bluuebunny/crossref_metadata_2025 huggingface dataset:
Simple and robust model to estimate liveweight of Ethiopian Menz sheep
Authors: Wamatu Jane , Alkhtib Ashraf , Rischkowsky Barbara
Published: September 2019

Heart girth (HG) bands have been predominantly used in Ethiopia by smallholder farmers, traders and extension workers to estimate liveweight (LW) of livestock. They are produced using recommended and published predictive models from Ethiopia. More recently, some farmers and traders have abandoned the bands due to perceived inaccuracy of LW estimation and reverted to eye-ball estimations. The present study generated a novel algorithm using multiple criteria to develop a robust predictive model for LW estimation of Ethiopian Menz sheep by using HG. Subsequently, recommended models currently in use in Ethiopia were evaluated for accuracy in predicting LW, using data of the present study. Liveweight and HG of 420 Menz sheep were measured. Simple linear model (SLM), Box–Cox (SLM with LW0.75), quadratic and allometric models were used to describe the relationship between LW and HG. Algorithms used to validate the models included data exploration, model construction and model redeployment. Results showed that all models had similar R2 (≈0.82). All models fitted the criteria of residual analysis and robustness against extreme values. However, only Box–Cox was robust against data redeployment, with 95th percentile of prediction error (PE) less than 10%. Accordingly, a Box–Cox model (LW0.75 = –9.71 + 0.289 (HG)) is robust and can be used to accurately predict LW of Menz sheep. The 95th percentile of PE of existing, recommended models was higher than 10; thus, they cannot be recommended to accurately predict LW of Menz sheep. The present study concludes that an approach based on regressing LW on HG, and then selecting models with the highest R2, is inadequate to generate accurate and robust prediction models. This highlights the importance of model redeployment to generate accurate prediction models. Calibrated HG bands are suitable alternatives to weighing scales in rural areas of Ethiopia because they are cheaper and not subject to maintenance. Thus, their accuracy and robustness in estimation of LW is vital for sustainable use.
The germination success of Acacia longifolia subsp. longifolia (Fabaceae): a comparison between its native and exotic ranges
Authors: Welgama Amali , Florentine Singarayer , Marchante Hélia , Javaid Muhammad Mansoor , Turville Christopher
Published: September 2019

Acacia longifolia subsp. longifolia is native to South-eastern Australia and has naturalised in many regions across the globe, including in Portugal, Spain, and South Africa invading extensive areas. Prolific seed production and a long-lived seedbank are considered key factors that enhance its invasiveness. Yet, the effects of different factors on germination are still underexplored. Seeds were collected from Portuguese and Australian populations, and germination was evaluated under different temperature regimes, photoperiods, pH levels, salt stress, osmotic potential and burial depths. Findings show both populations share some similar patterns but also reveal important differences related to their germination. Higher temperatures induce increased germination rates while the photoperiod has no effect on germination. Both populations had quicker seed emergence under dark conditions. Seeds from both populations decrease germination rate under increasing salt-stress and show a wide range of pH tolerance, but Australians seeds are more tolerant to increase of both parameters. Seeds from the Portuguese population are bigger and germinated from deeper depths than the Australian. Our results may provide information to improve management of this species seedbank. Germination can prevent by, tillage or other interventions that help to increase burial depths; adding lime (to increase the soil alkalinity) can reduce its germination rate in both geographical ranges.
Oil Spill Source Identification Using Colorimetric Detection
Authors: Woodland Walmiria , Lim Richard , Motti Cherie , Irving Paul , Wang Jun , Payne Mark , Junk Peter C. , Vamvounis George
Published: September 2019

The colorimetric detection of polycyclic aromatic hydrocarbons (PAHs) was investigated for the quick and easy identification of likely oil spill offenders. In this new technology, photochromic compounds were used to sense PAHs by varying their photoswitching capacity. To that end, three photochromes were designed and showed varying degrees of photoswitching inhibition, depending on PAH analyte, photochrome, and excitation wavelength. PAH mixtures that mimic oil spills showed the same varying response and demonstrated the accuracy of this technology. To prove the applicability of this technology, an array was assembled, using the three photochromes at three excitation wavelengths, and tested against authentic crude oil samples. Not only could these samples be differentiated, but also weathering of two distinctly different oil samples showed limited variation in response, demonstrating that this may be a viable technique for in situ oil identification.
Men's preconception health care in Australian general practice: GPs' knowledge, attitudes and behaviours
Authors: Hogg Kirsten , Rizio Taletha , Manocha Ramesh , McLachlan Robert I. , Hammarberg Karin
Published: September 2019

