bluuebunny/crossref_metadata_2025 huggingface dataset:
LOBSTER: an environment to design bioimage analysis workflows for large and complex fluorescence microscopy data
Authors: Tosi Sébastien , Bardia Lídia , Filgueira Maria Jose , Calon Alexandre , Colombelli Julien
Published: December 2019

Open source software such as ImageJ and CellProfiler greatly simplified the quantitative analysis of microscopy images but their applicability is limited by the size, dimensionality and complexity of the images under study. In contrast, software optimized for the needs of specific research projects can overcome these limitations, but they may be harder to find, set up and customize to different needs. Overall, the analysis of large, complex, microscopy images is hence still a critical bottleneck for many Life Scientists. We introduce LOBSTER (Little Objects Segmentation and Tracking Environment), an environment designed to help scientists design and customize image analysis workflows to accurately characterize biological objects from a broad range of fluorescence microscopy images, including large images exceeding workstation main memory. LOBSTER comes with a starting set of over 75 sample image analysis workflows and associated images stemming from state-of-the-art image-based research projects.

Availability and implementation

LOBSTER requires MATLAB (version ≥ 2015a), MATLAB Image processing toolbox, and MATLAB statistics and machine learning toolbox. Code source, online tutorials, video demonstrations, documentation and sample images are freely available from: https://sebastients.github.io.

Supplementary information

Supplementary data are available at Bioinformatics online.
Building a pipeline to solicit expert knowledge from the community to aid gene summary curation
Authors: Antonazzo Giulia , Urbano Jose M , Marygold Steven J , Millburn Gillian H , Brown Nicholas H
Published: December 2019

Brief summaries describing the function of each gene’s product(s) are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. However, manually writing such summaries, even for a single species, is a daunting task; for example, the Drosophila melanogaster genome contains almost 14 000 protein-coding genes. One solution is to use computational methods to generate summaries, but this often fails to capture the key functions or express them eloquently. Here, we describe how we solicited help from the research community to generate manually written summaries of D. melanogaster gene function. Based on the data within the FlyBase database, we developed a computational pipeline to identify researchers who have worked extensively on each gene. We e-mailed these researchers to ask them to draft a brief summary of the main function(s) of the gene’s product, which we edited for consistency to produce a ‘gene snapshot’. This approach yielded 1800 gene snapshot submissions within a 3-month period. We discuss the general utility of this strategy for other databases that capture data from the research literature.

Database URL: https://flybase.org/
Reconstruction of the Carbohydrate 6-O Sulfotransferase Gene Family Evolution in Vertebrates Reveals Novel Member, CHST16, Lost in Amniotes
Authors: Ocampo Daza Daniel , Haitina Tatjana
Published: December 2019

Glycosaminoglycans are sulfated polysaccharide molecules, essential for many biological processes. The 6-O sulfation of glycosaminoglycans is carried out by carbohydrate 6-O sulfotransferases (C6OSTs), previously named Gal/GalNAc/GlcNAc 6-O sulfotransferases. Here, for the first time, we present a detailed phylogenetic reconstruction, analysis of gene synteny conservation and propose an evolutionary scenario for the C6OST family in major vertebrate groups, including mammals, birds, nonavian reptiles, amphibians, lobe-finned fishes, ray-finned fishes, cartilaginous fishes, and jawless vertebrates.

The C6OST gene expansion likely started early in the chordate lineage, giving rise to four ancestral genes after the divergence of tunicates and before the emergence of extant vertebrates. The two rounds of whole-genome duplication in early vertebrate evolution (1R/2R) only contributed two additional C6OST subtype genes, increasing the vertebrate repertoire from four genes to six, divided into two branches. The first branch includes CHST1 and CHST3 as well as a previously unrecognized subtype, CHST16 that was lost in amniotes. The second branch includes CHST2, CHST7, and CHST5. Subsequently, local duplications of CHST5 gave rise to CHST4 in the ancestor of tetrapods, and to CHST6 in the ancestor of primates.

The teleost-specific gene duplicates were identified for CHST1, CHST2, and CHST3 and are result of whole-genome duplication (3R) in the teleost lineage. We could also detect multiple, more recent lineage-specific duplicates. Thus, the vertebrate repertoire of C6OST genes has been shaped by gene duplications and gene losses at several stages of vertebrate evolution, with implications for the evolution of skeleton, nervous system, and cell–cell interactions.
Does Sexual Orientation Relate to Health and Well-Being? Analysis of Adults 50+ Years of Age
Authors: Nelson Christi L , Andel Ross
Published: December 2019

Background and Objectives

Based on the Minority Stress Theory, this article examines the associations between sexual orientation and self-reported measures of physical, mental, and cognitive health, as well as health risk behaviors.

Research Design and Methods

The analytical sample included members of the 2016 wave of the Health and Retirement Study aged 50+ years. Binary and ordered logistic regressions were conducted to assess whether being a sexual minority was associated with poorer self-rated physical, mental, and cognitive health, as well as being more likely to engage in health risk behaviors.

