bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alterations in Ion Channel Expression Surrounding Implanted Microelectrode Arrays in the Brain
Authors: Salatino Joseph W. , Kale Arya P. , Purcell Erin K. 
Published: January 2019

AbstractMicroelectrode arrays designed to map and modulate neuronal circuitry have enabled greater understanding and treatment of neurological injury and disease. Reliable detection of neuronal activity over time is critical for the successful application of chronic recording devices. Here, we assess device-related plasticity by exploring local changes in ion channel expression and their relationship to device performance over time. We investigated four voltage-gated ion channels (Kv1.1, Kv4.3, Kv7.2, and Nav1.6) based on their roles in regulating action potential generation, firing patterns, and synaptic efficacy. We found that a progressive increase in potassium channel expression and reduction in sodium channel expression accompanies signal loss over 6 weeks (both LFP amplitude and number of units). This motivated further investigation into a mechanistic role of ion channel expression in recorded signal instability. We employed siRNA in neuronal culture to find that Kv7.2 knockdown (as a model for the transient downregulation observed at 1 day in vivo) mimics excitatory synaptic remodeling around devices. This work provides new insight into the mechanisms underlying signal loss over time.
Homologous recombination substantially delays sequence but not gene content divergence of prokaryotic populations
Authors: Iranzo Jaime , Wolf Yuri I. , Koonin Eugene V. , Sela Itamar 
Published: January 2019

AbstractEvolution of bacterial and archaeal genomes is a highly dynamic process that involves extensive gain and loss of genes. Therefore, phylogenetic trees of prokaryotes can be constructed both by the traditional sequence-based methods (gene trees) and by comparison of gene compositions (genome trees). Comparing the branch lengths in gene and genome trees with identical topologies for 34 clusters of closely related bacterial and archaeal genomes, we found that the terminal branches of gene trees were systematically compressed compared to those of genome trees. Thus, sequence evolution seems to be significantly delayed with respect to genome evolution by gene gain and loss. The extent of this delay widely differs among bacterial and archaeal lineages. We develop and explore mathematical models demonstrating that the delay of sequence divergence can be explained by sequence homogenization that is caused by homologous recombination. Once evolving genomes become isolated by barriers that impede homologous recombination, gene and genome evolution processes settle into parallel trajectories, and genomes diverge, resulting in speciation. This model of prokaryotic genome evolution gives a mechanistic explanation of our previous finding that archaeal genomes contain a class of genes that turn over rapidly, before significant sequence divergence occurs, and provides a framework for correcting phylogenetic trees, to make them consistent with the dynamics of gene turnover.
Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex
Authors: Weigt Martina , Gao Qingsong , Ban Hyoju , He Haijin , Mastrobuoni Guido , Kempa Stefan , Chen Wei , Li Fei 
Published: January 2019

AbstractSplicing factors have recently been shown to be involved in heterochromatin formation, but their role in controlling heterochromatin structure and function remains poorly understood. In this study, we identified a fission yeast homologue of human splicing factor RBM10, which has been linked to TARP syndrome. Overexpression of Rbm10 in fission yeast leads to strong global intron retention. Rbm10 also interacts with splicing factors in a pattern resembling that of human RBM10, suggesting that the function of Rbm10 as a splicing regulator is conserved. Surprisingly, our deep-sequencing data showed that deletion of Rbm10 caused only minor effect on genome-wide gene expression and splicing. However, the mutant displays severe heterochromatin defects. Further analyses indicated that the heterochromatin defects in the mutant did not result from mis-splicing of heterochromatin factors. Our proteomic data revealed that Rbm10 associates with the histone deacetylase Clr6 complex and chromatin remodelers known to be important for heterochromatin silencing. Deletion of Rbm10 results in significant reduction of Clr6 in heterochromatin. Our work together with previous findings further suggests that different splicing subunits may play distinct roles in heterochromatin regulation.
Nutrient availability affects the prevalence of a microsporidian parasite
Authors: Narr Charlotte F. , Ebert Dieter , Bastille‐Rousseau Guillaume , Frost Paul C. 
Published: January 2019

Abstract

Defining the relationship between nutrients and parasitism is complicated by shifts in host physiology and population density, which can both mediate the effects of host diet on parasites and vice versa.

