bluuebunny/crossref_metadata_2025 huggingface dataset:
Mild proteasomal stress improves photosynthetic performance in Arabidopsis chloroplasts
Authors: Grimmer Julia , Helm Stefan , Dobritzsch Dirk , Hause Gerd , Shema Gerta , Zahedi René P. , Baginsky Sacha
Published: April 2020

The proteasome is an essential protein-degradation machinery in eukaryotic cells that controls protein turnover and thereby the biogenesis and function of cell organelles. Chloroplasts import thousands of nuclear-encoded precursor proteins from the cytosol, suggesting that the bulk of plastid proteins is transiently exposed to the cytosolic proteasome complex. Therefore, there is a cytosolic equilibrium between chloroplast precursor protein import and proteasomal degradation. We show here that a shift in this equilibrium, induced by mild genetic proteasome impairment, results in elevated precursor protein abundance in the cytosol and significantly increased accumulation of functional photosynthetic complexes in protein import-deficient chloroplasts. Importantly, a proteasome lid mutant shows improved photosynthetic performance, even in the absence of an import defect, signifying that functional precursors are continuously degraded. Hence, turnover of plastid precursors in the cytosol represents a mechanism to constrain thylakoid membrane assembly and photosynthetic electron transport.
Activating primary care COPD patients with multi-morbidity through tailored self-management support
Authors: Ansari Sameera , Hosseinzadeh Hassan , Dennis Sarah , Zwar Nicholas
Published: April 2020

Given the dearth of COPD self-management interventions that specifically acknowledge multi-morbidity in primary care, we aimed to activate COPD patients through personalised self-management support that recognised the implications of co-morbidities. This single-group experimental study included patients aged 40−84 with a spirometry diagnosis of COPD and at least one co-morbidity. A self-management education programme for COPD in the context of multi-morbidity, based on the Health Belief Model, was tailored and delivered to participants by general practice nurses in face-to-face sessions. At 6 months’ follow-up, there was significant improvement in patient activation (p < 0.001), COPD-related quality of life (p = 0.012), COPD knowledge (p < 0.001) and inhaler device technique (p = 0.001), with no significant change in perception of multi-morbidity (p = 0.822) or COPD-related multi-morbidity (0.084). The programme improved patients’ self-efficacy for their COPD as well as overall health behaviour. The findings form an empirical basis for further testing the programme in a large-scale randomised controlled trial.
Children’s neurodevelopment of reading is affected by China’s language input system in the information era
Authors: Zhou Wei , Kwok Veronica P. Y. , Su Mengmeng , Luo Jin , Tan Li Hai
Published: April 2020

Communications through electronic devices require knowledge in typewriting, typically with the pinyin input method in China. Yet, the over utilization of the pronunciation-based pinyin input method may violate the traditional learning processes of written Chinese, which involves abundant visual orthographic analysis of characters and repeated writing. We used functional magnetic resonance imaging to examine the influence of pinyin typing on reading neurodevelopment of intermediate Chinese readers (age 9–11). We found that, relative to less frequent pinyin users, more frequent pinyin users showed an overall weaker pattern of cortical activations in the left middle frontal gyrus, left inferior frontal gyrus, and right fusiform gyrus in performing reading tasks. In addition, more frequent pinyin typists had relatively less gray matter volume in the left middle frontal region, a site known to be crucial for Chinese reading. This study demonstrates that Chinese children’s brain development in the information era is affected by the frequent use of the pinyin input method.
An interactive database of Leishmania species distribution in the Americas
Authors: Herrera Giovanny , Barragán Natalia , Luna Nicolás , Martínez David , De Martino Frasella , Medina Julián , Niño Sergio , Páez Luisa , Ramírez Angie , Vega Laura , Velandia Valeria , Vera Michelle , Zúñiga María Fernanda , Bottin Marius Jean , Ramírez Juan David
Published: April 2020

The Americas have an elevated number of leishmaniasis cases (accounting for two-thirds of the worldwide disease burden) and circulating Leishmania species, and are therefore of interest in terms of epidemiological surveillance. Here, we present a systematic review of Leishmania parasite species circulating in the countries of the American continent, together with complementary information on epidemiology and geospatial distribution. A database was built from data published between 1980 and 2018 on Leishmania species identified in most of the American countries. A total of 1499 georeferenced points were extracted from published articles and subsequently located to 14 countries in the Americas. This database could be used as a reference when surveilling the occurrence of Leishmania species in the continent.
Version 4 of the CRU TS monthly high-resolution gridded multivariate climate dataset
Authors: Harris Ian , Osborn Timothy J. , Jones Phil , Lister David
Published: April 2020

CRU TS (Climatic Research Unit gridded Time Series) is a widely used climate dataset on a 0.5° latitude by 0.5° longitude grid over all land domains of the world except Antarctica. It is derived by the interpolation of monthly climate anomalies from extensive networks of weather station observations. Here we describe the construction of a major new version, CRU TS v4. It is updated to span 1901–2018 by the inclusion of additional station observations, and it will be updated annually. The interpolation process has been changed to use angular-distance weighting (ADW), and the production of secondary variables has been revised to better suit this approach. This implementation of ADW provides improved traceability between each gridded value and the input observations, and allows more informative diagnostics that dataset users can utilise to assess how dataset quality might vary geographically.
The Impact of Voice Leading and Harmony on Musical Expectancy
Authors: Wall Leona , Lieck Robert , Neuwirth Markus , Rohrmeier Martin
Published: April 2020

