bluuebunny/crossref_metadata_2025 huggingface dataset:
Living machines in our cultural imagination
Authors: Szollosy Michael
Published: June 2018

Public perceptions of robots and artificial intelligence (AI)—both positive and negative—are hopelessly misinformed, based far too much on science fiction rather than science fact. However, these fictions can be instructive, and reveal to us important anxieties that exist in the public imagination, both towards robots and AI and about the human condition more generally. These anxieties are based on little-understood processes (such as anthropomorphization and projection), but cannot be dismissed merely as inaccuracies in need of correction. Our demonization of robots and AI illustrate two-hundred-year-old fears about the consequences of the Enlightenment and industrialization. Idealistic hopes projected onto robots and AI, in contrast, reveal other anxieties, about our mortality—and the transhumanist desire to transcend the limitations of our physical bodies—and about the future of our species. This chapter reviews these issues and considers some of their broader implications for our future lives with living machines.
Sustainability of living machines
Authors: Halloy José
Published: June 2018

Humankind is facing the reality of climate change and energy and resource transitions that could pose a major existential threat. Our future technological development must respond to these challenges. Artificial intelligence and robotics are making tremendous progress. However, in terms of power, energy, and materials consumptions the gap between these technologies and a living being is huge and non-sustainable in the long term. This chapter argues for a radical biomimetic, or Living Machines, approach to the development of next generation technologies; radical meaning including the type of chemistry and ecological processes found in living systems. This radical approach necessitates re-inventing our computational technologies in terms of materials, architectures, and processes, linking these processes within new technological ecosystems, and learning from the self-regulating ecological cycles of birth, growth, death, and re-use found in the natural world.
Canada
Authors: Parker George L.
Published: June 2018

This chapter discusses the history of fiction publishing in Canada since 1950. It begins with the arrival of New York publisher Alfred Knopf in Canada in August 1955, a month after the Canadian Writers' Conference was held at Queen's University in Kingston, Ontario. During the conference, the sorry plight of the English-language book scene was tackled: bookstores, for example, were dominated by British and American authors, and Canadian literature was practically ignored in schools and universities. The chapter examines how many of these complaints were resolved by the 2000s. It considers changes in Canadian fiction from traditional realism towards modernism and postmodernism, and the importance of the New Canadian Library quality paperback series (1958). It also describes other significant developments that reshaped the Canadian book market, including the emergence of independent small presses, Harlequin Enterprises, the proliferation of international conglomerates, the marketing of e-books, and the rise of Amazon.
Moral Personality in Emerging Adulthood
Authors: Pratt Michael W. , Matsuba M. Kyle
Published: June 2018

Chapter 5 begins with a brief overview of the field of moral development in recent years, touching on moral cognition, moral affect, and moral behavior. Patterns in the development of moral personality are then explained and reviewed, following the McAdams and Pals model. The authors then turn to research on morality from a narrative perspective (still quite limited) and describe their own work on stories of prosocial moral episodes and of empathy in emerging adulthood from the Futures Study data. The chapter ends with a case study of the emerging and young adulthood of Dr. Martin Luther King Jr., as a way of illustrating these issues of moral personality development.
Homelessness, social relations and institutional logics: property rights without property?
Authors: Luiz John M , Rycroft James
Published: June 2018

We explore whether there is evidence of property rights among the homeless, and if so, how these rights are governed. By conducting interviews with 52 homeless people in Cape Town, we show that although the homeless are able to derive some value from assets, and can exclude other members of their community, these rights are precarious and dependent upon state agents not seizing the ‘property’ and overriding the community’s rules of the game. We demonstrate the intersectionality of claims with respect to the same physical property from the varying perspectives of the claimants involved and how this differs depending on the property. Homeless people rely on a community logic to develop rules of the game which results in the appearance of a market logic. In the absence of formal institutions effectively operating in their spaces, they have constituted social norms which provide some semblance of property rights respected intra-group.
Volatile Compounds of Endophytic Bacillus spp. have Biocontrol Activity Against Sclerotinia sclerotiorum
Authors: Massawe Venance Colman , Hanif Alvina , Farzand Ayaz , Mburu David Kibe , Ochola Sylvans Ochieng , Wu Liming , Tahir Hafiz Abdul Samad , Gu Qin , Wu Huijun , Gao Xuewen
Published: June 2018

To develop an effective biological agent to control Sclerotinia sclerotiorum, three endophytic Bacillus spp. strains with high antagonistic activity were isolated from maize seed and characterized. In vitro assays revealed that the Bacillus endophytes could produce volatile organic compounds (VOC) that reduced sclerotial production and inhibited mycelial growth of S. sclerotiorum. Gas chromatography–mass spectrometry revealed that the selected strains produced 16 detectable VOC. Eight of the produced VOC exhibited negative effects on S. sclerotiorum, while a further four induced accumulation of reactive oxygen species in mycelial cells. A mixture of VOC produced by Bacillus velezensis VM11 caused morphological changes in the ultrastructure and organelle membranes of S. sclerotiorum mycelial cells. The bromophenol blue assay revealed a yellow color of untreated fungal mycelium, which grew faster and deeper from 24 to 72 h postinoculation, as an indication of reduced pH. The potassium permanganate (KMnO4) titration assay showed that the rate of oxalic acid accumulation was higher in minimal salt liquid medium cultures inoculated with untreated fungal plugs compared with the Bacillus VOC-treated ones. Interestingly, biological control assays using host-plant leaves challenged with treated fungal mycelial plugs produced reduced lesions compared with the control. These findings provide new viable possibilities of controlling diseases caused by S. sclerotiorum using VOC produced by Bacillus endophytes.
Temperature and Humidity Associated With Artificial Ventilation in the Premature Infant
Authors: Ralphe Jane L. , Dail Robin B.
Published: June 2018

Background:

Approximately half of the 55,000 very low birth-weight infants (<1500 g) born in the United States each year develop bronchopulmonary dysplasia (BPD). Many etiologies have been associated with the development of BPD, including aberrant temperature/humidity levels of artificial ventilation.

