bluuebunny/crossref_metadata_2025 huggingface dataset:
Ir/TiONx/C high-performance oxygen evolution reaction nanocomposite electrocatalysts in acidic media: synthesis, characterization and electrochemical benchmarking protocol
Authors: Loncar Anja , Moriau Leonard , Stojanovski Kevin , Ruiz-Zepeda Francisco , Jovanovic Primoz , Bele Marjan , Gaberscek Miran , Hodnik Nejc
Published: January 2020

More efficient utilization of iridium is of immense importance for the future development of proton exchange membrane electrolyzers. In this study, we introduce a new facile and scalable synthesis of an Ir-based high-performance oxygen evolution reaction (OER) electrocatalytic nanocomposite. The composite consists of Ir nanoparticles with an average size of 3–4 nm, which are effectively anchored on a titanium oxynitride support (TiONx), which is distributed across high-surface-area Ketjen Black carbon (Ir/TiONx/C). We provide complete structural, morphological and compositional characterization (x-ray diffraction, scanning transmission electron microscopy and energy-dispersive x-ray spectroscopy) and propose a proper benchmark protocol to measure true electrochemical performance. Compared to the state-of-the-art Ir Black electrocatalyst, Ir/TiONx/C exhibits approximately three times higher OER performance.
Root flavonoids are related to enhanced AMF colonization of an invasive tree
Authors: Pei Yingchun , Siemann Evan , Tian Baoliang , Ding Jianqing
Published: January 2020

Arbuscular mycorrhizal fungi (AMF) are important mutualistic microbes in soil, which have capacity to form mutualistic associations with most land plants. Arbuscular mycorrhizal fungi play an important role in plant invasions and their interactions with invasive plants have received increasing attention. However, the chemical mechanisms underlying the interactions of AMF and invasive plants are still poorly understood. In this study we aim to test whether root secondary chemicals are related to enhanced AMF colonization and rapid growth in an invasive tree. We conducted a common garden experiment in China with Chinese tallow tree (Triadica sebifera) to examine the relationships among AMF colonization and secondary metabolites in roots of plants from introduced (USA) and native (China) populations. We found that AMF colonization rate was higher in introduced populations compared to native populations. Roots of plants from introduced populations had lower levels of phenolics and tannins, but higher levels of flavonoids than those of plants from native populations. Flavonoids were positively correlated with AMF colonization, and this relationship was especially strong for introduced populations. Besides, AMF colonization was positively correlated with plant biomass suggesting that higher root flavonoids and AMF colonization may impact plant performance. This suggests that higher root flavonoids in plants from introduced populations may promote AMF spore germination and/or attract hyphae to their roots, which may subsequently increase plant growth. Overall, our results support a scenario in which invasive plants enhance their AMF association and invasion success via genetic changes in their root flavonoid metabolism. These findings advance our understanding of the mechanisms underlying plant invasion success and the evolutionary interactions between plants and AMF. Understanding such mechanisms of invasive plant success is critical for predicting and managing plant invasions in addition to providing important insights into the chemical mechanism of AMF–plant interactions.
FilTar: using RNA-Seq data to improve microRNA target prediction accuracy in animals
Authors: Bradley Thomas , Moxon Simon
Published: January 2020

Motivation

MicroRNA (miRNA) target prediction algorithms do not generally consider biological context and therefore generic target prediction based on seed binding can lead to a high level of false-positive predictions. Here, we present FilTar, a method that incorporates RNA-Seq data to make miRNA target prediction specific to a given cell type or tissue of interest.

Results

We demonstrate that FilTar can be used to: (i) provide sample specific 3′-UTR reannotation; extending or truncating default annotations based on RNA-Seq read evidence and (ii) filter putative miRNA target predictions by transcript expression level, thus removing putative interactions where the target transcript is not expressed in the tissue or cell line of interest. We test the method on a variety of miRNA transfection datasets and demonstrate increased accuracy versus generic miRNA target prediction methods.

Availability and implementation

FilTar is freely available and can be downloaded from https://github.com/TBradley27/FilTar. The tool is implemented using the Python and R programming languages, and is supported on GNU/Linux operating systems.

Supplementary information

Supplementary data are available at Bioinformatics online.
AnnoGen: annotating genome-wide pragmatic features
Authors: Sheng Quanhu , Yu Hui , Oyebamiji Olufunmilola , Wang Jiandong , Chen Danqian , Ness Scott , Zhao Ying-Yong , Guo Yan
Published: January 2020

Motivation

Genome annotation is an important step for all in-depth bioinformatics analysis. It is imperative to augment quantity and diversity of genome-wide annotation data for the latest reference genome to promote its adoption by ongoing and future impactful studies.

Results

We developed a python toolkit AnnoGen, which at the first time, allows the annotation of three pragmatic genomic features for the GRCh38 genome in enormous base-wise quantities. The three features are chemical binding Energy, sequence information Entropy and Homology Score. The Homology Score is an exceptional feature that captures the genome-wide homology through single-base-offset tiling windows of 100 continual nucleotide bases. AnnoGen is capable of annotating the proprietary pragmatic features for variable user-interested genomic regions and optionally comparing two parallel sets of genomic regions. AnnoGen is characterized with simple utility modes and succinct HTML report of informative statistical tables and plots.