In Western tonal music, voice leading (VL) and harmony are two central concepts influencing whether a musical sequence is perceived as well-formed. However, experimental studies have primarily focused on the effect of harmony on the cognitive processing of polyphonic music. The additional effect of VL remains unknown, despite music theory suggesting VL to be tightly connected to harmony. Therefore, the aim of this study was to investigate and compare the effects of both VL and harmony on listener expectations. Using a priming paradigm and a choice reaction time task, participants (N = 34) were asked to indicate whether the final chord in a sequence had a different timbre than the preceding ones (cover task), with the experimental conditions being good and poor VL or harmony, respectively. An analysis with generalised mixed effects models revealed a significant influence of both VL and harmony on reaction times (RTs). Moreover, pairwise comparison showed significantly faster RTs when VL was good as compared to both VL and harmony being poor, which was not the case when only harmony was good. This study thus provides evidence for the additional importance of VL for the processing of Western polyphonic music.
Characterisation of cuticular inflation development and ultrastructure in Trichuris muris using correlative X-ray computed tomography and electron microscopy
Authors: O’Sullivan James D. B. , Cruickshank Sheena M. , Starborg Tobias , Withers Philip J. , Else Kathryn J.
Published: April 2020

The parasitic nematode Trichuris trichiura is a significant burden on public health in developing countries, and currently available drugs exhibit a poor cure rate. Worms live within a specialised tunnel of host intestinal epithelial cells and have anterior-ventral projections of the cuticle termed “cuticular inflations”, which are thought to be involved in host-parasite interactions. This work aimed to characterise structure and suggest a function of cuticular inflations in the most tractable and widely-used model of trichuriasis, Trichuris muris. Using scanning electron microscopy, we show for the first time that most cuticular inflations develop between the second and third larval moults. Correlative X-ray computed tomography (CT)-steered Serial Block Face Scanning Electron Microscopy (SBF-SEM) and transmission electron microscopy enabled ultrastructural imaging of cuticular inflations, and showed the presence of an additional, web-like layer of cuticle between the median and cortical layers of the inflation. Additionally, we characterised variation in inflation morphology, resolving debate as to the inflations’ true shape in situ. Cells underlying the inflations had many mitochondria, and we highlight their potential capacity for active transport as an area for future investigation. Overall, insights from the powerful imaging techniques used provide an excellent basis for future study of cuticular inflation function.
Effect of High Intensity Interval Training on Matrix Metalloproteinases in Women with Breast Cancer Receiving Anthracycline-Based Chemotherapy
Authors: Lee Kyuwan , Kang Irene , Mack Wendy J. , Mortimer Joanne , Sattler Fred , Salem George , Dieli-Conwright Christina M.
Published: April 2020

Anthracycline chemotherapy is commonly used to treat breast cancer yet may increase the level of matrix metalloproteinases (MMP) -2 and -9, which increase the risk of atherosclerosis. While exercise has been shown to reduce the level of MMP in patients with diabetes, high intensity interval training (HIIT) has not been utilized to improve level of MMP in women with breast cancer receiving anthracycline chemotherapy. Thirty women were randomized to either 8-week HIIT or control (CON) group. The CON group was offered the HIIT intervention after 8 weeks. MMP-1, -2 -7, -9, tissue inhibitor of MMP (TIMP) -1, and-2 were measured at baseline and post-intervention. Repeated measures ANCOVA and paired t-test were performed to assess changes in MMP and TIMP. Post-intervention, no significant between-group differences were observed for MMP and TIMP. However, within-group decrease in MMP-9 was observed in the HIIT group [104.3(51.9) to 65.2(69.1); P = 0.01]. MMP-9 in the CON group was not significantly changed [115.5(47.2) to 90.4(67.9);]. MMP-2 significantly increased in both the HIIT group [76.6(11.2) to 83.2(13.1); P = 0.007) and the CON group [69.0(8.9) to 77.6(11.1) P = 0.003). It is unclear whether an 8-week HIIT intervention influences MMP-9 in breast cancer patients undergoing anthracycline chemotherapy. Additional investigations are required to understand the exercise-induced changes in MMP-2 and -9 in women undergoing anthracycline chemotherapy.
Copious positron production by femto-second laser via absorption enhancement in a microstructured surface target
Authors: Wang Ye-Chen , Yin Yan , Wang Wei-Quan , Zou De-Bin , Miao Wen-Xuan , Yu Tong-Pu , Shao Fu-Qiu
Published: April 2020

Laser-driven positron production is expected to provide a non-radioactive, controllable, radiation tunable positron source in laboratories. We propose a novel approach of positron production by using a femto-second laser irradiating a microstructured surface target combined with a high-Z converter. By numerical simulations, it is shown that both the temperature and the maximum kinetic energy of electrons can be greatly enhanced by using a microstructured surface target instead of a planar target. When these energetic electrons shoot into a high Z converter, copious positrons are produced via Bethe-Heitler mechanism. With a laser (wavelength λ = 1 μm) with duration ~36 fs, intensity ~5.5 × 1020 W/cm2 and energy ~6 Joule, ~109 positrons can be obtained.
Transmission of Superoscillations
Authors: Zarkovsky S. , Ben-Ezra Y. , Schwartz M.
Published: April 2020