Potentially modifiable factors can affect male fertility and reproductive outcomes, including smoking, obesity, and older paternal age. This study surveyed GPs’ knowledge about, attitudes towards, and needs for promoting fertility and preconception health to male patients. The survey, conducted February to June 2018 and completed by 304 GPs, included questions relating to men’s preconception health, the potential barriers and enablers to discussing preconception health with male patients, and the types of resources that would enable GPs to discuss parenthood intentions with men of reproductive age. Most GPs (90%) did not feel confident in their knowledge about modifiable factors that affect male fertility. Two-thirds agreed that it was their role to discuss these factors with male patients, but nearly 80% practised this only occasionally. Lack of knowledge, the sensitivity of the subject and fertility being perceived as a female issue, were identified as barriers to discussing fertility and preconception health with male patients. To facilitate discussions, GPs wanted trustworthy websites and factsheets to refer patients to. Men do not typically receive fertility or preconception health advice in general practice. A national framework for preconception health care that includes men, GP education and training, and reproductive health resources for men is needed.
Thermal and numerical simulation of mould electromagnetic stirring of GCr15 bearing steel
Authors: Jiang Danqing , Wang Rui , Zhu Longqiang , Zhang Qiong , Li Chuanjun , Wang Jiang , Ren Zhongming
Published: September 2019

The thermal and numerical simulation of the mould electromagnetic stirring (M-EMS) during continuous casting (CC) of the GCr15 bearing steel was performed. The thermal simulation apparatus with the M-EMS was used to examine the effect of stirring parameters on solidification structures. It was found that M-EMS enlarged the equiaxed grain regions, refined the grain size and resulted in more homogeneous distribution of the solute elements. The flow field in the mould was simulated to show the M-EMS intensity, which is in accordance with experimental observations. The mechanical properties of the blooms obtained at the current of 300A and frequency of 5 Hz are optimal.
CXCR6 regulates localization of tissue-resident memory CD8 T cells to the airways
Authors: Wein Alexander N. , McMaster Sean R. , Takamura Shiki , Dunbar Paul R. , Cartwright Emily K. , Hayward Sarah L. , McManus Daniel T. , Shimaoka Takeshi , Ueha Satoshi , Tsukui Tatsuya , Masumoto Tomoko , Kurachi Makoto , Matsushima Kouji , Kohlmeier Jacob E.
Published: September 2019

Resident memory T cells (TRM cells) are an important first-line defense against respiratory pathogens, but the unique contributions of lung TRM cell populations to protective immunity and the factors that govern their localization to different compartments of the lung are not well understood. Here, we show that airway and interstitial TRM cells have distinct effector functions and that CXCR6 controls the partitioning of TRM cells within the lung by recruiting CD8 TRM cells to the airways. The absence of CXCR6 significantly decreases airway CD8 TRM cells due to altered trafficking of CXCR6−/− cells within the lung, and not decreased survival in the airways. CXCL16, the ligand for CXCR6, is localized primarily at the respiratory epithelium, and mice lacking CXCL16 also had decreased CD8 TRM cells in the airways. Finally, blocking CXCL16 inhibited the steady-state maintenance of airway TRM cells. Thus, the CXCR6/CXCL16 signaling axis controls the localization of TRM cells to different compartments of the lung and maintains airway TRM cells.
Platelet-activating factor (PAF) mediates NLRP3-NEK7 inflammasome induction independently of PAFR
Authors: Deng Meng , Guo Haitao , Tam Jason W. , Johnson Brandon M. , Brickey W. June , New James S. , Lenox Austin , Shi Hexin , Golenbock Douglas T. , Koller Beverly H. , McKinnon Karen P. , Beutler Bruce , Ting Jenny P.-Y.
Published: September 2019

The role of lipids in inflammasome activation remains underappreciated. The phospholipid, platelet-activating factor (PAF), exerts multiple physiological functions by binding to a G protein–coupled seven-transmembrane receptor (PAFR). PAF is associated with a number of inflammatory disorders, yet the molecular mechanism underlying its proinflammatory function remains to be fully elucidated. We show that multiple PAF isoforms and PAF-like lipids can activate the inflammasome, resulting in IL-1β and IL-18 maturation. This is dependent on NLRP3, ASC, caspase-1, and NEK7, but not on NLRC4, NLRP1, NLRP6, AIM2, caspase-11, or GSDMD. Inflammasome activation by PAF also requires potassium efflux and calcium influx but not lysosomal cathepsin or mitochondrial reactive oxygen species. PAF exacerbates peritonitis partly through inflammasome activation, but PAFR is dispensable for PAF-induced inflammasome activation in vivo or in vitro. These findings reveal that PAF represents a damage-associated signal that activates the canonical inflammasome independently of PAFR and provides an explanation for the ineffectiveness of PAFR antagonist in blocking PAF-mediated inflammation in the clinic.
Effects of FGF14 and NaVβ4 deletion on transient and resurgent Na current in cerebellar Purkinje neurons
Authors: White Hayley V. , Brown Spencer T. , Bozza Thomas C. , Raman Indira M.
Published: September 2019