Availability and implementation

https://github.com/shengqh/annogen.
Anti-silencing factor 1A is associated with genome stability maintenance of mouse preimplantation embryos†
Authors: Deng Kai , Feng Wanyou , Liu Xiaohua , Su Xiaoping , Zuo Erwei , Du Shanshan , Huang Yongjun , Shi Deshun , Lu Fenghua
Published: January 2020

Genome stability is critical for the normal development of preimplantation embryos, as DNA damages may result in mutation and even embryo lethality. Anti-silencing factor 1A (ASF1A) is a histone chaperone and enriched in the MII oocytes as a maternal factor, which may be associated with the maintenance of genome stability. Thus, this study was undertaken to explore the role of ASF1A in maintaining the genome stability of early mouse embryos. The ASF1A expressed in the preimplantation embryos and displayed a dynamic pattern throughout the early embryonic development. Inhibition of ASF1A expression decreased embryonic development and increased DNA damages. Overexpression of ASF1A improved the developmental potential and decreased DNA damages. When 293T cells that had been integrated with RGS-NHEJ were co-transfected with plasmids of pcDNA3.1-ASF1A, gRNA-NHEJ, and hCas9, less cells expressed eGFP, indicating that non-homologous end joining was reduced by ASF1A. When 293T cells were co-transfected with plasmids of HR-donor, gRNA-HR, hCas9, and pcDNA3.1-ASF1A, more cells expressed eGFP, indicating that homologous recombination (HR) was enhanced by ASF1A. These results indicate that ASF1A may be associated with the genome stability maintenance of early mouse embryos and this action may be mediated by promoting DNA damage repair through HR pathway.
Tesmin, Metallothionein-Like 5, is Required for Spermatogenesis in Mice†
Authors: Oji Asami , Isotani Ayako , Fujihara Yoshitaka , Castaneda Julio M , Oura Seiya , Ikawa Masahito
Published: January 2020

In mammals, more than 2000 genes are specifically or abundantly expressed in testis, but gene knockout studies revealed several are not individually essential for male fertility. Tesmin (Metallothionein-like 5; Mtl5) was originally reported as a testis-specific transcript that encodes a member of the cysteine-rich motif containing metallothionein family. Later studies showed that Tesmin has two splicing variants and both are specifically expressed in male and female germ cells. Herein, we clarified that the long (Tesmin-L) and short (Tesmin-S) transcript forms start expressing from spermatogonia and the spermatocyte stage, respectively, in testis. Furthermore, while Tesmin-deficient female mice are fertile, male mice are infertile due to arrested spermatogenesis at the pachytene stage. We were able to rescue the infertility with a Tesmin-L transgene, where we concluded that TESMIN-L is critical for meiotic completion in spermatogenesis and indispensable for male fertility.
The Evolution of Corporate Accounts of Scandals From Exposure to Investigation
Authors: Gottschalk Petter , Benson Michael L
Published: January 2020

We extend research on how corporations respond to scandals by examining the evolution of the accounts that are developed by corporate agents after a scandal becomes public. Guided by the theory of accounts and a recently developed perspective on crisis management, we examine how the accounts developed by 12 corporations caught up in highly publicized scandals changed from the time of initial exposure to the issuance of an investigative report. Our analysis shows that denial of wrongdoing in several cases is replaced by admission of wrongdoing and scapegoating, while obfuscation of wrongdoing is replaced by denial or acceptance of responsibility and scapegoating. We conclude with a discussion of the broader managerial and social implications of our analysis and how it furthers our understanding of the ability of corporations to weather serious scandals.
Integrating the Familial and the Cultural: An Approach for Analysing Intergenerational Family Relationships in Social Work Practice
Authors: Koren Chaya , Simhi-Meidai Shiran
Published: January 2020

When analysing (intergenerational) family relationships for social work practice, it is often unclear what relates to familial and what to cultural bodies of knowledge. Often the conclusion is that ‘they are both’, which challenges family assessment processes. We aim to address this by suggesting an integration between the familial and the cultural, through presenting their shared parameters and constructs. This results in a non-judgemental approach for social work practice analysis. Integration is illustrated using data from a stepfamily that participated in a large qualitative study on the meaning of late-life repartnering, from an intergenerational family and multicultural perspective in Israel, as a case example. The stepfamily included both partners and an adult child and grandchild of each partner. Individual interviews were conducted with each stepfamily member separately and transcribed verbatim. In late-life repartnering, two multigenerational families with potentially diverse cultural backgrounds encounter each other late in their life history and become a stepfamily. This is especially relevant in immigration societies that practice both collectivist and individualist familial norms. A multigenerational stepfamily perspective provides a rich source for examining our familial–cultural integration approach for social work practice analysis and could be applied to other family contexts. Conclusions and implications are addressed.
Exploring the effect of Ni/Cr contents on the sheet-like NiCr-oxide-decorated CNT composites as highly active and stable catalysts for urea electrooxidation
Authors: Gan Qiuping , Wang Benzhi , Chen Judan , Tian Jianniao , Isimjan Tayirjan Taylor , Yang Xiulin
Published: January 2020