It is widely accepted that a signal bandlimited by σ cannot oscillate at higher frequencies. The phenomenon of superoscillation provides a refutation of that quite general belief. Temporal superoscillations have been rarely demonstrated and are mostly treated as a mathematical curiosity. In the present article we demonstrate experimentally for the first time to our best knowledge, the transmission of superoscillating signals through commercial low pass filters. The experimental system used for the demonstration is described, providing the insight into the transmission of superoscillations, or super-narrow pulses. Thus, while the phenomenon may seem rather esoteric, a very simple system is used for our demonstration.
The HSP90 inhibitor Onalespib exerts synergistic anti-cancer effects when combined with radiotherapy: an in vitro and in vivo approach
Authors: Spiegelberg Diana , Abramenkovs Andris , Mortensen Anja Charlotte Lundgren , Lundsten Sara , Nestor Marika , Stenerlöw Bo
Published: April 2020

Oncogenic client-proteins of the chaperone Heat shock protein 90 (HSP90) insure unlimited tumor growth and are involved in resistance to chemo- and radiotherapy. The HSP90 inhibitor Onalespib initiates the degradation of oncoproteins, and might also act as a radiosensitizer. The aim of this study was therefore to evaluate the efficacy of Onalespib in combination with external beam radiotherapy in an in vitro and in vivo approach. Onalespib downregulated client proteins, lead to increased apoptosis and caused DNA-double-strands. Monotherapy and combination with radiotherapy reduced colony formation, proliferation and migration assessed in radiosensitive HCT116 and radioresistant A431 cells. In vivo, a minimal treatment regimen for 3 consecutive days of Onalespib (3 × 10 mg/kg) doubled survival, whereas Onalespib with radiotherapy (3 × 2 Gy) caused a substantial delay in tumor growth and prolonged the survival by a factor of 3 compared to the HCT116 xenografted control group. Our results demonstrate that Onalespib exerts synergistic anti-cancer effects when combined with radiotherapy, most prominent in the radiosensitive cell models. We speculate that the depletion and downregulation of client proteins involved in signalling, migration and DNA repair mechanisms is the cause. Thus, individually, or in combination with radiotherapy Onalespib inhibits tumor growth and has the potential to improve radiotherapy outcomes, prolonging the overall survival of cancer patients.
Deep Learning Method for Mandibular Canal Segmentation in Dental Cone Beam Computed Tomography Volumes
Authors: Jaskari Joel , Sahlsten Jaakko , Järnstedt Jorma , Mehtonen Helena , Karhu Kalle , Sundqvist Osku , Hietanen Ari , Varjonen Vesa , Mattila Vesa , Kaski Kimmo
Published: April 2020

Accurate localisation of mandibular canals in lower jaws is important in dental implantology, in which the implant position and dimensions are currently determined manually from 3D CT images by medical experts to avoid damaging the mandibular nerve inside the canal. Here we present a deep learning system for automatic localisation of the mandibular canals by applying a fully convolutional neural network segmentation on clinically diverse dataset of 637 cone beam CT volumes, with mandibular canals being coarsely annotated by radiologists, and using a dataset of 15 volumes with accurate voxel-level mandibular canal annotations for model evaluation. We show that our deep learning model, trained on the coarsely annotated volumes, localises mandibular canals of the voxel-level annotated set, highly accurately with the mean curve distance and average symmetric surface distance being 0.56 mm and 0.45 mm, respectively. These unparalleled accurate results highlight that deep learning integrated into dental implantology workflow could significantly reduce manual labour in mandibular canal annotations.
Monitoring protease activity in biological tissues using antibody prodrugs as sensing probes
Authors: Vasiljeva Olga , Menendez Elizabeth , Nguyen Margaret , Craik Charles S. , Michael Kavanaugh W.
Published: April 2020

Proteases have been implicated in the development of many pathological conditions, including cancer. Detection of protease activity in diseased tissues could therefore be useful for diagnosis, prognosis, and the development of novel therapeutic approaches. Due to tight post-translational regulation, determination of the expression level of proteases alone may not be indicative of protease activities, and new methods for measuring protease activity in biological samples such as tumor biopsies are needed. Here we report a novel zymography-based technique, called the IHZTM assay, for the detection of specific protease activities in situ. The IHZ assay involves imaging the binding of a protease-activated monoclonal antibody prodrug, called a Probody® therapeutic, to tissue. Probody therapeutics are fully recombinant, masked antibodies that can only bind target antigen after removal of the mask by a selected protease. A fluorescently labeled Probody molecule is incubated with a biological tissue, thereby enabling its activation by tissue endogenous proteases. Protease activity is measured by imaging the activated Probody molecule binding to antigen present in the sample. The method was evaluated in xenograft tumor samples using protease specific substrates and inhibitors, and the measurements correlated with efficacy of the respective Probody therapeutics. Using this technique, a diverse profile of MMP and serine protease activities was characterized in breast cancer patient tumor samples. The IHZ assay represents a new type of in situ zymography technique that can be used for the screening of disease-associated proteases in patient samples from multiple pathological conditions.
Challenges and opportunities for strain verification by whole-genome sequencing
Authors: Gallegos Jenna E. , Hayrynen Sergei , Adames Neil R. , Peccoud Jean
Published: April 2020