Results

In analyses using overall and propensity-matched samples, lesbian, gay, and bisexual (LGB) participants were about twice as likely to report ever having depression as their heterosexual counterparts but were also more likely to report better self-rated health. The LGB group was more likely to report ever having smoked but were not significantly different in any of the other health risk behaviors.

Discussion and Implications

LGB individuals appear to be at greater risk of ever experiencing depression than heterosexual individuals but, at the same time, report better physical health. This may suggest a tendency for resilience. Differences in health risk behavior may also exist. Mental health and other medical professionals should receive special training to better understand the unique problems of LGB individuals.
Decolonizing History: Enquiry and Practice
Authors: Behm Amanda , Fryar Christienna , Hunter Emma , Leake Elisabeth , Lewis Su Lin , Miller-Davenport Sarah
Published: December 2019

On the back of the Royal Historical Society’s 2018 report on race and ethnicity, as well as ongoing discussions about ‘decolonizing the syllabus’, this is a conversation piece titled, ‘Decolonizing History: Enquiry and Practice’. While ‘decolonization’ has been a key framework for historical research, it has assumed increasingly varied and nebulous meanings in teaching, where calls for ‘decolonizing’ are largely divorced from the actual end of empire. How does ‘decolonizing history’ relate to the study of decolonization? And can history, as a field of practice and study, be ‘decolonized’ without directly taking up histories of empire? Using the RHS report as a starting point, this conversation explores how we ‘decolonize history’. We argue that, rather than occurring through tokenism or the barest diversification of reading lists and course themes, decolonizing history requires rigorous critical study of empire, power and political contestation, alongside close reflection on constructed categories of social difference. Bringing together scholars from several UK universities whose teaching and research ranges across modern historical fields, this piece emphasizes how the study of empire and decolonization can bring a necessary global perspective to what tend to be framed as domestic debates on race, ethnicity, and gender.
Forecasting for recreational fisheries management: a derby fishery case study with Gulf of Mexico Red Snapper
Authors: Farmer Nicholas A , Froeschke John T , Records David L
Published: December 2019

In a derby fishery, anglers race to catch as many fish as possible during a limited season. To meet legal mandates to prevent overfishing, forecasting accuracy is paramount. Red Snapper is among the most prized species in the US Gulf of Mexico and represents a politically charged derby fishery case study. We describe the management considerations, data, methods, and specialized statistical forecasting approaches used to estimate recreational component season lengths to maximize fishing opportunities while meeting mandates to constrain catch below legal limits. Retrospective analysis of model predictions for 2013–2017 indicated mean prediction error of 2626 ± 13 231, 3014 ± 15 744, and 42 975 ± 132 032 pounds whole weight per open day for charter, headboat, and private mode catch rates, respectively. Forecasting results using generalized linear models indicated that the annual harvest for 2017 would be caught in 2 d for the private angling component with an 18% probability of exceeding the component quota. The federal for-hire (charter and headboat) component season was estimated to be 48 d, with a 5% probability of exceeding the component quota. There is a broad scientific and management interest in identifying strategies to continue rebuilding the stock while increasing stakeholder access.
Preoperative neurological deficit in acute type A aortic dissection
Authors: Kreibich Maximilian , Desai Nimesh D , Bavaria Joseph E , Szeto Wilson Y , Vallabhajosyula Prashanth , Itagaki Ryo , Okamura Homare , Kimura Naoyuki , Yamaguchi Atsushi , Beyersdorf Friedhelm , Czerny Martin , Rylski Bartosz
Published: December 2019

OBJECTIVES

Our goal was to evaluate postoperative outcomes in patients with type A aortic dissection with preoperative neurological deficits independent of shock.

METHODS

Between 2002 and 2017, 150 of 1600 patients, operated on for aortic dissection type A in 3 centres, presented with preoperative new onset neurological deficits. Postoperative outcomes were classified using a modified Rankin Scale (mRS) as ‘no to moderate disability’ (mRS 0–3) or as ‘poor clinical outcome’ (mRS 4–6). Clinical and radiographic data were analysed.

RESULTS

Ninety-three patients (62%) had no to moderate disability and 57 (38%) had a poor clinical outcome. The in-hospital mortality rate was 18% (28 patients). Patients with poor clinical outcomes were significantly older (P = 0.01) and had a significantly higher incidence of hypertension (P = 0.04), history of stroke (P = 0.03) and common carotid artery occlusion (left common carotid artery: P = 0.01; right common carotid artery: P < 0.01). One-third of all patients developed haemodynamic instability (P = 0.27). Cardiopulmonary bypass (P < 0.01) and cross-clamp (P = 0.03) times were significantly longer in patients with poor clinical outcomes. Age (odds ratio 1.041; P = 0.02) and history of stroke (odds ratio 2.651; P = 0.03) were predictive of poor clinical outcome; coma was not. Haemorrhagic transformation occurred in 7 patients without any independent predictors.