Purpose:

The purpose of this literature review is to explore what is known regarding inspired air temperature/humidity levels from artificial ventilation in very premature infants, focusing on what levels these infants actually receive, and what factors impact these levels.

Methods/Search Strategy:

PubMed, CINAHL, Scopus, and Web of Science were searched. Of the 830 articles retrieved, 23 were synthesized for study purpose, sample/study design, and temperature/humidity findings.

Findings/Results:

Heating and humidification practices studied in neonatal ventilation did not maintain recommended levels. In addition, human neonatal studies and noninvasive neonatal ventilation research were limited. Furthermore, ventilation settings, environmental temperatures, and mouth position (in noninvasive ventilation) were found to impact temperature/humidity levels.

Implications for Practice:

Environmental temperatures and ventilatory settings merit consideration during artificial ventilation. In addition, aberrant temperature/humidity levels may impact infant body temperature stability; thus, employing measures to ensure adequate thermoregulation while receiving artificial ventilation must be a priority.

Implications for Research:

This review underscores the need for further research into current warming and humidification techniques for invasive and noninvasive neonatal ventilation. A focus on human studies and the impact of aberrant levels on infant body temperature are needed. Future research may provide management options for achieving and maintaining target temperature/humidity parameters, thus preventing the aberrant levels associated with BPD.
Critical Care Management of Anti-N-Methyl-d-Aspartate Receptor Encephalitis
Authors: Neyens Ron R. , Gaskill George E. , Chalela Julio A.
Published: June 2018

Objectives:

Anti-N-methyl-d-aspartate receptor encephalitis is considered an immune-mediated form of encephalitis with paraneoplastic and nonparaneoplastic forms. Delay in recognition is common and patients typically present to the ICU without a diagnosis or with complications following a delayed diagnosis. The aim of this review is to provide a focused overview for the ICU clinician regarding presentation, diagnosis, and critical care management.

Data Sources, Study Selection, and Data Extraction:

PubMed database search with manual review of articles involving anti-N-methyl-d-aspartate receptor encephalitis.

Data Synthesis:

Anti-N-methyl-d-aspartate receptor encephalitis is increasingly encountered in the ICU. The cascade of events initiating anti-N-methyl-d-aspartate receptor antibody formation may involve an infectious trigger particularly in the setting of teratoma. Following a prodrome, most patients develop psychiatric symptoms followed by movement disorder. Classical, psychiatric, and catatonic phenotypes may be distinguished based on the presence and severity of symptoms. Early immunotherapy and low initial cerebrospinal fluid inflammation are independent predictors of positive outcomes in ICU patients. Concomitant organ failure, status epilepticus, and the identification of a tumor did not influence outcome in critically ill patients. Supportive care in the ICU includes management of various manifestations of dyskinesia, status epilepticus, autonomic disorders, and the need for general sedation. Common treatment strategies and limitations are discussed including the emerging role of bortezomib.

Conclusions:

Intensivists should be familiar with the presentation and management of anti-N-methyl-d-aspartate receptor encephalitis. Early diagnosis and immediate implementation of steroids, immunoglobulins, and/or plasmapheresis and immune therapy are associated with a good neurologic outcome although response may be delayed. The selection and timing of second-line immune therapy requires further study.
Functional Optical Zone After Small-Incision Lenticule Extraction as Stratified by Attempted Correction and Optical Zone
Authors: Fu Dan , Wang Lin , Zhou Xingtao , Yu Zhiqiang
Published: June 2018

Purpose:

To compare the functional optical zone (OZ) with different levels of myopia and different OZ groups after small-incision lenticule extraction.

Methods:

This retrospective study included 249 patients (120 men) after small-incision lenticule extraction correction. We grouped participants according to attempted correction [low: spherical equivalent (SE) > −3.0 D; moderate: −6.0 D ≥ SE ≥ −3.0 D; high: SE ≥ −6.0 D] and planned functional optical zone (PFOZ) (OZ-1: PFOZ ≤ 6.3 mm; OZ-2: 6.3 mm < PFOZ ≤ 6.5; OZ-3: PFOZ > 6.5 mm), and we compared the achieved functional optical zone (AFOZ) and total corneal aberration, using Scheimpflug imaging, 1 month postoperatively. Correlations between corneal aberration and AFOZ were analyzed.

Results:

The AFOZ was smaller than the PFOZ in all 3 refraction groups (reduction: low, 0.78 ± 0.72 mm; moderate, 1.22 ± 0.60 mm; and high: 1.49 ± 0.58 mm, P < 0.001). There was no difference in the AFOZ among the 3 OZ groups. Total corneal aberration increased more in the high myopia group (total higher-order aberration, coma, and spherical aberration, P < 0.001), which also correlated with the AFOZ.