Laboratory strains, cell lines, and other genetic materials change hands frequently in the life sciences. Despite evidence that such materials are subject to mix-ups, contamination, and accumulation of secondary mutations, verification of strains and samples is not an established part of many experimental workflows. With the plummeting cost of next generation technologies, it is conceivable that whole genome sequencing (WGS) could be applied to routine strain and sample verification in the future. To demonstrate the need for strain validation by WGS, we sequenced haploid yeast segregants derived from a popular commercial mutant collection and identified several unexpected mutations. We determined that available bioinformatics tools may be ill-suited for verification and highlight the importance of finishing reference genomes for commonly used laboratory strains.
Mitigation of greenhouse gas emissions through optimized irrigation and nitrogen fertilization in intensively managed wheat–maize production
Authors: Zhang Xin , Xiao Guangmin , Li Hu , Wang Ligang , Wu Shuxia , Wu Wenliang , Meng Fanqiao
Published: April 2020

In the wheat–maize rotation cultivation system in northern China, excessive irrigation and over-fertilization have depleted groundwater and increased nitrogen (N) losses. These problems can be addressed by optimized N fertilization and water-saving irrigation. We evaluated the effects of these practices on greenhouse gas emissions (GHG), net profit, and soil carbon (C) sequestration. We conducted a field experiment with flood irrigation (FN0, 0 kg N ha−1 yr−1, FN600, 600 kg N ha−1 yr−1) and drip fertigation treatments (DN0, 0 kg N ha−1 yr−1; DN420, 420 kg N ha−1 yr−1; DN600, 600 kg N ha−1 yr−1) in 2015–2017. Compared with FN600, DN600 decreased direct GHGs (N2O + CH4) emissions by 21%, and increased the net GHG balance, GHG intensity, irrigation water-use efficiency (IWUE), and soil organic C content (ΔSOC) by 13%, 12%, 88%, and 89.8%, respectively. Higher costs in DN600 (for electricity, labour, polyethylene) led to a 33.8% lower net profit than in FN600. Compared with FN600, DN420 reduced N and irrigation water by 30% and 46%, respectively, which increased partial factor productivity and IWUE (by 49% and 94%, respectively), but DN420 did not affect GHG mitigation or net profit. Because lower profit is the key factor limiting the technical extension of fertigation, financial subsidies should be made available for farmers to install fertigation technology.
Microbial lag phase can be indicative of, or independent from, cellular stress
Authors: Hamill Philip G. , Stevenson Andrew , McMullan Phillip E. , Williams James P. , Lewis Abiann D. R. , S Sudharsan , Stevenson Kath E. , Farnsworth Keith D. , Khroustalyova Galina , Takemoto Jon Y. , Quinn John P. , Rapoport Alexander , Hallsworth John E.
Published: April 2020

Measures of microbial growth, used as indicators of cellular stress, are sometimes quantified at a single time-point. In reality, these measurements are compound representations of length of lag, exponential growth-rate, and other factors. Here, we investigate whether length of lag phase can act as a proxy for stress, using  a number of model systems (Aspergillus penicillioides; Bacillus subtilis; Escherichia coli; Eurotium amstelodami, E. echinulatum, E. halophilicum, and E. repens; Mrakia frigida; Saccharomyces cerevisiae; Xerochrysium xerophilum; Xeromyces bisporus) exposed to mechanistically distinct types of cellular stress including low water activity, other solute-induced stresses, and dehydration-rehydration cycles. Lag phase was neither proportional to germination rate for X. bisporus (FRR3443) in glycerol-supplemented media (r2 = 0.012), nor to exponential growth-rates for other microbes. In some cases, growth-rates varied greatly with stressor concentration even when lag remained constant. By contrast, there were strong correlations for B. subtilis in media supplemented with polyethylene-glycol 6000 or 600 (r2 = 0.925 and 0.961), and for other microbial species. We also  analysed data from independent studies of food-spoilage fungi under glycerol stress (Aspergillus aculeatinus and A. sclerotiicarbonarius); mesophilic/psychrotolerant bacteria under diverse, solute-induced stresses (Brochothrix thermosphacta, Enterococcus faecalis, Pseudomonas fluorescens, Salmonella typhimurium, Staphylococcus aureus); and fungal enzymes under acid-stress (Terfezia claveryi lipoxygenase and Agaricus bisporus tyrosinase). These datasets also exhibited diversity, with some strong- and moderate correlations between length of lag and exponential growth-rates; and sometimes none. In conclusion, lag phase is not  a reliable measure of stress because length of lag and growth-rate inhibition are sometimes highly correlated, and sometimes not at all.
Scavenging crustacean fauna in the Chilean Patagonian Sea
Authors: Figueroa-Muñoz Guillermo , Retamal Marco , De Los Ríos Patricio R. , Esse Carlos , Pérez-Schultheiss Jorge , Vega-Aguayo Rolando , Boyero Luz , Correa-Araneda Francisco
Published: April 2020

