bluuebunny/crossref_metadata_2025 huggingface dataset:
Of Sound Heart and Mind
Authors: Greenman Paul S. , Viau Pascale , Morin Francis , Lapointe-Campagna Marie-Ève , Grenier Jean , Chomienne Marie-Hélène , Jbilou Jalila
Published: August 2018

Background:

Heart disease is related to the etiology of mental health problems such as depression, anxiety, and posttraumatic stress.

Objective:

The goal of this scoping review was to determine which factors pose a significant risk for the onset of symptoms of depression, anxiety, and posttraumatic stress in patients with heart disease, as well as to identify what might protect them from these afflictions.

Method:

We conducted a thorough search of relevant medical and psychological databases (Scopus, PsycARTICLES, Psychology and Behavioral Sciences Collection, Sage Journals, and MEDLINE) and identified 41 studies that met inclusion criteria, which included all types of heart disease.

Results:

The results of our review indicate that mental health history, the tendency to stifle negative emotional experiences (known as “type D personality”), and social support in patients with heart disease are related to the onset of or protection from depression, anxiety, and posttraumatic stress. These factors, along with gender and younger age, seem to be relatively consistent predictors of mental health problems in this population.

Conclusions:

As per our results, it is important for clinicians to attend to the mental health history, type D personality, and presence and quality of social support in patients with heart disease. More research into prevention and gender differences is necessary to hone the detection and treatment of these problems in people with heart disease.

Clinical Implications:

Attention to their mental health history, their ability to express and regulate affect, their age, and their gender will most likely assist in identifying symptoms of depression, anxiety, and posttraumatic stress in people with cardiac disease. Gender differences, particularly in the manifestation of depression, ought to be taken into account.
Activation in Children and Adolescents Treated With Selective Serotonin Reuptake Inhibitors
Authors: Garcia-Delgar Blanca , Morer Astrid , Varela Eva , Romero Soledad , García Marta , Coffey Barbara J. , Lázaro Luisa
Published: August 2018

Background

Activation is a behavioral adverse event related to the use of psychotropic medication. Its high incidence in pediatrics and in childhood-onset neuropsychiatric disorders suggests it may be linked to neurodevelopment. However, previous studies have scarcely examined the role that factors relevant to developmental pharmacokinetics, such as body weight, may play in the onset of activation in children and adolescents.

Methods

We conducted a retrospective analysis of hospitalized patients to identify the risk factors for activation in children and adolescents treated with selective serotonin reuptake inhibitors. Our focus was on factors related to development, including body weight, to explore the relationship between activation and neurodevelopmental processes.

Results

Among the 139 participants (mean age, 14 ± 2.3 years), activation appeared in 29 (20.9%). Age 12 years or younger and comorbid diagnosis of autism spectrum disorder were associated with statistically significant increases in the risk of activation, but no association was found regarding body weight.

Conclusions

Our findings support the hypothesis that activation is closely linked to brain development processes. Longitudinal studies are needed to explore this line of research further.
New guidelines for hospital-acquired pneumonia/ventilator-associated pneumonia: USA vs. Europe
Authors: Martin-Loeches Ignacio , Rodriguez Alejandro H. , Torres Antoni
Published: August 2018

Purpose of review

The International ERS/ESICM/ESCMID/ALAT guidelines for the management of hospital-acquired pneumonia and ventilator-associated pneumonia were published in 2017 whilst the American guidelines for Management of Adults With Hospital-acquired and Ventilator-associated Pneumonia were launched in 2016 by the Infectious Diseases Society of America/ATS. Both guidelines made updated recommendations based on the most recent evidence sharing not only some parallelisms but also important conceptual differences.

Recent findings

Contemporary therapy for hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP) emphasizes the importance of prompt and appropriate antimicrobial therapy. There is an implicit risk, when appropriate means broad spectrum, that liberal use of antimicrobial combinations will encourage the emergence of multidrug resistant (MDR), extensively drug-resistant (XDR) and pandrug-resistant bacteria (PDR) and generate untreatable infections, including carbapenemase resistant infections.

American and European guidelines have many areas of common agreement such as limiting antibiotic duration. Both guidelines were in favour of a close clinical assessment. Neither recommended a regular use of biomarkers but only in specific circumstances such as dealing with MDR and treatment failure. Risk factor prediction for MDR differed and whilst American guidelines focus on organ failure, the European ones did it in local ecology and septic shock.
Physical activity and weight maintenance: the utility of wearable devices and mobile health technology in research and clinical settings
Authors: Riffenburg Kaitlyn M. , Spartano Nicole L.
Published: August 2018

Purpose of review

The integration of wearable devices and mobile health (mHealth) technology to facilitate behavior change has the potential to transform the efficacy of interventions and implementation programs for weight maintenance. The purpose of this review was to provide a comprehensive analysis of the overall utility of wearable devices for assessing and promoting weight maintenance in research and clinical settings.