CONCLUSIONS

Most patients with preoperative neurological deficit have no to moderate disability postoperatively but commonly develop preoperative haemodynamic instability. This study suggests that an immediate surgical approach may be reasonable in patients with preoperative neurological deficit or coma.
Ontological Counter-securitization in Asymmetric Power Relations: Lessons from Israel
Authors: Jamal Amal
Published: December 2019

This article seeks to enhance the understanding of ontological counter-securitization and the constitution of securitized subjects in the context of asymmetrical power relations. It builds on the available critique of the conceptualization of counter-securitization and the differentiation between physical and ontological securitization in order to facilitate a better understanding of the identity formation of securitized subjects as resistance. It argues that whereas the current literature deals with the differentiation between physical and ontological dimensions of securitization and recently with the meaning of counter-securitization, nonetheless the treatment of the later as a resistance is limited. It remains in the realm of the physical dimensions of securitization, rendering ontological ones unaddressed. The article argues that ontological counter-securitization emerges as an analytical category when the mismatch between the physical and ontological securitization policies is utilized as a structural opportunity for resisting asymmetrical power relations. The article exemplifies its theoretical arguments through exploring the complicated securitization policies of Israel toward its Palestinian citizens and the resistance of the latter to such policies. It argues that despite the fact that the Israeli physical and ontological securitization of its Palestinian citizens have not matched, they have been constructed as complementary and therefore have not been morally justifiable. This lack of moral justifiability has had repercussions on the legitimacy of the securitization policy, leading to the rise of the securitized subject as a securitizing agency that is able to practice counter-securitization. Since the power relations between the state and its Palestinian citizens has been asymmetrical, the latter limited their counter-securitization to the ontological dimension, manifested through politicizing their indigenous identity. The conceptualization of politicizing indigeneity as an ontological counter-securitization strategy of resistance has not been addressed in the available literature on securitization theory. Thus, exploring its analytical merits is a central goal of this article.
The Behavioral Response of Blattella germanica (Blattodea: Ectobiidae) Exposed to DEET Varies Throughout Its Life Cycle
Authors: Reynoso M M N , Mengoni S , Alzogaray R A
Published: December 2019

The German cockroach, Blattella germanica L., is a hemimetabolous insect pest of economical and medical importance. N,N-diethyl-3-methylbenzamide (DEET) is an insect repellent whose effect on this species has received very little attention. The objective of this work was to determine whether the behavioral response of B. germanica to DEET varies along its life cycle. DEET repellence was assessed in small, medium, and large nymphs, and in adults of both sexes, all originated from the same laboratory colony (CIPEIN). The experimental arena consisted in a piece of filter paper treated with repellent on one half (195 µg/cm2) and solvent alone on the other half. A cockroach was placed on the filter paper, and its behavior was filmed. An image analyzer was used to quantify how long the insect spent on each side of the paper. As a control, a cockroach was exposed to a piece of filter paper treated with solvent (acetone) alone. Each assay was repeated independently six times. Distribution coefficient (DC) values were calculated, a parameter that ranges between 0 (attraction) and 1 (repellence). Small nymphs were more sensitive to DEET (mean DC = 0.93). The mean DC values of the other groups varied between 0.62 (medium nymphs) and 0.71 (male adults). The group of medium nymphs was the only one whose behavior was not significantly altered by exposure to DEET. The results show the importance of assessing insect repellents at different stages of the insect’s life cycle in order to obtain a complete panorama of its effect.
Mapping Quantitative Trait Loci for Resistance to Fall Armyworm (Lepidoptera: Noctuidae) Leaf-Feeding Damage in Maize Inbred Mp705
Authors: Womack E D , Williams W P , Smith J S , Warburton M L , Bhattramakki D
Published: December 2019

The fall armyworm, Spodoptera frugiperda (J. E. Smith), is an agronomically important pest that severely limits maize (Zea mays (Linnaeus) [Poales: Poaceae]) production. This migrant insect devastates maize plants in many countries threatening the livelihood of millions. Quantitative trait loci (QTL) were mapped to identify chromosomal regions that control resistance to fall armyworm leaf-feeding and to identify molecular markers linked to the target loci for use in marker-assisted selection (MAS). A bi-parental mapping population, comprising 243 F2:3 families from the cross Mp705 (resistant) × Mp719 (susceptible), was evaluated for fall armyworm leaf-feeding damage under artificial infestation over 3 yr. A linkage map comprised of 1,276 single-nucleotide polymorphism and simple sequence repeat molecular markers was constructed. Quantitative trait loci analyses identified two major QTL in bins 4.06 and 9.03 that when combined, explained 35.7% of the phenotypic variance over all environments. Mp705 was responsible for the leaf-feeding damage reducing alleles for both large effect QTL and most of the small effect QTL identified in this study. The QTL identified in bin 9.03 co-locates with a previously identified QTL that controls resistance to leaf-feeding damage in maize by fall armyworm and other lepidopteran insects. The QTL in bin 4.06 is a new source of resistance identified in this study. Beneficial alleles derived from Mp705 for the application of an integrated QTL-MAS approach could accelerate breeding efforts to minimize fall armyworm leaf-feeding in maize.
Evaluating the Efficacy of Oxalic Acid Vaporization and Brood Interruption in Controlling the Honey Bee Pest Varroa destructor (Acari: Varroidae)
Authors: Jack Cameron J , van Santen Edzard , Ellis James D
Published: December 2019