We examined the relationship between nutrient availability and an abundant parasite capable of both horizontal and vertical transmission (Hamiltosporidium tvaerminnensis) of a planktonic crustacean, Daphnia magna, in rock pools on Baltic Sea Skerry islands.

We found that the relative availability of nutrients directly affected infection prevalence; parasite prevalence was higher in pools with higher particulate N:P ratios. Infection prevalence was not related to Daphnia population densities. A complementary experiment that examined host responses to an N:P gradient in mesocosms indicated that high N:P ratios can increase spore load in the hosts.

We surmise that high N:P food increases Daphnia feeding rate, which increases their contact with parasite spores and leads to higher prevalence and more intense infections. We found no direct evidence that parasite‐induced changes in host nutrient use affected nutrient dynamics in pools. However, the relationship between diet N:P and the parasite's prevalence and load is consistent with previously documented patterns of this parasite's effect on host nutrient use.

Taken together, this study suggests that high N:P ratios in food may benefit the parasite in multiple ways and could create environments that favour horizontal transmission over vertical transmission for parasites capable of both transmission routes. If so, nutrient limitation could have long‐term consequences for host–parasite evolution.
The Construction of the Efficient Office: Scientific Management, Accountability, and the Neo‐Liberal State
Authors: Parker Lee D. , Jeacle Ingrid 
Published: January 2019

ABSTRACTThe office has been a central site of organizational planning, accountability, and control since the 19th century. Yet it has been the subject of relatively little accounting research. Through the dual theoretical lenses of Foucaultian and Labour Process theories, this study employs historical photo‐elicitation methodology to investigate the implementation of management control and accountability in the scientifically managed office which emerged in the United States during the late 19th and early 20th centuries. Our analysis reveals the manner in which accounting records created new modes of disciplinary control and surveillance within the office and how accounting tasks were de‐skilled in a gradually feminized and mechanized office environment. We also witness the role of accounting in the physical structuring of office space through the assembly line arrangement of office furniture to facilitate paper flows and the installation of record‐keeping systems of surveillance. In addition, our visually derived historical account of these transformations in office administration allows us to reflect on some contemporary issues. The production‐line design and efficiency so promoted by scientific management served as a forerunner to today's open‐plan office, as well as influencing contemporary office management philosophies such as Activity‐Based Working. Furthermore, we seek to inform current debates on the role of accounting in contemporary neo‐liberal society. In the history of the scientific office, we gain an early glimpse of the subsequent role that accounting comes to play within a neo‐liberal agenda as a powerful technology of micro‐measurement and micro‐management.
bmotif: A package for motif analyses of bipartite networks
Authors: Simmons Benno I. , Sweering Michelle J. M. , Schillinger Maybritt , Dicks Lynn V. , Sutherland William J. , Di Clemente Riccardo 
Published: January 2019

Abstract

Bipartite networks are widely used to represent a diverse range of species interactions, such as pollination, herbivory, parasitism and seed dispersal. The structure of these networks is usually characterised by calculating one or more indices that capture different aspects of network architecture. While these indices capture useful properties of networks, they are relatively insensitive to changes in network structure. Consequently, variation in ecologically‐important interactions can be missed. Network motifs are a way to characterise network structure that is substantially more sensitive to changes in pairwise interactions and is gaining in popularity. However, there is no software available in R, the most popular programming language among ecologists, for conducting motif analyses in bipartite networks. Similarly, no mathematical formalisation of bipartite motifs has been developed.

Here we introduce bmotif: a package for motif analyses of bipartite networks. Our code is primarily an r package, but we also provide matlab and Python code of the core functionality. The software is based on a mathematical framework where, for the first time, we derive formal expressions for motif frequencies and the frequencies with which species occur in different positions within motifs. This framework means that analyses with bmotif are fast, making motif methods compatible with the permutational approaches often used in network studies, such as null model analyses.