Recent findings

Recent intervention trials using wearable devices have been successful in increasing physical activity and decreasing or maintaining body weight, but complex study designs involving multiple behavioral strategies make it difficult to assess whether wearable devices can independently influence weight status. The daily feedback that wearable devices and mHealth technology provide may assist in motivating higher levels of physical activity achievement. However, the integration of wearable devices into the healthcare setting and implementation of mHealth programs still need to be tested.

Recent studies add concrete implications for providers and researchers to better assess and promote physical activity in healthcare settings by identifying how wearable devices can be advantageous for physical activity and health promotion.
The potential of chronopharmacology for treatment of atherosclerosis
Authors: Winter Carla , Soehnlein Oliver
Published: August 2018

Purpose of review

Development of atherosclerosis contributes to cardiovascular diseases that still are the leading cause of mortality worldwide. Successful strategies for treating inflammatory aspects of atherosclerotic lesion development are rare. Here, we review new insights into the impact of circadian rhythmicity on atherogenesis and their potential for innovative time-optimized pharmacological treatment strategies.

Recent findings

Studies on the circadian clock revealed an extensive influence on immune cell activity. Immune cell functionality and their recruitment to injured tissues exhibit circadian rhythmicity. Many indications that the circadian clock also modulates atherogenesis were given in the past. Transcriptome analysis of the aorta reveals a time-dependent expression profile. Furthermore, deficiency of the core clock proteins Bmal1 and Clock consistently accelerates atherosclerosis. Recent work provided new insights on time-dependent leukocyte recruitment to atherosclerotic lesions and its regulatory mechanisms through the CCR2-CCL2 axis. Based on timed CCR2-CCL2 signaling blockage, an effective chronopharmacological treatment strategy was established to reduce early lesion development with concomitant reduction of systemic side effects.

Circadian rhythmicity impacts on the pathogenesis of atherosclerosis. Circadian oscillation in the expression of drug targets may license timed intervention strategies with improved efficacy and lower risk.
Anti‐Cytomegalovirus Activity in Human Milk and Colostrum From Mothers of Preterm Infants
Authors: Donalisio Manuela , Rittà Massimo , Tonetto Paola , Civra Andrea , Coscia Alessandra , Giribaldi Marzia , Cavallarin Laura , Moro Guido E. , Bertino Enrico , Lembo David
Published: August 2018

Objectives:

This study aimed to investigate the anti‐human cytomegalovirus (CMV) activity of milk from seropositive and seronegative mothers of preterm infants and to analyze its changes throughout the different stages of lactation and after Holder pasteurization, a procedure adopted by donor human milk banks.

Methods:

Eighteen mothers of preterm infants were enrolled in the study. Colostrum, transitional milk, and mature milk samples were collected and tested for anti‐CMV activity. Depletion of immunoglobulins A from milk samples was carried out by jacalin resin. Pools of milk samples were pasteurized according to Holder technique.

Results:

All samples were endowed with anti‐CMV activity, although to a different extent. In CMV IgG‐positive mothers, colostra were significantly more active than the transitional milk and mature milk samples. Moreover, they were more potent than colostra from seronegative mothers. Immunoglobulins A depletion in colostra from IgG‐positive mothers resulted in a partial loss of anti‐CMV activity. Holder pasteurization significantly reduced the antiviral activity.

Conclusions:

Human milk is endowed with anti‐CMV activity and its potency may vary depending on the stage of lactation and the serological status of the mother. This biological property could partially neutralize CMV particles excreted in the milk of CMV IgG‐positive mothers thus reducing the risk of transmitting infectious viruses to the infant.
First Intracardiac Kaposiform Hemangioendothelioma in an Infant Resolved With Sirolimus: A Case Report
Authors: Zaidi Syed Javed , Shaik Shaista , Agrawal Caitlin , Cossor Waseem
Published: August 2018

Introduction:

Kaposiform hemangioendothelioma (KHE) is a rare and aggressive vascular tumor that can be associated with a consumptive coagulopathy and thrombocytopenia (Kasabach-Merritt phenomenon). Only one case of an intracardiac KHE has been reported which was treated with surgical excision and then expectant management.

Case Presentation:

We present a patient with an intracardiac KHE which presented as a large mass surrounding the atria, pulmonary veins, superior vena cava, and infiltrating the atrial septum with moderate compression of the superior vena cava and mild compression of the pulmonary veins. This tumor clinically presented as persistent tachypnea and was unresponsive to conventional therapy with vincristine and steroids but responded dramatically to Sirolimus with almost complete regression on follow-up.

Conclusions:

None of the current treatments for KHE, alone or in combination therapy have been found to be effective in a uniform or reproducible manner. Well designed, preferably randomized trials are required for a better understanding of the appropriate dosage and duration as well as response to treatment and a consensus of first and second line therapies.
Retinal Thickness Changes throughout the Natural History of Drusen in Age-related Macular Degeneration
Authors: Nivison-Smith Lisa , Wang Henrietta , Assaad Nagi , Kalloniatis Michael
Published: August 2018

SIGNIFICANCE

Drusen are associated with retinal thinning in age-related macular degeneration (AMD). These changes, however, have mostly been examined at single time points, ignoring the evolution of drusen from emergence to regression. Understanding the full breadth of retinal changes associated with drusen will improve understanding of disease pathogenesis.