A successful Integrated Pest Management approach to Varroa destructor Anderson and Trueman control in managed colonies of western honey bees Apis mellifera Linnaeus (Hymenoptera: Apidae) must be an improvement over conventional control methods and include cost-effective treatments that can be readily employed by beekeepers. Herein, we tested the efficacy of oxalic acid (OA) vaporization and brood interruption as Varroa controls. Sixty experimental colonies were randomly assigned to one of six treatment groups with 10 colonies per group. The six treatments were: 1) OA applied once, 2) OA applied three times, 3) brood interruption, 4) OA applied once + brood interruption, 5) OA applied three times + brood interruption, and 6) no OA or brood interruption. The OA was applied via vaporization, with each application being 1 g OA applied through the hive entrance (label rate), on the bottom board. Brood interruption was accomplished by caging a colony’s queen in a queen cage for a period of 24 d. An additional 10 colonies were treated with amitraz (Apivar - positive control). Varroa levels were estimated before, during, and after treatment applications using sticky boards left in colonies for 3 d. Our data suggest that queen caging to achieve brood interruption during the fall season can negatively impact colony strength and survival. We observed high colony mortality in some treatments, despite diligent colony management to alleviate the side effects of the treatments. Colonies treated with amitraz were healthier and had better survival than those treated with OA vaporization. In conclusion, OA and/or brood interruption did not provide sufficient Varroa control.
Limbic Predominant Age-Related TDP-43 Encephalopathy (LATE): Clinical and Neuropathological Associations
Authors: Besser Lilah M , Teylan Merilee A , Nelson Peter T
Published: December 2019

Recently, a consensus working group provided new terminology for a common disease entity, limbic predominant age-related TDP-43 encephalopathy (LATE), and its neuropathological substrate (LATE-NC). LATE-NC not only often co-occurs with Alzheimer disease neuropathological change (ADNC), but also may present in isolation. The present study aimed to investigate potential risk factors and neuropathological characteristics associated with LATE-NC. A sample of 616 autopsied participants (>75 years at death), with TDP-43 immunohistochemical studies performed, was obtained from the National Alzheimer’s Coordinating Center. Logistic regression analyses examined associations between demographic, clinical and neuropathological characteristics and LATE-NC (TDP-43 in amygdala, hippocampus, or entorhinal/inferior temporal cortex) (alpha = 0.05). Adjusted models indicated that ADNC, hippocampal sclerosis (HS), arteriolosclerosis, and limbic or amygdala-predominant Lewy body disease (LBD), but not other LBD subtypes, were associated with higher odds of LATE-NC, whereas congestive heart failure (CHF) and motor problems as first predominant symptom were associated with lower odds of LATE-NC. Our findings corroborate previous studies indicating associations between LATE-NC and ADNC, HS, and arteriolosclerosis. Novel findings suggest the association with LATE-NC is restricted to amygdala/limbic-predominant subtype of LBD, and a possible protective (or competing risk) association with CHF. This study may inform future hypothesis-driven research on LATE-NC, a common brain disease of aging.
Aboveground biomass and seasonal patterns of aboveground net primary productivity in five bamboo species in northern Laos
Authors: Xayalath Singkone , Hirota Isao , Tomita Shinsuke , Nakagawa Michiko
Published: December 2019

Aims

Accurate estimates of bamboo biomass and net primary productivity (NPP) are required to evaluate the carbon sequestration potential of bamboo forests. However, relevant data that are important for climate change mitigation, have rarely been collected in regions outside of East Asia and India. Information on seasonal patterns of NPP and its components will enable the quantification of factors that influence the carbon balance in bamboo forests. In this study, we quantified the aboveground biomass (AGB) and aboveground NPP of five major bamboo species in northern Laos using monthly data collected over a 12-month period.

Methods

All live culms in 10, 2 m × 2 m plots (for one monopodial bamboo species: Indosasa sinica) and 30 clumps per species (for four sympodial bamboo species: Bambusa tulda, Cephalostachyum virgatum, Dendrocalamus membranaceus and Gigantochloa sp.) were numbered and measured at breast height. We set 10 or 20 litter traps per species to collect litterfall. Censuses of dead and recruited culms and litterfall collection were performed once per month for 12 months.