The marine ecosystem of the Chilean Patagonia is considered structurally and functionally unique, because it is the transition area between the Antarctic climate and the more temperate Pacific region. However, due to its remoteness, there is little information about Patagonian marine biodiversity, which is a problem in the face of the increasing anthropogenic activity in the area. The aim of this study was to analyze community patterns and environmental characteristics of scavenging crustaceans in the Chilean Patagonian Sea, as a basis for comparison with future situations where these organisms may be affected by anthropogenic activities. These organisms play a key ecological role in marine ecosystems and constitute a main food for fish and dolphins, which are recognized as one of the main tourist attractions in the study area. We sampled two sites (Puerto Cisnes bay and Magdalena sound) at four different bathymetric strata, recording a total of 14 taxa that included 7 Decapoda, 5 Amphipoda, 1 Isopoda and 1 Leptostraca. Taxon richness was low, compared to other areas, but similar to other records in the Patagonian region. The crustacean community presented an evident differentiation between the first stratum (0–50 m) and the deepest area in Magdalena sound, mostly influenced byPseudorchomenesp. and a marked environmental stratification. This species andIsaeopsissp. are two new records for science. The discovery of undescribed species evidences that this region needs further studies exploring its biodiversity, which is most likely being already impacted by anthropogenic pressure.
MicroRNA-124 Reduces Arsenic-induced Endoplasmic Reticulum Stress and Neurotoxicity and is Linked with Neurodevelopment in Children
Authors: Park Hae-Ryung , Sun Ryan , Panganiban Ronald A. , Christiani David C. , Lu Quan
Published: April 2020

Arsenic (As) exposure adversely affects neurodevelopment in children. Accumulation of misfolded proteins in cells exposed to As leads to endoplasmic reticulum (ER) stress response, which, if not relieved, results in cell death. Despite the potential role of ER stress for As-induced neurotoxicity, the underlying mechanisms remain poorly understood. Here we aimed to investigate the roles of microRNA(miR)-124, a novel ER stress suppressor, in As-induced ER stress response and cytotoxicity in neural cells. We further aimed to link these in vitro findings to neurodevelopmental outcomes in children who were exposed to As. Using Quantitative RT-PCR and Cyquant assay, we showed that miR-124 protects against As-induced cytotoxicity in neural cells with concomitant suppression of As-induced ER stress. In addition, As-induced cytotoxicity was exacerbated in miR-124 knockout cells generated by CRISPR-based gene editing compared scramble control. Furthermore, we identified two miR-124 SNPs rs67543816 (p = 0.0003) and rs35418153 (p = 0.0004) that are significantly associated with a mental composite score calculated from the Bayley Scales of Infant Development III in Bangladesh children. Our study reveals As-induced ER stress as a crucial mechanism underlying the toxic effects of As on neural cell function and neurodevelopment and identifies miR-124 as a potential preventative and therapeutic target against detrimental effects of As exposure in children.
Taxogenomic assessment and genomic characterisation of Weissella cibaria strain 92 able to metabolise oligosaccharides derived from dietary fibres
Authors: Månberger Anna , Verbrugghe Phebe , Guðmundsdóttir Elísabet Eik , Santesson Sara , Nilsson Anne , Hreggviðsson Guðmundur Óli , Linares-Pastén Javier A. , Nordberg Karlsson Eva
Published: April 2020

The importance of the gut microbiota in human health has led to an increased interest to study probiotic bacteria. Fermented food is a source of already established probiotics, but it also offers an opportunity to discover new taxa. Four strains of Weissella sp. isolated from Indian fermented food have been genome sequenced and classified into the species W. cibaria based on whole-genome phylogeny. The genome of W. cibaria strain 92, known to utilise xylooligosaccharides and produce lactate and acetate, was analysed to identify genes for oligosaccharide utilisation. Clusters including genes involved in transportation, hydrolysis and metabolism of xylooligosaccharides, arabinooligosaccharides and β-glucosides were identified. Growth on arabinobiose and laminaribiose was detected. A 6-phospho-β-glucosidase clustered with a phosphotransferase system was found upregulated during growth on laminaribiose, indicating a mechanism for laminaribiose utilisation. The genome of W. cibaria strain 92 harbours genes for utilising the phosphoketolase pathway for the production of both acetate and lactate from pentose and hexose sugars but lacks two genes necessary for utilising the pentose phosphate pathway. The ability of W. cibaria strain 92 to utilise several types of oligosaccharides derived from dietary fibres, and produce lactate and acetate makes it interesting as a probiotic candidate for further evaluation.
Interaction of atomic systems with quantum vacuum beyond electric dipole approximation
Authors: Kosik Miriam , Burlayenko Oleksandr , Rockstuhl Carsten , Fernandez-Corbaton Ivan , Słowik Karolina
Published: April 2020

The photonic environment can significantly influence emission properties and interactions among atomic systems. In such scenarios, frequently the electric dipole approximation is assumed that is justified as long as the spatial extent of the atomic system is negligible compared to the spatial variations of the field. While this holds true for many canonical systems, it ceases to be applicable for more contemporary nanophotonic structures. To go beyond the electric dipole approximation, we propose and develop in this article an analytical framework to describe the impact of the photonic environment on emission and interaction properties of atomic systems beyond the electric dipole approximation. Particularly, we retain explicitly magnetic dipolar and electric quadrupolar contributions to the light-matter interactions. We exploit a field quantization scheme based on electromagnetic Green’s tensors, suited for dispersive materials. We obtain expressions for spontaneous emission rate, Lamb shift, multipole-multipole shift and superradiance rate, all being modified with dispersive environment. The considered influence could be substantial for suitably tailored nanostructured photonic environments, as demonstrated exemplarily.
In vivo biodistribution analysis of transmission competent and defective RNA virus-based episomal vector
Authors: Komatsu Yumiko , Tanaka Chiaki , Komorizono Ryo , Tomonaga Keizo
Published: April 2020

