julilili42/papers huggingface dataset:
Decision-making in plants under competition
2017-12-15

Abstract Plants can plastically respond to light competition in three strategies, comprising vertical growth, which promotes competitive dominance; shade tolerance, which maximises performance under shade; or lateral growth, which offers avoidance of competition. Here, we test the hypothesis that plants can ‘choose’ between these responses, according to their abilities to competitively overcome their neighbours. We study this hypothesis in the clonal plant Potentilla reptans using an experimental setup that simulates both the height and density of neighbours, thus presenting plants with different light-competition scenarios. Potentilla reptans ramets exhibit the highest vertical growth under simulated short-dense neighbours, highest specific leaf area (leaf area/dry mass) under tall-dense neighbours, and tend to increase total stolon length under tall-sparse neighbours. These responses suggest shifts between ‘confrontational’ vertical growth, shade tolerance and lateral-avoidance, respectively, and provide evidence that plants adopt one of several alternative plastic responses in a way that optimally corresponds to prevailing light-competition scenarios.
Lipid moieties on lipoproteins of commensal and non-commensal staphylococci induce differential immune responses
2017-12-15

Abstract Lipoproteins (Lpp) of Gram-positive bacteria are major players in alerting our immune system. Here, we show that the TLR2 response induced by commensal species Staphylococcus aureus and Staphylococcus epidermidis is almost ten times lower than that induced by noncommensal Staphylococcus carnosus , and this is at least partially due to their different modifications of the Lpp lipid moieties. The N terminus of the lipid moiety is acylated with a long-chain fatty acid (C17) in S. aureus and S. epidermidis , while it is acylated with a short-chain fatty acid (C2) in S. carnosus . The long-chain N -acylated Lpp, recognized by TLR2–TLR1 receptors, silences innate and adaptive immune responses, while the short-chain N -acetylated Lpp, recognized by TLR2–TLR6 receptors, boosts it.
The Evolution of Corneal Transplantation
2017-12-15

BACKGROUND The aim of this study was to investigate the evolution of surgical methods in and leading indications for corneal transplantation from 2005 to 2016. MATERIAL AND METHODS Data from the corneal graft waiting list and from all keratoplasties carried out between 2005 and 2016 at the University Eye Hospital Tübingen were retrospectively evaluated. RESULTS A total of 1259 keratoplasties were performed between 2005 and 2016 at the University Eye Hospital Tübingen. The most common surgical indications for corneal transplantation were Fuchs endothelial corneal dystrophy (45.5%) and keratoconus (14.2%). The mean rate of corneal transplantations almost doubled from 71 keratoplasties per year in the first 6-year period to 139 keratoplasties per year in the second 6-year period (P=0.005). The number of penetrating keratoplasties remained similar. The number of Descemet membrane endothelial keratoplasties (DMEK) increased significantly from 2008 to 2016 (P<0.0001). One DMEK procedure was performed in 2008 (representing 1.4% of all transplantations), while 75 DMEK procedures were performed in 2016 (representing 60.5% of all transplantations) (P<0.0001). DMEK became the favored surgical method for endothelial disorders, exceeding penetrating keratoplasty in 2013. CONCLUSIONS Our study shows evolutionary changes in preferred corneal transplantation techniques and leading indications for keratoplasty from 2005 to 2016. Since its introduction a decade ago, DMEK is currently the golden standard in the management of corneal endothelial dysfunction.
Microplastics as an emerging threat to terrestrial ecosystems
2017-12-16