Conclusions:

The discrepancy between the AFOZ and PFOZ increased with greater attempted correction. Attempted correction and AFOZ influence corneal aberration.
Dysthyroid Optic Neuropathy
Authors: Saeed Peerooz , Tavakoli Rad Shahzad , Bisschop Peter H. L. T.
Published: June 2018

Purpose:

Dysthyroid optic neuropathy (DON) is a serious complication of Graves orbitopathy that can result in irreversible and profound visual loss. Controversy exists regarding the pathogenesis and management of the disease. The authors provide an overview of the current understanding of DON and present a therapeutic guideline.

Methods:

A review of the literature.

Results:

The mechanism of DON appears to be multifactorial: direct compression of the optic nerve by enlarged extraocular muscles, stretching of the optic nerve by proptosis, orbital pressure, vascular insufficiency, and inflammation. Some or all of these factors may be involved in an individual patient. There has only been one controlled trial comparing high-dose intravenous methylprednisolone to bony orbital decompression for DON. Both 2-wall and 3-wall decompression techniques successfully improve visual functions of patients with DON. There are few case reports/case series that suggest biologic agents may improve visual function in DON.

Conclusions:

DON is a serious complication of Graves orbitopathy, the diagnosis and management of which is complex and requires a multidisciplinary approach. There is little evidence regarding the optimum management strategy. Based on the current literature, the first line of treatment is intravenous methylprednisolone, with the exact timing and indication of bony orbital decompression still to be determined. In addition, there may be a role for the use of biologic agents that will require a systematic program to determine efficacy.
Extraocular Muscle Enlargement and Thyroid Eye Disease-like Orbital Inflammation Associated with Immune Checkpoint Inhibitor Therapy in Cancer Patients
Authors: Sagiv Oded , Kandl Thomas J. , Thakar Sudip D. , Thuro Bradley A. , Busaidy Naifa L. , Cabanillas Maria , Jimenez Camilo , Dadu Ramona , Graham Paul H. , Debnam J. Matthew , Esmaeli Bita
Published: June 2018

Purpose:

To describe thyroid eye disease (TED)-like orbital inflammatory syndrome in 3 cancer patients treated with immune checkpoint inhibitors.

Methods:

All consecutive patients treated by the senior author who were receiving immune checkpoint inhibitors and developed TED-like orbital inflammation were included.

Results:

Three cancer patients treated with immune checkpoint inhibitors developed orbital inflammation. The first patient was treated with a combination of a cytotoxic T-lymphocyte antigen-4 inhibitor and a programmed cell death protein 1 inhibitor and developed TED-like orbital inflammation with normal thyroid function and antibody levels. The second patient had a previous diagnosis of Graves disease without TED, and developed TED soon after initiating treatment with a programmed cell death protein 1 inhibitor. The third patient developed acute hyperthyroidism with symptomatic TED following treatment with an investigational cytotoxic T-lymphocyte antigen-4 inhibitor agent. All 3 patients were managed with either systemic steroids or observation, with resolution of their symptoms and without the need to halt immune checkpoint inhibitor treatment for their cancer.

Discussion and Conclusions:

TED-like orbital inflammation may occur as a side effect of immune checkpoint inhibitor therapy with anti–cytotoxic T-lymphocyte antigen-4 or anti-PD-1 inhibitors. To the best of their knowledge, this is the first reported case of TED as a result of programmed cell death protein 1 inhibitor monotherapy. All 3 patients were treated with systemic steroids and responded quickly while continuing treatment with immune checkpoint inhibitors for their cancer. With increasing use of this class of drugs, clinicians should be familiar with the clinical manifestations and treatments for this adverse reaction.
Association of Inflow Cannula Position with Left Ventricular Unloading and Clinical Outcomes in Patients with HeartMate II Left Ventricular Assist Device
Authors: Imamura Teruhiko , Nguyen Ann , Chung Ben , Rodgers Daniel , Sarswat Nitasha , Kim Gene , Raikhelkar Jayant , Adatya Sirtaz , Ota Takeyoshi , Song Tae , Juricek Colleen , Estep Jerry D. , Burkhoff Daniel , Jeevanandam Valluvan , Sayer Gabriel , Uriel Nir
Published: June 2018

The relationship between the HeartMate II left ventricular assist device (LVAD) position and pump thrombosis has been reported. However, further clinical implications of device position are unknown. This study aimed to investigate optimal device position for better left ventricular (LV) unloading and patient prognosis. Patients undergoing a ramp test with right heart catheterization after HeartMate II LVAD implantation were enrolled to this study. Device position was quantified from the chest X-ray obtained at the time of the ramp test: (1) inflow cannula angle relative to horizontal line, (2) pump angle relative to spine, (3) pump depth, (4) angle between inflow cannula and pump, and (5) angle between pump and outflow graft. LV unloading was assessed by pulmonary capillary wedge pressure at set LVAD speed. Fifty-four patients (60 years old and 34 male [63%]) were enrolled. Nobody experienced device malfunction during the study period. Increased LV unloading (i.e., lower pulmonary capillary wedge pressure) was associated with a narrower inflow cannula angle relative to horizontal line. Inflow cannula angle <75° was associated with higher 1 year heart failure readmission-free survival rate (p < 0.05, hazards ratio 7.56 [95% confidence interval 2.32–24.7]). In conclusion, HeartMate II LVAD inflow cannula position was associated with LV unloading and patient prognosis. Prospective studies to ensure optimal device positioning and target better clinical outcomes are warranted.
Acute hyperalgesia and delayed dry eye after corneal abrasion injury
Authors: Hegarty Deborah M. , Hermes Sam M. , Morgan Michael M. , Aicher Sue A.
Published: June 2018

Introduction:

Corneal nerves mediate pain from the ocular surface, lacrimation, and blinking, all of which protect corneal surface homeostasis and help preserve vision. Because pain, lacrimation and blinking are rarely assessed at the same time, it is not known whether these responses and their underlying mechanisms have similar temporal dynamics after acute corneal injury.