PURPOSE

The purpose of this study was to assess how the natural history of drusen affects retinal thickness, focusing on the photoreceptor and retinal pigment epithelium (RPE) layers.

METHODS

Spectral domain optical coherence tomography of subjects with intermediate AMD (n = 50) who attended the Centre for Eye Health, Sydney, Australia, for two separate visits (476 ± 16 days between visits) was extracted. Scans were automatically segmented with manufacturer software then assessed for drusen that had emerged, grown, or regressed between visits. For each identified lesion, the thickness of each retinal layer at the drusen peak and at adjacent drusen-free areas (150 μm nasal and temporal to the druse) was compared between visits.

RESULTS

Before drusen emergence, the RPE was significantly thicker at the drusen site (14.2 ± 2.6%) compared with neighboring drusen-free areas. There was a 71% sensitivity of RPE thickening predicting drusen emergence. Once drusen emerged, significant thinning of all outer retinal layers was observed, consistent with previous studies. Drusen growth was significantly correlated with thinning of the outer retina (r = −0.38, P < .001). Drusen regression resulted in outer retinal layers returning to thicknesses not significantly different from baseline.

CONCLUSIONS

The natural history of drusen is associated with RPE thickening before drusen emergence, thinning of the outer nuclear layer as well as photoreceptor and RPE layers proportional to drusen growth, and return to baseline thickness after drusen regression. These findings have useful clinical applications, providing a potential marker for predicting drusen emergence for AMD prognostic and intervention studies and highlighting that areas of normal retinal thickness in AMD may be former sites of regressed drusen.
Brief Report: Identification of Elite and Viremic Controllers From a Large Urban HIV Ambulatory Center in Kampala, Uganda
Authors: Kayongo Alex , Gonzalo-Gil Elena , Gümüşgöz Emrah , Niwaha Anxious J. , Semitala Fred , Kalyesubula Robert , Bagaya Bernard S. , Joloba Moses L. , Sutton Richard E.
Published: August 2018

Background:

Throughout the world, there are antiretroviral therapy–naive HIV+ individuals who maintain elevated peripheral CD4+ T-cell counts, historically referred to as long-term nonprogressors (LTNPs). With recent improvements in viral load (VL) detection methods to levels as low as 20 copies per milliliter, 2 subsets of LTNPs have been defined: elite controllers (ECs), with undetectable VLs for at least 6–12 months, and viremic controllers (VCs), with VLs between 200 and 2000 copies per milliliter. ECs and VCs have been extensively studied in the developed world to determine underlying mechanisms responsible for virologic control. In sub-Saharan Africa, most studies have characterized LTNPs based on immunologic criteria making it difficult to compare findings with the Western cohorts, which use virologic criteria. Here, we describe a cohort of Uganda ECs and VCs attending a large HIV ambulatory center in Kampala, Uganda, based initially on CD4 counts and confirmed by repeated VL measurements.

Methods:

A cross-sectional study was conducted among 14,492 HIV-infected, antiretroviral therapy–naive individuals aged 18 years and older under care for at least 5 years with serial peripheral CD4 counts ≥500 cells/μL. Among those, we determined the frequency of individuals with VLs <2000 copies per milliliter for at least 6 months.

Results:

We report a prevalence of 0.26% (38/14,492) of HIV controllers in the clinic. We identified 36 ECs and 2 VCs. These individuals were middle-aged with an average CD4 count of 858 ± 172 (mean ± SD, 95% confidence interval: 795 to 921). Their average duration in HIV care was 7.4 ± 2.1 years (mean ± SD, 95% confidence interval: 6.6 to 8.1). The majority of EC/VCs were women (87%, 33/38), reflecting the demographics of the urban clinic.

Conclusions:

For the first time, this study demonstrates the frequency of EC/VCs in a large urban clinic in Uganda. Further study of these East African subjects may provide insights into how some individuals are able to control HIV in the absence of medications.
Lipofilling of Fingertips for Volume Defects after Fingertip Injuries
Authors: Cerny Michael K. , Moog Philipp , Bauer Anna-Theresa , Schmauss Daniel , Varga Laszlo , Aitzetmueller Matthias M. , Machens Hans-Günther , Duscher Dominik , Erne Holger
Published: August 2018

Introduction

Regardless of the good outcomes of conservatively treated fingertip injuries, many patients complain about volume defects and hypoesthesia. Injection of autologous fat into the defect zone may resolve the volume problem and stimulate digital nerve regeneration by adipose derived stem cell transplantation.

Methods

We analyzed 5 volume defects resulting from conservatively treated fingertip injuries in 4 patients (male to female ratio, 2:2), 6 months after the injection of autologous abdominal fat into the defect zone retrospectively. The fat transplantation was performed after complete wound healing was achieved (2.5–13.5 months; mean, 6.5 months). Assessment of 2-point discrimination; finger pulp circumference; the Disability of the Arm, Shoulder, and Hand score; visual analog scale score; and a questionnaire regarding the treatment satisfaction were carried out both preoperatively and at a 6 month follow-up according to the standard of our clinic.

