bluuebunny/crossref_metadata_2025 huggingface dataset:
Regime shifts occur disproportionately faster in larger ecosystems
Authors: Cooper Gregory S. , Willcock Simon , Dearing John A.
Published: March 2020

Regime shifts can abruptly affect hydrological, climatic and terrestrial systems, leading to degraded ecosystems and impoverished societies. While the frequency of regime shifts is predicted to increase, the fundamental relationships between the spatial-temporal scales of shifts and their underlying mechanisms are poorly understood. Here we analyse empirical data from terrestrial (n = 4), marine (n = 25) and freshwater (n = 13) environments and show positive sub-linear empirical relationships between the size and shift duration of systems. Each additional unit area of an ecosystem provides an increasingly smaller unit of time taken for that system to collapse, meaning that large systems tend to shift more slowly than small systems but disproportionately faster. We substantiate these findings with five computational models that reveal the importance of system structure in controlling shift duration. The findings imply that shifts in Earth ecosystems occur over ‘human’ timescales of years and decades, meaning the collapse of large vulnerable ecosystems, such as the Amazon rainforest and Caribbean coral reefs, may take only a few decades once triggered.
Diverse nanostructures underlie thin ultra-black scales in butterflies
Authors: Davis Alexander L. , Nijhout H. Frederik , Johnsen Sönke
Published: March 2020

Recently, it has been shown that animals such as jumping spiders, birds, and butterflies have evolved ultra-black coloration comparable to the blackest synthetic materials. Of these, certain papilionid butterflies have reflectances approaching 0.2%, resulting from a polydisperse honeycomb structure. It is unknown if other ultra-black butterflies use this mechanism. Here, we examine a phylogenetically diverse set of butterflies and demonstrate that other butterflies employ simpler nanostructures that achieve ultra-black coloration in scales thinner than synthetic alternatives. Using scanning electron microscopy, we find considerable interspecific variation in the geometry of the holes in the structures, and verify with finite-difference time-domain modeling that expanded trabeculae and ridges, found across ultra-black butterflies, reduce reflectance up to 16-fold. Our results demonstrate that butterflies produce ultra-black by creating a sparse material with high surface area to increase absorption and minimize surface reflection. We hypothesize that butterflies use ultra-black to increase the contrast of color signals.
High energy acceptor states strongly enhance exciton transfer between metal organic phosphorescent dyes
Authors: de Vries Xander , Coehoorn Reinder , Bobbert Peter A.
Published: March 2020

Exciton management in organic light-emitting diodes (OLEDs) is vital for improving efficiency, reducing device aging, and creating new device architectures. In particular in white OLEDs, exothermic Förster-type exciton transfer, e.g. from blue to red emitters, plays a crucial role. It is known that a small exothermicity partially overcomes the spectral Stokes shift, enhancing the fraction of resonant donor-acceptor pair states and thus the Förster transfer rate. We demonstrate here a second enhancement mechanism, setting in when the exothermicity exceeds the Stokes shift: transfer to multiple higher-lying electronically excited states of the acceptor molecules. Using a recently developed computational method we evaluate the Förster transfer rate for 84 different donor–acceptor pairs of phosphorescent emitters. As a result of the enhancement the Förster radius tends to increase with increasing exothermicity, from around 1 nm to almost 4 nm. The enhancement becomes particularly strong when the excited states have a large spin-singlet character.
Deep high-temperature hydrothermal circulation in a detachment faulting system on the ultra-slow spreading ridge
Authors: Tao Chunhui , Seyfried W. E. , Lowell R. P. , Liu Yunlong , Liang Jin , Guo Zhikui , Ding Kang , Zhang Huatian , Liu Jia , Qiu Lei , Egorov Igor , Liao Shili , Zhao Minghui , Zhou Jianping , Deng Xianming , Li Huaiming , Wang Hanchuang , Cai Wei , Zhang Guoyin , Zhou Hongwei , Lin Jian , Li Wei
Published: March 2020

