zinc starvation machinery an attractive target for improving rhizobial symbiotic compatibility.
Cryptococcus neoformans Chitin Synthase 3 Plays a Critical Role in Dampening Host Inflammatory Responses
Authors: Hole Camaron R. , Lam Woei C. , Upadhya Rajendra , Lodge Jennifer K.
Published: February 2020

Cryptococcus neoformansis the most common disseminated fungal pathogen in AIDS patients, resulting in ∼200,000 deaths each year. There is a pressing need for new treatments for this infection, as current antifungal therapy is hampered by toxicity and/or the inability of the host’s immune system to aid in resolution of the disease. An ideal target for new therapies is the fungal cell wall. The cryptococcal cell wall is different from the cell walls of many other pathogenic fungi in that it contains chitosan. Strains that have decreased chitosan are less pathogenic and strains that are deficient in chitosan are avirulent and can induce protective responses. In this study, we investigated the host responses to achs3Δstrain, a chitosan-deficient strain, and found that mice inoculated with thechs3Δstrain all died within 36 h and that death was associated with an aberrant hyperinflammatory immune response driven by neutrophils, indicating that chitosan is critical in modulating the immune response toCryptococcus.
Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling
Authors: Contador Carolina A. , Lo Siu-Kit , Chan Siu H. J. , Lam Hon-Ming
Published: February 2020

Nitrogen is the most limiting macronutrient for plant growth, and rhizobia are important bacteria for agriculture because they can fix atmospheric nitrogen and make it available to legumes through the establishment of a symbiotic relationship with their host plants. In this work, we studied the nitrogen fixation process in the microsymbiont
Sinorhizobium fredii
at the genome level. A metabolic model was built using genome annotation and literature to reconstruct the symbiotic form of
S. fredii
. Genes controlling the nitrogen fixation process were identified by simulating gene knockouts. Additionally, the nitrogen-fixing capacities of
S. fredii
CCBAU45436 in symbiosis with cultivated and wild soybeans were evaluated. The predictions suggested an outperformance of
S. fredii
with cultivated soybean, consistent with published experimental evidence. The reconstruction presented here will help to understand and improve nitrogen fixation capabilities of
S. fredii
and will be beneficial for agriculture by reducing the reliance on fertilizer applications.
Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of
Zetaproteobacteria
Iron Mats at Marine Hydrothermal Vents
Authors: McAllister Sean M. , Polson Shawn W. , Butterfield David A. , Glazer Brian T. , Sylvan Jason B. , Chan Clara S.
Published: February 2020

Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron oxidation gene,
cyc2
, in iron-rich hydrothermal vents, where iron-oxidizing microbes dominate. We pieced together diverse
Zetaproteobacteria
genomes, compared these genomes, and analyzed expression of
cyc2
and other hypothetical iron oxidation genes. We show that
cyc2
is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity. These findings will help us understand and potentially quantify the impacts of neutrophilic iron oxidizers in a wide variety of marine and terrestrial environments.
Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics
Authors: Alexa (Oniciuc) Elena A. , Walsh Calum J. , Coughlan Laura M. , Awad Amal , Simon Cezara A. , Ruiz Lorena , Crispie Fiona , Cotter Paul D. , Alvarez-Ordóñez Avelino
Published: February 2020

The study shows the potential of functional metagenomics analyses to uncover the diversity of functions in microbial communities prevailing in dairy products and their processing environments, evidencing that lactic acid bacteria (LAB) dominate the cheese microbiota, whereas Gram-negative microorganisms of animal or soil origin dominate the microbiota of milk and cheese-processing environments. The functional and
in silico
screening of the library allowed the identification of LAB, and especially
Lactococcus lactis
, as a relevant reservoir of antimicrobial resistance (AR) determinants in cheese. Quorum-quenching (QQ) determinants were not recovered through the execution of wet-lab function-based screenings but were detected through
in silico
sequencing-based analyses.
Posterior reversible encephalopathy syndrome associated with the use of chemotherapeutic agents: a rare complication after treatment with vinorelbine
Authors: Gil Ines , Serrazina Filipa , Pinto Miguel , Viana-Baptista Miguel
Published: February 2020