Methods:

We examined changes in corneal nerve density, evoked and spontaneous pain, and ocular homeostasis in Sprague-Dawley male rats after a superficial epithelial injury with heptanol. We also measured changes in calcitonin gene-related peptide (CGRP), which has been implicated in both pain and epithelial repair.

Results:

Hyperalgesia was seen 24 hours after abrasion injury, while basal tear production was normal. One week after abrasion injury, pain responses had returned to baseline levels and dry eye symptoms emerged. There was no correlation between epithelial nerve density and pain responses. Expression of both ATF3 (a nerve injury marker) and CGRP increased in trigeminal ganglia 24 hours after injury when hyperalgesia was seen, and returned to normal one week later when pain behavior was normal. These molecular changes were absent in the contralateral ganglion, despite reductions in corneal epithelial nerve density in the uninjured eye. By contrast, CGRP was upregulated in peripheral corneal endings 1 week after injury, when dry eye symptoms emerged.

Conclusion:

Our results demonstrate dynamic trafficking of CGRP within trigeminal sensory nerves following corneal injury, with elevations in the ganglion correlated with pain behaviors and elevations in peripheral endings correlated with dry eye symptoms.
The Use of Antidotes for Calcium Gluconate Extravasation: An Experimental Study in Mice
Authors: Pacheco Compaña Francisco Javier , Midón Míguez José , de Toro Santos Francisco Javier , Centeno Cortés Alberto , López San Martín Patricia , Yebra-Pimentel Vidal María Teresa , Mosquera Osés Joaquín José
Published: June 2018

Background:

Calcium gluconate extravasation is a process that can cause serious lesions, such as necrosis and calcification of the soft tissues. The aim of the present study was to analyze the beneficial effects of four possible local antidotes for calcium gluconate extravasation: hyaluronidase, sodium thiosulfate, triamcinolone acetonide, and physiologic saline solution.

Methods:

Seventy-four BALB/c mice were used in the study. The substances selected for use in this study were calcium gluconate (4.6 mEq/ml), hyaluronidase (1500 IU/ml), sodium thiosulfate (25%), triamcinolone acetonide (40 mg/ml 0.5 mg/kg), and saline solution 0.9%. Five minutes were allowed to lapse after the calcium gluconate infiltration, and then an antidote was infiltrated. After 3 weeks, a skin biopsy was performed and a radiographic and histologic study was carried out.

Results:

Only in the group infiltrated with sodium thiosulfate did all skin lesions disappear after the 3-week period after infiltration. In the radiographic study, calcium deposits larger than 0.5 mm were observed in 40 percent of cases without an antidote, in 33 percent with triamcinolone acetonide, in 13 percent with a saline solution, and in none with thiosulfate and hyaluronidase. In the histologic study, calcium deposits were found in 53 percent of cases without antidote, 100 percent of cases with triamcinolone acetonide, 33 percent of cases with saline solution, and 13 percent of cases with sodium thiosulfate or hyaluronidase.

Conclusion:

Sodium thiosulfate and hyaluronidase prevent the development of calcium deposits after calcium gluconate extravasation.
Critical Ischemia Time, Perfusion, and Drainage Function of Vascularized Lymph Nodes
Authors: Yang Chin-Yu , Ho Olivia A. , Cheng Ming-Huei , Hsiao Hui-Yi
Published: June 2018

Background:

Vascularized lymph node transfer is a promising surgical treatment for lymphedema. This study investigated the effect of ischemia on the lymphatic drainage efficiency of vascularized lymph node flaps and the critical ischemia time of lymph nodes.

Methods:

Twenty-four lymph nodes containing groin flaps in 12 Sprague-Dawley rats were dissected. Clamping of the vascular pedicle was performed for 0, 1, 3, 5, 6, or 7 hours; then, each was allowed to reperfuse by means of the vascular pedicle for 1 hour. Perfusion and ischemic changes were assessed using indocyanine green lymphography; laser Doppler flowmetry; and histologic studies with associated lymphatic vessel endothelial hyaluronan receptor-1, CD68, 4′,6-diamidino-2-phenylindole, terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling, and glutathione assay stains.

Results:

The mean latency period of the groin lymph node flaps was 247 ± 67, 83 ± 15, 72 ± 42, 30 ± 18, and 245 ± 85 seconds in the 0-, 1-, 3-, 5-, and 6-hour groups, respectively. Perfusion detected by laser Doppler was 85.2 ± 14.5, 87.2 ± 36.7, 129.8 ± 33.7, 140.4 ± 148.5, 156.1 ± 91.4, and 41.2 ± 34.8 perfusion units at ischemia times of 0, 1, 3, 5, 6, and 7 hours, respectively. Cell damage measured by glutathione was 46.8 ± 10.2, 67.7 ± 14.2, 62.8 ± 15.4, 126.6 ± 5.9, 259.0 ± 70.3, and 109.1 ± 27.5 at ischemia times of 0, 1, 3, 5, 6, and 7 hours, respectively. Histologically, as ischemia time increased, hemorrhage and congestion became more severe.