Results

In 3 patients, one session of lipofilling was sufficient to correct the contour, whereas 1 patient with 2 fingertip injuries was treated a second time. There was no significant change in finger pulp circumference, in the 2-point discrimination values and the Disability of the Arm, Shoulder, and Hand score results. There was a significant improvement in the visual analog scale scores in 4 of 5 cases, and all patients were very satisfied with the results of the procedure regarding the improvement in hand function in sports, at work and their daily routine.

Conclusions

Lipofilling can be performed with little operative risks, might alleviate the patient’s symptoms and reduce pain after conservative treatment of fingertip injuries.
Endoscopic Management of Spontaneous Cerebrospinal Fluid Fistula Caused by Clival Defect
Authors: Karli Rifat , Yildirim Ugur
Published: August 2018

Cerebrospinal fluid (CSF) rhinorrhea is that the fluid in subarachnoid space leaks into the nasal passage in any way as a transparent discharge. Cerebrospinal fluid fistulas generally develop as secondary to trauma. Only 3% of CSF fistulas develop spontaneously. Spontaneous CSF fistulas are mostly originated from ethmoid roof and cribriform plate; however, the development of spontaneous CSF fistula due to defect in clivus is very rare. To our knowledge, till date only 13 patients with spontaneous CSF fistulae due to Clivus defect have been reported in English literature. In this clinical report, the authors aimed to contribute to the literature by reporting a 56-year-old patient who has been treated in our clinic with spontaneous CSF fistula due to clivus defect.
Advances in management of Guillain–Barré syndrome
Authors: Doets Alex Y. , Jacobs Bart C. , van Doorn Pieter A.
Published: August 2018

Purpose of review

The clinical presentation of Guillain–Barré syndrome (GBS) is highly variable, which can make the diagnosis challenging. Intravenous immunoglobulin (IVIg) and plasma exchange are the cornerstones of treatment since decades. But despite these treatments, 25% initially progress in muscle weakness, 25% require artificial ventilation, 20% is still not able to walk independently after 6 months, and 2–5% die, emphasizing the need for better treatment. We summarize new developments regarding the diagnosis, prognosis, and management of GBS.

Recent findings

GBS is a clinical diagnosis that can be supported by cerebrospinal fluid examination and nerve conduction studies. Nerve ultrasound and MRI are potentially useful techniques to diagnose inflammatory neuropathies. Several novel infections have recently been associated to GBS. Evidence from experimental studies and recent phase 2 clinical trials suggests that complement inhibition combined with IVIg might improve outcome in GBS, but further studies are warranted. Prognostic models could guide the selection of patients with a relatively poor prognosis that might benefit most from additional IVIg or otherwise intensified treatment.

New diagnostic tools may help to have early and accurate diagnosis in difficult GBS cases. Increased knowledge on the pathophysiology of GBS forms the basis for development of new, targeted, and personalized treatments that hopefully improve outcome.
Electrokinetic remediation of heavy metals from municipal solid waste incineration fly ash pretreated by nitric acid
Authors: Li Huilin , Muhammad Faheem , Yan Yujie , Zhang Manli , Jiao Binquan , Yu Lin , Li Dongwei
Published: August 2018

Municipal solid waste incineration (MSWI) fly ash has a high concentration of heavy metals (HMs) which are hazardous to the environment. Moreover, it has high pH and buffering capacity which hinders the removal of HMs. Another constraining factor is the considerable fraction of HMs which exist in oxidizable and reducible states. The acid pretreatment of MSWI fly ash is a key solution to this problem. Therefore, the current experiment is carried out to evaluate the effect of acid pretreatment of MSWI fly ash and reaction/proposed time on the removal efficiency of HMs through an electrokinetic experiment. The leaching experiment results show that acid pretreatment has increased the desorption/release of heavy metal ions (Pb2+, Cd2+, Cu2+and Zn2+). It enhances the migration of HM ions in electrolytic cells which get precipitated at the cathode, thereby increasing the removal efficiency of HMs in the electrokinetic experiment. Moreover, it is found that prolonged proposed time (12 d) has significant effect on the removal efficiency of HMs. Finally, it is concluded that acid pretreatment and prolonged proposed time have enhanced the removal electrokinetic remediation of HMs which is carried out via three processes, i.e. desorption (enhanced by acidification), migration and precipitation.
Scalable population-level modelling of biological cells incorporating mechanics and kinetics in continuous time
Authors: Engblom Stefan , Wilson Daniel B. , Baker Ruth E.
Published: August 2018

The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this detailed knowledge of the individual cell to be able to explain at the population level how cells interact and respond with each other and their environment. In particular, the goal is to understand how organisms develop, maintain and repair functional tissues and organs. In this paper, we propose a novel computational framework for modelling populations of interacting cells. Our framework incorporates mechanistic, constitutive descriptions of biomechanical properties of the cell population, and uses a coarse-graining approach to derive individual rate laws that enable propagation of the population through time. Thanks to its multiscale nature, the resulting simulation algorithm is extremely scalable and highly efficient. As highlighted in our computational examples, the framework is also very flexible and may straightforwardly be coupled with continuous-time descriptions of biochemical signalling within, and between, individual cells.
New MRI contrast agents based on silicon nanotubes loaded with superparamagnetic iron oxide nanoparticles
Authors: Gonzalez-Rodriguez Roberto , Granitzer Petra , Rumpf Klemens , Coffer Jeffery L.
Published: August 2018

