bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetics and the conservation of natural populations: allozymes to genomes
Authors: Allendorf Fred W. 
Published: December 2016

I consider how the study of genetic variation has influenced efforts to conserve natural populations over the last 50 years. Studies with allozymes in the 1970s provided the first estimates of the amount of genetic variation within and between natural populations at multiple loci. These early studies played an important role in developing plans to conserve species. The description of genetic variation in mitochondrial DNA in the early 1980s laid the foundation for the field of phylogeography, which provided a deeper look in time of the relationships and connectivity among populations. The development of microsatellites in the 1990s provided much more powerful means to describe genetic variation at nuclear loci, including the ability to detect past bottlenecks and estimate current effective population size with a single temporal sample. In the 2000s, single nucleotide polymorphisms presented a cornucopia of loci that has greatly improved power to estimate genetic and population demographic parameters important for conservation. Today, population genomics presents the ability to detect regions of the genome that are affected by natural selection (e.g. local adaptation or inbreeding depression). In addition, the ability to genotype historical samples has provided power to understand how climate change and other anthropogenic phenomena have affected populations. Modern molecular techniques provide unprecedented power to understand genetic variation in natural populations. Nevertheless, application of this information requires sound understanding of population genetics theory. I believe that current training in conservation genetics focuses too much on the latest techniques and too little on understanding the conceptual basis which is needed to interpret these data and ask good questions.
Shifts in the distribution of ixodid ticks parasitizing cattle in Zimbabwe
Authors: SUNGIRAI M. , ABATIH E. N. , MOYO D. Z. , CLERCQ P. De , MADDER M. 
Published: December 2016

Abstract.In an attempt to update information on the ecological distribution of ixodid ticks (Ixodida: Ixodidae) in Zimbabwe, a cross‐sectional survey was carried out between September 2013 and May 2015 at 322 dip tanks. A total of 15 tick species were collected, namely: Amblyomma hebraeum Koch (65.2%, n = 210/322), Amblyomma variegatum Fabricius (14.9%, n = 48/322), Hyalomma rufipes Koch (62.4%, n = 201/322), Hyalomma truncatum Koch (37.9%, n = 122/322), Rhipicephalus appendiculatus Neumann (60.6%, n = 195/322), Rhipicephalus compositus Neumann (0.3%, n = 1/322,), Rhipicephalus decoloratus Koch (61.8%, n = 199/322), Rhipicephalus evertsi evertsi Neumann (65.2%, n = 210/322), Rhipicephalus lunulatus Neumann (4%, n = 13/322), Rhipicephalus microplus Canestrini (32%, n = 103/322), Rhipicephalus near punctatus Walker and Horak (7.1%, n = 23/322), Rhipicephalus simus Koch (5.6%, n = 18/322) and Rhipicephalus cf. turanicus Pomerantsev (3.4%, n = 11/322). Compared with previous surveys, changes in the distribution of A. hebraeum, A. variegatum and R. microplus were recorded. The distributions of other tick species have largely remained unchanged. Factors which might have influenced these changes and the possible impacts on the epidemiology of tick‐borne diseases are discussed.
Engineering chloroplasts to improve Rubisco catalysis: prospects for translating improvements into food and fiber crops
Authors: Sharwood Robert E. 
Published: December 2016

SummaryThe uncertainty of future climate change is placing pressure on cropping systems to continue to provide stable increases in productive yields. To mitigate future climates and the increasing threats against global food security, new solutions to manipulate photosynthesis are required. This review explores the current efforts available to improve carbon assimilation within plant chloroplasts by engineering Rubisco, which catalyzes the rate‐limiting step of CO2 fixation. Fixation of CO2 and subsequent cycling of 3‐phosphoglycerate through the Calvin cycle provides the necessary carbohydrate building blocks for maintaining plant growth and yield, but has to compete with Rubisco oxygenation, which results in photorespiration that is energetically wasteful for plants. Engineering improvements in Rubisco is a complex challenge and requires an understanding of chloroplast gene regulatory pathways, and the intricate nature of Rubisco catalysis and biogenesis, to transplant more efficient forms of Rubisco into crops. In recent times, major advances in Rubisco engineering have been achieved through improvement of our knowledge of Rubisco synthesis and assembly, and identifying amino acid catalytic switches in the L‐subunit responsible for improvements in catalysis. Improving the capacity of CO2 fixation in crops such as rice will require further advances in chloroplast bioengineering and Rubisco biogenesis.