Conclusions:

The critical ischemia time of vascularized lymph nodes is 5 hours in the rodent animal model, verified by indocyanine green lymphatic fluid uptake, laser Doppler perfusion, and histologic assessments. Interestingly, lymphatic drainage and perfusion of vascularized lymph nodes were improved with an increased ischemia time before the critical 5 hours was reached.
Anatomical Characterization and Three-Dimensional Modeling of the Muscles at the Corner of the Mouth: An Iodine Staining Technique Based on Micro–Computed Tomography
Authors: Sun Min , Chen Guo C. , Wang Yong Q. , Song Tao , Li Hai D. , Wu Di , Yin Ning B.
Published: June 2018

The anatomy of the modiolus and surrounding muscles is complicated and contributes to the morphology of the mouth corner. The authors used iodine staining and micro–computed tomography to observe the anatomy of the modiolus and surrounding muscles. Based on the micro–computed tomographic images and the three-dimensional model construction, the authors found that the muscle fibers in the modiolus were oriented continuously in the running direction of the muscle itself and that there were no chaotic clumps in the region of muscle fiber convergence. The pars marginalis of the orbicularis oris muscle connects with the deep buccinator muscle, which may account for how the pars marginalis fibers act to press the upper lip against the maxillary teeth or invert it closer to the oral cavity. These findings may be helpful for plastic surgeons who perform commissuroplasty.
Concepts and Artistry in the Treatment of Scapholunate Ligament Injuries
Authors: Elzinga Kate E. , Kamnerdnakta Sirichai , Chung Kevin C.
Published: June 2018

Background:

Scapholunate ligament injuries are highly challenging injuries to treat. Great uncertainly remains in determining which operative procedures are most effective. Furthermore, there is no consensus on whether surgical intervention changes the natural course of scapholunate injuries.

Methods:

The authors present their assessment of scapholunate injuries and the senior author’s preferred surgical techniques. Surgical videos are included. The authors’ postoperative management is described.

Results:

Operative procedures are selected based on the patient’s timing and pattern of injury, degree of associated carpal changes and arthritis, and goals.

Conclusion:

Over the past 20 years, the senior author has had good success with these techniques, but prospective, longterm outcome studies are needed to critically assess whether these surgical techniques improve patients’ long-term function and pain.
Electrical-charge accumulation enables integrative quality control duringB. subtilissporulation
Authors: Sirec Teja , Buffard Pauline , Garcia-Ojalvo Jordi , Asally Munehiro
Published: June 2018

Quality control of offspring is important for the survival of cells. However, the mechanism by which quality of offspring cells may be monitored while running genetic programs of cellular differentiation remains largely unclear. Here we investigated a quality control system duringBacillus subtilisspore formation by combining single-cell time-lapse microscopy, molecular biology and mathematical modelling. Our results revealed that the quality-control system via premature germination is coupled with the accumulation of cations on the surface of developing forespores. Specifically, the forespores accumulating less cations on their surface are more likely to be aborted. This charge accumulation system enables the projection of multidimensional information about the external environment and morphological development of the forespore onto a one-dimensional information of cation accumulation. Based on the insight we gain, we propose a novel use of Nernstian chemicals for reducing the yield and quality ofBacillusendospores.
Neural Mechanisms Associated with Semantic and Basic Self-Oriented Memory Processes Interact to Modulate Self-Esteem
Authors: Amey Rachel C. , Leitner Jordan B. , Liu Mengting , Forbes Chad E.
Published: June 2018

Individuals constantly encounter feedback from others and process this feedback in various ways to maintain positive situational state self-esteem (SSE) in relation to semantic-based or trait self-esteem (TSE). Individuals may utilize a data-driven, or episodic-based process that encodes positive, but not negative, self-relevant information automatically, or employ a semantic-driven process that manipulates encoded negative feedback post-hoc. It’s unclear, however, how these processes work either alone or in concert while individuals receive positive and negative feedback to modulate feedback encoding and subsequent SSE. Utilizing neural regions associated with semantic self-oriented and basic encoding processes (mPFC and PCC respectively), and time-frequency and Granger causality analyses to assess mPFC and PCC interactions, this study examined how encoding of positive and negative self-relevant feedback modulated individuals’ post-task SSE in relation to their TSE while continuous EEG was recorded. Among those with higher levels of TSE, the encoding of positive or negative feedback was not associated with SSE. Rather, higher SSE was associated with mPFC activity to all feedback and higher TSE. The relationship between TSE and SSE was moderated by mPFC-PCC communication such that increases in mPFC-PCC communication led to SSE levels that were consistent with TSE levels. Furthermore, Granger causality analyses indicated that individuals exhibited higher SSE to the extent mPFC influenced PCC in response to positive and negative feedback. Findings highlight the dynamic interplay between semantic self-oriented and basic encoding processes that modulate SSE in relation to TSE, to maintain more positive global selfperceptions in the moment and over time.
Soil variation response is mediated by growth trajectories rather than functional traits in a widespread pioneer Neotropical tree
Authors: Levionnois Sébastien , Tysklind Niklas , Nicolini Eric , Ferry Bruno , Troispoux Valérie , Le Moguedec Gilles , Morel Hélène , Stahl Clément , Coste Sabrina , Caron Henri , Heuret Patrick
Published: June 2018

Abstract

Trait-environment relationships have been described at the community level across tree species. However, whether interspecific trait-environment relationships are consistent at the intraspecific level is yet unknown. Moreover, we do not know how consistent is the response between organ vs. whole-tree level.