This article describes the preparation and fundamental properties of a new possible material as a magnetic resonance imaging contrast agent based on the incorporation of preformed iron oxide (Fe
3
O
4
) nanocrystals into hollow silicon nanotubes (Si NTs). Specifically, superparamagnetic Fe
3
O
4
nanoparticles of two different average sizes (5 nm and 8 nm) were loaded into Si NTs of two different shell thicknesses (40 nm and 70 nm). To achieve proper aqueous solubility, the NTs were functionalized with an outer polyethylene glycol-diacid (600) moiety via an aminopropyl linkage. Relaxometry parameters
r
1
and
r
2
were measured, with the corresponding
r
2
/
r
1
ratios in phosphate buffered saline confirming the expected negative contrast agent behaviour for these materials. For a given nanocrystal size, the observed
r
2
values are found to be inversely proportional to NT wall thickness, thereby demonstrating the role of nanostructured silicon template on associated relaxometry properties.
Analytical estimation of non-local deformation-mediated magneto-electric coupling in soft composites
Authors: Rambausek M. , Keip M.-A.
Published: August 2018

For a long time, the search for magneto-electric materials concentrated on multi-ferroics and hard-matter composites. By contrast, rather recently the exploitation of strain-mediated magneto-electric (ME) coupling in soft composites was proposed. The basic idea behind this approach is to combine the magneto- and electro-mechanical responses of composites consisting of a soft matrix carrying magnetic inclusions. Despite that such composites are straightforward to manufacture and have cheap constituents, they did not gain much attention up to now. In this contribution, we demonstrate that ME coupling induced by finite deformations could be of significant magnitude. Our approach relies on shape effects as a special non-local phenomenon in magneto- and electro-elasticity. Based on that we characterize an up to now overlooked ME coupling mechanism which purely relies on these shape effects in soft-matter-based magnetic and electric media. While soft magnetic media are commonly realized as composites, the coupling effect to be highlighted exists independently of the origin of a body's magnetic and electric properties. We show that the magnitude of the effect is indeed significant and, among ellipsoidal bodies, most pronounced for those of spherical to moderately prolate shape. Finite-element simulations are performed to assess the quality of the analytical predictions.
Ecological conditions alter cooperative behaviour and its costs in a chemically defended sawfly
Authors: Lindstedt Carita , Miettinen Antti , Freitak Dalial , Ketola Tarmo , López-Sepulcre Andres , Mäntylä Elina , Pakkanen Hannu
Published: August 2018

The evolution of cooperation and social behaviour is often studied in isolation from the ecology of organisms. Yet, the selective environment under which individuals evolve is much more complex in nature, consisting of ecological and abiotic interactions in addition to social ones. Here, we measured the life-history costs of cooperative chemical defence in a gregarious social herbivore,Diprion pinipine sawfly larvae, and how these costs vary under different ecological conditions. We ran a rearing experiment where we manipulated diet (resin content) and attack intensity by repeatedly harassing larvae to produce a chemical defence. We show that forcing individuals to allocate more to cooperative defence (high attack intensity) incurred a clear cost by decreasing individual survival and potency of chemical defence. Cooperative behaviour and the magnitude of its costs were further shaped by host plant quality. The number of individuals participating in group defence, immune responses and female growth decreased on a high resin diet under high attack intensity. We also found some benefits of cheating: non-defending males had higher growth rates across treatments. Taken together, these results suggest that ecological interactions can shape the adaptive value of cooperative behaviour and maintain variation in the frequency of cooperation and cheating.
Evidence for sexual conflict over major histocompatibility complex diversity in a wild songbird
Authors: Roved Jacob , Hansson Bengt , Tarka Maja , Hasselquist Dennis , Westerdahl Helena
Published: August 2018

Sex differences in parasite load and immune responses are found across a wide range of animals, with females generally having lower parasite loads and stronger immune responses than males. Intrigued by these general patterns, we investigated if there was any sign of sex-specific selection on an essential component of adaptive immunity that is known to affect fitness, the major histocompatibility complex class I (MHC-I) genes, in a 20-year study of great reed warblers. Our analyses on fitness related to MHC-I diversity showed a highly significant interaction between MHC-I diversity and sex, where males with higher, and females with lower, MHC-I diversity were more successful in recruiting offspring. Importantly, mean MHC-I diversity did not differ between males and females, and consequently neither sex reached its MHC-I fitness optimum. Thus, there is an unresolved genetic sexual conflict over MHC-I diversity in great reed warblers. Selection from pathogens is known to maintain MHC diversity, but previous theory ignores that the immune environments are considerably different in males and females. Our results suggest that sexually antagonistic selection is an important, previously neglected, force in the evolution of vertebrate adaptive immunity, and have implications for evolutionary understanding of costs of immune responses and autoimmune diseases.
Trends and perspectives on the use of social network analysis in behavioural ecology: a bibliometric approach
Authors: Webber Quinn M.R. , Wal Eric Vander
Published: August 2018