Contents

Summary
494

I.
Introduction
495

II.
Prokaryotic ancestry of chloroplasts influences gene regulatory mechanisms
496

III.
The target enzyme of CO2 fixation within chloroplasts – Rubisco
496

IV.
Oxygenation of RuBP leads to photorespiration and hampers C3 plant photosynthesis
499

V.
Exploring nature for improved Rubisco
499

VI.
Prospects for improving rice photosynthesis by altering Rubisco catalysis
501

VII.
Engineering CO2 assimilation in higher plants by plastid transformation
501

VIII.
Direct bioengineering of Rubisco in higher plants
502

IX.
The next challenges that need to be met for Rubisco engineering
505

X.
Conclusions
506

Acknowledgements
507

References
507
The role of electrical and jasmonate signalling in the recognition of captured prey in the carnivorous sundew plant Drosera capensis
Authors: Krausko Miroslav , Perutka Zdeněk , Šebela Marek , Šamajová Olga , Šamaj Jozef , Novák Ondřej , Pavlovič Andrej 
Published: December 2016

Summary

The carnivorous sundew plant (Drosera capensis) captures prey using sticky tentacles. We investigated the tentacle and trap reactions in response to the electrical and jasmonate signalling evoked by different stimuli to reveal how carnivorous sundews recognize digestible captured prey in their traps.

We measured the electrical signals, phytohormone concentration, enzyme activities and Chla fluorescence in response to mechanical stimulation, wounding or insect feeding in local and systemic traps. Seven new proteins in the digestive fluid were identified using mass spectrometry.

Mechanical stimuli and live prey induced a fast, localized tentacle‐bending reaction and enzyme secretion at the place of application. By contrast, repeated wounding induced a nonlocalized convulsive tentacle movement and enzyme secretion in local but also in distant systemic traps. These differences can be explained in terms of the electrical signal propagation and jasmonate accumulation, which also had a significant impact on the photosynthesis in the traps.

The electrical signals generated in response to wounding could partially mimic a mechanical stimulation of struggling prey and might trigger a false alarm, confirming that the botanical carnivory and plant defence mechanisms are related. To trigger the full enzyme activity, the traps must detect chemical stimuli from the captured prey.
Focusing on situation‐specific expectations in major depression as basis for behavioural experiments – Development of the Depressive Expectations Scale
Authors: Kube Tobias , D'Astolfo Lisa , Glombiewski Julia A. , Doering Bettina K. , Rief Winfried 
Published: December 2016

ObjectivesDysfunctional expectations are considered to be core features of various mental disorders. The aim of the study was to develop the Depressive Expectations Scale (DES) as a depression‐specific measure for the assessment of dysfunctional expectations. Whereas previous research primarily focused on general cognitions and attitudes, the DES assesses 25 future‐directed expectations (originally 75 items) which are situation‐specific and falsifiable.Design and methodsTo evaluate the psychometric properties of the DES, the scale was completed by 175 participants with and without severe depressive symptoms in an online survey. Participants additionally completed the Patient Health Questionnaire modules for depression (PHQ‐9) and anxiety (GAD‐7). People experiencing depressive symptoms were informed about the study with the help of self‐help organizations.ResultsReliability analyses indicated excellent internal consistency of the scale. An exploratory factor analyses revealed four factors: social rejection, social support, mood regulation, and ability to perform. The DES sum score strongly correlated with the severity of depressive symptoms. The DES sum score also significantly correlated with symptoms of generalized anxiety.ConclusionThe DES was shown to have excellent reliability; validity analyses were promising. As the DES items are situation‐specific and falsifiable, they can be tested by the individual using behavioural experiments and may therefore facilitate cognitive restructuring. Thus, a structured assessment of patients’ expectation with help of the DES can provide a basis for interventions within cognitive–behavioural treatment of depression.Practitioner points

Assessing situation‐specific expectations in patients experiencing depressive symptoms can provide a basis for the conduction of behavioural experiments to test patients’ expectations.

For the use of behavioural experiments, therapists should choose those dysfunctional expectations which a patient strongly agrees on.