RNA virus-based episomal vector (REVec) is an emerging viral vector system that mediates long-term stable gene expression in variety of cell typesin vitro. However, little is known about its tissue tropism and persistence of gene expressionin vivo. Here, to evaluate the feasibility of REVec forin vivogene delivery, we conducted biodistribution analysis of transmission competent REVec and transmission defective ΔG-REVec in Lewis rats. Following intracranial administration of REVec, transgene expression was detected in various tissues. In contrast, transgene expression was only observed in the brain after ΔG-REVec administration. Low levels of vector shedding in the feces and blood and of neutralizing antibody in the serum were detected after REVec injection. In the brain, microglia, astrocytes and neurons were susceptible to REVec-mediated transduction. However, the animals administered with REVec, but not with ΔG-REVec showed a significant decrease in body weight compared to mock treated animals. Additionally, CD8 T cell infiltration was observed in the brain of these animals. In summary, we demonstrated that REVec promotes long-term transgene expressionin vivowithout causing high vector shedding or neutralizing antibody production; however, suggests the need to attenuate vector associated pathogenicity in the future.
Lactobacillus acidophilus and L. plantarum improve health status, modulate gut microbiota and innate immune response of marron (Cherax cainii)
Authors: Foysal Md Javed , Fotedar Ravi , Siddik Muhammad A. B. , Tay Alfred
Published: April 2020

This study aimed to investigate the combined effects of two most potent probiotic bacteria Lactobacillus acidophilus and Lactobacillus plantarum on overall health and immune status of freshwater crayfish, marron under laboratory conditions. A total of 36 marron were distributed into six different tanks and two different feeding groups, control and probiotic-fed group. After acclimation, control group was fed with basal diet while probiotic group was fed 109 CFU/mL per kg of bacterial supplemented feed for 60 days. The results showed no significant differences in weight gain, however, probiotic feed significantly enhanced some hemolymph parameters and biochemical composition of tail muscle. Histology data revealed better hepatopancreas health and higher microvilli counts in the marron gut fed probiotic diet. The probiotic bacteria triggered significant shift of microbial communities at different taxa level, mostly those reported as beneficial for crayfish. The probiotic diet also enriched the metabolic functions and genes associated with innate immune response of crayfish. Further correlation analysis revealed significant association of some taxa with increased activity for hemolymph and immune genes. Therefore, dietary Lactobacillus supplementation can modulate the overall health and immunity as well as gut microbial composition and interaction network between gut microbiota and immune system in crayfish.
Publisher Correction: Optimizing the dynamics of protein expression
Authors: Trösemeier Jan-Hendrik , Rudorf Sophia , Loessner Holger , Hofner Benjamin , Reuter Andreas , Schulenborg Thomas , Koch Ina , Bekeredjian-Ding Isabelle , Lipowsky Reinhard , Kamp Christel
Published: April 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Plant resistance does not compromise parasitoid-based biocontrol of a strawberry pest
Authors: Weber Daniela , Egan Paul A. , Muola Anne , Ericson Lars E. , Stenberg Johan A.
Published: April 2020

Plant nutritional  quality can influence interactions between herbivores and their parasitoids. While most previous work has focused on a limited set of secondary plant metabolites, the tri-trophic effects of overall phenotypic resistance have been understudied. Furthermore, the joint effects of secondary and primary metabolites on parasitoids are almost unexplored. In this study, we compared the performance and survival of the parasitoid species Asecodes parviclava Thompson on wild woodland strawberry (Fragaria vesca L.) genotypes showing variation in resistance against the parasitoid’s host, the strawberry leaf beetle (Galerucella tenella L.). Additionally, we related the metabolic profiles of these plant genotypes to the tritrophic outcomes in order to identify primary and secondary metabolites involved in regulating plant potential to facilitate parasitism. We found that parasitoid performance was strongly affected by plant genotype, but those differences in plant resistance to the herbivore were not reflected in parasitoid survival. These findings could be explained in particular by a significant link between parasitoid survival and foliar carbohydrate levels, which appeared to be the most important compounds for parasitism success. The fact that plant quality strongly affects parasitism should be further explored and utilized in plant breeding programs for a synergistic application in sustainable pest management.
Metal concentrations and biological effects from one of the largest mining disasters in the world (Brumadinho, Minas Gerais, Brazil)
Authors: Vergilio Cristiane dos Santos , Lacerda Diego , Oliveira Braulio Cherene Vaz de , Sartori Echily , Campos Gabriela Munis , Pereira Anna Luiza de Souza , Aguiar Diego Borges de , Souza Tatiana da Silva , Almeida Marcelo Gomes de , Thompson Fabiano , Rezende Carlos Eduardo de
Published: April 2020

The rupture of the Brumadinho mining tailings dam in Brazil is considered one of the largest mining disasters in the world, resulting in 244 deaths and 26 missing people, in addition to the environmental consequences. The present study aims to evaluate the concentrations of multiple elements and the biological effects on water and sediments of the Paraopeba River after the Brumadinho Dam rupture. The tailings are formed by fine particulate material with large amounts of Fe, Al, Mn, Ti, rare earth metals and toxic metals. In the water, the levels of Fe, Al, Mn, Zn, Cu, Pb, Cd and U were higher than those allowed by Brazilian legislation. In the sediments, Cr, Ni, Cu and Cd levels were higher than the established sediment quality guidelines (TEL-NOAA). The differences in metal concentrations in the water and sediments between the upstream and downstream sides of the dam illustrate the effect of the tailings in the Paraopeba River. Toxicological tests demonstrated that the water and sediments were toxic to different trophic levels, from algae to microcrustaceans and fish. The fish exposed to water and sediments containing mine ore also accumulated metals in muscle tissue. This evaluation emphasizes the necessity of long-term monitoring in the affected area.
On the widespread enhancement in fine particulate matter across the Indo-Gangetic Plain towards winter
Authors: Ojha Narendra , Sharma Amit , Kumar Manish , Girach Imran , Ansari Tabish U. , Sharma Som K. , Singh Narendra , Pozzer Andrea , Gunthe Sachin S.
Published: April 2020