Abstract Microplastics (plastics &lt;5 mm, including nanoplastics which are &lt;0.1 μm) originate from the fragmentation of large plastic litter or from direct environmental emission. Their potential impacts in terrestrial ecosystems remain largely unexplored despite numerous reported effects on marine organisms. Most plastics arriving in the oceans were produced, used, and often disposed on land. Hence, it is within terrestrial systems that microplastics might first interact with biota eliciting ecologically relevant impacts. This article introduces the pervasive microplastic contamination as a potential agent of global change in terrestrial systems, highlights the physical and chemical nature of the respective observed effects, and discusses the broad toxicity of nanoplastics derived from plastic breakdown. Making relevant links to the fate of microplastics in aquatic continental systems, we here present new insights into the mechanisms of impacts on terrestrial geochemistry, the biophysical environment, and ecotoxicology. Broad changes in continental environments are possible even in particle‐rich habitats such as soils. Furthermore, there is a growing body of evidence indicating that microplastics interact with terrestrial organisms that mediate essential ecosystem services and functions, such as soil dwelling invertebrates, terrestrial fungi, and plant‐pollinators. Therefore, research is needed to clarify the terrestrial fate and effects of microplastics. We suggest that due to the widespread presence, environmental persistence, and various interactions with continental biota, microplastic pollution might represent an emerging global change threat to terrestrial ecosystems.
Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis
2017-12-16

Histone deacetylases have central functions in regulating stress defenses and development in plants. However, the knowledge about the deacetylase functions is largely limited to histones, although these enzymes were found in diverse subcellular compartments. In this study, we determined the proteome‐wide signatures of the RPD3/HDA1 class of histone deacetylases in Arabidopsis. Relative quantification of the changes in the lysine acetylation levels was determined on a proteome‐wide scale after treatment of Arabidopsis leaves with deacetylase inhibitors apicidin and trichostatin A. We identified 91 new acetylated candidate proteins other than histones, which are potential substrates of the RPD3/HDA1‐like histone deacetylases in Arabidopsis, of which at least 30 of these proteins function in nucleic acid binding. Furthermore, our analysis revealed that histone deacetylase 14 (HDA14) is the first organellar‐localized RPD3/HDA1 class protein found to reside in the chloroplasts and that the majority of its protein targets have functions in photosynthesis. Finally, the analysis of HDA14 loss‐of‐function mutants revealed that the activation state of RuBisCO is controlled by lysine acetylation of RuBisCO activase under low‐light conditions.
Sleep spindles and cognition in depression
2017-12-17

Sleep plays a critical role in orchestrating several cognitive functions. Sleep spindles are particularly at the forefront of studies on the consolidation of cognitive abilities, such as procedural and declarative memory. Despite that major depressive disorder (MDD) has been linked to sleep spindle alterations, their role in MDD pathogenesis and symptomatology (including memory deficits) is still scarcely investigated. Here, we first provide an overview of sleep and sleep spindle alterations in MDD and their potential effects on memory and cognition. Secondly, limited data suggest that sleep spindles deficits in severe MDD might not only lead to cognitive impairments but primarily affect memory consolidation processes during sleep. Furthermore, it seems likely that many sleep spindle related effects are masked by interacting (antidepressant) medication, selection of mixed patient groups with mild symptomatology as well as use of incomprehensive methodology in analyzing sleep. We propose a preliminary model predicting that impairments in sleep spindle related activity during sleep are mainly responsible for memory consolidation deficits in depressed patients, but that medication augmenting sleep spindle activity can enhance and restore sleep-mediated consolidation. Future studies thus need to scrutinize previous findings on sleep spindle effects in MDD.
Sustainable computational science: the ReScience initiative
2017-12-18

Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results; however, computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research is reproducible. But this is not exactly true. James Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. The actual scholarship is the full software environment, code, and data that produced the result. This implies new workflows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested and are hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically different from other traditional scientific journals. ReScience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and software tests.
Is It Possible to Develop Cancer Vaccines to Neoantigens, What Are the Major Challenges, and How Can These Be Overcome?
2017-12-18