To modify patients’ expectations, they should be exposed to situations where the discrepancy between patients’ expectations and actual situational outcomes can be maximized.

The Depressive Expectations Scale can be completed repeatedly to monitor a patient's progress within cognitive–behavioural treatment.
The influence of facultative endosymbionts on honeydew carbohydrate and amino acid composition of the black bean aphid Aphis fabae
Authors: Schillewaert Sharon , Parmentier Thomas , Vantaux Amelie , Van den Ende Wim , Vorburger Christoph , Wenseleers Tom 
Published: December 2016

AbstractThe facultative endosymbionts Hamiltonella defensa and Regiella insecticola are commonly found in aphids. They are linked with various ecological benefits but generally occur at low prevalence, which indicates a possible harbouring cost. Little is known about how the presence of facultative endosymbionts is reflected in honeydew composition. Honeydew is the key mediator of the mutualism between aphids and their tending ants. The present study examines whether endosymbionts have an influence on aphid honeydew quality by comparing the amino acid and carbohydrate concentrations between infected and uninfected aphids. To this end, two genetic lines of the aphid Aphis fabae Scopoli are experimentally infected with different strains of Hamiltonella and Regiella. Infected aphids are shown to have reduced concentrations of amino acids in the honeydew compared with uninfected aphids. However, the presence of endosymbionts has no effect on the absolute amount of carbohydrates produced. Nevertheless, interclonal variation in honeydew composition between aphid genotypes is observed for both carbohydrate and amino acid production. These results imply that the nutritional value of honeydew depends on aphid genotype, as well as on the presence of secondary bacterial endosymbionts, which suggests that there is a physiological cost of harbouring endosymbionts and which could also impact aphid attractiveness to tending ants.
Damaging Effects of Ultraviolet Radiation on the Cornea
Authors: Delic Naomi C. , Lyons J. Guy , Di Girolamo Nick , Halliday Gary M. 
Published: December 2016

AbstractThe cornea sits at the anterior aspect of the eye and, like the skin, is highly exposed to ultraviolet radiation (UVR). The cornea blocks a significant proportion of UVB from reaching the posterior structures of the eye. However, UVA can penetrate the full thickness of the cornea, even reaching the anterior portion of the lens. Epidemiological data indicate that UVR is a contributing factor for a multitude of diseases of the cornea including pterygium, photokeratitis, climatic droplet keratopathy and ocular surface squamous neoplasia (OSSN), although the pathogenic mechanisms of each require further elucidation. UVR is a well‐known genotoxic agent, and its effects have been well characterized in organs such as the skin. However, we are only beginning to identify its effects on the cornea, such as the UVR signature C → T and CC → TT transversions identified by sequencing and increased proliferative and shedding rates in response to UVR exposure. Alarmingly, a single low‐dose exposure of UVR to the cornea is sufficient to elicit genetic, molecular and cellular changes, supporting the consideration of using protective measures, such as wearing sunglasses when outdoors. The aim of this review was to describe the adverse effects of UVR on the cornea.
Bimodal Targeting Using Sulfonated, Mannosylated PEI for Combined Gene Delivery and Photodynamic Therapy
Authors: Chitgupi Upendra , Li Yi , Chen Mingfu , Shao Shuai , Beitelshees Marie , Tan Myles Joshua , Neelamegham Sriram , Pfeifer Blaine A. , Jones Charles , Lovell Jonathan F. 
Published: December 2016

AbstractPhotodynamic therapy (PDT) and gene delivery have both been used to target both cancer cells and tumor‐associated macrophages (TAMs). Given the complex nature of tumor tissue, there could be merit in combining these strategies simultaneously. In this study, we developed a bimodal targeting approach to both cancer cells and macrophages, employing materials conducive to both gene delivery and PDT. Polymers libraries were created that consisted of cationic polyethyleneimine (PEI) conjugated to the photosensitizer pyropheophorbide‐a, with sulfonation (to target selectin‐expressing cells) and mannosylation (to target TAMs). Polyplexes, consisting of these polymers electrostatically bound to DNA, were analyzed for transfection efficacy and cytotoxicity toward epithelial cells and macrophages to assess dual‐targeting. This study provides preliminary proof of principle for using modified PEI for targeted gene delivery and PDT.
Daughters of Mothers Who Smoke: A Population‐based Cohort Study of Maternal Prenatal Tobacco use and Subsequent Prenatal Smoking in Offspring
Authors: Ncube Collette N. , Mueller Beth A. 
Published: December 2016