The increased popularity and improved accessibility of social network analysis has improved our ability to test hypotheses about the complexity of animal social structure. To gain a deeper understanding of the use and application of social network analysis, we systematically surveyed the literature and extracted information on publication trends from articles using social network analysis. We synthesize trends in social network research over time and highlight variation in the use of different aspects of social network analysis. Our primary finding highlights the increase in use of social network analysis over time and from this finding, we observed an increase in the number of review and methods of social network analysis. We also found that most studies included a relatively small number (median = 15, range = 4–1406) of individuals to generate social networks, while the number and type of social network metrics calculated in a given study varied zero to nine (median = 2, range 0–9). The type of data collection or the software programs used to analyze social network data have changed; SOCPROG and UCINET have been replaced by various R packages over time. Finally, we found strong taxonomic and conservation bias in the species studied using social network analysis. Most species studied using social networks are mammals (111/201, 55%) or birds (47/201, 23%) and the majority tend to be species of least concern (119/201, 59%). We highlight emerging trends in social network research that may be valuable for distinct groups of social network researchers: students new to social network analysis, experienced behavioural ecologists interested in using social network analysis, and advanced social network users interested in trends of social network research. In summary we address the temporal trends in social network publication practices, highlight potential bias in some of the ways we employ social network analysis, and provide recommendations for future research based on our findings.
Approach direction prior to landing explains patterns of colour learning
Authors: Langridge Keri V. , Wilke Claudia , Riabinina Olena , Vorobyev Misha , de Ibarra Natalie Hempel
Published: August 2018

Gaze direction is closely coupled with body movement in insects and other animals. If movement patterns interfere with the acquisition of visual information, insects can actively adjust them to seek relevant cues. Alternatively, where multiple visual cues are available, an insect’s movements may influence how it perceives a scene. We show that the way a foraging bumblebee approaches a floral pattern could determine what it learns about the pattern. When trained to vertical bicoloured patterns, bumblebees consistently approached from below centre in order to land in the centre of the target where the reward was located. In subsequent tests, the bees preferred the colour of the lower half of the pattern that they predominantly faced during the approach and landing sequence. A predicted change of learning outcomes occurred when the contrast line was moved up or down off-centre: learned preferences again reflected relative frontal exposure to each colour during the approach, independent of the overall ratio of colours. This mechanism may underpin learning strategies in both simple and complex visual discriminations, highlighting that morphology and action patterns determines how animals solve sensory learning tasks. The deterministic effect of movement on visual learning may have substantially influenced the evolution of floral signals, particularly where plants depend on fine-scaled movements of pollinators on flowers.
Visual Long-term Memory Can Replace Active Maintenance in Visual Working Memory
Authors: Schurgin Mark W. , Cunningham Corbin A. , Egeth Howard E. , Brady Timothy F.
Published: August 2018

Humans have remarkable visual long-term memory abilities, capable of storing thousands of objects with significant detail. However, it remains unknown how such memory is utilized during the short-term maintenance of information. Specifically, if people have a previously encoded memory for an item, how does this affect subsequent working memory for that same item? Here, we demonstrate people can quickly and accurately make use of visual long-term memories and therefore maintain less perceptual information actively in working memory. We assessed how much perceptual information is actively maintained in working memory by measuring neural activity during the delay period of a working memory task using electroencephalography. We find that despite maintaining less perceptual information in working memory when long-term memory representations are available, there is no decrement in memory performance. This suggests under certain circumstances people can dynamically disengage working memory maintenance and instead use long-term memories when available. However, this does not mean participants always utilize long-term memory. In a follow-up experiment, we introduced additional perceptual interference into working memory and found participants actively maintained items in working memory even when they had existing long-term memories available. These results clarify the kinds of conditions under which long-term and working memory operate. Specifically, working memory is engaged when new information is encountered or perceptual interference is high. Visual long-term memory may otherwise be rapidly accessed and utilized in lieu of active perceptual maintenance. These data demonstrate the interactions between working memory and long-term memory are more dynamic and fluid than previously thought.
Moving in complex environments: a biomechanical analysis of locomotion on inclined and narrow substrates
Authors: Clemente Christofer J. , Dick Taylor J.M. , Wheatley Rebecca , Gaschk Joshua , Abdul Nasir Ami Fadhillah Amir , Cameron Skye F. , Wilson Robbie S.
Published: August 2018