Fine particulate matter (PM2.5, aerodynamic diameter ≤2.5 µm) impacts the climate, reduces visibility and severely influences human health. The Indo-Gangetic Plain (IGP), home to about one-seventh of the world’s total population and a hotspot of aerosol loading, observes strong enhancements in the PM2.5 concentrations towards winter. We performed high-resolution (12 km × 12 km) atmospheric chemical transport modeling (WRF-Chem) for the post-monsoon to winter transition to unravel the underlying dynamics and influences of regional emissions over the region. Model, capturing the observed variations to an extent, reveals that the spatial distribution of PM2.5 having patches of enhanced concentrations (≥100 µgm−3) during post-monsoon, evolves dramatically into a widespread enhancement across the IGP region during winter. A sensitivity simulation, supported by satellite observations of fires, shows that biomass-burning emissions over the northwest IGP play a crucial role during post-monsoon. Whereas, in contrast, towards winter, a large-scale decline in the air temperature, significantly shallower atmospheric boundary layer, and weaker winds lead to stagnant conditions (ventilation coefficient lower by a factor of ~4) thereby confining the anthropogenic influences closer to the surface. Such changes in the controlling processes from post-monsoon to winter transition profoundly affect the composition of the fine aerosols over the IGP region. The study highlights the need to critically consider the distinct meteorological processes of west-to-east IGP and changes in dominant sources from post-monsoon to winter in the formulation of future pollution mitigation policies.
Multi-objective optimization for EEG channel selection and accurate intruder detection in an EEG-based subject identification system
Authors: Moctezuma Luis Alfredo , Molinas Marta
Published: April 2020

We present a four-objective optimization method for optimal electroencephalographic (EEG) channel selection to provide access to subjects with permission in a system by detecting intruders and identifying the subject. Each instance was represented by four features computed from two sub-bands, extracted using empirical mode decomposition (EMD) for each channel, and the feature vectors were used as input for one-class/multi-class support vector machines (SVMs). We tested the method on data from the event-related potentials (ERPs) of 26 subjects and 56 channels. The optimization process was performed by the non-dominated sorting genetic algorithm (NSGA), which found a three-channel combination that achieved an accuracy of 0.83, with both a true acceptance rate (TAR) and a true rejection rate (TRR) of 1.00. In the best case, we obtained an accuracy of up to 0.98 for subject identification with a TAR of 0.95 and a TRR 0.93, all using seven EEG channels found by NSGA-III in a subset of subjects manually created. The findings were also validated using 10 different subdivisions of subjects randomly created, obtaining up to 0.97 ± 0.02 of accuracy, a TAR of 0.81 ± 0.12 and TRR of 0.85 ± 0.10 using eight channels found by NSGA-III. These results support further studies on larger datasets for potential applications of EEG in identification and authentication systems.
Similar history biases for distinct prospective decisions of self-performance
Authors: Mei Ning , Rankine Sean , Olafsson Einar , Soto David
Published: April 2020

Metacognition can be deployed retrospectively -to reflect on the correctness of our behavior- or prospectively -to make predictions of success in one’s future behavior or make decisions about strategies to solve future problems. We investigated the factors that determine prospective decision making. Human participants performed a visual discrimination task followed by ratings of visibility and response confidence. Prior to each trial, participants made prospective judgments. In Experiment 1, they rated their belief of future success. In Experiment 2, they rated their decision to adopt a focused attention state. Prospective beliefs of success were associated with no performance changes while prospective decisions to engage attention were followed by better self-evaluation of the correctness of behavioral responses. Using standard machine learning classifiers we found that the current prospective decision could be predicted from information concerning task-correctness, stimulus visibility and response confidence from previous trials. In both Experiments, awareness and confidence were more diagnostic of the prospective decision than task correctness. Notably, classifiers trained with prospective beliefs of success in Experiment 1 predicted decisions to engage in Experiment 2 and vice-versa. These results indicate that the formation of these seemingly different prospective decisions share a common, dynamic representational structure.
Genomic characterization and outcome of prosthetic joint infections caused by Staphylococcus aureus
Authors: Wildeman Peter , Tevell Staffan , Eriksson Carl , Lagos Amaya Campillay , Söderquist Bo , Stenmark Bianca
Published: April 2020