The developing high-efficiency urea fuel cells have an irreplaceable role in solving the increasingly severe environmental crisis and energy shortages. The sluggish six-electron dynamic anodic oxidation reaction is the bottleneck of the rapid progress of urea fuel-cell technology. To tackle this challenge, we select the NiCr bimetallic system due to the unique synergic effect between the Ni and the Cr. Moreover, better conductivity is assured using carbon nanotubes (CNTs) as the support. Most importantly, we use a simple hydrothermal method in catalyst preparation for easy scale-up at a low cost. The results show that the hybrid catalysts of NiCrx-oxide-CNTs with different Ni/Cr ratios show much better catalytic performance in terms of active surface area and current density as compared to that of Ni-hydro-CNTs. The optimized NiCr2-oxide-CNTs catalyst exhibits not only the largest electrochemically active surface area (ESA, 50.7 m2 g−1) and the highest urea electrocatalytic current density (115.6 mA cm−2), but also outstanding long-term stability. The prominent performance of the NiCr2-oxide-CNTs catalyst is due to the combined effect of the improved charge transfer between Ni and Cr species, the large ESA, along with an elegant balance between the oxygen-defect sites and hydrophilicity. Moreover, we have proposed a synergistically enhanced urea catalytic mechanism.
Biosecurity Dogs Detect Live Insects after Training with Odor-Proxy Training Aids: Scent Extract and Dead Specimens
Authors: Moser Ariella Y , Brown Wendy Y , Bizo Lewis A , Andrew Nigel R , Taylor Michelle K
Published: January 2020

Detector dogs could be trained to find invasive insect pests at borders before they establish in new areas. However, without access to the live insects themselves, odor training aids are needed to condition dogs to their scent. This proof-of-concept study assessed 2 potential training aids for insect detection: a scent extract and dead specimens of the target species. Using Musgraveia sulciventris (Hemiptera: Tessaratomidae) as an experimental model, gas chromatography–mass spectrometry (GC-MS) analyses were carried out to compare the chemical headspaces that make up the odors of live specimens and these 2 training aids. This was then followed by canine scent-detection testing to investigate biosecurity detector dogs’ (n = 4) responses to training in an ecologically valid context. Both the scent extract and the dead specimens shared the majority of their volatile organic compounds (VOCs) with live insects. Of the dogs trained with scent extract (n = 2), both were able to detect the live insects accurately, and of those trained with dead specimens (n = 2), one detected the live insects accurately. These findings lend support for these training aids as odor-proxies for live insects—particularly scent extract, which is a relatively novel product with the potential for broad application to facilitate and improve insect-detection training.
Discontinuing Contact Precautions for Vancomycin-Resistant Enterococcus (VRE) Is Associated With Rising VRE Bloodstream Infection Rates in Ontario Hospitals, 2009–2018: A Quasi-experimental Study
Authors: Johnstone Jennie , Shing Emily , Saedi Arezou , Adomako Kwaku , Li Ye , Brown Kevin A , Garber Gary
Published: January 2020

In Ontario, Canada, since 2012, some hospitals discontinued contact precautions for vancomycin-resistant Enterococcus (VRE). Between 2009 and 2018, there was an associated rise in VRE bloodstream infections in hospitals where contact precautions were discontinued but not in hospitals that maintained contact precautions. These data suggest contact precautions are important for hospital VRE control programs.
Impact of a Publicly Funded Herpes Zoster Immunization Program on the Burden of Disease in Ontario, Canada: A Population-based Study
Authors: Martins Diana , McCormack Daniel , Tadrous Mina , Gomes Tara , Kwong Jeffrey C , Mamdani Muhammad M , Buchan Sarah A , Antoniou Tony
Published: January 2020

Background

In September 2009, a live attenuated herpes zoster vaccine (ZVL) became available in Canada. Beginning in September 2016, ZVL was made available to all Ontario residents aged 65–70 through a publicly funded immunization program. We assessed the impact of ZVL availability and its subsequent public funding on herpes zoster burden in this population.

Methods

A population-based study of Ontario residents aged 65–70 between January 2005 and September 2018. We used interventional autoregressive integrated moving average models to examine the impact of ZVL market availability and the publicly funded ZVL program on monthly incidence rate of medically attended herpes zoster, defined as an outpatient visit for herpes zoster with a prescription for a herpes zoster antiviral dispensed ≤5 days before or after the visit, or a herpes zoster–related emergency department (ED) visit or hospitalization. In secondary analyses, we examined impacts on any herpes zoster–related ED visits and hospitalizations.

Results

We found no association between ZVL market availability and monthly incidence of herpes zoster (P = .32) or monthly rates of ED visits and hospitalizations (P = .88). Conversely, the introduction of publicly funded ZVL reduced the monthly rate of medically attended herpes zoster by 19.1% (from 4.8 to 3.8 per 10 000 population; P < .01) and herpes zoster–related ED visits and hospitalizations by 38.2% (from 1.7 to 1.0 per 10 000 population; P < .05).

Conclusions

The introduction of a publicly funded immunization program for herpes zoster was associated with reduced disease burden and related acute healthcare service use.
Nasopharyngeal Microbiota Profiles in Rural Venezuelan Children Are Associated With Respiratory and Gastrointestinal Infections
Authors: Verhagen Lilly M , Rivera-Olivero Ismar A , Clerc Melanie , Chu Mei Ling J N , van Engelsdorp Gastelaars Jody , Kristensen Maartje I , Berbers Guy A M , Hermans Peter W M , de Jonge Marien I , de Waard Jacobus H , Bogaert Debby
Published: January 2020

Background

Recent research suggests that the microbiota affects susceptibility to both respiratory tract infections (RTIs) and gastrointestinal infections (GIIs). In order to optimize global treatment options, it is important to characterize microbiota profiles across different niches and geographic/socioeconomic areas where RTI and GII prevalences are high.