Voltage-gated Na channels of Purkinje cells are specialized to maintain high availability during high-frequency repetitive firing. They enter fast-inactivated states relatively slowly and undergo a voltage-dependent open-channel block by an intracellular protein (or proteins) that prevents stable fast inactivation and generates resurgent Na current. These properties depend on the pore-forming α subunits, as well as modulatory subunits within the Na channel complex. The identity of the factors responsible for open-channel block remains a question. Here we investigate the effects of genetic mutation of two Na channel auxiliary subunits highly expressed in Purkinje cells, NaVβ4 and FGF14, on modulating Na channel blocked as well as inactivated states. We find that although both NaVβ4 and the FGF14 splice variant FGF14-1a contain sequences that can generate resurgent-like currents when applied to Na channels in peptide form, deletion of either protein, or both proteins simultaneously, does not eliminate resurgent current in acutely dissociated Purkinje cell bodies. Loss of FGF14 expression does, however, reduce resurgent current amplitude and leads to an acceleration and stabilization of inactivation that is not reversed by application of the site-3 toxin, anemone toxin II (ATX). Tetrodotoxin (TTX) sensitivity is higher for resurgent than transient components of Na current, and loss of FGF14 preferentially affects a highly TTX-sensitive subset of Purkinje α subunits. The data suggest that NaV1.6 channels, which are known to generate the majority of Purkinje cell resurgent current, bind TTX with high affinity and are modulated by FGF14 to facilitate open-channel block.
2. Is knowledge impossible?
Authors: Pritchard Duncan
Published: September 2019

‘Is knowledge impossible?’ considers an influential argument that purports to show that we do not know much of what we take ourselves to know. If this argument works, then it licenses a radical sceptical doubt. It first looks at Descartes’s formulation of radical scepticism—Cartesian scepticism—which employs an important theoretical innovation known as a radical sceptical hypothesis. The closure principle is also discussed along with the radical sceptical paradox. If this radical sceptical argument works, then we not only lack knowledge of much of what we believe, but we do not even have any good epistemic reasons for believing what we do.
3. Defending knowledge
Authors: Pritchard Duncan
Published: September 2019

‘Defending knowledge’ considers some of the different philosophical responses to the problem of radical scepticism. It begins with the natural response to a philosophical puzzle: to insist on our commonsense principles and work back from there, focusing on the work of G.E. Moore. It then looks at a different kind of response to the sceptical problem, which involves the idea that perhaps there is some sort of context-shift in play in the sceptical reasoning. Finally, it discusses a more radical approach to the problem of radical scepticism outlined by Ludwig Wittgenstein. There is no one particular solution to radical scepticism, but numerous philosophical responses to the problem.
5. Genealogy
Authors: Gutting Gary
Published: September 2019

In using the term ‘genealogy’, Foucault proclaimed his connection to Nietzsche. ‘Genealogy’ analyses what Foucault thought about the genealogical method, how it compared to Nietzsche’s, and to what extent he used it. Both Nietzsche and Foucault offer many problematic, yet different, remarks on genealogy. Foucault is thoroughly Nietzschean in one respect: the critical intent with which he employs his genealogy. Foucault’s genealogies deconstruct, by showing their real origin, official meanings and evaluations involved in a society’s self-understanding. Foucault saw an intimate bond between knowledge and power. The mere fact that a cognitive state is an effect of power does not exclude it from the realm of knowledge.
6. The masked philosopher
Authors: Gutting Gary
Published: September 2019

Foucault sometimes admitted and sometimes denied that he was a philosopher. ‘The masked philosopher’ asks what a philosopher is and ponders whether Foucault really was a philosopher. Is philosophy an academic, perhaps technical and specialist, subject? Did Foucault’s work contribute to the modern (Kantian) philosophical project? Foucault’s interest in philosophy comes from his interest in how contemporary philosophy fits into the general scheme of history. Philosophy should be focused not on perennial questions, but on the question of what is distinctive about our current situation. To Foucault, the difficulty is in understanding how a single, unified being can be the transcendental source of all possible knowledge at the same time as being the object of knowledge.
7. Madness
Authors: Gutting Gary
Published: September 2019

Foucault felt outrage towards a perception of madness that admits no meaningful alternatives to standards of normality, one which rejects any beliefs or behaviours that deviate from these standards. ‘Madness’ examines Foucault’s ideas about insanity and how madness has come to be perceived by culture. Madness, stated Foucault, suffers from both a conceptual exclusion and a physical exclusion and this reflects a moral condemnation. His History of Madness sustains this argument. The moral fault occurs because madness corresponds to a radical choice to reject humanity and the human community in favour of animality. Despite the voice of madness being silenced, Foucault was particularly fascinated by the idea that probing the limits of reason will reveal truths.
10. Ancient sex
Authors: Gutting Gary
Published: September 2019

Towards the end of his life, Foucault’s topic of exploration turned to the ethical formation of the self, which emerged from his analysis of modern power relations. ‘Ancient sex’ looks at Foucault’s analysis of the historical constitution of ethical identity beyond the Christian hermeneutics of the self and its modern secular equivalent. According to Foucault, there are few differences between the ancients and the Christians on the level of moral codes and conducts, but fundamental differences emerge when we look at the formation of ethical subjects. What does Foucault mean by his phrase ‘living the truth’? He means truth as the product of individual self-creation and truth-telling as a social virtue.
3. How to be happy
Authors: Evans Dylan
Published: September 2019

The range of things that can make us joyful or distressed is simply vast. Is there any pattern underlying this bewildering diversity? ‘How to be happy’ explores what makes us happy by considering some of the main findings in contemporary research on the psychology of positive emotions and happiness. It discusses the ‘technologies of mood’ that promise to provide us with short cuts to happiness, from psychotherapy and art to drugs and meditation. It asks whether or not they work and discusses the dangers that beset some of these attempts to circumvent the more circuitous path to happiness that natural selection laid out for us.
Afterword
Authors: Evans Dylan
Published: September 2019