The posterior reversible encephalopathy syndrome (PRES) is a clinicoradiological syndrome characterised by a combination of headache, encephalopathy, seizures and visual disturbances, associated with high-intensity abnormalities on T2-weighted images affecting subcortical white and grey matter of the occipital and parietal lobes. Among other causes, PRES has been associated with the use of several medications including chemotherapeutic agents. Here we report a case of a 65-year-old patient with squamous cell carcinoma of the lung treated with cisplatin/vinorelbine. Following the second administration of vinorelbine, she was admitted to the hospital for a generalised seizure. Blood pressure was just slightly elevated and, except for drowsiness, she had a near-normal neurological examination. MRI corroborated the diagnosis. Vinorelbine-induced PRES has been reported only once in the literature, also in association with cisplatin. Our case underlines the role of vinorelbine and suggests that its association with cisplatin in this setting may enhance the risk of PRES.
Metastatic malignancy mimics: a rare case of traumatic splenosis mimicking intra-abdominal malignancy
Authors: Nadesalingam Vinoth , Davis Laura May , Vivian Gill , Corcoran Benjamin
Published: February 2020

We present a case of a patient, undergoing imaging for an unrelated presentation, whose adolescent abdominal trauma had caused an unrecognised disseminated intra-abdominal splenosis, resulting in an imaging presentation on CT that suggested intra-abdominal malignancy. The lack of correlative symptoms of disseminated malignancy, in addition to imaging findings suggesting previous upper abdominal trauma, led to a suggestion that the intra-abdominal lesion might represent spleen tissue. A denatured red cell scan with radio-labelled technetium-99m, allowed this tissue to be confirmed as splenic in nature, and an invasive, and potentially risky biopsy was averted.
Practice recommendations for the use of sedation in routine hospital-based colonoscopy
Authors: Dossa Fahima , Dubé Catherine , Tinmouth Jill , Sorvari Anne , Rabeneck Linda , McCurdy Bronwen R , Dominitz Jason A , Baxter Nancy N
Published: February 2020

Objective

Although sedation improves patient experience during colonoscopy, there is great jurisdictional variability in sedative practices. The objective of this study was to develop practice recommendations for the use of moderate and deep sedation in routine hospital-based colonoscopy to facilitate standardisation of practice.

Design

We recruited 32 multidisciplinary panellists to participate in a modified Delphi process to establish consensus-based recommendations for the use of sedation in colonoscopy. Panel members participated in a values assessment survey followed by two rounds of anonymous online voting on preliminary practice recommendations. An inperson meeting was held between voting rounds to facilitate consensus-building. Consensus was defined as >60% agreement/disagreement with recommendation statements; >80% agreement/disagreement was considered indicative of strong consensus.

Results

Twenty-nine panellists participated in the values assessment survey. Panellists ranked all factors presented as important to the development of practice recommendations. The factor considered most important was patient safety. Patient satisfaction, procedural efficiency, and cost were considered less important. Strong consensus was achieved for all nine practice recommendations presented to the panel. These recommendations included that all endoscopists be able to perform colonoscopy with moderate sedation, that an endoscopist and a single trained nurse are sufficient for performing colonoscopy with moderate sedation, and that anaesthesia-provided deep sedation be used for select patients.

Conclusion

The recommendations presented in this study were agreed on by a multidisciplinary group and provide guidance for the use of sedation in routine hospital-based colonoscopy. Standardised sedation practices will promote safe, effective, and efficient colonoscopy for all patients.
Randomised controlled trial to investigate the relationship between mild hypercapnia and cerebral oxygen saturation in patients undergoing major surgery
Authors: Wong Clarence , Churilov Leonid , Cowie Dean , Tan Chong Oon , Hu Raymond , Tremewen David , Pearce Brett , Pillai Param , Karalapillai Dharshi , Bellomo Rinaldo , Weinberg Laurence
Published: February 2020

Objectives

The effects of hypercapnia on regional cerebral oxygen saturation (rSO2) during surgery are unclear. We conducted a randomised controlled trial to investigate the relationship between mild hypercapnia and rSO2. We hypothesised that, compared with targeted normocapnia (TN), targeted mild hypercapnia (TMH) during major surgery would increase rSO2.

Design

A prospective, randomised, controlled trial in adult participants undergoing elective major surgery.

Setting

A single tertiary centre in Heidelberg, Victoria, Australia.

Participants

40 participants were randomised to either a TMH or TN group (20 to each).

Interventions

TMH (partial pressure of carbon dioxide in arterial blood, PaCO2, 45–55 mm Hg) or TN (PaCO235–40 mm Hg) was delivered via controlled ventilation throughout surgery.