We examined phenotypic variability for 16 functional leaf (dimensions, nutrient, chlorophyll) and wood traits (density) across two soil types, Ferralitic Soil (FS) vs. White Sands (WS), on two sites for 70 adult trees ofCecropia obtusaTrécul (Urticaceae) in French Guiana.Cecropiais a widespread pioneer Neotropical genus that generally dominates early successional forest stages. To understand how soil types impact resource-use through the processes of growth and branching, we examined the architectural development with a retrospective analysis of growth trajectories. We expect soil types to affect both, functional traits in relation to resource acquisition strategy as already described at the interspecific level, and growth strategies due to resource limitations with reduced growth on poor soils.

Functional traits were not involved in the soil response, as only two traits-leaf residual water content and K content-showed significant differences across soil types. Soil effects were stronger on growth trajectories, with WS trees having the slowest growth trajectories and less numerous branches across their lifespan.

The analysis of growth trajectories based on architectural analysis improved our ability to characterise the response of trees with soil types. The intraspecific variability is higher for growth trajectories than functional traits forC. obtusa, revealing the complementarity of the architectural approach with the functional approach to gain insights on the way trees manage their resources over their lifetime. Soil-related responses ofCecropiafunctional traits are not the same as those at the interspecific level, suggesting that the effects of the acting ecological processes are different between the two levels. Apart from soil differences, much variation was found across sites, which calls for further investigation of the factors shaping growth trajectories in tropical forests.
Three-dimensional organization of transzonal projections and other cytoplasmic extensions in mouse ovarian follicles
Authors: Baena Valentina , Terasaki Mark
Published: June 2018

Each mammalian oocyte is nurtured by its own multi-cellular structure, the ovarian follicle. We used new methods for serial section electron microscopy to examine entire cells and their projections in mouse antral ovarian follicles. It is already known that cumulus cells send towards the oocyte thin cytoplasmic projections called transzonal projections (TZPs), which are crucial for normal oocyte development. We found that most TZPs do not reach the oocyte, and that they often branch and make gap junctions with each other. Furthermore, the connected TZPs are usually contacted on their shaft by oocyte microvilli. Mural granulosa cells were found to possess randomly oriented cytoplasmic projections that are strikingly similar to free-ended TZPs. We propose that granulosa cells use cytoplasmic projections to search for the oocyte, and cumulus cell differentiation results from a contact-mediated paracrine interaction with the oocyte.
The sequences near Chi sites allow the RecBCD pathway to avoid genomic rearrangements
Authors: Li Chastity , Danilowicz Claudia , Tashjian Tommy F. , Godoy Veronica G. , Prévost Chantal , Prentiss Mara
Published: June 2018

Bacterial recombinational repair is initiated by RecBCD, which creates a 3′ single-stranded DNA (ssDNA) tail on each side of a double strand break (DSB). Each tail terminates in a Chi site sequence that is usually distant from the break. Once an ssDNA-RecA filament forms on a tail, the tail searches for homologous double-stranded DNA (dsDNA) to use as template for DSB repair. Here we show that the nucleoprotein filaments rarely trigger sufficient synthesis to form an irreversible repair unless a long strand exchange product forms at the 3′ end of the filament. Our experimental data and modeling suggest that terminating both filaments with Chi sites allows recombinational repair to strongly suppress fatal genomic rearrangements resulting from mistakenly joining different copies of a repeated sequence after a DSB has occurred within a repeat. Taken together our evidence highlights cellular safe fail mechanisms that bacteria use to avoid potentially lethal situations.
Effects of Pathological Mutations on the Prion-Like Polymerisation of MyD88
Authors: O’Carroll Ailís , Chauvin Brieuc , Brown James , Meagher Ava , Coyle Joanne , Hunter Dominic , Bhumkhar Akshay , Ve Thomas , Kobe Bostjan , Sierecki Emma , Gambin Yann
Published: June 2018