Methods

We performed 16S sequencing of nasopharyngeal swabs from 209 Venezuelan Amerindian children aged 6 weeks–59 months who were participating in a 13-valent pneumococcal conjugate vaccine (PCV13) study. Using random forest models, differential abundance testing, and regression analysis, we determined whether specific bacteria were associated with RTIs or GIIs and variation in PCV13 response.

Results

Microbiota compositions differed between children with or without RTIs (P = .018) or GIIs (P = .001). Several species were associated with the absence of infections. Some of these health-associated bacteria are also observed in developed regions, such as Corynebacterium (log2(fold change [FC]) = 3.30 for RTIs and log2(FC) = 1.71 for GIIs), while others are not commonly observed in developed regions, such as Acinetobacter (log2(FC) = 2.82 and log2(FC) = 5.06, respectively). Klebsiella spp. presence was associated with both RTIs (log2(FC) = 5.48) and GIIs (log2(FC) = 7.20).

Conclusions

The nasopharyngeal microbiota of rural Venezuelan children included several bacteria that thrive in tropical humid climates. Interestingly, nasopharyngeal microbiota composition not only differed in children with an RTI but also in those with a GII, which suggests a reciprocal interplay between the 2 environments. Knowledge of region-specific microbiota patterns enables tailoring of preventive and therapeutic approaches.
Homotypic and Heterotypic Protection and Risk of Reinfection Following Natural Norovirus Infection in a Highly Endemic Setting
Authors: Chhabra Preeti , Rouhani Saba , Browne Hannah , Peñataro Yori Pablo , Siguas Salas Mery , Paredes Olortegui Maribel , Moulton Lawrence H , Kosek Margaret N , Vinjé Jan
Published: January 2020

Background

Norovirus is a leading cause of acute gastroenteritis worldwide, yet there is limited information on homotypic or heterotypic protection following natural infection to guide vaccine development.

Methods

A total of 6020 stools collected from 299 Peruvian children between 2010 and 2014 were tested by norovirus real-time reverse-transcription polymerase chain reaction followed by sequence-based genotyping. Cox proportional hazards models were used to derive adjusted hazard ratios (HRs) of infection among children with vs without prior exposure.

Results

Norovirus was detected in 1288 (21.3%) samples. GII.4 (26%), GII.6 (19%), and GI.3 (9%) viruses accounted for 54% of infections. Homotypic protection for GI.3 (HR, 0.35; P = .015), GI.7 (HR, 0.19; P = .022), GII.4 (HR, 0.39; P < .001), and GII.6 (HR, 0.52; P = .006) infections was observed. Hazard analysis showed that children with prior GII.4 infection exhibited heterotypic protection with a 48% reduction of subsequent GI.3 infection (HR, 0.52; P = .005). Prior exposure to GI.3, GII.2, and GII.17 infections enhanced susceptibility to subsequent infections with several other norovirus genotypes.

Conclusions

Children up to 2 years of age infected with GII.4 noroviruses demonstrated both homotypic and heterotypic protection to reinfection with other genotypes. These data support the need for ongoing vaccine development efforts with GII.4 as the main component and caution the inclusion of genotypes that may enhance susceptibility to infections.
Joubert syndrome diagnosed renally late
Authors: Collard Elizabeth , Byrne Catherine , Georgiou Michalis , Michaelides Michel , Dixit Abhijit
Published: January 2020

Joubert syndrome is a genetically heterogeneous multisystem disorder typically diagnosed in childhood. Nephronophthisis is the most common renal pathology in Joubert syndrome, and renal failure usually occurs in childhood or in young adults. We report a 61-year-old female diagnosed with AHI1-related oculorenal Joubert syndrome, who presented initially with decline in renal function in her 50s. Our report describes exceptionally late presentation of renal disease in Joubert syndrome and highlights the importance of continued renal function monitoring in older adults with Joubert syndrome.
PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding
Authors: Banchi Elisa , Ametrano Claudio G , Greco Samuele , Stanković David , Muggia Lucia , Pallavicini Alberto
Published: January 2020

DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called ‘better clustering for QIIME’ (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100 224 sequences), PLANiTS2 (96 771 sequences) and PLANiTS (97 550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering.

Database URL: https://github.com/apallavicini/bc4q; https://github.com/apallavicini/PLANiTS.
In vivo relationship between near-infrared spectroscopy-detected lipid-rich plaques and morphological plaque characteristics by optical coherence tomography and intravascular ultrasound: a multimodality intravascular imaging study
Authors: Zanchin Christian , Ueki Yasushi , Losdat Sylvain , Fahrni Gregor , Daemen Joost , Ondracek Anna S , Häner Jonas D , Stortecky Stefan , Otsuka Tatsuhiko , Siontis George C M , Rigamonti Fabio , Radu Maria , Spirk David , Kaiser Christoph , Engstrom Thomas , Lang Irene , Koskinas Konstantinos C , Räber Lorenz
Published: January 2020

Aims

We assessed morphological features of near-infrared spectroscopy (NIRS)-detected lipid-rich plaques (LRPs) by using optical coherence tomography (OCT) and intravascular ultrasound (IVUS).