When people speak of cognition and emotion, or of reason and the passions, they are usually referring to two distinct mental faculties. One of them is cool, calm, and collected and works towards its conclusions slowly by means of explicit logical rules. The other is hot, colourful, and jumps to conclusions by consulting gut feelings. However, just because the heart works independently of reason does not mean it lacks reasons. On the contrary, the Afterword concludes that the things that emotions do all have their reasons, and sometimes these reasons are very good ones. Not only are there passions within reason, but there are reasons within passion.
2. Poetry’s areas of authority and application
Authors: O'Donoghue Bernard
Published: September 2019

‘Poetry’s areas of authority and application’ first considers the distinction between poetry and prose, which then raises the question of the prose-poem. What is the effect of claiming the status of poetry for something that seems to be structured according to the rules of its syntactic antitype, in prose? In using the words that everyone uses for communication and the expression of emotion, poetry can achieve an explicitness that music in itself or other formal arts, despite their regularity, cannot match. But what are poets good at and what are their obligations? Areas in which poetry seems to have particular authority and aptness are love, death, and nature.
Conclusion
Authors: O'Donoghue Bernard
Published: September 2019

Having started with grand claims for poetry, by Shelley, Wallace Stevens, and others, on grounds of public utility, this brief consideration of what poetry is has encountered a series of recurrent features. Its primary effect seems to be to satisfy what the reader or hearer wants by surprising them in some way. It is never the statement of the obvious. It may be abnormal in language or in opinion or in organization. But it must not be abnormal for the sake of it; it must not be perverse, because its endeavour is to expose the truth in some sense that is not obvious. It works in the service of reality. It is in that sense that it is an enhancement of life as we end where we began....
Wine Regulations
Authors: Meloni Giulia , Anderson Kym , Deconinck Koen , Swinnen Johan
Published: September 2019

This paper provides an overview and analysis of wine regulations in an international and historical comparative perspective. Wine is an excellent sector to study government interventions because for centuries wine markets have been subject to many government regulations that differ greatly within and between countries. Wine consumption taxes, for example, range from zero in some countries to more than 100% in others. The European Union has extensive quantity and quality regulations for wine, while other major producers such as Australia and the United States are much less regulated. After a general overview of current regulations and historical evolutions, we analyze three key wine regulations in more detail: consumption taxes, planting rights, and geographical indications. Most wine regulations reveal a tension between the public interest and vested private interests.
The Value of Terroir: A Historical Analysis of the Bordeaux and Champagne Geographical Indications
Authors: Haeck Catherine , Meloni Giulia , Swinnen Johan
Published: September 2019

Previous studies on the value ofterroir, or more generally geographical indications (GI), used hedonic techniques. We use historical data and exploit temporal and geographical variations in the introduction of wine GIs in early twentieth century France to study the impact on the price of specific wines in the years and decades following their introduction. We find large effects of GIs on prices of some Champagne wines, but no significant impact on Bordeaux or other Champagne wines.
Exploring evolutionary theories of plant defence investment using field populations of the deadly carrot
Authors: Martinez-Swatson Karen , Kjøller Rasmus , Cozzi Federico , Simonsen Henrik Toft , Rønsted Nina , Barnes Christopher
Published: September 2019

Background and Aims

There are a number of disparate models predicting variation in plant chemical defences between species, and within a single species over space and time. These can give conflicting predictions. Here we review a number of these theories, before assessing their power to predict the spatial–temporal variation of thapsigargins between and within populations of the deadly carrot (Thapsia garganica). By utilizing multiple models simultaneously (optimum defence theory, growth rate hypothesis, growth–differentiation balance hypothesis, intra–specific framework and resource exchange model of plant defence), we will highlight gaps in their predictions and evaluate the performance of each.

Methods

Thapsigargins are potent anti-herbivore compounds that occur in limited richness across the different plant tissues of T. garganica, and therefore represent an ideal system for exploring these models. Thapsia garganica plants were collected from six locations on the island of Ibiza, Spain, and the thapsigargins quantified within reproductive, vegetative and below-ground tissues. The effects of sampling time, location, mammalian herbivory, soil nutrition and changing root-associated fungal communities on the concentrations of thapsigargins within these in situ observations were analysed, and the results were compared with our model predictions.

Key Results

The models performed well in predicting the general defence strategy of T. garganica and the above-ground distribution of thapsigargins, but failed to predict the considerable proportion of defences found below ground. Models predicting variation over environmental gradients gave conflicting and less specific predictions, with intraspecific variation remaining less understood.

