bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuraminidase inhibitor resistance in influenza: a clinical perspective
Authors: Lee Nelson , Hurt Aeron C. 
Published: October 2018

Purpose of review
Neuraminidase inhibitors (NAIs), including oseltamivir, zanamivir, and peramivir, is the main class of antiviral available for clinical use. As such, development of resistance toward these agents is of great clinical and public health concern.

Recent findings
At present, NAI resistance remains uncommon among the circulating viruses (oseltamivir <3.5%, zanamivir <1%). Resistance risk is slightly higher in A(H1N1) than A(H3N2) and B viruses. Resistance may emerge during drug exposure, particularly among young children (<5 years), the immunocompromised, and individuals receiving prophylactic regimens. H275Y A(H1N1) variant, showing high-level oseltamivir resistance, is capable of causing outbreaks. R294K A(H7N9) variant shows reduced inhibition across NAIs. Multi-NAI resistance has been reported in the immunocompromised.

Summary
These findings highlight the importance of continuous surveillance, and assessment of viral fitness and transmissibility of resistant virus strains. Detection can be challenging, especially in a mix of resistant and wild-type viruses. Recent advances in molecular techniques (e.g. targeted mutation PCR, iART, ddPCR, pyrosequencing, next-generation sequencing) have improved detection and our understanding of viral dynamics. Treatment options available for oseltamivir-resistant viruses are limited, and susceptibility testing of other NAIs may be required, but non-NAI antivirals (e.g. polymerase inhibitors) that are active against these resistant viruses are in late-stage clinical development.
Hepatitis B virus and hepatitis C virus infection in immunocompromised patients
Authors: Hwang Jessica P. , Torres Harrys A. 
Published: October 2018

Purpose of review
To provide an update on recent studies of hepatitis B virus (HBV) and hepatitis C virus (HCV) infections in cancer patients with an emphasis on viral reactivation after cancer treatment, new antiviral therapies, and safety concerns.

Recent findings
The diagnostic criteria for HBV reactivation in patients receiving cancer therapy were revised in 2018. HBV reactivation in these patients is preventable, even with the use of new cancer therapies. HCV reactivation also has been reported in cancer patients, particularly those with hematologic malignancies, and is not a virologic condition usually associated with poor outcome. Prophylaxis to prevent HCV reactivation is not recommended because therapy with direct-acting antivirals eradicates the infection in the majority of cancer patients.

Summary
Cancer patients with HBV or HCV infection are at risk for viral reactivation, with many similarities between these two infections. Patients at high risk for reactivation will benefit significantly from taking oral antivirals, which will reduce the risk of HBV reactivation or prevent development of HCV reactivation following its virologic cure.
Inter-comparison and assessment of gridded climate products over tropical forests during the 2015/2016 El Niño
Authors: Burton C. , Rifai S. , Malhi Y. 
Published: October 2018

To understand the impacts of extreme climate events, it is first necessary to understand the spatio-temporal characteristics of the event. Gridded climate products are frequently used to describe climate patterns but have been shown to perform poorly over data-sparse regions such as tropical forests. Often, they are uncritically employed in a wide range of studies linking tropical forest processes to large-scale climate variability. Here, we conduct an inter-comparison and assessment of near-surface air temperature fields supplied by four state-of-the-art reanalysis products, along with precipitation estimates supplied by four merged satellite-gauge rainfall products. Firstly, spatio-temporal patterns of temperature and precipitation anomalies during the 2015–2016 El Niño are shown for each product to characterize the impact of the El Niño on the tropical forest biomes of Equatorial Africa, Southeast Asia and South America. Using meteorological station data, a two-stage assessment is then conducted to determine which products most reliably model tropical climates during the 2015–2016 El Niño, and which perform best over the longer-term satellite observation period (1980–2016). Results suggest that eastern Amazonia, parts of the Congo Basin and mainland Southeast Asia all experienced significant monthly mean temperature anomalies during the El Niño, while northeastern Amazonia, eastern Borneo and southern New Guinea experienced significant precipitation deficits. Our results suggest ERA-Interim and MERRA2 are the most reliable air temperature datasets, while TRMM 3B42 V7 and CHIRPS v2.0 are the best-performing rainfall datasets.
This article is part of a discussion meeting issue ‘The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications’.
The impact of the 2015/2016 El Niño on global photosynthesis using satellite remote sensing
Authors: Luo Xiangzhong , Keenan Trevor F. , Fisher Joshua B. , Jiménez-Muñoz Juan-Carlos , Chen Jing M. , Jiang Chongya , Ju Weimin , Perakalapudi Naga-Vineet , Ryu Youngryel , Tadić Jovan M. 
Published: October 2018