Methods and results

IVUS-NIRS and OCT were performed in the two non-infarct-related arteries (non-IRAs) in patients undergoing percutaneous coronary intervention for treatment of an acute coronary syndrome. A lesion was defined as the 4 mm segment with the maximum amount of lipid core burden index (maxLCBI4mm) of each LRP detected by NIRS. We divided the lesions into three groups based on the maxLCBI4mm value: <250, 250–399, and ≥400. OCT analysis and IVUS analysis were performed blinded for NIRS. We measured fibrous cap thickness (FCT) by using a semi-automated method. A total of 104 patients underwent multimodality imaging of 209 non-IRAs. NIRS detected 299 LRPs. Of those, 41% showed a maxLCBI4mm <250, 39% a maxLCBI4mm 251–399, and 19% a maxLCBI4mm ≥400. LRPs with a maxLCBI4mm ≥400, as compared with LRPs with a maxLCBI4mm 250–399 and <250, were more frequently thin-cap fibroatheroma (TCFA) (42.1% vs. 5.1% and 0.8%; P < 0.001) with a smaller minimum FCT (80 μm vs. 110 μm and 120 μm; P < 0.001); a higher IVUS-derived percent atheroma volume (53% vs. 53% and 44%; P < 0.001) and a higher remodelling index (1.08 vs. 1.02 and 1.01; P < 0.001). MaxLCBI4mm correlated with OCT-derived FCT (r = 0.404; P < 0.001) and was the best predictor for TCFA with an optimal cut-off value of 401 (area under the curve = 0.882; P < 0.001).

Conclusion

LRPs with increasing maxLCBI4mm exhibit OCT and IVUS features of presumed plaque vulnerability including TCFA morphology, increased plaque burden, and positive remodelling.
Very short vs. long dual antiplatelet therapy after second generation drug-eluting stents in 35 785 patients undergoing percutaneous coronary interventions: a meta-analysis of randomized controlled trials
Authors: Benenati Stefano , Galli Mattia , De Marzo Vincenzo , Pescetelli Fabio , Toma Matteo , Andreotti Felicita , Bona Roberta Della , Canepa Marco , Ameri Pietro , Crea Filippo , Porto Italo
Published: January 2020

Aim

To provide an updated assessment of the efficacy–safety profile of very short (1 or 3 months) dual antiplatelet therapy (DAPT) compared with long (12 months) DAPT in patients undergoing percutaneous coronary interventions (PCIs).

Methods and results

Seven randomized controlled trials (RCTs) comparing very short vs. long DAPT in 35 785 patients undergoing PCI were selected. The primary efficacy endpoint was major adverse cardiovascular events (MACE) and the primary safety endpoint trial-defined major bleeding through at least 1 year. Compared with longer duration, very short DAPT yielded comparable rates of MACE [odds ratio (OR) 0.93, 95% confidence interval (CI) 0.84–1.03, P = 0.19], all-cause mortality (OR 0.92, 95% CI 0.80–1.06, P = 0.25), myocardial infarction (OR 1.01, 95% CI 0.88–1.15, P = 0.91), stroke (OR 1.04, 95% CI 0.72–1.50, P = 0.83), stent thrombosis (OR 1.05, 95% CI 0.80–1.37, P = 0.73), target vessel revascularization (OR 0.99, 95% CI 0.82–1.18, P = 0.89), and comparable net clinical benefit (OR 0.92, 95% CI 0.84–1.01, P = 0.08). Very short DAPT was associated with reduced rates of major bleeding (OR 0.61, 95% CI 0.40–0.94, P = 0.03) or any bleeding (OR 0.65, 95% CI 0.47–0.90, P = 0.009). Subgroup analyses showed consistent results for 1 vs. 3 month DAPT and for aspirin vs. P2Y12 inhibitor monotherapy following very short DAPT.

Conclusions

Compared with long DAPT, very short DAPT did not increase the odds of ischaemic complications, while reducing the odds of major or any bleeding by over 30%.
Molecular identification of bronchopulmonary neuroendocrine tumours and neuroendocrine genotype in lung neoplasia using the NETest liquid biopsy
Authors: Filosso Pier Luigi , Öberg Kjell , Malczewska Anna , Lewczuk Anna , Roffinella Matteo , Aslanian Harry , Bodei Lisa
Published: January 2020

OBJECTIVES

Diagnosing lung neuroendocrine neoplasia (NEN) requires a biopsy or an operation. We evaluated a ‘liquid biopsy’ (NETest) as an in vitro diagnostic tool for identifying NEN and compared it to chromogranin A (CgA).

METHODS

We identified 4 study cohorts: patients with bronchopulmonary carcinoids (n = 99, including 62 typical and 37 atypical carcinoids), lung cancers [n = 101, including 41 adenocarcinomas, 37 squamous carcinomas (SQC), 16 small-cell lung cancers and 7 large-cell neuroendocrine carcinomas]; benign disease (50 idiopathic pulmonary fibrosis) and healthy controls (n = 102). Transcript levels measured quantitatively (activity scores: 0–100) were compared to CgA (enzyme-linked immunosorbent assay; normal < 109 ng/ml) levels.