Coupled magmatic and tectonic activity plays an important role in high-temperature hydrothermal circulation at mid-ocean ridges. The circulation patterns for such systems have been elucidated by microearthquakes and geochemical data over a broad spectrum of spreading rates, but such data have not been generally available for ultra-slow spreading ridges. Here we report new geophysical and fluid geochemical data for high-temperature active hydrothermal venting at Dragon Horn area (49.7°E) on the Southwest Indian Ridge. Twin detachment faults penetrating to the depth of 13 ± 2 km below the seafloor were identified based on the microearthquakes. The geochemical composition of the hydrothermal fluids suggests a long reaction path involving both mafic and ultramafic lithologies. Combined with numerical simulations, our results demonstrate that these hydrothermal fluids could circulate ~ 6 km deeper than the Moho boundary and to much greater depths than those at Trans-Atlantic Geotraverse and Logachev-1 hydrothermal fields on the Mid-Atlantic Ridge.
The substrate specificity switch FlhB assembles onto the export gate to regulate type three secretion
Authors: Kuhlen Lucas , Johnson Steven , Zeitler Andreas , Bäurle Sandra , Deme Justin C. , Caesar Joseph J.  E. , Debo Rebecca , Fisher Joseph , Wagner Samuel , Lea Susan M.
Published: March 2020

Protein secretion through type-three secretion systems (T3SS) is critical for motility and virulence of many bacteria. Proteins are transported through an export gate containing three proteins (FliPQR in flagella, SctRST in virulence systems). A fourth essential T3SS protein (FlhB/SctU) functions to “switch” secretion substrate specificity once the growing hook/needle reach their determined length. Here, we present the cryo-electron microscopy structure of an export gate containing the switch protein from a Vibrio flagellar system at 3.2 Å resolution. The structure reveals that FlhB/SctU extends the helical export gate with its four predicted transmembrane helices wrapped around FliPQR/SctRST. The unusual topology of the FlhB/SctU helices creates a loop wrapped around the bottom of the closed export gate. Structure-informed mutagenesis suggests that this loop is critical in gating secretion and we propose that a series of conformational changes in the T3SS trigger opening of the gate through interactions between FlhB/SctU and FliPQR/SctRST.
Structure of E3 ligase E6AP with a proteasome-binding site provided by substrate receptor hRpn10
Authors: Buel Gwen R. , Chen Xiang , Chari Raj , O’Neill Maura J. , Ebelle Danielle L. , Jenkins Conor , Sridharan Vinidhra , Tarasov Sergey G. , Tarasova Nadya I. , Andresson Thorkell , Walters Kylie J.
Published: March 2020

Regulated proteolysis by proteasomes involves ~800 enzymes for substrate modification with ubiquitin, including ~600 E3 ligases. We report here that E6AP/UBE3A is distinguished from other E3 ligases by having a 12 nM binding site at the proteasome contributed by substrate receptor hRpn10/PSMD4/S5a. Intrinsically disordered by itself, and previously uncharacterized, the E6AP-binding domain in hRpn10 locks into a well-defined helical structure to form an intermolecular 4-helix bundle with the E6AP AZUL, which is unique to this E3. We thus name the hRpn10 AZUL-binding domain RAZUL. We further find in human cells that loss of RAZUL by CRISPR-based gene editing leads to loss of E6AP at proteasomes. Moreover, proteasome-associated ubiquitin is reduced following E6AP knockdown or displacement from proteasomes, suggesting that E6AP ubiquitinates substrates at or for the proteasome. Altogether, our findings indicate E6AP to be a privileged E3 for the proteasome, with a dedicated, high affinity binding site contributed by hRpn10.
Observation of dissipative chlorophyll-to-carotenoid energy transfer in light-harvesting complex II in membrane nanodiscs
Authors: Son Minjung , Pinnola Alberta , Gordon Samuel C. , Bassi Roberto , Schlau-Cohen Gabriela S.
Published: March 2020