AbstractBackgroundPrenatal exposure to tobacco is associated with adverse health outcomes for the mother and child, and has been associated with an increased risk of tobacco smoking and nicotine dependence in offspring. The objective of this study was to examine the risk of prenatal smoking, among daughters, associated with maternal prenatal smoking.MethodsWe used a population‐based cohort study design, with linked vital records data of mothers and daughters delivering 1984–96 and 1996–2013, respectively, in Washington State. The exposure of interest was mothers’ prenatal smoking (any vs. no smoking at any time during pregnancy), while the outcome was daughters’ prenatal smoking (similarly assessed). We used multivariable log‐binomial regression to obtain estimates of the relative risk (RR) and 95% confidence interval (CI).ResultsDaughters exposed to maternal prenatal smoking were more likely to smoke during their pregnancy, compared to unexposed daughters (RR 1.78, 95% CI 1.72, 1.84, adjusted for the year the daughter delivered, her marital status and educational attainment, and the mothers’ race/ethnicity).ConclusionsIn this relatively young population, we found that daughters exposed to maternal prenatal smoking have an increased risk of smoking later on during their own pregnancy, emphasizing the importance of exposures during the prenatal period. The mechanisms leading to prenatal smoking are multifactorial and likely include behavioural, genetic, epigenetic and environmental factors. An understanding of this risk factor for prenatal smoking may guide health care providers to better target smoking cessation interventions to at‐risk populations.
Assessing fear learning via conditioned respiratory amplitude responses
Authors: Castegnetti Giuseppe , Tzovara Athina , Staib Matthias , Gerster Samuel , Bach Dominik R. 
Published: December 2016

AbstractRespiratory physiology is influenced by cognitive processes. It has been suggested that some cognitive states may be inferred from respiration amplitude responses (RAR) after external events. Here, we investigate whether RAR allow assessment of fear memory in cued fear conditioning, an experimental model of aversive learning. To this end, we built on a previously developed psychophysiological model (PsPM) of RAR, which regards interpolated RAR time series as the output of a linear time invariant system. We first establish that average RAR after CS+ and CS− are different. We then develop the response function of fear‐conditioned RAR, to be used in our PsPM. This PsPM is inverted to yield estimates of cognitive input into the respiratory system. We analyze five validation experiments involving fear acquisition and retention, delay and trace conditioning, short and medium CS‐US intervals, and data acquired with bellows and MRI‐compatible pressure chest belts. In all experiments, CS+ and CS− are distinguished by their estimated cognitive inputs, and the sensitivity of this distinction is higher for model‐based estimates than for peak scoring of RAR. Comparing these data with skin conductance responses (SCR) and heart period responses (HPR), we find that, on average, RAR performs similar to SCR in distinguishing CS+ and CS−, but is less sensitive than HPR. Overall, our work provides a novel and robust tool to investigate fear memory in humans that may allow wide and straightforward application to diverse experimental contexts.
Effects of CPAP therapy on visceral fat thickness, carotid intima‐media thickness and adipokines in patients with obstructive sleep apnoea
Authors: Ng Susanna S.S. , Liu Eric K.H. , Ma Ronald C.W. , Chan Tat‐On , To Kin‐Wang , Chan Ken K.P. , Ngai Jenny , Yip Wing‐Ho , Ko Fanny W.S. , Wong Chun‐Kwok , Hui David S.C. 
Published: December 2016