The term "neoantigen," as applied to molecules newly expressed on tumor cells, has a long history. The groundbreaking discovery of a cancer causing virus in chickens by Rous over 100 years ago, followed by discoveries of other tumor-causing viruses in animals, suggested a viral etiology of human cancers. The search for other oncogenic viruses in the 1960s and 1970s resulted in the discoveries of Epstein-Barr virus (EBV), hepatitis B virus (HBV), and human papilloma virus (HPV), and continues until the present time. Contemporaneously, the budding field of immunology was posing the question can the immune system of animals or humans recognize a tumor that develops from one's own tissues and what types of antigens would distinguish the tumor from normal cells. Molecules encoded by oncogenic viruses provided the most logical candidates and evidence was quickly gathered for both humoral and cellular recognition of viral antigens, referred to as neoantigens. Often, however, serologic responses to virus-bearing tumors revealed neoantigens unrelated to viral proteins and expressed on multiple tumor types, foreshadowing later findings of multiple changes in other genes in tumor cells creating nonviral neoantigens.
The development of narcissistic admiration and machiavellianism in early adulthood.
2017-12-18

We investigated the development of narcissistic admiration (i.e., the assertive or extraverted dimension of narcissism; Back et al., 2013) and Machiavellianism (Mach) in early adulthood. Specifically, we examined (a) mean-level changes in narcissistic admiration and Mach during early adulthood and (b) how studying economics and experiencing any of 30 life events were related to individual differences in changes in narcissistic admiration and Mach. We used longitudinal data from 2 cohorts of young adults in Germany (N1 = 4,962 and N2 = 2,572). The mean levels of narcissistic admiration remained stable over time. Life events analyses indicated that narcissistic admiration increased among people who experienced a positively evaluated change in their eating or sleeping habits, a positively evaluated romantic break-up, or a negatively evaluated failure on an important exam. The mean levels of Mach decreased during early adulthood in both cohorts. Life events analyses showed that Mach decreased for only the 91% of young adults who had started a new job and evaluated it positively, suggesting that mastering occupational roles mitigates Mach in early adulthood. The results will be discussed in the light of previous longitudinal studies on narcissism and the Big Five and cross-sectional studies on how age is related to narcissism and Mach. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Cognitive Abilities and Mathematical Competencies at School Entry
2017-12-18

ABSTRACT The aim of this study was to identify mathematical competencies in early childhood and cognitive correlates of those competencies in a prospective longitudinal sample of children ( N = 1,292) in predominantly low‐income and nonurban communities in the United States. General mental ability, processing speed, vocabulary, and the working memory (WM), inhibitory control (IC), and cognitive flexibility components of executive function (EF) were assessed when children were aged 4 and 5 years. Math ability was assessed prior to school entry using a norm‐referenced assessment. Exploratory factor analysis indicated that items from the math assessment loaded onto factors representing conceptual and procedural skill. General mental ability, processing speed, vocabulary, and a unitary EF composite all related to both conceptual and procedural skill. When EF components were examined separately, however, only the IC aspect of EF was related to conceptual skill and only the WM aspect of EF was related to procedural skill.
New roles for nuclear EGFR in regulating the stability and translation of mRNAs associated with VEGF signaling
2017-12-18

Cell membrane-associated epidermal growth factor receptor (EGFR) translocates into a perinuclear/nuclear location upon stimulation, where it complexes with mRNAs. Treatment with radiation and cisplatin decreases the amounts of mRNAs present within this complex. Gene array analyses of mRNAs in complex with immunoprecipitated nEGFR revealed significant enrichment of different mRNA species compared to the control immunoprecipitation. Functional annotation with help of DAVID Gene Ontology Analysis identified under other terms the HIF-1A/VEGF signaling pathway as one of the top scoring KEGG pathways. RT-PCR and western blots revealed the radiation-induced expression of mRNAs and proteins involved in HIF-1A/VEGF signaling. Simultaneously, the levels of the corresponding validated miRNAs within the complex containing nEGFR and mRNAs were decreased. This finding argues that an mRNA/miRNA/nEGFR complex regulates protein expression. Indeed, we detected the GW182, AGO2, PABPC1 and cNOT1 proteins, which belong to the deadenylase complex, in a complex with nuclear EGFR. Erlotinib-mediated inhibition of EGFR kinase reduced the radiation-induced increase in mRNA expression. In this context, erlotinib reduced AGO2 phosphorylation by the EGFR kinase at residue Y393, which was associated with increased cNOT1 deadenylase activity and reduced mRNA stability. To prove the roles of miRNAs in this context, we transfected cells with an inhibitor of Hsa-mir-1180p5, which targets the NFATC4 mRNA, an mRNA associated with VEGF signaling, or pretreated cells with erlotinib. Indeed, Hsa-mir-1180p5 knockdown increased and the erlotinib treatment decreased the expression of the NFATC4 protein. The expression of the NFATC4 protein controlled the cloning efficiency and radiosensitivity of A549 and FaDu tumor cells. Thus, this study is the first to show that a membrane-located tyrosine kinase receptor, such as EGFR, is internalized to a nuclear/perinuclear location upon exposure to stress and modulates the stability and translation of miRNA-selected mRNAs. This mechanism enables cells to directly express proteins in response to EGFR activation and may contribute to treatment resistance in EGFR-overexpressing tumors.
Comparing Recalibration Strategies for Electroencephalography-Based Decoders of Movement Intention in Neurological Patients with Motor Disability
2017-12-18