Plants prevent photodamage under high light by dissipating excess energy as heat. Conformational changes of the photosynthetic antenna complexes activate dissipation by leveraging the sensitivity of the photophysics to the protein structure. The mechanisms of dissipation remain debated, largely due to two challenges. First, because of the ultrafast timescales and large energy gaps involved, measurements lacked the temporal or spectral requirements. Second, experiments have been performed in detergent, which can induce non-native conformations, or in vivo, where contributions from homologous antenna complexes cannot be disentangled. Here, we overcome both challenges by applying ultrabroadband two-dimensional electronic spectroscopy to the principal antenna complex, LHCII, in a near-native membrane. Our data provide evidence that the membrane enhances two dissipative pathways, one of which is a previously uncharacterized chlorophyll-to-carotenoid energy transfer. Our results highlight the sensitivity of the photophysics to local environment, which may control the balance between light harvesting and dissipation in vivo.
Cancer associated fibroblast FAK regulates malignant cell metabolism
Authors: Demircioglu Fevzi , Wang Jun , Candido Juliana , Costa Ana S. H. , Casado Pedro , de Luxan Delgado Beatriz , Reynolds Louise E. , Gomez-Escudero Jesus , Newport Emma , Rajeeve Vinothini , Baker Ann-Marie , Roy-Luzarraga Marina , Graham Trevor A. , Foster Julie , Wang Yu , Campbell James J. , Singh Rajinder , Zhang Penglie , Schall Thomas J. , Balkwill Frances R. , Sosabowski Jane , Cutillas Pedro R. , Frezza Christian , Sancho Patricia , Hodivala-Dilke Kairbaan
Published: March 2020

Emerging evidence suggests that cancer cell metabolism can be regulated by cancer-associated fibroblasts (CAFs), but the mechanisms are poorly defined. Here we show that CAFs regulate malignant cell metabolism through pathways under the control of FAK. In breast and pancreatic cancer patients we find that low FAK expression, specifically in the stromal compartment, predicts reduced overall survival. In mice, depletion of FAK in a subpopulation of CAFs regulates paracrine signals that increase malignant cell glycolysis and tumour growth. Proteomic and phosphoproteomic analysis in our mouse model identifies metabolic alterations which are reflected at the transcriptomic level in patients with low stromal FAK. Mechanistically we demonstrate that FAK-depletion in CAFs increases chemokine production, which via CCR1/CCR2 on cancer cells, activate protein kinase A, leading to enhanced malignant cell glycolysis. Our data uncover mechanisms whereby stromal fibroblasts regulate cancer cell metabolism independent of genetic mutations in cancer cells.
Author Correction: A simulated Northern Hemisphere terrestrial climate dataset for the past 60,000 years
Authors: Armstrong Edward , Hopcroft Peter O. , Valdes Paul J.
Published: March 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
The temporal structure of the inner retina at a single glance
Authors: Zhao Zhijian , Klindt David A. , Maia Chagas André , Szatko Klaudia P. , Rogerson Luke , Protti Dario A. , Behrens Christian , Dalkara Deniz , Schubert Timm , Bethge Matthias , Franke Katrin , Berens Philipp , Ecker Alexander S. , Euler Thomas
Published: March 2020

The retina decomposes visual stimuli into parallel channels that encode different features of the visual environment. Central to this computation is the synaptic processing in a dense layer of neuropil, the so-called inner plexiform layer (IPL). Here, different types of bipolar cells stratifying at distinct depths relay the excitatory feedforward drive from photoreceptors to amacrine and ganglion cells. Current experimental techniques for studying processing in the IPL do not allow imaging the entire IPL simultaneously in the intact tissue. Here, we extend a two-photon microscope with an electrically tunable lens allowing us to obtain optical vertical slices of the IPL, which provide a complete picture of the response diversity of bipolar cells at a “single glance”. The nature of these axial recordings additionally allowed us to isolate and investigate batch effects, i.e. inter-experimental variations resulting in systematic differences in response speed. As a proof of principle, we developed a simple model that disentangles biological from experimental causes of variability and allowed us to recover the characteristic gradient of response speeds across the IPL with higher precision than before. Our new framework will make it possible to study the computations performed in the central synaptic layer of the retina more efficiently.
Author Correction: A new microdispersed albumin derivative potentially useful for radio-guided surgery of occult breast cancer lesions
Authors: Caviglioli Gabriele , Chinol Marco , Baldassari Sara , Garaboldi Lucia , Zuccari Guendalina , Petretto Andrea , Drava Giuliana , Sinico Chiara , Paganelli Giovanni
Published: March 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Using the circulating proteome to assess type I interferon activity in systemic lupus erythematosus
Authors: Smith Michael A. , Chiang Chia-Chien , Zerrouki Kamelia , Rahman Saifur , White Wendy I. , Streicher Katie , Rees William A. , Schiffenbauer Adam , Rider Lisa G. , Miller Frederick W. , Manna Zerai , Hasni Sarfaraz , Kaplan Mariana J. , Siegel Richard , Sinibaldi Dominic , Sanjuan Miguel A. , Casey Kerry A.
Published: March 2020