Important Findings

The AGB was highest in I. sinica (59.87 Mg ha−1) and lowest in C. virgatum (11.54 Mg ha−1), and was mostly below the plausible global range for bamboos (32–256 Mg ha−1). The sympatric distribution of multiple bamboo species at the study sites may have suppressed the AGB in four of the five studied species. The aboveground NPP estimates were between 3.43 and 14.25 Mg ha−1 yr−1; those for D. membranaceus (8.20 Mg ha−1 yr−1) and I. sinica (14.25 Mg ha−1 yr−1) were comparable to mean global estimates for temperate evergreen forests (8.78 Mg ha−1 yr−1) and tropical moist forests (10.56 Mg ha−1 yr−1). High culm recruitment rates (15.20–23.39% yr−1) were major contributors to aboveground NPP estimates. Seasonal patterns of aboveground NPP were largely influenced by the phenology of the new culms. In the four sympodial bamboo species, new culms began to emerge following the onset of persistent rainfall, mainly in July and August. However, the sprouting of new culms in the monopodial species I. sinica followed a trend of increasing temperatures, mainly in March and April. Thus, our results indicate that bamboos have considerable potential for sequestering carbon in northern Laos, but that this potential may be affected by climate change.
High incidence of dengue in Israel travelers to Kathmandu, Nepal, in 2019
Authors: Lachish Tamar , Lustig Yaniv , Leshem Eyal , Katz-Likvornik Shiri , Biber Asaf , Nadir Eyal , Schwartz Eli
Published: December 2019

We describe the emergence of dengue in Kathmandu in Nepal in 2019. We found a high incidence in Israeli travelers. The circulating serotypes were identified as DENV-2 and DENV-3 with phylogenetic analysis suggesting that the latter serotype originated from India. Travelers to Nepal should be aware of the potential dengue risk beyond the Terai.
Indications for Mechanical Circulatory Support
Authors: Dickinson Michael , Wilkinson Stephen , Jani Milena
Published: December 2019

Optimal patient selection for mechanical circulatory support depends on a while accurate assessment of a given patient’s anticipated trajectory from advanced heart failure and early intervention before end organ damage occurs. Life-limiting non-cardiac diagnoses must be ruled out and goals of therapy should be defined according to the patient’s long-term wishes. This chapter reviews many of the commonly used tools that can aid the heart failure provider in planning for advanced therapies. Options and goals will vary according to what the duration of intended use may be. While guidelines are available, it is often the bedside clinical judgement that determines what device and when to implement. Most often the error is in waiting too long to initiate therapy which runs the risk of poor outcomes.
Palliative Care in Mechanical Circulatory Support
Authors: Mackey Regina M. , Strand Jacob J.
Published: December 2019

Palliative care teams are increasingly involved in the care of patients with advanced circulatory failure and play an important role in the care of patients undergoing implantation of left ventricular assist devices. Palliative care teams focus on symptom management, caregiver support, and robust advance care planning for patients in the pre-implantation and post-implantation phase of care. Preoperative envolvement of Palliative care is effective in helping the patient articulate his/her goals and reason for pursuing surgical intervention as well as declaring just how committed the patient is to long term medical care should various types of complications occur in the perioperative period. This provides comfort to the family when a difficult decision has to be made at a time when the patient can’t take an active part in making that decision. Effective Palliative care teams are present to celebrate the victories as well as the failures in patient care.
The Abbott CentriMag™ Acute Circulatory Support System and the HeartMate Percutaneous Heart Pump™
Authors: Farrar David J.
Published: December 2019

Abbott currently offers two short-term circulatory support systems. The Abbott CentriMag™ Acute Circulatory Support System has a magnetically levitated impeller in a centrifugal blood pump that provides hemocompatible left and/or right ventricular support across a range of clinical conditions. Clinical experience with the CentriMag system is extensive, with more than 40,000 sold and more than 150 articles in the literature. The HeartMate Percutaneous Heart Pump (PHP) System is a catheter-based heart pump and console designed to provide short-term left ventricular support to rapidly stabilize hemodynamics or to maintain adequate cardiac output. The key feature of the pump is an integrated 14 Fr arterial sheath that is placed through the femoral artery. The distal portion of the catheter then expands to 24 F after it is inserted into the left ventricle across the aortic valve. This feature is made possible by a collapsible elastomeric impeller and cannula that the operator expands during use. The impeller pumps blood from the left ventricle through the collapsible, nitinol-reinforced polyurethane cannula into the ascending aorta.
EVAHEART® 2 Left Ventricular Assist Device System
Authors: Motomura Tadashi
Published: December 2019

The EVAHEART® left ventricular assist device (LVAD) system has been used in over 170 patients as bridge to transplantation (BTT) in Japan. Sixty percent of the patients are supported over 2 years, with the longest support time being 10.5 years. EVAHEART® is a centrifugal pump that has demonstrated high pulse pressure, excellent hemocompatibility, and low pump thrombosis. Recently, the EVAHEART® 2 was developed, which incorporates a smaller pump housing and a unique tip-less inflow cannula design. EVAHEART® 2 is currently approved by the PMDA in Japan and is under clinical trial in the United States for BTT and extended support.
Concomitant Cardiac Valve Procedures with Circulatory Support Device Implantation
Authors: Dembitsky Walt , Adamson Robert , Limmer Karl , Larson Craig
Published: December 2019