The El Niño-Southern Oscillation exerts a large influence on global climate regimes and on the global carbon cycle. Although El Niño is known to be associated with a reduction of the global total land carbon sink, results based on prognostic models or measurements disagree over the relative contribution of photosynthesis to the reduced sink. Here, we provide an independent remote sensing-based analysis on the impact of the 2015–2016 El Niño on global photosynthesis using six global satellite-based photosynthesis products and a global solar-induced fluorescence (SIF) dataset. An ensemble of satellite-based photosynthesis products showed a negative anomaly of −0.7 ± 1.2 PgC in 2015, but a slight positive anomaly of 0.05 ± 0.89 PgC in 2016, which when combined with observations of the growth rate of atmospheric carbon dioxide concentrations suggests that the reduction of the land residual sink was likely dominated by photosynthesis in 2015 but by respiration in 2016. The six satellite-based products unanimously identified a major photosynthesis reduction of −1.1 ± 0.52 PgC from savannahs in 2015 and 2016, followed by a highly uncertain reduction of −0.22 ± 0.98 PgC from rainforests. Vegetation in the Northern Hemisphere enhanced photosynthesis before and after the peak El Niño, especially in grasslands (0.33 ± 0.13 PgC). The patterns of satellite-based photosynthesis ensemble mean were corroborated by SIF, except in rainforests and South America, where the anomalies of satellite-based photosynthesis products also diverged the most. We found the inter-model variation of photosynthesis estimates was strongly related to the discrepancy between moisture forcings for models. These results highlight the importance of considering multiple photosynthesis proxies when assessing responses to climatic anomalies.
This article is part of a discussion meeting issue ‘The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications'.
Quasi-universality in single-cell sequencing data
Authors: Aparicio Luis , Bordyuh Mykola , Blumberg Andrew J. , Rabadan Raul 
Published: October 2018

ABSTRACTThe development of single-cell technologies provides the opportunity to identify new cellular states and reconstruct novel cell-to-cell relationships. Applications range from understanding the transcriptional and epigenetic processes involved in metazoan development to characterizing distinct cells types in heterogeneous populations like cancers or immune cells. However, analysis of the data is impeded by its unknown intrinsic biological and technical variability together with its sparseness; these factors complicate the identification of true biological signals amidst artifact and noise. Here we show that, across technologies, roughly 95% of the eigenvalues derived from each single-cell data set can be described by universal distributions predicted by Random Matrix Theory. Interestingly, 5% of the spectrum shows deviations from these distributions and present a phenomenon known as eigenvector localization, where information tightly concentrates in groups of cells. Some of the localized eigenvectors reflect underlying biological signal, and some are simply a consequence of the sparsity of single cell data; roughly 3% is artifactual. Based on the universal distributions and a technique for detecting sparsity induced localization, we present a strategy to identify the residual 2% of directions that encode biological information and thereby denoise single-cell data. We demonstrate the effectiveness of this approach by comparing with standard single-cell data analysis techniques in a variety of examples with marked cell populations.
DNA analysis of a large collection of shark fins from a US retail shop: species composition, global extent of trade and conservation - a Technical Report from the Monterey Bay Aquarium
Authors: Palumbi Stephen R. , Robinson Kristin M. , Van Houtan Kyle S. , Jorgensen Salvador J. 
Published: October 2018

ABSTRACTWe identified shark fins sampled across the entirety of a shark fin shop that had operated on the west coast of the United States until 2014. From these specimens we obtained 963 species identifications with Cytochrome oxidase (COI) sequencing and 1,720 identifications with control region (CR) sequences. We found 36-39 distinct species with COI and 38-41 with CR. Of the species identified, 16-23 are currently listed as Endangered or Vulnerable on the IUCN Red List, an additional 2 are considered data deficient, and 7 currently listed under CITES Appendix II. Of the 2.5 tonnes of fins from this collection, we estimated 56-66% (CR or COI, respectively) come from CITES-listed species or those the IUCN considers threatened or data deficient. Most of these species occur outside of the United States EEZ, comprising a global set of species that is common in most fin surveys. The principal target shark fishery in the United States (spiny dogfish; Squalus acanthias) has no fins in our collection. Fins seen abundantly in our collection include pelagic species such as thresher, mako, oceanic whitetip, silky, blue and hammerhead sharks, as in previous samples of the shark fin supply chain. However, in addition, we see a large flood of blacktip, dusky, sandbar, and smalltail sharks that are common in shallow coastal waters. This may indicate that the global market for shark fins takes sharks from nearshore coastal zones, all over the world. Abundant species in the fin shop included globally-distributed species such as scalloped hammerheads and shortfin mako sharks, but also regionally-restricted species such as finetooth, blacknose, and Caribbean Reef sharks found only in the western Atlantic or Caribbean. Specimens identified from rare species of particular conservation concern included the wedgefish genus Rhyncobatus and the white shark. Both molecular markers performed well in identifying most fins, achieving a similar degree of taxonomic certainty. The universal primers for COI regularly amplified bacteria in wet fin samples, but the CR primers were able to return shark sequences even from these degraded samples. However, the CR primers amplified a second gene, likely a pseudogene, in some important and abundant species, and seriously underestimated some species of high conversation concern such as the thresher sharks.
Detection of a novel insect specific flavivirus across ecologically diverse populations of Aedes aegypti on the Caribbean Island of Saint Lucia
Authors: Jeffries C.L. , White M. , Wilson L. , Yakob L. , Walker T. 
Published: October 2018