Staphylococcus aureus is a commensal colonizing the skin and mucous membranes. It can also act as a pathogen, and is the most common microorganism isolated from prosthetic joint infections (PJIs). The aim of this study was to explore the genomic relatedness between commensal and PJI S. aureus strains as well as microbial traits and host-related risk factors for treatment failure. Whole-genome sequencing (WGS) was performed on S. aureus isolates obtained from PJIs (n = 100) and control isolates from nares (n = 101). Corresponding clinical data for the PJI patients were extracted from medical records. No PJI-specific clusters were found in the WGS phylogeny, and the distribution of the various clonal complexes and prevalence of virulence genes among isolates from PJIs and nares was almost equal. Isolates from patients with treatment success and failure were genetically very similar, while the presence of an antibiotic-resistant phenotype and the use of non-biofilm-active antimicrobial treatment were both associated with failure.In conclusion, commensal and PJI isolates of S. aureus in arthroplasty patients were genetically indistinguishable, suggesting that commensal S. aureus clones are capable of causing PJIs. Furthermore, no association between genetic traits and outcome could be demonstrated, stressing the importance of patient-related factors in the treatment of S. aureus PJIs.
Dynamics at the crystal-melt interface in a supercooled chalcogenide liquid near the glass transition
Authors: Li Jianheng , Jangid Rahul , Zhu Weidi , Kohne Chris , Fluerasu Andrei , Zhang Yugang , Sen Sabyasachi , Kukreja Roopali
Published: April 2020

Direct quantitative measurements of nanoscale dynamical processes associated with structural relaxation and crystallization near the glass transition are a major experimental challenge. These type of processes have been primarily treated as macroscopic phenomena within the framework of phenomenological models and bulk experiments. Here, we report x-ray photon correlation spectroscopy measurements of dynamics at the crystal-melt interface during the radiation induced formation of Se nano-crystallites in pure Se and in binary AsSe4 glass-forming liquids near their glass transition temperature. We observe a heterogeneous dynamical behaviour where the intensity correlation functions g2(q, t) exhibits either a compressed or a stretched exponential decay, depending on the size of the Se nano-crystallites. The corresponding relaxation timescale for the AsSe4 liquid increases as the temperature is raised, which can be attributed to changes in the chemical composition of the melt at the crystal-melt interface with the growth of the Se nano-crystallites.
Nitrogen Pollution Impact and Remediation through Low Cost Starch Based Biodegradable polymers
Authors: Ibrahim K. A. , Naz M. Y. , Shukrullah S. , Sulaiman S. A. , Ghaffar A. , AbdEl-Salam N. M.
Published: April 2020

The world does not have too much time to ensure that the fast-growing population has enough land, food, water and energy. The rising food demand has brought a positive surge in fertilizers’ demand and agriculture-based economy. The world is using 170 million tons of fertilizer every year for food, fuel, fiber, and feed. The nitrogenous fertilizers are being used to meet 48% of the total food demand of the world. High fertilizer inputs augment the reactive nitrogen levels in soil, air, and water. The unassimilated reactive nitrogen changes into a pollutant and harms the natural resources. The use of controlled-release fertilizers for slowing down the nutrients’ leaching has recently been practiced by farmers. However, to date, monitoring of the complete discharge time and discharge rate of controlled released fertilizers is not completely understood by the researchers. In this work, corn starch was thermally processed into a week gel-like coating material by reacting with urea and borate. The granular urea was coated with native and processed starch in a fluidized bed reactor having bottom-up fluid delivery system. The processed starch exhibited better thermal and mechanical stability as compared to the native starch. Unlike the pure starch, the storage modulus of the processed starch dominated the loss modulus. The release time of urea, coated with processed starch, remained remarkably larger than the uncoated urea.
Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau
Authors: Roy Chayan , Rameez Moidu Jameela , Haldar Prabir Kumar , Peketi Aditya , Mondal Nibendu , Bakshi Utpal , Mapder Tarunendu , Pyne Prosenjit , Fernandes Svetlana , Bhattacharya Sabyasachi , Roy Rimi , Mandal Subhrangshu , O’Neill William Kenneth , Mazumdar Aninda , Mukhopadhyay Subhra Kanti , Mukherjee Ambarish , Chakraborty Ranadhir , Hallsworth John Edward , Ghosh Wriddhiman
Published: April 2020

Little is known about life in the boron-rich hot springs of Trans-Himalayas. Here, we explore the geomicrobiology of a 4438-m-high spring which emanates ~70 °C-water from a boratic microbialite calledShivlinga. Due to low atmospheric pressure, the vent-water is close to boiling point so can entropically destabilize biomacromolecular systems. Starting from the vent,Shivlinga’s geomicrobiology was revealed along the thermal gradients of an outflow-channel and a progressively-drying mineral matrix that has no running water; ecosystem constraints were then considered in relation to those of entropically comparable environments. The spring-water chemistry and sinter mineralogy were dominated by borates, sodium, thiosulfate, sulfate, sulfite, sulfide, bicarbonate, and other macromolecule-stabilizing (kosmotropic) substances. Microbial diversity was high along both of the hydrothermal gradients. Bacteria, Eukarya and Archaea constituted >98%, ~1% and <1% ofShivlinga’s microbiome, respectively. Temperature constrained the biodiversity at ~50 °C and ~60 °C, but not below 46 °C. Along each thermal gradient, in the vent-to-apron trajectory, communities were dominated byAquificae/Deinococcus-Thermus, thenChlorobi/Chloroflexi/Cyanobacteria, and finallyBacteroidetes/Proteobacteria/Firmicutes. Interestingly, sites of >45 °C were inhabited by phylogenetic relatives of taxa for which laboratory growth is not known at >45 °C.Shivlinga’s geomicrobiology highlights the possibility that the system’s kosmotrope-dominated chemistry mitigates against the biomacromolecule-disordering effects of its thermal water.