Conclusion

Here we found that multiple models predicting the general defence strategy of plant species could likely be integrated into a single model, while also finding a clear need to better incorporate below-ground defences into models of plant chemical defences. We found that constitutive and induced thapsigargins differed in their regulation, and suggest that models predicting intraspecific defences should consider them separately. Finally, we suggest that in situ studies be supplemented with experiments in controlled environments to identify specific environmental parameters that regulate variation in defences within species.
XII—What’s Wrong with the Consequence Argument: A Compatibilist Libertarian Response
Authors: List Christian
Published: September 2019

The most prominent argument for the incompatibility of free will and determinism is Peter van Inwagen’s consequence argument. I offer a new diagnosis of what is wrong with this argument. Proponents and critics typically accept the way the argument is framed, and only disagree on whether the premisses and rules of inference are true. I suggest that the argument involves a category mistake: it conflates two different levels of description, namely, the physical level at which we describe the world from the perspective of fundamental physics and the agential level at which we describe agents and their actions. My diagnosis is based on an account of free will as a higher-level phenomenon. I call this account ‘compatibilist libertarianism’, for reasons that will become clear. Although the paper addresses a primarily metaphysical question, it uses tools similar to those employed in philosophy-of-science work on determinism and indeterminism, higher-level phenomena, and dynamical systems.
Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
Authors: Davín Adrián A , Tricou Théo , Tannier Eric , de Vienne Damien M , Szöllősi Gergely J
Published: September 2019

Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages. It also incorporates various features that have not to date been combined in a single simulator, such as the possibility of generating species trees with a pre-defined variation of speciation and extinction rates through time, simulating explicitly intergenic sequences of variable length and outputting gene tree—species tree reconciliations.

Availability and implementation

Source code and manual are freely available in https://github.com/AADavin/ZOMBI/.

Supplementary information

Supplementary data are available at Bioinformatics online.
A fast and memory efficient MLCS algorithm by character merging for DNA sequences alignment
Authors: Liu Sen , Wang Yuping , Tong Wuning , Wei Shiwei
Published: September 2019

Motivation

Multiple longest common subsequence (MLCS) problem is searching all longest common subsequences of multiple character sequences. It appears in many fields such as data mining, DNA alignment, bioinformatics, text editing and so on. With the increasing in sequence length and number of sequences, the existing dynamic programming algorithms and the dominant point-based algorithms become ineffective and inefficient, especially for large-scale MLCS problems.

Results

In this paper, by considering the characteristics of DNA sequences with many consecutively repeated characters, we first design a character merging scheme which merges the consecutively repeated characters in the sequences. As a result, it shortens the length of sequences considered and saves the space of storing all sequences. To further reduce the space and time costs, we construct a weighted directed acyclic graph which is much smaller than widely used directed acyclic graph for MLCS problems. Based on these techniques, we propose a fast and memory efficient algorithm for MLCS problems. Finally, the experiments are conducted and the proposed algorithm is compared with several state-of-the art algorithms. The experimental results show that the proposed algorithm performs better than the compared state-of-the art algorithms in both time and space costs.

Availability and implementation

https://www.ncbi.nlm.nih.gov/nuccore and https://github.com/liusen1006/MLCS.
Metric learning on expression data for gene function prediction
Authors: Makrodimitris Stavros , Reinders Marcel J T , van Ham Roeland C H J
Published: September 2019

Motivation

Co-expression of two genes across different conditions is indicative of their involvement in the same biological process. However, when using RNA-Seq datasets with many experimental conditions from diverse sources, only a subset of the experimental conditions is expected to be relevant for finding genes related to a particular Gene Ontology (GO) term. Therefore, we hypothesize that when the purpose is to find similarly functioning genes, the co-expression of genes should not be determined on all samples but only on those samples informative for the GO term of interest.

Results

To address this, we developed Metric Learning for Co-expression (MLC), a fast algorithm that assigns a GO-term-specific weight to each expression sample. The goal is to obtain a weighted co-expression measure that is more suitable than the unweighted Pearson correlation for applying Guilt-By-Association-based function predictions. More specifically, if two genes are annotated with a given GO term, MLC tries to maximize their weighted co-expression and, in addition, if one of them is not annotated with that term, the weighted co-expression is minimized. Our experiments on publicly available Arabidopsis thaliana RNA-Seq data demonstrate that MLC outperforms standard Pearson correlation in term-centric performance. Moreover, our method is particularly good at more specific terms, which are the most interesting. Finally, by observing the sample weights for a particular GO term, one can identify which experiments are important for learning that term and potentially identify novel conditions that are relevant, as demonstrated by experiments in both A. thaliana and Pseudomonas Aeruginosa.

Availability and implementation

MLC is available as a Python package at www.github.com/stamakro/MLC.

Supplementary information

Supplementary data are available at Bioinformatics online.
Three Years of Progress Toward Achieving Hepatitis C Elimination in the Country of Georgia, April 2015–March 2018
Authors: Tsertsvadze Tengiz , Gamkrelidze Amiran , Chkhartishvili Nikoloz , Abutidze Akaki , Sharvadze Lali , Kerashvili Vakhtang , Butsashvili Maia , Metreveli David , Gvinjilia Lia , Shadaker Shaun , Nasrullah Muazzam , Adamia Ekaterine , Zeuzem Stefan , Afdhal Nezam , Arora Sanjeev , Thornton Karla , Skaggs Beth , Kuchuloria Tinatin , Lagvilava Maia , Sergeenko David , Averhoff Francisco
Published: September 2019

Background

In April 2015, in collaboration with the US Centers for Disease Control and Prevention and Gilead Sciences, the country of Georgia embarked on the world’s first hepatitis C elimination program. We aimed to assess progress toward elimination targets 3 years after the start of the elimination program.