RESULTS

The results of the NETest were positive (>20) in 94% of patients with bronchopulmonary carcinoid compared to 8% of the controls (Fisher’s exact test; P < 0.001) and were significantly more accurate as a diagnostic test (McNemar’s test; P < 0.001, χ2 = 72) than was CgA (positive: 19% bronchopulmonary carcinoid, 15% controls). Small-cell lung cancers (87%), large-cell neuroendocrine carcinomas (86%), adenocarcinoma (42%) and SQC (35%) were also NETest-positive. Increasing the NETest cut-off score to >40 was useful for detecting all NENs and differentiating these tumours from either controls/benign lung diseases (specificity 97%) or adenocarcinoma/SQC (specificity 94%). CgA was positive in 15–44% irrespective of pathology and had no diagnostic value.

CONCLUSIONS

A gene-based liquid biopsy is an effective and accurate method for diagnosing lung tumours with neuroendocrine gene expression. CgA has no value. An NETest score >40 provides an accurate (94–97%) rule-in for the diagnosis of NEN and a rule-out for benign and other neoplastic diseases. Because neuroendocrine gene expression is associated with a poor prognosis, NETest levels may have utility both in the diagnosis of and the treatment stratification for lung neoplasia.
Mapping pre-dissection aortic wall abnormalities: a multiparametric assessment
Authors: Houben Ignas B , Nama Nitesh , Moll Frans L , van Herwaarden Joost A , Nordsletten David A , Williams David M , Patel Himanshu J , Figueroa C Alberto , Burris Nicholas S
Published: January 2020

OBJECTIVES

Maximal aortic diameter is commonly used to assess aortic risk but poorly predicts the timing and location of dissection events in patients with connective tissue disease who undergo regular imaging surveillance. Hence, we aimed to use available surveillance computed tomography angiography (CTA) scans to investigate the correlation between 3-dimensional (3D) growth and cyclic transmural wall stress with the location of intimal tear formation.

METHODS

Three type B aortic dissection patients with 2 available electrocardiogram (ECG)-gated pre-dissection CTA scans and without surgical repair during the pre-dissection interval were retrospectively identified at our institution. Vascular deformation mapping was used to measure 3D aortic growth between 2 pre-dissection clinical CTA studies. In addition, we performed a computational analysis to estimate cyclic transmural wall stress in patient-specific baseline CTA geometries.

RESULTS

In all 3 connective tissue disease patients, the site of type B aortic intimal tear co-localized with areas of peak 3D aortic wall growth. Aortic growth was detected by clinical radiological assessment in only 1 case. Co-localization of peak transmural stress and the site of intimal tear formation were found in all cases.

CONCLUSIONS

Focal areas of growth and transmural wall stress co-localized with the site of intimal tear formation. These hypothesis-generating results suggest a possible new analytic pathway for a more sophisticated assessment of the factors leading to the initiation of dissection in patients with connective tissue disease. These methods could improve on current risk-stratification techniques.
Prediction of sudden cardiac death in Japanese heart failure patients: international validation of the Seattle Proportional Risk Model
Authors: Fukuoka Ryoma , Kohno Takashi , Kohsaka Shun , Shiraishi Yasuyuki , Sawano Mitsuaki , Abe Takayuki , Nagatomo Yuji , Goda Ayumi , Mizuno Atsushi , Fukuda Keiichi , Shadman Ramin , Dardas Todd F , Levy Wayne C , Yoshikawa Tsutomu
Published: January 2020

Aims

Heart failure (HF) is associated with an increased risk of sudden cardiac death (SCD). This study sought to demonstrate the incidence of SCD within a multicentre Japanese registry of HF patients hospitalized for acute decompensation, and externally validate the Seattle Proportional Risk Model (SPRM).

Methods and results

We consecutively registered 2240 acute HF patients from academic institutions in Tokyo, Japan. The discrimination and calibration of the SPRM were assessed by the c-statistic, Hosmer–Lemeshow statistic, and visual plotting among non-survivors. Patient-level SPRM predictions and implantable cardioverter-defibrillator (ICD) benefit [ICD estimated hazard ratio (HR), derived from the Cox proportional hazards model in the Sudden Cardiac Death in Heart Failure Trial (SCD-HeFT)] was calculated. During the 2-year follow-up, 356 deaths (15.9%) occurred, which included 76 adjudicated SCDs (3.4%) and 280 non-SCDs (12.5%). The SPRM showed acceptable discrimination [c-index = 0.63; 95% confidence interval (CI) 0.56–0.70], similar to that of original SPRM-derivation cohort. The calibration plot showed reasonable conformance. Among HF patients with reduced ejection fraction (EF; < 40%), SPRM showed improved discrimination compared with the ICD eligibility criteria (e.g. New York Heart Association functional Class II–III with EF ≤ 35%): c-index = 0.53 (95% CI 0.42–0.63) vs. 0.65 (95% CI 0.55–0.75) for SPRM. Finally, in the subgroup of 246 patients with both EF ≤ 35% and SPRM-predicted risk of ≥ 42.0% (SCD-HeFT defined ICD benefit threshold), mean ICD estimated HR was 0.70 (30% reduction of all-cause mortality by ICD).