ABSTRACT
Background and objectiveObstructive sleep apnoea (OSA) is associated with an increased prevalence of metabolic syndrome. This study explores the effects of continuous positive airway pressure (CPAP) for patients with OSA on visceral and mesenteric fat thickness, carotid intima‐media thickness (IMT) and adipokines.MethodsA randomized controlled study was conducted at a teaching hospital on 90 patients newly diagnosed with OSA to receive either therapeutic CPAP or subtherapeutic CPAP for 3 months. Visceral fat thickness and carotid IMT were measured with B‐mode ultrasound; adipokine levels were assessed at baseline and 3 months.ResultsAltogether, 45 patients received therapeutic CPAP and 45 received subtherapeutic CPAP without significant differences in age 50.3 (10.1) versus 48.7 (9.0) years, BMI 28.2 (3.9) versus 28.2 (4.5) kg/m2, Epworth Sleepiness Scale (ESS) 12.4 (5.9) versus 11.3 (4.7), apnoea–hypopnoea index (AHI) 30.6 (21.4) versus 35.2 (25.5) /h, minimum SaO2
79.6 (10.8) versus 76.7 (12.4) % and existing co‐morbidities. CPAP usage was therapeutic 4.2 (2.1) versus subtherapeutic 4.1 (2.0) h/night over 3 months. Adiponectin and irisin levels changed significantly following therapeutic CPAP for 3 months versus subtherapeutic CPAP (−1.6 vs 7.3, P = 0.042; 0.1 vs −0.1, P = 0.028 respectively) while only serum level of monocyte chemotactic protein 1 (MCP‐1) at baseline was positively correlated with AHI (r = 0.278). No significant changes were observed in other adipokines, visceral fat thickness and IMT.ConclusionShort‐term therapeutic CPAP versus subtherapeutic CPAP does not significantly reduce visceral fat thickness and IMT, although it reduces adiponectin and increases irisin.
Bayesian Causality Test for Integer-Valued Time Series Models with Applications to Climate and Crime Data
Authors: Chen Cathy W. S. , Lee Sangyeol 
Published: December 2016

SummaryWe investigate the causal relationship between climate and criminal behaviour. Considering the characteristics of integer-valued time series of criminal incidents, we propose a modified Granger causality test based on the generalized auto-regressive conditional heteroscedasticity type of integer-valued time series models to analyse the relationship between the number of crimes and the temperature as an environmental factor. More precisely, we employ the Poisson, negative binomial and log-linear Poisson integer-valued generalized auto-regressive conditional heteroscedasticity models and particularly adopt a Bayesian method for our analysis. The Bayes factors and posterior probability of the null hypothesis help to determine the causality between the variables considered. Moreover, employing an adaptive Markov chain Monte Carlo sampling scheme, we estimate model parameters and initial values. As an illustration, we evaluate our test through a simulation study and, to examine whether or not temperature affects crime activities, we apply our method to data sets categorized as sexual offences, drug offences, theft of motor vehicles, and domestic-violence-related assault in Ballina, New South Wales, Australia. The result reveals that more sexual offences, drug offences and domestic-violence-related assaults occur during the summer than in other seasons of the year. This evidence strongly advocates a causal relationship between crime and temperature.
Quantifying the risk of nosocomial infection within Ebola Holding Units: a retrospective cohort study of negative patients discharged from five Ebola Holding Units in Western Area, Sierra Leone
Authors: Arkell Paul , Youkee Daniel , Brown Colin S. , Kamara Abdul , Kamara Thaim B. , Johnson Oliver , Lado Marta , George Viginia , Koroma Fatmata , King Matilda B. , Parker Benson E. , Baker Peter 
Published: December 2016

AbstractObjectivesA central pillar in the response to the 2014 Ebola virus disease (EVD) epidemic in Sierra Leone was the role of Ebola Holding Units (EHUs). These units isolated patients meeting a suspect case definition, tested them for EVD, initiated appropriate early treatment and discharged negative patients to onward inpatient care or home. Positive patients were referred to Ebola Treatment Centres. We aimed to estimate the risk of nosocomial transmission within these EHUs.MethodsWe followed up a cohort of 543 patients discharged with a negative EVD test from five EHUs in the Western Area, Sierra Leone, and examined all line‐listed subsequent EVD tests from any facility in the Western Area to see whether the patient was retested within 30 days, matching by name, age and address. We defined possible readmissions as having the same name and age but uncertain address, and confirmed readmissions where name, age and address matched.ResultsWe found a positive readmission rate of 3.3% (18 cases), which included 1.5% confirmed readmissions (8 cases) and 1.8% possible readmissions (10 cases). This is lower than rates previously reported. We cannot ascertain whether EVD was acquired within the EHUs or from re‐exposure in the community. No demographic or clinical variables were identified as risk factors for positive readmission, likely due to our small sample size.ConclusionsThese findings support the EHU model as a safe method for isolation of suspect EVD patients and their role in limiting the spread of EVD.