Motor rehabilitation based on the association of electroencephalographic (EEG) activity and proprioceptive feedback has been demonstrated as a feasible therapy for patients with paralysis. To promote long-lasting motor recovery, these interventions have to be carried out across several weeks or even months. The success of these therapies partly relies on the performance of the system decoding movement intentions, which normally has to be recalibrated to deal with the nonstationarities of the cortical activity. Minimizing the recalibration times is important to reduce the setup preparation and maximize the effective therapy time. To date, a systematic analysis of the effect of recalibration strategies in EEG-driven interfaces for motor rehabilitation has not yet been performed. Data from patients with stroke (4 patients, 8 sessions) and spinal cord injury (SCI) (4 patients, 5 sessions) undergoing two different paradigms (self-paced and cue-guided, respectively) are used to study the performance of the EEG-based classification of motor intentions. Four calibration schemes are compared, considering different combinations of training datasets from previous and/or the validated session. The results show significant differences in classifier performances in terms of the true and false positives (TPs) and (FPs). Combining training data from previous sessions with data from the validation session provides the best compromise between the amount of data needed for calibration and the classifier performance. With this scheme, the average true (false) positive rates obtained are 85.3% (17.3%) and 72.9% (30.3%) for the self-paced and the cue-guided protocols, respectively. These results suggest that the use of optimal recalibration schemes for EEG-based classifiers of motor intentions leads to enhanced performances of these technologies, while not requiring long calibration phases prior to starting the intervention.
Prevention and management of adverse events of Novel agents in multiple myeloma: A consensus of the european myeloma network
2017-12-18

During the last few years, several new drugs have been introduced for treatment of patients with multiple myeloma, which have significantly improved treatment outcome. All of these novel substances differ at least in part in their mode of action from similar drugs of the same drug class, or are representatives of new drugs classes, and as such present with very specific side effect profiles. In this review, we summarize these adverse events, provide information on their prevention, and give practical guidance for monitoring of patients and for management of adverse events.Leukemia accepted article preview online, 18 December 2017. doi:10.1038/leu.2017.353.
Growth and evolution of satellites in a Jovian massive disc
2017-12-18

The formation of satellite systems in circum-planetary discs is considered to be similar to the formation of rocky planets in a proto-planetary disc, especially super-Earths. Thus, it is possible to use systems with large satellites to test formation theories that are also applicable to extrasolar planets. Furthermore, a better understanding of the origin of satellites might yield important information about the environment near the growing planet during the last stages of planet formation. In this work, we investigate the formation and migration of the Jovian satellites through N-body simulations. We simulated a massive, static, low-viscosity, circumplanetary disc in agreement with the minimum mass sub-nebula model prescriptions for its totalmass. In hydrodynamic simulations,we found no signs of gaps, therefore type II migration is not expected. Hence, we used analytic prescriptions for type I migration, eccentricity and inclination damping, and performed N-body simulations with damping forces added. Detailed parameter studies showed that the number of final satellites is strong influenced by the initial distribution of embryos, the disc temperature, and the initial gas density profile. For steeper initial density profiles, it is possible to form systems with multiple satellites in resonance while a flatter profile favours the formation of satellites close to the region of the Galilean satellites. We show that the formation of massive satellites such as Ganymede and Callisto can be achieved for hotter discs with an aspect ratio of H/r ~ 0.15 for which the ice line was located around 30RJ.
Silica‐Grafted Neodymium Catalysts for the Production of Ultrahigh‐Molecular‐Weight cis‐1,4‐Polyisoprene
2017-12-18