Characterisation of an organisms’ performance in different habitats provides insight into the conditions that allow it to survive and reproduce. In recent years, Northern quolls (Dasyurus hallucatus)—a medium-sized semi-arboreal marsupial native to northern Australia—have undergone significant population declines within open forest, woodland and riparian habitats, but less so in rocky areas. To explore this decline, we quantified the biomechanical performance of wild Northern quolls over inclined narrow (13 mm pole) and inclined wide (90 mm platform) substrates. We predicted that quolls may possess biomechanical adaptations to increase stability on narrow surfaces, which are more common in rocky habitats. Our results display that quolls have some biomechanical characteristics consistent with a stability advantage on narrow surfaces. This includes the coupled use of limb pairs and high grip torques (Max = 68.9 N.m, Min = −69.9 N.m), highlighting their ability to generate corrective forces to counteract the toppling moments commonly encountered during gait on narrow surfaces. However, unlike other arboreal specialists such as primates, speed was constrained on narrow surfaces, and quolls did not adopt diagonal sequence gaits. Quolls appear to adopt similar performance characteristics to cats and dogs which may limit their ability to outperform these key predators (invasive or otherwise) in particular habitats. This overlap may contribute to the declining population of Northern quolls on mainland Australia.
Diagnostic value of blood gene expression-based classifiers as exemplified for acute myeloid leukemia
Authors: Warnat-Herresthal Stefanie , Perrakis Konstantinos , Taschler Bernd , Becker Matthias , Seep Lea , Baßler Kevin , Günther Patrick , Schulte-Schrepping Jonas , Klee Kathrin , Ulas Thomas , Haferlach Torsten , Mukherjee Sach , Schultze Joachim L.
Published: August 2018

Acute Myeloid Leukemia (AML) is a severe, mostly fatal hematopoietic malignancy. Despite nearly two decades of promising results using gene expression profiling, international recommendations for diagnosis and differential diagnosis of AML remain based on classical approaches including assessment of morphology, immunophenotyping, cytochemistry, and cytogenetics. Concerns about the translation of whole transcriptome profiling include the robustness of derived predictors when taking into account factors such as study- and site-specific effects and whether achievable levels of accuracy are sufficient for practical use. In the present study, we sought to shed light on these issues via a large-scale analysis using machine learning methods applied to a total of 12,029 samples from 105 different studies. Taking advantage of the breadth of data and the now much improved understanding of high-dimensional modeling, we show that AML can be predicted with high accuracy. High-dimensional approaches - in which multivariate signatures are learned directly from genome-wide data with no prior biological knowledge - are highly effective and robust. We explore also the relationship between predictive signatures, differential expression and known AML-related genes. Taken together, our results support the notion that transcriptome assessment could be used as part of an integrated genomic approach in cancer diagnosis and treatment to be implemented early on for diagnosis and differential diagnosis of AML.

One Sentence Summary

Blood gene expression data and machine learning were used to develop robust and accurate classifiers for diagnosis and differential diagnosis of acute myeloid leukemia based on analysis of more than 12,000 samples derived from more than 100 individual studies
Molecular and topological reorganizations in mitochondrial architecture interplay during Bax-mediated steps of apoptosis
Authors: Ader Nicholas R. , Hoffmann Patrick C. , Ganeva Iva , Borgeaud Alicia C. , Wang Chunxin , Youle Richard J. , Kukulski Wanda
Published: August 2018

During apoptosis, Bcl-2 proteins such as Bax and Bak mediate the release of pro-apoptotic proteins from the mitochondria by clustering on the outer mitochondrial membrane and thereby permeabilizing it. However, it remains unclear how outer membrane openings form. Here, we combined different correlative microscopy and electron cryo-tomography approaches to visualize the effects of Bax activity on mitochondria in human cells. Our data show that Bax clusters localize near outer membrane ruptures of highly variable size. Bax clusters contain structural elements suggesting a higher-order organization of their components. Furthermore, unfolding of inner membrane cristae is coupled to changes in the supramolecular assembly of ATP synthases, particularly pronounced at membrane segments exposed to the cytosol by ruptures. Based on our results, we propose a comprehensive model in which molecular reorganizations of the inner membrane and sequestration of outer membrane components into Bax clusters interplay in the formation of outer membrane ruptures.
KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency
Authors: Di Giammartino Dafne Campigli , Kloetgen Andreas , Polyzos Alexander , Liu Yiyuan , Kim Daleum , Murphy Dylan , Abuhashem Abderhman , Cavaliere Paola , Aronson Boaz , Shah Veevek , Dephoure Noah , Stadtfeld Matthias , Tsirigos Aristotelis , Apostolou Effie
Published: August 2018

Cell fate transitions are accompanied by global transcriptional, epigenetic and topological changes driven by transcription factors (TFs), as is strikingly exemplified by reprogramming somatic cells to pluripotent stem cells (PSCs) via expression of OCT4, KLF4, SOX2 and cMYC. How TFs orchestrate the complex molecular changes around their target gene loci in a temporal manner remains incompletely understood. Here, using KLF4 as a paradigm, we provide the first TF-centric view of chromatin reorganization and its association to 3D enhancer rewiring and transcriptional changes of linked genes during reprogramming of mouse embryonic fibroblasts (MEFs) to PSCs. Inducible depletion of KLF factors in PSCs caused a genome-wide decrease in the connectivity of enhancers, while disruption of individual KLF4 binding sites from PSC-specific enhancers was sufficient to impair enhancer-promoter contacts and reduce expression of associated genes. Our study provides an integrative view of the complex activities of a lineage-specifying TF during a controlled cell fate transition and offers novel insights into the order and nature of molecular events that follow TF binding.
Behavioral response to visual motion impacts population coding in the mouse visual thalamus
Authors: Socha Karolina , Whiteway Matt , Butts Daniel A. , Bonin Vincent
Published: August 2018