Conclusion

The cumulative incidence of SCD was 3.4% in Japanese HF registry. The SPRM performed reasonably well in Japanese patients and may aid in improving SCD prediction.
Microbial abundance, composition, and function in nectar are shaped by flower visitor identity
Authors: Morris Megan M , Frixione Natalie J , Burkert Alexander C , Dinsdale Elizabeth A , Vannette Rachel L
Published: January 2020

Microbial dispersal is essential for establishment in new habitats, but the role of vector identity is poorly understood in community assembly and function. Here, we compared microbial assembly and function in floral nectar visited by legitimate pollinators (hummingbirds) and nectar robbers (carpenter bees). We assessed effects of visitation on the abundance and composition of culturable bacteria and fungi and their taxonomy and function using shotgun metagenomics and nectar chemistry. We also compared metagenome-assembled genomes (MAGs) of Acinetobacter, a common and highly abundant nectar bacterium, among visitor treatments. Visitation increased microbial abundance, but robbing resulted in 10× higher microbial abundance than pollination. Microbial communities differed among visitor treatments: robbed flowers were characterized by predominant nectar specialists within Acetobacteraceae and Metschnikowiaceae, with a concurrent loss of rare taxa, and these resulting communities harbored genes relating to osmotic stress, saccharide metabolism and specialized transporters. Gene differences were mirrored in function: robbed nectar contained a higher percentage of monosaccharides. Draft genomes of Acinetobacter revealed distinct amino acid and saccharide utilization pathways in strains isolated from robbed versus pollinated flowers. Our results suggest an unrecognized cost of nectar robbing for pollination and distinct effects of visitor type on interactions between plants and pollinators. Overall, these results suggest vector identity is an underappreciated factor structuring microbial community assembly and function.
Differential impact of top-down and bottom-up forces in structuring freshwater bacterial communities
Authors: Pradeep Ram A S , Keshri J , Sime-Ngando T
Published: January 2020

Limited data exist on the simultaneous impact of bottom-up (nutrients) and top-down (viruses and heterotrophic nanoflagellates) forces in shaping freshwater bacterial communities. In our laboratory microcosms, nutrient additions (organic and inorganic) and viral reduction approach led to the proliferation of high nucleic acid (HNA) bacterial subpopulation without an increase in phage abundance. High viral-mediated bacterial lysis in the presence of nanoflagellates yielded high proportion of low nucleic acid bacterial subpopulation. 16S rRNA gene sequence analysis indicated that members of classes Proteobacteria and Bacteroidetes evoked differential responses to nutrients and mortality forces, thereby resulting in differences (P < 0.001) in bacterial community composition and diversity, as observed from analysis of similarities and UniFrac analysis. Bacterial species richness (Chao) and diversity (Shannon) index was significantly higher (P < 0.001) in the presence of both the top-down factors and viruses alone, whereas lower host diversity was observed under nutrient relaxation of growth-limiting substrates due to the explosive growth of opportunistic HNA bacterial subpopulation. Our results are in agreement with the theoretical model of ‘killing the winner’, where the availability of growth-limiting substrates can act as a stimulating factor for host community composition while top-down forces can operate in the control of host diversity.
A subcellular proteome atlas of the yeastKomagataella phaffii
Authors: Valli Minoska , Grillitsch Karlheinz , Grünwald-Gruber Clemens , Tatto Nadine E , Hrobath Bernhard , Klug Lisa , Ivashov Vasyl , Hauzmayer Sandra , Koller Martina , Tir Nora , Leisch Friedrich , Gasser Brigitte , Graf Alexandra B , Altmann Friedrich , Daum Günther , Mattanovich Diethard
Published: January 2020

The compartmentalization of metabolic and regulatory pathways is a common pattern of living organisms. Eukaryotic cells are subdivided into several organelles enclosed by lipid membranes. Organelle proteomes define their functions. Yeasts, as simple eukaryotic single cell organisms, are valuable models for higher eukaryotes and frequently used for biotechnological applications. While the subcellular distribution of proteins is well studied in Saccharomyces cerevisiae, this is not the case for other yeasts like Komagataella phaffii (syn. Pichia pastoris). Different to most well-studied yeasts, K. phaffii can grow on methanol, which provides specific features for production of heterologous proteins and as a model for peroxisome biology. We isolated microsomes, very early Golgi, early Golgi, plasma membrane, vacuole, cytosol, peroxisomes and mitochondria of K. phaffii from glucose- and methanol-grown cultures, quantified their proteomes by liquid chromatography-electrospray ionization-mass spectrometry of either unlabeled or tandem mass tag-labeled samples. Classification of the proteins by their relative enrichment, allowed the separation of enriched proteins from potential contaminants in all cellular compartments except the peroxisomes. We discuss differences to S. cerevisiae, outline organelle specific findings and the major metabolic pathways and provide an interactive map of the subcellular localization of proteins in K. phaffii.
Adolescence and Aging: Impact of Adolescence Inflammatory Stress and Microbiota Alterations on Brain Development, Aging, and Neurodegeneration
Authors: Yahfoufi Nour , Matar Chantal , Ismail Nafissa
Published: January 2020

Puberty/adolescence is a critical phase during neurodevelopment with numerous structural, neurochemical, and molecular changes occurring in response to genetic and environmental signals. A consequence of this major neuronal reorganizing and remodeling is a heightened level of vulnerability to stressors and immune challenges. The gut microbiota is a fundamental modulator of stress and immune responses and has been found to play a role in mental health conditions and neurodegenerative disorders. Environmental insults (stress, infection, neuroinflammation, and use of antibiotics) during adolescence can result in dysbiosis subsidizing the development of brain disorders later in life. Also, pubertal neuroinflammatory insults can alter neurodevelopment, impact brain functioning in an enduring manner, and contribute to neurological disorders related to brain aging, such as Alzheimer’s disease, Parkinson’s disease, and depression. Exposure to probiotics during puberty can mitigate inflammation, reverse dysbiosis, and decrease vulnerabilities to brain disorders later in life. The goal of this review is to reveal the consequences of pubertal exposure to stress and immune challenges on the gut microbiota, immune reactivity within the brain, and the risk or resilience to stress-induced mental illnesses and neurodegenerative disorders. We propose that the consumption of probiotics during adolescence contribute to the prevention of brain pathologies in adulthood.
Dynamic time warping of palaeomagnetic secular variation data
Authors: Hagen Cedric J , Reilly Brendan T , Stoner Joseph S , Creveling Jessica R
Published: January 2020