Primary and secondary outcome measures

The primary endpoint was the absolute difference between the two groups in percentage change in rSO2from baseline to completion of surgery. Secondary endpoints included intraoperative pH, bicarbonate concentration, base excess, serum potassium concentration, incidence of postoperative delirium and length of stay (LOS) in hospital.

Results

The absolute difference between the two groups in percentage change in rSO2from the baseline to the completion of surgery was 19.0% higher in both hemispheres with TMH (p<0.001). On both sides, the percentage change in rSO2was greater in the TMH group than the TN group throughout the duration of surgery. The difference between the groups became more noticeable over time. Furthermore, postoperative delirium was higher in the TN group (risk difference 0.3, 95% CI 0.1 to 0.5, p=0.02). LOS was similar between groups (5 days vs 5 days; p=0.99).

Conclusion

TMH was associated with a stable increase in rSO2from the baseline, while TN was associated with a decrease in rSO2in both hemispheres in patients undergoing major surgery. This resulted in a clear separation of percentage change in rSO2from the baseline between TMH and TN over time. Our findings provide the rationale for larger studies on TMH during surgery.

Trial registration number

The Australian New Zealand Clinical Trials Registry (ACTRN12616000320459).
Post-traumatic stress reactions and doctor-certified sick leave after a workplace terrorist attack: Norwegian cohort study
Authors: Dale Maria Teresa Grønning , Nissen Alexander , Berthelsen Mona , Heir Trond
Published: February 2020

Objective

To explore the association between the psychosocial work environment and the risk of sick leave among governmental employees with symptom-defined post-traumatic stress disorder (PTSD) after a workplace bomb attack.

Design

A prospective study on employees who met the symptom criteria for PTSD. Questionnaire data on the psychosocial work environment 10 months after the terrorist attack was linked to registry data on doctor-certified sick leave in the period 12–22 months after the attack.

Setting

The bombing of the government ministries in Oslo, Norway, 22 July 2011.

Participants

The study sample consists of 94 Norwegian governmental employees, all with symptom-defined PTSD from the Norwegian version of the PTSD checklist (Post-traumatic Stress Disorder Checklist-Specific) measured 10 months after the attack.

Results

After adjustment for sex and severity of PTSD symptoms, predictability at work reduced the odds of sick leave (adjusted OR=0.62, 95% CI 0.40 to 0.98). Sense of control over decisions at work was associated with fewer absence days for employees with sick leave (adjusted rate ratio=0.61, 95% CI 0.38 to 0.98).

Conclusions

Employees with PTSD after workplace terrorism would benefit from control over their workplace conditions and increased predictability to reduce the risk of sick leave. The findings suggest that the work environment can facilitate employees’ work ability after stressful events, independent of severity of PTSD symptoms.
Effectiveness of a culturally adapted biopsychosocial intervention (POHON SIHAT) in improving self-efficacy in patients with diabetes attending primary healthcare clinics in Putrajaya, Malaysia: study protocol of a randomised controlled trial
Authors: Suhaimi Aida Farhana , Ibrahim Normala , Tan Kit-Aun , Silim Umi Adzlin , Moore Gaye , Ryan Brigid , Castle David J
Published: February 2020

Introduction

People with diabetes are often associated with multifaceted factors and comorbidities. Diabetes management frameworks need to integrate a biopsychosocial, patient-centred approach. Despite increasing efforts in promotion and diabetes education, interventions integrating both physical and mental health components are still lacking in Malaysia. The Optimal Health Programme (OHP) offers an innovative biopsychosocial framework to promote overall well-being and self-efficacy, going beyond education alone and has been identified as relevant within the primary care system. Following a comprehensive cultural adaptation process, Malaysia’s first OHP was developed under the name ‘Pohon Sihat’ (OHP). The study aims to evaluate the effectiveness of the mental health-based self-management and wellness programme in improving self-efficacy and well-being in primary care patients with diabetes mellitus.

Methods and analysis

This biopsychosocial intervention randomised controlled trial will engage patients (n=156) diagnosed with type 2 diabetes mellitus (T2DM) from four primary healthcare clinics in Putrajaya. Participants will be randomised to either OHP plus treatment as usual. The 2-hour weekly sessions over five consecutive weeks, and 2-hour booster session post 3 months will be facilitated by trained mental health practitioners and diabetes educators. Primary outcomes will include self-efficacy measures, while secondary outcomes will include well-being, anxiety, depression, self-care behaviours and haemoglobin A1c glucose test. Outcome measures will be assessed at baseline, immediately postintervention, as well as at 3 months and 6 months postintervention. Where appropriate, intention-to-treat analyses will be performed.