A novel concept has emerged whereby the higher-order self-assembly of proteins provides a simple and robust mechanism for signal amplification. This appears to be a universal signalling mechanism within the innate immune system, where the recognition of pathogens or danger-associated molecular patterns need to trigger a strong, binary response within cells. Previously, multiple structural studies have been limited to single domains, expressed and assembled at high protein concentrations. We therefore set out to develop new in vitro strategies to characterise the behaviour of full-length proteins at physiological levels. In this study we focus on the adaptor protein MyD88, which contains two domains with different self-assembly properties: a TIR domain that can polymerise similarly to the TIR domain of Mal, and a Death Domain that has been shown to oligomerise with helical symmetry in the Myddosome complex. To visualize the behaviour of full-length MyD88 without purification steps, we use single-molecule fluorescence coupled to eukaryotic cell-free protein expression. These experiments demonstrate that at low protein concentration, only full-length MyD88 forms prion-like polymers. We also demonstrate that the metastability of MyD88 polymerisation creates the perfect binary response required in innate signalling: the system is silenced at normal concentrations but upstream signalling creates a “seed” that triggers polymerisation and amplification of the response. These findings pushed us to re-interpret the role of polymerisation in MyD88-related diseases and we studied the impact of disease-associated point mutations L93P, R196C and L252P/L265P at the molecular level. We discovered that all mutations completely block the ability of MyD88 to polymerise. We also confirm that L252P, a gain-of-function mutation, allows the MyD88 mutant to form extremely stable oligomers, even when expressed at low nanomolar concentrations. Thus, our results are consistent with and greatly add to the findings on the Myddosomes digital ‘all-or-none’ responses and the behaviour of the oncogenic mutation of MyD88.
Epitope - based peptide vaccine againstFructose-bisphosphate aldolase (FBA)ofMadurella mycetomatisusing immunoinformatics approaches
Authors: Mohammed Arwa A. , ALnaby Ayman M. H. , Sabeel Solima M. , AbdElmarouf Fagr M. , Dirar Amina I. , Ali Mostafa M. , Khandgawi Mustafa A. , Yousif Abdelhameed M. , Abdulgadir Eman M. , Sabahalkhair Magdi A. , Abbas Ayman E. , Hassan Mohammed A.
Published: June 2018

Background

Mycetoma is a distinct flesh eating and destructive neglected tropical disease. It is endemic in many tropical and subtropical countries. Mycetoma is caused by bacterial infections (actinomycetoma) such as Streptomyces somaliensis and Nocardiae or true fungi (eumycetoma) such as Madurella mycetomatis. Until date, treatments fail to cure the infection and the available marketed drugs are expensive and toxic upon prolonged usage. Moreover, no vaccine was prepared yet against mycetoma.

The aimof this study is to predict effective epitope-based vaccine against fructose-bisphosphate aldolase enzymes of M. mycetomatis using immunoinformatics approaches.

Methods and Materials

Fructose-bisphosphate aldolase ofMadurella mycetomatisSequence was retrieved from NCBI. Different prediction tools were used to analyze the nominee’s epitopes in Immune Epitope Database for B-cell, T-cell MHC class II & I. Then the proposed peptides were docked using Autodock 4.0 software program.

Results and Conclusions

The proposed and promising peptides KYLQ shows a potent binding affinity to B-cell, FEYARKHAF with a very strong binding affinity to MHC1 alleles and FFKEHGVPL that show a very strong binding affinity to MHC11and MHC1 alleles. This indicates a strong potential to formulate a new vaccine, especially with the peptide FFKEHGVPL which is likely to be the first proposed epitope-based vaccine against Fructose-bisphosphate aldolase of Madurella mycetomatis. This study recommends an in-vivo assessment for the most promising peptides especially FFKEHGVPL.
Liquid biopsy for infectious diseases: Sequencing of cell-free plasma to detect pathogen DNA in patients with invasive fungal disease
Authors: Hong David K. , Blauwkamp Timothy A. , Kertesz Mickey , Bercovici Sivan , Truong Cynthia , Banaei Niaz
Published: June 2018

Diagnosis of life-threatening deep-seated infections currently requires invasive sampling of the infected tissue to provide a microbiologic diagnosis. These procedures can lead to high morbidity in patients and add to healthcare costs. Here we describe a novel next-generation sequencing assay that was used to detect pathogen-derived cell-free DNA in peripheral blood of patients with biopsy-proven invasive fungal infections. The non-invasive nature of this approach could provide rapid, actionable treatment information for invasive fungal infections when a biopsy is not possible.
Communication and quorum sensing in non-living mimics of eukaryotic cells
Authors: Niederholtmeyer Henrike , Chaggan Cynthia , Devaraj Neal K.
Published: June 2018

Cells in tissues or biofilms communicate with one another through chemical and mechanical signals to coordinate collective behaviors. Non-living cell mimics provide simplified models of natural systems, however, it has remained challenging to implement communication capabilities comparable to living cells. Here we present a porous artificial cell-mimic containing a nucleus-like DNA-hydrogel compartment that is able to express and display proteins, and communicate with neighboring cell-mimics through diffusive protein signals. We show that communication between cell-mimics allows distribution of tasks, quorum sensing, and cellular differentiation according to local environment. Cell-mimics can be manufactured in large quantities, easily stored, chemically modified, and spatially organized into diffusively connected tissue-like arrangements, offering a means for studying communication in large ensembles of artificial cells.
Covering all your bases: incorporating intron signal from RNA-seq data
Authors: Lee Stuart , Zhang Albert Y. , Su Shian , Ng Ashley P. , Holik Aliaksei Z. , Asselin-Labat Marie-Liesse , Ritchie Matthew E. , Law Charity W.
Published: June 2018

RNA-seq datasets can contain millions of intron reads per sequenced library that are typically removed from downstream analysis. Only reads overlapping annotated exons are considered to be informative since mature mRNA is assumed to be the major component sequenced, especially when examining poly(A) RNA samples. In this paper, we demonstrate that intron reads are informative and that pre-mRNA is the major source of intron signal. Making use of pre-mRNA signal, ourindexmethod combines differential expression analyses from intron and exon counts to categorise changes observed in each count set, giving additional genes with evidence of transcriptional changes when compared to a classic approach. Considering the importance of intron retention in some biological systems, another novel method,superintronic, looks for evidence of intron retention after accounting for the presence of pre-mRNA signal. The results presented here overcomes deficiencies and biases in previous works related to intron reads by exploring multiple sources for intron reads simultaneously using a data-driven approach, and provides a broad overview into how intron reads can be utilised in relation to multiple aspects of transcriptional biology.
Disturbance During Biofilm Community Succession Promotes Cooperation and Diversity
Authors: Stratford James P. , Hodgson Douglas M. , Beecroft Nelli J. , Smith Ann , Marchesi Julian R. , Avignone-Rossa Claudio
Published: June 2018