We present and make publicly available a dynamic programming algorithm to simultaneously align the inclination and declination vector directions of sedimentary palaeomagnetic secular variation data. This algorithm generates a library of possible alignments through the systematic variation of assumptions about the relative accumulation rate and shared temporal overlap of two or more time-series. The palaeomagnetist can then evaluate this library of reproducible and objective alignments using available geological constraints, statistical methods and expert knowledge. We apply the algorithm to align previously (visually) correlated medium to high accumulation rate northern North Atlantic Holocene deposits (101–102 cm ka–1) with strong radiocarbon control. The algorithm generates plausible alignments that largely conform with radiocarbon and magnetic acquisition process uncertainty. These alignments illustrate the strengths and limitations of this numerical approach.
Palaeoslab and plume signatures in the mantle transition zone beneath Eastern Himalaya and adjoining regions
Authors: Saikia Dipankar , Kumar M Ravi , Singh Arun
Published: January 2020

A comprehensive data set of 73 876 high quality receiver functions computed using waveforms recorded by 327 broad-band seismic stations is used to investigate the mantle transition zone (MTZ) structure beneath the eastern Himalaya, southern Tibet, Assam valley and the previously unexplored Burmese arc and Bengal basin regions. A highly variable and perturbed mantle transition zone, with depressed 410 and 660 km discontinuities, is observed beneath the Bengal basin and to the east of the eastern Himalayan syntaxis. The 410 is elevated by ∼10 km along the Himalayan collision front, while it deviates in the range of ±5 km beneath most parts of Tibet and the Himalayan Foredeep. In northern Tibet and along the Red River Fault, delayed conversions from the 410 reveal a deepening of more than 10 km. The 410 and 660 km discontinuities are uplifted by nearly 10 km beneath the Arunachal Himalaya, due to the presence of a subducting Indian lithosphere, as evident in the regional tomographic images. We observe a thick (>20 km) transition zone beneath the Burmese Arc and close to the Tengchong volcano. An uplifted 410 together with a depressed 660 km discontinuity requires presence of lithospheric slabs within the MTZ. Delayed P-to-s conversions from the 410 and 660 km discontinuities in the proximity of the Jinsha suture zone seem to be consistent with the earlier results that invoke flow of a hot Tibetan asthenosphere into the mantle transition zone, as an explanation. Interestingly, results from the Bengal basin reveal a deepening (∼10 km) of both the 410 and 660 km discontinuities. Similar results from other plume affected regions prompt us to interpret this as a signature of the Kergulean plume.
Upper mantle deformation signatures of craton–orogen interaction in the Carpathian–Pannonian region from SKS anisotropy analysis
Authors: Petrescu Laura , Stuart Graham , Houseman Gregory , Bastow Ian
Published: January 2020

Since the Mesozoic, central and eastern European tectonics have been dominated by the closure of the Tethyan Ocean as the African and European plates collided. In the Miocene, the edge of the East European Craton and Moesian Platform were reworked in collision during the Carpathian orogeny and lithospheric extension formed the Pannonian Basin. To investigate the mantle deformation signatures associated with this complex collisional-extensional system, we carry out SKS splitting analysis at 123 broad-band seismic stations in the region. We compare our measurements with estimates of lithospheric thickness and recent seismic tomography models to test for correlation with mantle heterogeneities. Reviewing splitting delay times in light of xenolith measurements of anisotropy yields estimates of anisotropic layer thickness. Fast polarization directions are mostly NW–SE oriented across the seismically slow West Carpathians and Pannonian Basin and are independent of geological boundaries, absolute plate motion direction or an expected palaeo-slab roll-back path. Instead, they are systematically orthogonal to maximum stress directions, implying that the indenting Adria Plate, the leading deformational force in Central Europe, reset the upper-mantle mineral fabric in the past 5 Ma beneath the Pannonian Basin, overprinting the anisotropic signature of earlier tectonic events. Towards the east, fast polarization directions are perpendicular to steep gradients of lithospheric thickness and align along the edges of fast seismic anomalies beneath the Precambrian-aged Moesian Platform in the South Carpathians and the East European Craton, supporting the idea that craton roots exert a strong influence on the surrounding mantle flow. Within the Moesian Platform, SKS measurements become more variable with Fresnel zone arguments indicating a shallow fossil lithospheric source of anisotropy likely caused by older tectonic deformation frozen in the Precambrian. In the Southeast Carpathian corner, in the Vrancea Seismic Zone, a lithospheric fragment that sinks into the mantle is sandwiched between two slow anomalies, but smaller SKS delay times reveal weaker anisotropy occurs mainly to the NW side, consistent with asymmetric upwelling adjacent to a slab, slower mantle velocities and recent volcanism.