ABSTRACTOutbreaks of mosquito-borne arboviral diseases including dengue virus (DENV), Zika virus (ZIKV), yellow fever virus (YFV) and chikungunya virus (CHIKV) have recently occurred in the Caribbean. The geographical range of the principle vectors responsible for transmission, Aedes (Ae.) aegypti and Ae. albopictus is increasing and greater mosquito surveillance is needed in the Caribbean given international tourism is so prominent. The island of Saint Lucia has seen outbreaks of DENV and CHIKV in the past five years but vector surveillance has been limited with the last studies dating back to the late 1970s. Natural disasters have changed the landscape of Saint Lucia and the island has gone through significant urbanisation. In this study, we conducted an entomological survey of Ae. aegypti and Ae. albopictus distribution across the island and analysed environmental parameters associated with the presence of these species. Although we collected Ae. aegypti across a range of sites across the island, no Ae. albopictus were collected despite traps being placed in diverse ecological settings. The number of Ae. aegypti collected was significantly associated with higher elevation and semi-urban settings yielded female mosquito counts per trap-day that were 5-fold lower than urban settings. Screening for arboviruses revealed a high prevalence of a novel insect-specific flavivirus closely related to cell fusing agent virus (CFAV). We discuss the implications that natural disasters, water storage and lack of mosquito surveillance have on arboviral outbreaks in Saint Lucia and implications for insect only flaviviruses on surveillance and detection of pathogenic flaviviruses.
KCC2 regulates neuronal excitability and hippocampal activity via interaction with Task-3 channels
Authors: Goutierre Marie , Awabdh Sana Al , François Emeline , Gomez-Dominguez Daniel , Irinopoulou Theano , de la Prida Liset Menendez , Poncer Jean Christophe 
Published: October 2018

AbstractThe K+/Cl− co-transporter KCC2 (SLC12A5) regulates neuronal transmembrane chloride gradients and thereby controls GABA signaling in the brain. KCC2 downregulation is observed in several neurological and psychiatric disorders including epilepsy, neuropathic pain and autism spectrum disorders. Paradoxical, excitatory GABA signaling is usually assumed to contribute to abnormal network activity underlying the pathology. We tested this hypothesis and explored the functional impact of chronic KCC2 downregulation in the rat dentate gyrus. Although the reversal potential of GABAA receptor currents was depolarized in KCC2 knockdown neurons, this shift was fully compensated by depolarization of their resting membrane potential. This effect was due to downregulation of Task-3 leak potassium channels that we show require KCC2 for membrane trafficking. Increased neuronal excitability upon KCC2 suppression altered dentate gyrus rhythmogenesis that could be normalized by chemogenetic hyperpolarization. Our data reveal KCC2 downregulation engages complex synaptic and cellular alterations beyond GABA signaling that concur to perturb network activity, thus offering novel targets for therapeutic intervention.
Quantitative proteomics of the 2016 WHONeisseria gonorrhoeaereference strains surveys vaccine candidates and antimicrobial resistance determinants
Authors: El-Rami Fadi E. , Zielke Ryszard A. , Wi Teodora , Sikora Aleksandra E. , Unemo Magnus 
Published: October 2018