In patients with advanced heart failure being considered for mechanical circulatory support (MCS), some degree of structural heart disease must often be considered in operative planning. The desire to surgically correct these structural lesions to improve long-term outcomes must be balanced against the goal of simplifying device implantation to improve short-term outcomes. This chapter discusses the rationale, approach, and outcomes related to adding concomitant cardiac surgical interventions during MCS device implantation.
Infectious Complications of Mechanical Circulatory Support
Authors: Sanchez Joyce L. , Baures Timothy J. , Mazi Patrick B. , Windham Samuel L.
Published: December 2019

Implanted mechanical circulatory support devices introduce both short- and long-term risks for infection. With the evolution of surgical techniques and current device technology, the incidence of major infections has decreased, but the overall incidence of infections has remained stable. The need for a percutaneous driveline means that these patients will remain at risk for infection in both superficial and deeper structures, including blood-stream infections. Over time, the spectrum of infecting organism(s) at each site has increasingly been characterized, allowing for early, appropriate antibiotic treatment and decreasing death from infections. The standardization of criteria has increased diagnostic specificity and allows studies to evaluate the optimal antibiotics and duration of therapy. Consultation with an infectious disease specialist familiar with device infections will minimize morbidity and potential delays in transplantation.
Renal Failure and Mechanical Circulatory Support Devices
Authors: Keri Krishna , Agarwal Mohit
Published: December 2019

Advanced heart failure patients typically have reduced renal reserve due to prolonged hemodynamic impairment and coexisting cardiorenal syndrome. This increases the risk of acute kidney injury following any type of surgical intervention. Even minimally compromised renal function can significantly increase the morbidity and mortality of these procedures. For these reasons, there is a critical need to carefully assess these risk factors in the preoperative setting, modifying them when possible in order to reduce the incidence of renal dysfunction. In cases where acute kidney injury occurs despite taking the appropriate preventative measures, a detailed understanding of the different modalities of renal replacement and the timing with which these methods are initiated can have a substantial impact on postoperative outcomes.
Introduction
Authors: Wainwright Elaine , Eccleston Christopher
Published: December 2019

This chapter sets out how the book achieves its aim of providing an authoritative, thought-provoking analysis of the relationship between all forms of occupation (school, employment, later life production) and pain. We begin with a brief introduction to why this aim is important, and show what a consideration of work and pain can offer. We introduce our life-span approach and scope of the book, covering Foundations (what is work, what is pain, how do they link), Investigations (into the interactions between pain and family life, learning, emerging adulthood, the occupational health workforce, and later life), and Interventions (from psychological, workplace, and policy-making perspectives). We signpost readers to our Discussion in which we bring together the book’s findings in a conceptual and analytical map of the forces of change in work, occupation, and pain management to suggest future ways of thinking about policy, practice, and research agendas.
The impact of chronic pain on school functioning in young people
Authors: Caes Line , Logan Deirdre
Published: December 2019

School plays a central role in young people’s lives, offering a developmental environment that fosters crucial academic, emotional, cognitive, and social milestones. This chapter presents a critical discussion of how a young person’s school functioning can be negatively affected by chronic pain. We highlight how the impact of chronic pain, and associated psychosocial factors, goes beyond school absenteeism to influence school engagement, executive functioning skills, and social skills development. Furthermore, the challenges teachers face to provide an inclusive school environment for young people with chronic pain will be discussed in depth. The chapter ends with suggestions of how to overcome the barriers to implementing a comprehensive approach towards school functioning within both research and clinical practice, including reviewing standardized tools to assess school impairment and offering guidance for biopsychosocially informed approaches to foster adaptive school functioning in young people with chronic pain.
Cancer Registries
Authors: Siesling Sabine , Bray Freddie , Zanetti Roberto , Matsuda Tomohiro , Gavin Anna , Voogd Adri , Kohler Betsy , McCabe Ryan
Published: December 2019

Abstract: Cancer registries provide insight into the burden of cancer by systematically recording data on new (pre)malignancies and/or in-situ tumours within a specific region, area, or treatment setting (e.g. hospital-based care). An understanding of the burden for a patient group at the population level is given by indicators such as incidence, survival, treatment modalities and timing, and prevalence. Mortality data are often obtained through national or regional death registries. Registries play a vital role in research into the causes of cancer, both by providing data on patterns and trends, and in different types of epidemiological studies (in particular, in their ability to follow up groups of persons exposed to a potential hazard). They comprise an essential element in the planning and monitoring of cancer control strategies as well as for identifying priorities in public health. Increasingly, registries in developed countries have begun to gather more data on treatments and outcomes (such as recurrences), which can be used for monitoring quality of care, guideline adherence, and outcome research.
What Defines a Breast Centre? An NAPBC Vision
Authors: Kaufman Cary S , Sarantou Terry
Published: December 2019

Abstract: The definition of a breast centre includes leadership with authority, multidisciplinary care and conferences, database maintenance, quality improvement, research, and community outreach. The National Accreditation Program for Breast Centers (NAPBC) in the USA has defined a set of standards to monitor compliance with the underlying goals of a breast centre.
Educational and Training Harmonization in Breast Care
Authors: Wyld Lynda , Markopoulos Christos
Published: December 2019