We describe the package and demonstrate how it can be used to conduct ecological analyses, using two examples of plant–pollinator networks. We first use motifs to examine the assembly and disassembly of an Arctic plant–pollinator community and then use them to compare the roles of native and introduced plant species in an unrestored site in Mauritius.

bmotif will enable motif analyses of a wide range of bipartite ecological networks, allowing future research to characterise these complex networks without discarding important meso‐scale structural detail.
AllergoOncology: Microbiota in allergy and cancer—A European Academy for Allergy and Clinical Immunology position paper
Authors: Untersmayr Eva , Bax Heather J. , Bergmann Christoph , Bianchini Rodolfo , Cozen Wendy , Gould Hannah J. , Hartmann Karin , Josephs Debra H. , Levi‐Schaffer Francesca , Penichet Manuel L. , O'Mahony Liam , Poli Aurelie , Redegeld Frank A. , Roth‐Walter Franziska , Turner Michelle C. , Vangelista Luca , Karagiannis Sophia N. , Jensen‐Jarolim Erika 
Published: January 2019

AbstractThe microbiota can play important roles in the development of human immunity and the establishment of immune homeostasis. Lifestyle factors including diet, hygiene, and exposure to viruses or bacteria, and medical interventions with antibiotics or anti‐ulcer medications, regulate phylogenetic variability and the quality of cross talk between innate and adaptive immune cells via mucosal and skin epithelia. More recently, microbiota and their composition have been linked to protective effects for health. Imbalance, however, has been linked to immune‐related diseases such as allergy and cancer, characterized by impaired, or exaggerated immune tolerance, respectively. In this AllergoOncology position paper, we focus on the increasing evidence defining the microbiota composition as a key determinant of immunity and immune tolerance, linked to the risk for the development of allergic and malignant diseases. We discuss novel insights into the role of microbiota in disease and patient responses to treatments in cancer and in allergy. These may highlight opportunities to improve patient outcomes with medical interventions supported through a restored microbiome.
The functional biology of peanut allergens and possible links to their allergenicity
Authors: Ozias‐Akins Peggy , Breiteneder Heimo 
Published: January 2019

AbstractPeanut is one of the most common food triggers of fatal anaphylaxis worldwide although peanut allergy affects only 1%‐2% of the general population. Peanuts are the source of highly potent allergenic proteins. It is emerging that the allergenicity of certain proteins is linked to their biological function. Peanut is an unusual crop in that it flowers aboveground but produces its seed‐containing pods underground. This so‐called geocarpic fruiting habit exposes pods and seeds during their development to soilborne pathogens and pests. Pest damage can also open routes of entry for opportunistic fungi such as Aspergillus. Although seed proteins have primary functions in nutrient reservoirs, lipid storage bodies, or the cytoskeleton, they have also evolved to act as part of the plant's defense system to enhance fitness and survival of the species. When interacting with pathogens or pests, these proteins modify and damage cells' membranes, interact with immune receptors, and modulate signaling pathways. Moreover, following exposure, the immune system of predisposed individuals reacts to these proteins with the production of specific IgE. This review explores the evolutionary biology of peanut and its seed proteins and highlights possible links between the proteins' biological function and their allergenicity.
Anterior segment optical coherence tomography (AS‐OCT) as a new method of detecting copper deposits forming the Kayser–Fleischer ring in patients with Wilson disease
Authors: Broniek‐Kowalik Karina , Dzieżyc Karolina , Litwin Tomasz , Członkowska Anna , Szaflik Jacek P. 
Published: January 2019

AbstractPurposeKayser–Fleischer ring pathognomonic for Wilson disease (WD) is formed of corneal copper deposits present predominantly within the anterior chamber angle at the Schwalbe's line. The slit‐lamp assessment commonly used as a standard of care cannot detect them early enough, as the angle view is obscured by the corneal limbus. The aim of the research was to evaluate the anterior segment optical coherence tomography (AS‐OCT), as objective diagnostic assessment of copper deposits forming KF ring in patients with WD.MethodsTwenty‐nine subjects (17 women) and twenty‐nine controls (14 women) were enrolled and underwent slit lamp and AS‐OCT assessment.ResultsKayser–Fleischer ring was not detected – either with a slit lamp or with AS‐OCT – in any of the controls. Fifteen subjects presenting without KF ring at a slit‐lamp examination were found to have a KF ring when examined with AS‐OCT (p < 0.001), which confirms improved accuracy of AS‐OCT, as compared to the slit‐lamp examination.ConclusionOur results support AS‐OCT as a diagnostic procedure to offer better objectivity and accuracy as compared to a slit‐lamp examination, both at the diagnostic stage and when monitoring changes in KF ring during medical therapy to assess its efficacy and patient compliance.
Acute intrarenal angiotensin (1‐7) infusion decreases diabetes‐induced glomerular hyperfiltration but increases kidney oxygen consumption in the rat
Authors: Persson Patrik , Fasching Angelica , Palm Fredrik 
Published: January 2019