Diversity-disturbance relationships have found widespread application in ecology, conservation and biodiversity management. In spite of their explanatory power, these conceptual frameworks have yet to be systematically applied to understanding succession in diverse microbial biofilms. Here we investigate community assembly in biofilms formed in replicate microbial bioelectrochemical systems using time-course sequencing of community 16S rRNA genes, corresponding to hundreds of operational taxonomic units (OTUs). For the first time we present a statistical model showing that a simple diversity-disturbance relationship can be used to explain dynamic changes in high diversity biofilm communities. This simple model reveals that succession in these systems is guided towards either a low diversity, generalist-dominated biofilm or a high diversity, cooperative-specialist biofilm, depending on the level of endogenous disturbance measured within the community. The pattern observed shows remarkable symmetry with findings from macro-scale communities such as grasslands, forests and coral reefs.
Recent secondary contacts, background selection and variable recombination rates shape genomic diversity in the model speciesAnolis carolinensis
Authors: Bourgeois Yann , Ruggiero Robert P. , Manthey Joseph D. , Boissinot Stéphane
Published: June 2018

Gaining a better understanding on how selection and neutral processes affect genomic diversity is essential to gain better insights into the mechanisms driving adaptation and speciation. However, the evolutionary processes affecting variation at a genomic scale have not been investigated in most vertebrate lineages. Previous studies have been limited to a small number of model species, mostly mammals, and no studies have investigated genomic variation in non avian reptiles. Here we present the first population genomics survey using whole genome re sequencing in the green anole (Anolis carolinensis). This species has emerged as a model for the study of genomic evolution in squamates. We quantified how demography, recombination and selection have led to the current genetic diversity of the green anole by using whole-genome resequencing of five genetic clusters covering the entire species range. The differentiation of green anole’s populations is consistent with a northward expansion from South Florida followed by genetic isolation and subsequent gene flow among adjacent genetic clusters. Dispersal out-of-Florida was accompanied by a drastic population bottleneck followed by a rapid population expansion. This event was accompanied by male-biased dispersal and/or selective sweeps on the X chromosome. We show that the combined effect of background selection and recombination rates is the main contributor to the genomic landscape of differentiation in the anole genome. We further demonstrate that recombination rates are positively correlated with GC content at third codon position (GC3) and confirm the importance of biased gene conversion in shaping genome wide patterns of diversity in reptiles.
Spatial distribution of benthic macrofauna in the Central Arctic Ocean
Authors: Vedenin Andrey , Gusky Manuela , Gebruk Andrey , Kremenetskaia Antonina , Rybakova Elena , Boetius Antje
Published: June 2018

Permanent ice coverage and the low primary production in the mostly ice-covered Central Arctic ocean basins result in significantly lower biomass and density of macrobenthos in the abyssal plains compared to the continental slopes. However, little is known on bathymetric and regional effects on macrobenthos diversity. This study synthesizes new and available macrobenthos data to provide a baseline for future studies of the effects of Arctic change on macrofauna community composition in the Arctic basins. Samples taken during three expeditions (in 1993, 2012 and 2015) at 37 stations on the slope of the Barents and Laptev Seas and in the abyssal of the Nansen and Amundsen Basins in the depth range from 38 m to 4381 m were used for a quantitative analysis of species composition, abundance and biomass. Benthic communities clustered in five depth ranges across the slope and basin. A parabolic pattern of species diversity change with depth was found, with the diversity maximum for macrofauna at the shelf edge at depths of 100-300 m. This deviates from the typical species richness peak at mid-slope depths of 1500-3000 m in temperate oceans. Due to the limited availability of standardized benthos data, it remains difficult to assess the massive sea ice retreat observed in the past decade has affected benthic community composition. The polychaeteYmerana pteropodaand the bryozoanNolellasp. were found for the first time in the deep Nansen and Amundsen Basins, as a potential first sign of increasing productivity and carbon flux with the thinning ice.
ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases
Authors: Domingo-Fernández Daniel , Hoyt Charles Tapley , Bobis-Álvarez Carlos , Marín-Llaó Josep , Hofmann-Apitius Martin
Published: June 2018

Although pathways are widely used for the analysis and representation of biological systems, their lack of clear boundaries, their dispersion across numerous databases, and the lack of interoperability impedes the evaluation of the coverage, agreements, and discrepancies between them. Here, we present ComPath, an ecosystem that supports curation of pathway mappings between databases and fosters the exploration of pathway knowledge through several novel visualizations. We have curated mappings between three of the major pathway databases and present a case study focusing on Parkinson’s disease that illustrates how ComPath can generate new biological insights by identifying pathway modules, clusters, and cross-talks with these mappings. The ComPath source code and resources are available at https://github.com/ComPath and the web application can be accessed at http://compath.scai.fraunhofer.de/.