Methods

We constructed a hepatitis C virus (HCV) care cascade for adults in Georgia, based on the estimated 150 000 persons aged ≥18 years with active HCV infection. All patients who were screened or entered the treatment program during April 2015–March 2018 were included in the analysis. Data on the number of persons screened for HCV were extracted from the national HCV screening database. For the treatment component, we utilized data from the Georgia National HCV treatment program database. Available treatment options included sofosbuvir and ledipasvir/sofosbuvir–based regimens.

Results

Since April 2015, a cumulative 974 817 adults were screened for HCV antibodies; 86 624 persons tested positive, of whom 61 925 underwent HCV confirmatory testing. Among the estimated 150 000 adults living with chronic hepatitis C in Georgia, 52 856 (35.1%) were diagnosed, 45 334 (30.2%) initiated treatment with direct-acting antivirals, and 29 090 (19.4%) achieved a sustained virologic response (SVR). Overall, 37 256 persons were eligible for SVR assessment; of these, only 29 620 (79.5%) returned for evaluation. The SVR rate was 98.2% (29 090/29 620) in the per-protocol analysis and 78.1% (29 090/37 256) in the intent-to-treat analysis.

Conclusions

Georgia has made substantial progress in the path toward eliminating hepatitis C. Scaling up of testing and diagnosis, along with effective linkage to treatment services, is needed to achieve the goal of elimination.
Alendronate Improves Bone Mineral Density in Children and Adolescents Perinatally Infected With Human Immunodeficiency Virus With Low Bone Mineral Density for Age
Authors: Jacobson Denise L , Lindsey Jane C , Gordon Catherine , Hazra Rohan , Spiegel Hans , Ferreira Flavia , Amaral Fabiana R , Pagano-Therrien Jesica , Gaur Aditya , George Kathy , Benson Jane , Siberry George K
Published: September 2019

Background

Children and adolescents with perinatal human immunodeficiency virus (HIV) infection and with low bone mineral density (BMD) may be at higher risk of osteoporosis and fractures in later life than their uninfected peers. Bisphosphonate therapy has been shown to reduce fractures in adults with osteoporosis, but has not been formally studied in youths living with HIV.

Methods

Fifty-two children and adolescents (aged 11–24 years) perinatally infected with HIV with low lumbar spine (LS) BMD (Z score < −1.5) were randomized to receive once-weekly alendronate or placebo in a double-blind cross-over study designed to assess the safety and efficacy of 48 and 96 weeks of alendronate in the United States and Brazil. All participants received daily calcium carbonate and vitamin D supplementation and were asked to engage in regular weight-bearing exercise. Safety and efficacy are summarized for the initial 48 weeks of the trial.

Results

Grade 3 or higher abnormal laboratory values, signs, or symptoms developed in 5 of 32 (16%) participants on alendronate and 2 of 18 (11%) on placebo (P > .99). No cases of jaw osteonecrosis, atrial fibrillation, or nonhealing fractures were reported. Mean increases (95% confidence interval) in LS BMD over 48 weeks were significantly larger on alendronate (20% [14%–25%]) than placebo (7% [5%–9%]) (P < .001). Similar improvements were seen for whole body BMD.

Conclusions

In this small study in children and adolescents perinatally infected with HIV with low LS BMD, 48 weeks of alendronate was well-tolerated, showed no safety concerns, and significantly improved LS and whole body BMD compared to participants on vitamin D/calcium supplementation and exercise alone.

Clinical Trials Registration

NCT00921557.
Investigating Transfusion-related Sepsis Using Culture-Independent Metagenomic Sequencing
Authors: Crawford Emily , Kamm Jack , Miller Steve , Li Lucy M , Caldera Saharai , Lyden Amy , Yokoe Deborah , Nichols Amy , Tran Nam K , Barnard Sarah E , Conner Peter M , Nambiar Ashok , Zinter Matt S , Moayeri Morvarid , Serpa Paula Hayakawa , Prince Brian C , Quan Jenai , Sit Rene , Tan Michelle , Phelps Maira , Derisi Joseph L , Tato Cristina M , Langelier Charles
Published: September 2019

Background

Transfusion-related sepsis remains an important hospital infection control challenge. Investigation of septic transfusion events is often restricted by the limitations of bacterial culture in terms of time requirements and low yield in the setting of prior antibiotic administration.

Methods

In 3 gram-negative septic transfusion cases, we performed metagenomic next-generation sequencing (mNGS) of direct clinical blood specimens in addition to standard culture-based approaches utilized for infection control investigations. Pathogen detection leveraged IDSeq, a new open-access microbial bioinformatics portal. Phylogenetic analysis was performed to assess microbial genetic relatedness and understand transmission events.