AbstractAimCommon kidney alterations early after the onset of insulinopenic diabetes include glomerular hyperfiltration, increased oxygen consumption and tissue hypoxia. Increased activity of the renin‐angiotensin‐aldosterone system (RAAS) has been implicated in most of these early alterations. The RAAS peptide angiotensin (1‐7) has the potential to modulate RAAS‐mediated alterations in kidney function. Thus, the aim of the present study was to determine the acute effects of angiotensin (1‐7) in the kidney of insulinopenic type 1 diabetic rat and the results compared to that of normoglycaemic controls.MethodsRenal haemodynamics and oxygen homeostasis were measured 3 weeks after administration of streptozotocin before and after acute intrarenal infusion of angiotensin (1‐7) at a dose of 400 ng min−1.ResultsArterial pressure and renal blood flow were similar between groups and not affected by exogenous angiotensin (1‐7). Diabetics presented with glomerular hyperfiltration, increased urinary sodium excretion and elevated kidney oxygen consumption. Angiotensin (1‐7) infusion normalized glomerular filtration, increased urinary sodium excretion, decreased proximal tubular reabsorption, and elevated kidney oxygen consumption even further. The latter resulting in tubular electrolyte transport inefficiency. Angiotensin (1‐7) did not affect tissue oxygen tension and had no significant effects in controls on any of the measured parameters.ConclusionDiabetes results in increased responsiveness to elevated levels of angiotensin (1‐7) which is manifested as inhibition of tubular sodium transport and normalization of glomerular filtration. Furthermore, elevated angiotensin (1‐7) levels increase kidney oxygen consumption in the diabetic kidney even further which affects tubular electrolyte transport efficiency negatively.
Roles of oestradiol receptor alpha and beta against hypertension and brain mitochondrial dysfunction under intermittent hypoxia in female rats
Authors: Laouafa Sofien , Roussel Damien , Marcouiller François , Soliz Jorge , Gozal David , Bairam Aida , Joseph Vincent 
Published: January 2019

AbstractAimChronic intermittent hypoxia (CIH) induces systemic (hypertension) and central alterations (mitochondrial dysfunction underlying cognitive deficits). We hypothesized that agonists of oestradiol receptors (ER) α and β prevent CIH‐induced hypertension and brain mitochondrial dysfunction.MethodsOvariectomized female rats were implanted with osmotic pumps delivering vehicle (Veh), the ERα agonist propylpyraoletriol (PPT — 30 μg/kg/day) or the ERβ agonist diarylpropionitril (DPN — 100 μg/kg/day). Animals were exposed to CIH (21%‐10% FIO2 — 10 cycles/hour – 8 hours/day – 7 days) or normoxia. Arterial blood pressure was measured after CIH or normoxia exposures. Mitochondrial respiration and H2O2 production were measured in brain cortex with high‐resolution respirometry, as well as activity of complex I and IV of the electron transport chain, citrate synthase, pyruvate, and lactate dehydrogenase (PDH and LDH).ResultsPropylpyraoletriol but not DPN prevented the rise of arterial pressure induced by CIH. CIH exposures decreased O2 consumption, complex I activity, and increased H2O2 production. CIH had no effect on citrate synthase activity, but decreased PDH activity and increased LDH activity indicating higher anaerobic glycolysis. Propylpyraoletriol and DPN treatments prevented all these alterations.ConclusionsWe conclude that in OVX female rats, the ERα agonist prevents from CIH‐induced hypertension while both ERα and ERβ agonists prevent the brain mitochondrial dysfunction and metabolic switch induced by CIH. These findings may have implications for menopausal women suffering of sleep apnoea regarding hormonal therapy.
Don't forget astrocytes when targeting Alzheimer's disease
Authors: Sadick Jessica S. , Liddelow Shane A. 
Published: January 2019