Ethics and dissemination

This study has ethics approval from the Medical Research and Ethics Committee, Ministry of Health Malaysia (NMRR-17-3426-38212). Study findings will be shared with the Ministry of Health Malaysia and participating healthcare clinics. Outcomes will also be shared through publication, conference presentations and publication in a peer-reviewed journal.

Trial registration number

NCT03601884.
Left ventricular filling pressure and survival following aortic valve replacement for severe aortic stenosis
Authors: Thaden Jeremy J , Balakrishnan Mahesh , Sanchez Jose , Adigun Rosalyn , Nkomo Vuyisile T , Eleid Mackram , Dahl Jordi , Scott Christopher , Pislaru Sorin , Oh Jae K , Schaff Hartzell , Pellikka Patricia A
Published: February 2020

Objective

To determine whether echocardiography-derived left ventricular filling pressure influences survival in patients with severe aortic stenosis (AS) undergoing aortic valve replacement (AVR).

Methods

We retrospectively reviewed 1383 consecutive patients with severe AS, normal ejection fraction and interpretable filling pressure undergoing AVR. Left ventricular filling pressure was determined according to current guidelines using mitral inflow, mitral annular tissue Doppler, estimated right ventricular systolic pressure and left atrial volume index. Cox proportional hazards regression was used to assess the influence of various parameters on mortality.

Results

Age was 75±10 years and 552 (40%) were female. Left ventricular filling pressure was normal in 325 (23%), indeterminate in 463 (33%) and increased in 595 (43%). Mean follow-up was 7.3±3.7 years, and mortality was 1.2%, 4.2% and 18.9% at 30 days and 1 and 5 years, respectively. Compared with patients with normal filling pressure, patients with increased filling pressure were older (78±9 vs 70±12, p<0.001), more often female (45% vs 35%, p=0.002) and were more likely to have New York Heart Association class III–IV symptoms (35% vs 24%, p=0.004), coronary artery disease (55% vs 42%, p<0.001) and concentric left ventricular hypertrophy (63% vs 37%, p<0.001). After correction for other factors, increased left ventricular filling pressure remained an independent predictor of mortality after successful AVR (adjusted HR 1.45 (95% CI 1.16 to 1.81), p=0.005).

Conclusions

Preoperative increased left ventricular filling pressure is common in patients with AS undergoing AVR and has important prognostic implications, regardless of symptom status. Future prospective studies should consider whether patients with increased filling pressure would benefit from earlier operation.
Clinical Impact of a Pharmacist-Led Antimicrobial Stewardship Initiative Evaluating Patients with Clostridioides Difficile Colitis
Authors: Bishop Paige A , Isache Carmen , McCarter Yvette S , Smotherman Carmen , Gautam Shiva , Jankowski Christopher A
Published: February 2020

Clostridioides difficile is the most common cause of healthcare-associated infection and gastroenteritis-associated death in the USA. Adherence to guideline recommendations for treatment of severe C. difficile infection (CDI) is associated with improved clinical success and reduced mortality. The purpose of this study was to determine whether implementation of a pharmacist-led antimicrobial stewardship program (ASP) CDI initiative improved adherence to CDI treatment guidelines and clinical outcomes. This was a single-center, retrospective, quasi-experimental study evaluating patients with CDI before and after implementation of an ASP initiative involving prospective audit and feedback in which guideline-driven treatment recommendations were communicated to treatment teams and documented in the electronic health record via pharmacy progress notes for all patients diagnosed with CDI. The primary endpoint was the proportion of patients treated with guideline adherent definitive regimens within 72 hours of CDI diagnosis. Secondary objectives were to evaluate the impact on clinical outcomes, including length of stay (LOS), infection-related LOS, 30-day readmission rates, and all-cause, in-hospital mortality. A total of 233 patients were evaluated. The proportion of patients on guideline adherent definitive CDI treatment regimen within 72 hours of diagnosis was significantly higher in the post-interventional group (pre: 42% vs post: 58%, p=0.02). No differences were observed in clinical outcomes or proportions of patients receiving laxatives, promotility agents, or proton pump inhibitors within 72 hours of diagnosis. Our findings demonstrate that a pharmacist-led stewardship initiative improved adherence to evidence-based practice guidelines for CDI treatment.