Results

mNGS of direct clinical blood specimens afforded precision detection of pathogens responsible for each case of transfusion-related sepsis and enabled discovery of a novel Acinetobacter species in a platelet product that had become contaminated despite photochemical pathogen reduction. In each case, longitudinal assessment of pathogen burden elucidated the temporal sequence of events associated with each transfusion-transmitted infection. We found that informative data could be obtained from culture-independent mNGS of residual platelet products and leftover blood specimens that were either unsuitable or unavailable for culture or that failed to grow due to prior antibiotic administration. We additionally developed methods to enhance accuracy for detecting transfusion-associated pathogens that share taxonomic similarity to contaminants commonly found in mNGS library preparations.

Conclusions

Culture-independent mNGS of blood products afforded rapid and precise assessment of pathogen identity, abundance, and genetic relatedness. Together, these challenging cases demonstrated the potential for metagenomics to advance existing methods for investigating transfusion-transmitted infections.
Resilience and Urban Capabilities in Denise Mina’s Garnethill Trilogy
Authors: Rodríguez González Carla
Published: September 2019

This essay examines Denise Mina’s Garnethill trilogy from the standpoint of spatial and capabilities studies. It analyzes the representation of spaces of resilience and their role in the gendered redistribution of urban and domestic power portrayed in the narratives. In order to do so, it contextualizes these books within the framework of contemporary Scottish crime fiction and subsequently studies the contraposition and subversion of emotional spaces in Glasgow and London in the process of recovery from the trauma of the child sexual abuse their protagonist has undergone.
Parsimonious Eurolung risk models to predict cardiopulmonary morbidity and mortality following anatomic lung resections: an updated analysis from the European Society of Thoracic Surgeons database
Authors: Brunelli Alessandro , Cicconi Silvia , Decaluwe Herbert , Szanto Zalan , Falcoz Pierre Emmanuel
Published: September 2019

OBJECTIVES

To develop a simplified version of the Eurolung risk model to predict cardiopulmonary morbidity and 30-day mortality after lung resection from the ESTS database.

METHODS

A total of 82 383 lung resections (63 681 lobectomies, 3617 bilobectomies, 7667 pneumonectomies and 7418 segmentectomies) recorded in the ESTS database (January 2007–December 2018) were analysed. Multiple imputations with chained equations were performed on the predictors included in the original Eurolung models. Stepwise selection was then applied for determining the best logistic model. To develop the parsimonious models, different models were tested eliminating variables one by one starting from the less significant. The models’ prediction power was evaluated estimating area under curve (AUC) with the 10-fold cross-validation technique.

RESULTS

Cardiopulmonary morbidity model (Eurolung1): the best parsimonious Eurolung1 model contains 5 variables. The logit of the parsimonious Eurolung1 model was as follows: −2.852 + 0.021 × age + 0.472 × male −0.015 × ppoFEV1 + 0.662×thoracotomy + 0.324 × extended resection. Pooled AUC is 0.710 [95% confidence interval (CI) 0.677–0.743]. Mortality model (Eurolung2): the best parsimonious model contains 6 variables. The logit of the parsimonious Eurolung2 model was as follows: −6.350 + 0.047 × age + 0.889 × male −0.055 × BMI −0.010 × ppoFEV1 + 0.892 × thoracotomy + 0.983 × pneumonectomy. Pooled AUC is 0.737 (95% CI 0.702–0.770). An aggregate parsimonious Eurolung2 was also generated by repeating the logistic regression after categorization of the numeric variables. Patients were grouped into 7 risk classes showing incremental risk of mortality (P < 0.0001).

CONCLUSIONS

We were able to develop simplified and updated versions of the Eurolung risk models retaining the predictive ability of the full original models. They represent a more user-friendly tool designed to inform the multidisciplinary discussion and shared decision-making process of lung resection candidates.
New High-Quality Draft Genome of the Brown Rot Fungal Pathogen Monilinia fructicola
Authors: De Miccolis Angelini Rita Milvia , Romanazzi Gianfranco , Pollastro Stefania , Rotolo Caterina , Faretra Francesco , Landi Lucia
Published: September 2019

Brown rot is a worldwide fungal disease of stone and pome fruit that is caused by several Monilinia species. Among these, Monilinia fructicola can cause severe preharvest and postharvest losses, especially for stone fruit. Here, we present a high-quality draft genome assembly of M. fructicola Mfrc123 strain obtained using both Illumina and PacBio sequencing technologies. The genome assembly comprised 20 scaffolds, including 29 telomere sequences at both ends of 10 scaffolds, and at a single end of 9 scaffolds. The total length was 44.05 Mb, with a scaffold N50 of 2,592 kb. Annotation of the M. fructicola assembly identified a total of 12,118 genes and 13,749 proteins that were functionally annotated. This newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within Monilinia species.
5. Employers’ Liability and Vicarious Liability
Authors: Dyer Dr Karen
Published: September 2019

Each Concentrate revision guide is packed with essential information, key cases, revision tips, exam Q&As, and more. Concentrates show you what to expect in a law exam, what examiners are looking for, and how to achieve extra marks. This chapter discusses the law on employer' liability and vicarious. To answer questions on this topic, students need to understand the following: tort of negligence; statutory duties, and the effect of breach of statutory duty; the Employers' Liability (Defective Equipment) Act 1969, and the meaning ‘PPE’; vicarious liability, and specifically The Catholic Child Welfare Society and others v Various Claimants and The Institute of the Brothers of the Christian Schools [2012] UKSC 56; and defences to negligence.
6. Product Liability
Authors: Dyer Dr Karen
Published: September 2019