Astrocytes are essential for CNS health, regulating homeostasis, metabolism, and synaptic transmission. In addition to these and many other physiological roles, the pathological impact of astrocytes (“reactive astrocytes”) in acute trauma and chronic disease like Alzheimer's disease (AD) is well established. Growing evidence supports a fundamental and active role of astrocytes in multiple neurodegenerative diseases. With a growing interest in normal astrocyte biology, and countless studies on changes in astrocyte function in the context of disease, it may be a surprise that no therapies exist incorporating astrocytes as key targets. Here, we examine unintentional effects of current AD therapies on astrocyte function and theorize how astrocytes may be intentionally targeted for more efficacious therapeutic outcomes. Given their integral role in normal neuronal functioning, incorporating astrocytes as key criteria for AD drug development can only lead to more effective therapies for the millions of AD sufferers worldwide.Linked ArticlesThis article is part of a themed section on Therapeutics for Dementia and Alzheimer's Disease: New Directions for Precision Medicine. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.18/issuetoc
Betulinic acid alleviates endoplasmic reticulum stress‐mediated nonalcoholic fatty liver disease through activation of farnesoid X receptors in mice
Authors: Gu Ming , Zhao Ping , Zhang Shiying , Fan Shengjie , Yang Li , Tong Qingchun , Ji Guang , Huang Cheng 
Published: January 2019

Background and PurposeThe molecular mechanism for the pathogenesis of nonalcoholic fatty liver disease (NAFLD) remains elusive. Both farnesoid X receptor (FXR) signalling and endoplasmic reticulum (ER) stress contribute to the progression of NAFLD; however, it is not clear whether the actions of these two pathways are dependent on each other. Moreover, the pharmacological benefits and mechanism of betulinic acid (BA) in controlling metabolic syndrome and NAFLD are largely unknown.Experimental ApproachA reporter assay and a time‐resolved FRET assay were used to identify BA as an agonist of the FXR. NAFLD was induced by a methionine and choline‐deficient L‐amino acid diet (MCD) and high‐fat diet (HFD). The pharmacological effects of BA (100 mg·kg−1·day−1) and potential interactions between hepatic FXR activation and ER stress pathways were evaluated by FXR silencing, Western blot and RT‐PCR analyses using control and FXR−/− mice.Key ResultsActivation of the FXR inhibited intracellular PERK/EIF2α/ATF4 and CHOP signalling, thereby alleviating hepatic ER stress, whereas FXR silencing resulted in an opposite effect. Furthermore, we identified BA as an FXR agonist that effectively attenuated the progression of NAFLD and metabolic disorders in both HFD‐ and MCD diet‐fed mice and restored the hepatocellular ER homeostasis by stimulating the FXR signalling pathway and blocking PERK/EIF2α signalling. In contrast, the effects of BA were attenuated in FXR−/− mice.Conclusions and ImplicationsOur data demonstrate that pharmacological activation of the FXR by BA reduces hepatocellular ER stress and attenuates NAFLD in an animal model of hepatic steatosis.
Design and antimicrobial activities of LL‐37 derivatives inhibiting the formation of Streptococcus mutans biofilm
Authors: Chen Zhao , Yang Guang , Lu Shengsheng , Chen Daiwei , Fan Sheng , Xu Junyang , Wu Buling , He Jian 
Published: January 2019

AbstractDental plaque is closely related to the occurrence of dental caries, of which the main causative bacterium is Streptococcus mutans (S. mutans). In this study, to create potent antibiofilm agents, we chose a human antimicrobial peptide LL‐37 as our starting material and modified it by cutting it shorter and varying its charge and hydrophobicity. The results of anti‐S. mutans as well as biofilm inhibitory activity tests indicated that two derivatives, IG‐13‐1 and IG‐13‐2, were the most potent one toward both planktonic and biofilm S. mutans cells with the minimal inhibitory concentration of 5.0 μM and minimal biofilm inhibitory concentrations of 5.91 ± 0.91 μM and 7.58 ± 0.23 μM, respectively. The modes of action study showed that IG‐13‐1 and IG‐13‐2 were functioned by disrupting the bacterial membrane, causing the leakage of inner contents, thereby leading to the death of bacterial cells eventually. In addition, IG‐13‐1 and IG‐13‐2 were able to suppress the expression of proinflammatory cytokine of TNF‐α and reduce the level of nuclear transcription factor‐κB, which indicated the potential anti‐inflammatory activity of these peptides. Conclusively, this study indicated that IG‐13‐1 and IG‐13‐2 are potent peptides in both anti‐S. mutans and anti‐inflammatory activities, therefore, showing a potential application for the prevention and treatment of dental caries.