Visual motion is a ubiquitous component of animals’ sensory experience and its encoding is critical for navigation and movement. Yet its impact on behavior and neural coding is not well understood. Combining pupillometry with cellular calcium imaging measurements of thalamocortical axons in awake behaving mice, we examined the impact of arousal and behavioral state on encoding of visual motion in the visual thalamus. We discovered that back-to-front visual motions elicits a robust behavioral response that shapes tunings of visual thalamic responses. Consistent with an arousal mechanism, the effects were pronounced during stillness and weak or absent during locomotor activity and under anesthesia. The impact on neuronal tuning was specific, biasing population response patterns in favor of back-to-front motion. The potent influence of visual motion on behavioral state dynamically affect sensory coding at early visual processing stages. Further research is required to reveal the circuitry and function of this novel mechanism.
Thylakoid-integrated recombinant Hcf106 participates in the chloroplast Twin Arginine Transport (cpTat) system
Authors: Ma Qianqian , Fite Kristen , Paul New Christopher , Dabney-Smith Carole
Published: August 2018

The chloroplast Twin arginine transport (cpTat) system distinguishes itself as a protein transport pathway by translocating fully-folded proteins, using the proton-motive force (PMF) as the sole source of energy. The cpTat pathway is evolutionarily conserved with the Tat pathway found in the plasma membrane of many prokaryotes. The cpTat (E. coli) system uses three proteins, Tha4 (TatA), Hcf106 (TatB), and cpTatC (TatC), to form a transient translocase allowing the passage of precursor proteins. Briefly, cpTatC and Hcf106, with Tha4, form the initial receptor complex responsible for precursor protein recognition and binding in an energy-independent manner, while a separate pool of Tha4 assembles with the precursor-bound receptor complex in the presence the PMF. Analysis by blue-native polyacrylamide gel electrophoresis (BN-PAGE) shows that the receptor complex, in the absence of precursor, migrates near 700 kDa and contains cpTatC and Hcf106 with little Tha4 remaining after detergent solubilization. To investigate the role that Hcf106 may play in receptor complex oligomerization and/or stability, systematic cysteine substitutions were made in positions from the N-terminal transmembrane domain to the end of the predicted amphipathic helix of the protein. BN-PAGE analysis allowed us to identify the locations of amino acids in Hcf106 that were critical for interacting with cpTatC. Oxidative cross-linking allowed us to map interactions of the transmembrane domain and amphipathic helix region of Hcf106. In addition, we showed thatin vitroexpressed, integrated Hcf106 can interact with the precursor signal peptide domain and imported cpTatC, strongly suggesting that a subpopulation of the integrated Hcf106 is participating in competent cpTat complexes.
Insights from Comparison of the Renal and Skin Single Cell Transcriptomes in Lupus Nephritis
Authors: Der Evan , Suryawanshi Hemant , Morozov Pavel , Kustagi Manjunath , Goilav Beatrice , Ranabathou Saritha , Izmirly Peter , Clancy Robert , Belmont H. Michael , Koenigsberg Mordecai , Mokrzycki Michele , Rominieki Helen , Graham Jay A. , Rocca Juan P. , Bornkamp Nicole , Jordan Nicole , Schulte Emma , Wu Ming , Pullman James , Slowikowski Kamil , Raychaudhuri Soumya , Guthridge Joel , James Judith ,   Accelerating Medicines Partnership in RA/SLE network, Buyon Jill , Tuschl Thomas , Putterman Chaim
Published: August 2018

Lupus nephritis (LN) occurs in up to 50% of patients with systemic lupus erythematosus (SLE), and is a major contributor to mortality and morbidity. LN presents as a highly heterogeneous disease both in histopathology and response to therapy. The molecular and cellular processes leading to renal damage and to the heterogeneity of the disease are not well understood. To elucidate the processes underpinning the heterogeneity of LN, we applied singlecell RNA-sequencing (scRNA-seq) to renal biopsies from LN patients. Skin biopsies were evaluated as a source of biomarkers for monitoring kidney disease. Type-I interferon (IFN) response signatures were identified in tubular cells and keratinocytes, differentiating LN patients from healthy controls. Non-responders associated with higher IFN signatures in both tissue compartments. Moreover, non-response was also associated with a fibrotic signature in the tubular cells. Receptor-ligand interaction analysis indicated that the fibrotic process is likely mediated by FGF receptors with the initiating signal originating from infiltrating leukocytes. Differential expression analysis of tubular cells between proliferative and membranous LN pointed to several fibrosis-relevant pathways, which may offer insight into their histological differences. In summary, scRNA-seq was applied to LN to deconstruct its heterogeneity and provide novel targets for personalized approaches to therapy.