Abstract: The primary treatment modality for breast cancer is surgery, which is a craft specialty requiring lengthy, high-quality training to achieve competency. This is especially true in an era of complex multidisciplinary oncology regimes and oncoplastic and reconstructive surgeries. Globally, training in breast surgery is highly variable in length, content, and quality, contributing to significant variation in the quality of care and outcomes. This chapter reviews training and its assessment and validation globally.
The Multidisciplinary Meeting
Authors: Sarantou Terry , Kaufman Cary , Eniu Alexandru , Siesling Sabine , Espié Marc , Verbeek Xander , Salgado Roberto
Published: December 2019

Abstract: Team-based care for a patient diagnosed with breast cancer is critical. The breast cancer disease-based team is composed of physicians from different specialties as well as nurses and other support staff. Breast cancer conference and tumour boards allow experts to review a complex case and work together to develop and refine therapeutic strategy. In each case presented, patient history with clinical, radiological, and pathological findings should be reviewed. Applicable treatment algorithms or care paths should be discussed as part of the overall process and to elevate the standard of care. Patients can be given access to clinical trials and important research. The multidisciplinary team (MDT) should meet at a given time (whether physically in one place or by video or teleconferencing) to discuss patients with breast cancer. The presence of an MDT, which meets at least biweekly, is often a requirement or indicator for audits and accreditation. Breast conferences should be accessible to MDT members, participation should be tracked on scorecards, and MDT programmes should be accountable.
Radiology
Authors: Junkermann Hans , Buchberger Wolfgang , Heywang-Köbrunner Sylvia , Michell Michael , Mundinger Alexander , Benn Carol , Zackrisson Sophia
Published: December 2019

Abstract: The three most important imaging methods for breast disease—mammography, ultrasound, and magnetic resonance imaging (MRI)—are discussed regarding their imaging principle, the advantages and disadvantages, and cost and cost-effectiveness in different contexts. The conditions to achieve a high-quality service with these methods are also mentioned. For imaging of symptomatic breast disease, the triple diagnostic approach is strongly advised: (a) clinical assessment, (b) imaging with ultrasound ± mammography, and (c) needle biopsy where appropriate. This approach prevents delay in the diagnosis in nearly all cases. The role of MRI in the primary investigation of symptomatic breast disease is strictly limited to special rare constellations. For screening of women of average risk, mammography is the preferred method in developed countries. Additional imaging for dense tissue is hampered by significant lowering of the specificity and is generally not recommended. In low- and middle-income countries, screening for breast cancer is not cost-effective. Only in high-risk women (genetic or otherwise) is screening with MRI plus mammography the method of choice. A short look into the future addresses upcoming and possible methodological developments in the imaging of breast disease with the prospect of further improving an already well-developed discipline.
Systemic Therapy
Authors: Verhoeven Didier , Brain Etienne , Duhoux François , Schwartsmann Gilberto , Cardoso Fatima
Published: December 2019

Abstract: Quality management of systemic treatment of breast cancer is a high priority, but few quality indicators have been identified so far. As structure indicators, education, day clinic facilities, and a dedicated pharmacy are proposed. As process indicators, access to appropriate experts, equity, and report of the given treatment in accordance to the guidelines are suggested. Overuse can burden the patients with unnecessary toxicity and society with unnecessary costs. Overall survival is the reference standard of outcome, but this is difficult to compare. Just as important are quality of life, patient-reported outcome, and safety. The essential antineoplastic agents for breast cancer are regularly updated by the World Health Organization. Tailored therapy, optimal patient selection, and clinical benefit are becoming key factors for all patients. In the future, a new funding model, precision medicine, and the molecular revolution will require sufficient human resources and networks to organize the best strategies.
Nursing Issues
Authors: Harmer Victoria , Hughes Cathy
Published: December 2019

Abstract: High-quality nurse–patient interaction has the potential to improve patient experience and outcomes of care. Specialist nursing is evolving to include a range of roles to support more complex care in a changing healthcare landscape, where there is an increase in incidence, an ageing population with comorbidities, more treatments, and new and novel therapies all delivered under increasing financial pressures. This chapter discusses the main specialist nursing roles in breast cancer care and the key issues facing breast cancer nursing.
The Changing Clinical Research Pathway
Authors: Verhoeven Didier , de Azambuja Evandro , Demey Wim , Teixeira Luis , Schwartsmann Gilberto , Brain Etienne , Cardoso Fatima , Awada Ahmad
Published: December 2019