AbstractThe sexually transmitted disease gonorrhea (causative agent:Neisseria gonorrhoeae) remains an urgent public health threat globally due to the repercussions on reproductive health, high incidence, widespread antimicrobial resistance (AMR), and absence of a vaccine. To mine gonorrhea antigens and enhance our understanding of gonococcal AMR at the proteome level, we performed the first large-scale proteomic profiling of a diverse panel (n=15) of gonococcal strains, including the 2016 World Health Organization (WHO) reference strains. These strains show all existing AMR profiles, previously described in regard to phenotypic and reference genome characteristics, and are intended for quality assurance in laboratory investigations. Herein, these isolates were subjected to subcellular fractionation and labeling with tandem mass tags coupled to mass spectrometry and multi-combinatorial bioinformatics. Our analyses detected 901 and 723 common proteins in cell envelope and cytoplasmic subproteomes, respectively. We identified nine novel gonorrhea vaccine candidates. Expression and conservation of new and previously selected antigens were investigated. In addition, established gonococcal AMR determinants were evaluated for the first time using quantitative proteomics. Six new proteins, WHO_F_00238, WHO_F_00635, WHO_F_00745, WHO_F_01139, WHO_F_01144, and WHO_F_01226, were differentially expressed in all strains, suggesting that they represent global proteomic AMR markers, indicate a predisposition toward developing or compensating gonococcal AMR, and/or act as new antimicrobial targets. Finally, phenotypic clustering based on the isolates’ defined antibiograms and common differentially expressed proteins yielded seven matching clusters between established and proteome-derived AMR signatures. Together, our investigations provide a reference proteomics databank for gonococcal vaccine and AMR research endeavors, which enables microbiological, clinical, or epidemiological projects and enhances the utility of the WHO reference strains.
Improving on hash-based probabilistic sequence classification using multiple spaced seeds and multi-index Bloom filters
Authors: Chu Justin , Mohamadi Hamid , Erhan Emre , Tse Jeffery , Chiu Readman , Yeo Sarah , Birol Inanc 
Published: October 2018

ABSTRACTAlignment-free classification of sequences against collections of sequences has enabled high-throughput processing of sequencing data in many bioinformatics analysis pipelines. Originally hash-table based, much work has been done to improve and reduce the memory requirement of indexing ofk-mer sequences with probabilistic indexing strategies. These efforts have led to lower memory highly efficient indexes, but often lack sensitivity in the face of sequencing errors or polymorphism because they arek-mer based. To address this, we designed a new memory efficient data structure that can tolerate mismatches using multiple spaced seeds, called a multi-index Bloom Filter. Implemented as part of BioBloom Tools, we demonstrate our algorithm in two applications, read binning for targeted assembly and taxonomic read assignment. Our tool shows a higher sensitivity and specificity for read-binning than BWA MEM at an order of magnitude less time. For taxonomic classification, we show higher sensitivity than CLARK-S at an order of magnitude less time while using half the memory.
Alpha diversity metrics for noisy OTUs
Authors: Edgar Robert C. , Flyvbjerg Henrik 
Published: October 2018

AbstractNext-generation sequencing (NGS) of marker genes such as 16S ribosomal RNA is widely used to survey microbial communities. The in-sample (alpha) diversity of Operational Taxonomic Units (OTUs) is often summarized by metrics such as richness or entropy which are calculated from observed abundances, or by estimators such as Chao1 which extrapolate to unobserved OTUs. Most such measures are adopted from traditional biodiversity studies, where observational error can often be neglected. However, errors introduced by next-generation amplicon sequencing tend to induce spurious OTUs and spurious counts in OTU tables, both of which are especially prevalent at low abundances. In consequence, traditional metrics may be grossly inaccurate if they are naively applied to NGS OTU tables. In this work, we describe two novel alpha diversity estimators which are calculated from OTU abundances above a specified threshold. The singleton-free estimator (SFE) is a non-parametric estimator which is derived from a similar approach to Chao1 but extrapolates using doublet and triplet abundances rather than singletons and doublets. The octave estimator (OE) fits a log-normal distribution to non-singleton bars of an octave plot. We show that these estimators are effective under suitable conditions, but these conditions rarely apply in practice. We conclude that extrapolating to unobserved OTUs remains an open problem which is unlikely to be solved in the near future.
Rapid growth and defence evolution following multiple introductions
Authors: van Boheemen Lotte A. , Bou-Assi Sarah , Uesugi Akane , Hodgins Kathryn A. 
Published: October 2018

AbstractRapid adaptation can aid invasive populations in their competitive success. Resource-allocation trade-off hypotheses predict higher resource availability or the lack of natural enemies in introduced ranges allow for increased growth and reproduction, thus contributing to invasive success. Evidence for such hypotheses are however equivocal and tests among multiple ranges over productivity gradients are required to provide a better understanding of the general applicability of these theories.Using common gardens, we investigated the adaptive divergence of various constitutive and inducible defence-related traits between the native North American and introduced European and Australian ranges, whilst controlling for divergence due to latitudinal trait clines, individual resource budgets and population differentiation, using >11,000 SNPs.Rapid, repeated clinal adaptation in defence-related traits was apparent despite distinct demographic histories. We also identified divergence among ranges in some defence-related traits, although differences in energy budgets among ranges may explain some, but not all, defence-related trait divergence. We do not identify a general reduction in defence in concert with an increase in growth among the multiple introduced ranges as predicted trade-off hypotheses.Synthesis: The rapid spread of invasive species is affected by a multitude of factors, likely including adaptation to climate and escape from natural enemies. Unravelling the mechanisms underlying invasives’ success enhances understanding of eco-evolutionary theory and is essential to inform management strategies in the face of ongoing climate change.