Abstract Supported neodymium‐based Ziegler‐type catalysts are obtained by grafting homoleptic methylaluminate Nd(AlMe 4 ) 3 onto high‐surface silica materials including periodic mesoporous silicas MCM‐41, SBA‐15, and KIT‐6. Low [Et 2 AlCl]‐cocatalyst contents allow for the fabrication of polyisoprenes with ultrahigh molecular weight (UHMWPI). The synthetic rubbers display molecular weights as high as 3×10 6 g mol −1 , polydispersity indices as low as 1.2, and microstructures with 99 % cis ‐stereospecificity. Combined analysis of the organolanthanide/silica hybrid materials by nitrogen physisorption, FTIR and magic angle spinning NMR spectroscopies, and elemental (metal) analysis assist in elucidating the intrapore surface organometallic chemistry and suggest the formation of unprecedented organolanthanide species.
The Digital Discotheque. Club Events in the Internet Age
2017-12-18

This paper aims to explore the receptive and aesthetic characteristics of the discotheque (or club) event as it has become a digitized and globally shared phenomenon of internet culture. By analyzing DJ Harvey’s performance at the Boiler Room Milan, I will point out, first, the immediate experience of this new form of entertainment in juxtaposition to traditional clubbing; second, the wider implications of this shift, particularly in terms of the roles of the DJ and the club space, aspects of performance, participation as well as social practices.
Impact of Sickle Cell Trait and Naturally Acquired Immunity on Uncomplicated Malaria after Controlled Human Malaria Infection in Adults in Gabon
2017-12-19

Controlled human malaria infection (CHMI) by direct venous inoculation (DVI) with 3,200 cryopreserved Plasmodium falciparum sporozoites (PfSPZ) consistently leads to parasitemia and malaria symptoms in malaria-naive adults. We used CHMI by DVI to investigate infection rates, parasite kinetics, and malaria symptoms in lifelong malaria–exposed (semi-immune) Gabonese adults with and without sickle cell trait. Eleven semi-immune Gabonese with normal hemoglobin (IA), nine with sickle cell trait (IS), and five nonimmune European controls with normal hemoglobin (NI) received 3,200 PfSPZ by DVI and were followed 28 days for parasitemia by thick blood smear (TBS) and quantitative polymerase chain reaction (qPCR) and for malaria symptoms. End points were time to parasitemia and parasitemia plus symptoms. PfSPZ Challenge was well tolerated and safe. Five of the five (100%) NI, 7/11 (64%) IA, and 5/9 (56%) IS volunteers developed parasitemia by TBS, and 5/5 (100%) NI, 9/11 (82%) IA, and 7/9 (78%) IS by qPCR, respectively. The time to parasitemia by TBS was longer in IA (geometric mean 16.9 days) and IS (19.1 days) than in NA (12.6 days) volunteers ( P = 0.016, 0.021, respectively). Five of the five, 6/9, and 1/7 volunteers with parasitemia developed symptoms ( P = 0.003, NI versus IS). Naturally adaptive immunity (NAI) to malaria significantly prolonged the time to parasitemia. Sickle cell trait seemed to prolong it further. NAI plus sickle cell trait, but not NAI alone, significantly reduced symptom rate. Twenty percent (4/20) semi-immunes demonstrated sterile protective immunity. Standardized CHMI with PfSPZ Challenge is a powerful tool for dissecting the impact of innate and naturally acquired adaptive immunity on malaria.