Abstract: Breast cancer is one of the fastest-growing research areas, where preclinical studies remain very important for understanding the tumour biology. Here, basic and applied science, though different, are very closely related and can be two sides of the same coin. Traditionally, clinical cancer research can be separated into four different phases, I–IV; however, today there is a clear evolution in the methodology of drug development. Adaptive phase II trials in the neoadjuvant setting of locally advanced breast cancer, for example, now provide a model for more rapid assessment of novel phase II drugs and for determining which subtypes will benefit from treatment. An evolution towards more selected patent populations is also being observed. Indeed, conducting clinical research requires not only an efficient design but also important ethical considerations. Pharma industry-only research, which today accounts for some 70% of breast cancer clinical research, raises concerns about objectivity. Finally, bureaucratic regulation is limiting cancer research and should be thoughtfully reconsidered.
Challenges and Threats
Authors: de Azambuja Evandro , Cardoso Fatima , Schwartsmann Gilberto , Verhoeven Didier , Demey Wim , Teixeira Luis , Aftimos Philippe , Brain Etienne , Awada Ahmad
Published: December 2019

Abstract: Breast cancer research requires collaboration between many stakeholders: scientists, the pharmaceutical industry, and patients. The design of trials must be done more in accordance with patients’ needs. More relevant endpoints must be selected. The gap between innovation and clinical practice must be closed. Power and fashion limit optimal achievement of clinical trials.
XMP gas-rich dwarfs in nearby voids: candidate selection
Authors: Pustilnik S A , Egorova E S , Perepelitsyna Y A , Kniazev A Y
Published: December 2019

We introduce a project aimed at systematically searching for eXtremely Metal-Poor (XMP) very gas-rich blue dwarfs in voids in the nearby Universe. Several such galaxies were first identified in the course of an unbiased study of the galaxy population in the nearby Lynx-Cancer void. These very rare and unusual galaxies appear to be the best proxies for the so-called Very Young Galaxies defined recently in the model simulations by Tweed et al. (2018). We discuss the main properties of 10 prototype objects residing in nearby voids and formulate criteria to search for similar dwarfs in other voids. The recently published sample of 1354 Nearby Void Galaxies is used to identify a subsample of 60 void dwarf XMP candidates. We provide a list of these XMP candidates with their main parameters and finding charts. These candidates are the subjects of subsequent spectral, photometric, and H i studies in the accompanying papers. Looking ahead, with reference to the submitted accompanying papers, we find that this study results in the discovery of many new XMP dwarfs with 12+log (O/H) ∼ 7.0–7.3 dex.
Te-REX: a sample of extragalactic TeV-emitting candidates
Authors: Balmaverde Barbara , Caccianiga A , Della Ceca R , Wolter A , Belfiore A , Ballo L , Berton M , Gioia I , Maccacaro T , Sbarufatti B
Published: December 2019

The REX (Radio-Emitting X-ray sources) is a catalogue produced by cross-matching X-ray data from the ROSAT-PSPC archive of pointed observations and radio data from the NRAO VLA Sky Survey, aimed at the selection of blazars. From the REX catalogue, we select a well-defined and statistically complete sample of high-energy peaked BL Lac (HBL). HBL are expected to be the most numerous class of extragalactic TeV-emitting sources. Specifically, we have considered only the REX sources in the currently planned CTA extragalactic survey area satisfying specific criteria and with an optical spectroscopic confirmation. We obtain 46 HBL candidates that we called Te-REX (TeV-emitting REX). We estimate the very high-energy gamma-ray emission, in the TeV domain, using an empirical approach i.e. using specific statistical relations between gamma-rays (at GeV energies) and radio/X-rays properties observed in bright HBL from the literature. We compare the spectral energy distributions (SEDs) with the sensitivities of current and upcoming Cherenkov telescopes and we predict that 14 Te-REX could be detectable with 50 h of observations of CTA and 7 of them also with current Cherenkov facilities in 50 h. By extrapolating these numbers on the total extragalactic sky, we predict that about 800 HBL could be visible in pointed CTA observations and ∼400 with current Cherenkov telescopes in 50 h. Interestingly, our predictions show that a non-negligible fraction (∼30 per cent) of the HBL that will be detectable by CTA is composed of relatively weak objects whose optical nuclear emission is swamped by the host-galaxy light and not (yet) detected by Fermi-LAT.
Evidence of proteins, chromosomes and chemical markers of DNA in exceptionally preserved dinosaur cartilage
Authors: Bailleul Alida M , Zheng Wenxia , Horner John R , Hall Brian K , Holliday Casey M , Schweitzer Mary H
Published: December 2019

A histological ground-section from a duck-billed dinosaur nestling (Hypacrosaurus stebingeri) revealed microstructures morphologically consistent with nuclei and chromosomes in cells within calcified cartilage. We hypothesized that this exceptional cellular preservation extended to the molecular level and had molecular features in common with extant avian cartilage. Histochemical and immunological evidence supports in situ preservation of extracellular matrix components found in extant cartilage, including glycosaminoglycans and collagen type II. Furthermore, isolated Hypacrosaurus chondrocytes react positively with two DNA intercalating stains. Specific DNA staining is only observed inside the isolated cells, suggesting endogenous nuclear material survived fossilization. Our data support the hypothesis that calcified cartilage is preserved at the molecular level in this Mesozoic material, and suggest that remnants of once-living chondrocytes, including their DNA, may preserve for millions of years.