Each Concentrate revision guide is packed with essential information, key cases, revision tips, exam Q&As, and more. Concentrates show you what to expect in a law exam, what examiners are looking for, and how to achieve extra marks. The chapter discusses the law on product liability. It covers key debates, sample questions, diagram answer plan, tips for getting extra marks, and online resources. To answer questions on this topic, students need to understand the following: the general principles of negligence; the meaning of strict liability; and the Consumer Protection Act 1987 and its relationship with the common law regarding consumer protection.
7. Occupiers’ Liability
Authors: Dyer Dr Karen
Published: September 2019

Each Concentrate revision guide is packed with essential information, key cases, revision tips, exam Q&As, and more. Concentrates show you what to expect in a law exam, what examiners are looking for, and how to achieve extra marks. This chapter discusses the issue of occupiers' liability. In order to answer questions on this topic, students need to understand the following: the Occupiers' Liability Act 1957; the Occupiers' Liability Act 1984; the ‘control test’ — how ‘occupiers’ have been identified by the courts; the difference between a ‘visitor’ and a ‘non-visitor’, and the legal differences that arise; how the courts have interpreted ‘reasonable care’; the concept of ‘breach of duty’ and ‘causation’ in negligence; excluding or restricting negligence liability under s. 65 Consumer Rights Act 2015; and general defences in tort law.
8. Intentional Torts
Authors: Dyer Dr Karen
Published: September 2019

Each Concentrate revision guide is packed with essential information, key cases, revision tips, exam Q&As, and more. Concentrates show you what to expect in a law exam, what examiners are looking for, and how to achieve extra marks. This chapter discusses intentional torts. It covers key debates, sample questions, diagram answer plan, tips for getting extra marks, and online resources. To answer questions on this topic, students need to understand the following: trespass to the person: assault, battery, false imprisonment, the rule in Wilkinson v Downton, and Protection from Harassment Act 1997; trespass to land; trespass to goods and the tort of conversion; and defences to intentional torts: necessity, lawful arrest, consent, and self-defence.
11. General Defences
Authors: Dyer Dr Karen
Published: September 2019

Each Concentrate revision guide is packed with essential information, key cases, revision tips, exam Q&As, and more. Concentrates show you what to expect in a law exam, what examiners are looking for, and how to achieve extra marks. This chapter discusses general defences, covering key debates, sample questions, diagram answer plan, tips for getting extra marks, and online resources. To answer questions on this topic, students need to understand the following: the concept of negligence; the Occupier's Liability Acts; the defence of volenti non fit injuria; the defence of contributory negligence and the Law Reform (Contributory Negligence) Act 1945; and the defence of illegality — ex turpi causa non oritur action.
14. Skills for Success in Coursework Assessments
Authors: Dyer Dr Karen
Published: September 2019

Each Concentrate revision guide is packed with essential information, key cases, revision tips, exam Q&As, and more. Concentrates show you what to expect in a law exam, what examiners are looking for, and how to achieve extra marks. This chapter discusses how students can structure their answers to coursework questions, and exposes common errors that students make when undertaking coursework. The starting point for obtaining a good grade in an exam is to answer the question set. It is even more important to do so for coursework questions, as students are usually given plenty of time to plan and prepare their answers, and to ask for additional support if needed. Whether answering a problem question or an essay question, students are required to produce a convincing argument using ‘evidence’ from case law, statutory provisions, and academic literature.
3. Establishing Liability in Principle: Duty of Care
Authors: Deakin Simon , Adams Zoe
Published: September 2019

This chapter discusses the following: the duty concept and the elements of the tort of negligence; formulating the duty of care; kinds of damage; the manner of infliction; and the way in which the notion of duty confines liability by reference to the nature of the parties involved.
4. Liability for Fault: Breach
Authors: Deakin Simon , Adams Zoe
Published: September 2019

This chapter examines the principal element of the cause of action in negligence, namely breach of duty. The issue of breach of duty is concerned with whether the defendant was careless, in the sense of failing to conform to the standard of care applicable to him. The discussions cover the concept of breach of duty; the objective standard; professional and regulatory standards; updating of standards in the light of new information; the role of cost-benefit analysis and the ‘Learned Hand’ test; weighing the risk and gravity of harm against the cost of prevention; and proof of carelessness, including discussion of the res ipsa loquitur principle.
5. Liability for Damage Caused: Causation and Remoteness
Authors: Deakin Simon , Adams Zoe
Published: September 2019

This chapter examines the third element of the tort of negligence, namely, causation. The defendant’s carelessness must be shown to have caused the loss or damage in question. The finding of a sufficient causal link is an essential ingredient in all forms of tort liability (with the exception of torts actionable without proof of damage). The discussions cover the nature of the causal inquiry; but-for causation; and remoteness of damage. There is extensive discussion of the Fairchild principle and the issue of causation in complex cases of liability for occupational illness and disease, with particular reference to the mesothelioma case law.