Type I interferon (IFN) drives pathology in systemic lupus erythematosus (SLE) and can be tracked via IFN-inducible transcripts in blood. Here, we examined whether measurement of circulating proteins, which enter the bloodstream from inflamed tissues, also offers insight into global IFN activity. Using a novel protocol we generated 1,132 aptamer-based protein measurements from anti-dsDNApos SLE blood samples and derived an IFN protein signature (IFNPS) that approximates the IFN 21-gene signature (IFNGS). Of 82 patients with SLE, IFNPS was elevated for 89% of IFNGS-high patients (49/55) and 26% of IFNGS-low patients (7/27). IFNGS-high/IFNPS-high patients exhibited activated NK, CD4, and CD8 T cells, while IFNPS-high only patients did not. IFNPS correlated with global disease activity in lymphopenic and non-lymphopenic patients and decreased following type I IFN neutralisation with anifrolumab in the SLE phase IIb study, MUSE. In summary, we developed a protein signature that reflects IFNGS and identifies a new subset of patients with SLE who have IFN activity.
Chemokine releasing particle implants for trapping circulating prostate cancer cells
Authors: Huang YiHui , Hakamivala Amirhossein , Li Shuxin , Nair Ashwin , Saxena Ramesh , Hsieh Jer-Tsong , Tang Liping
Published: March 2020

Prostate cancer (PCa) is the most prevalent cancer in U.S. men and many other countries. Although primary PCa can be controlled with surgery or radiation, treatment options of preventing metastatic PCa are still limited. To develop a new treatment of eradicating metastatic PCa, we have created an injectable cancer trap that can actively recruit cancer cells in bloodstream. The cancer trap is composed of hyaluronic acid microparticles that have good cell and tissue compatibility and can extend the release of chemokines to 4 days in vitro. We find that erythropoietin (EPO) and stromal derived factor-1α can attract PCa in vitro. Animal results show that EPO-releasing cancer trap attracted large number of circulating PCa and significantly reduced cancer spreading to other organs compared with controls. These results support that cancer trap may serve as a unique device to sequester circulating PCa cells and subsequently reduce distant metastasis.
Author Correction: Mobile Real-Time Grasshopper Detection and Data Aggregation Framework
Authors: Chudzik Piotr , Mitchell Arthur , Alkaseem Mohammad , Wu Yingie , Fang Shibo , Hudaib Taghread , Pearson Simon , Al-Diri Bashir
Published: March 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Purity determination of synthetic glucagon using a mass balance approach
Authors: Wang Xinxue , Zhang Fangyan , Li Hongmei , Xiao Peng , Su Fuhai , Xu Bei , Sun Wei , Song Dewei
Published: March 2020

Due to the widespread use of synthetic peptide drugs, their quantification and the analysis of impurities have become increasingly important in clinical and medical settings. Moreover, quantifying proteins using synthetic peptides as internal or external standards is a general approach, and the key to this approach is the knowing purities of the peptides. In this paper, synthetic glucagon was quantified using a mass balance method. The impurities in glucagon were analyzed and then accurately quantified separately. Karl Fischer (KF) titration and ion chromatography (IC) were used to determine the water and trifluoroacetic acid (TFA) contents in the samples, respectively. Furthermore, the inorganic ion content in the samples was determined by inductively coupled plasma mass spectrometry (ICP-MS). The sequence of peptide impurities was identified by a Thermo Fisher Orbitrap mass. Samples were determined to be 896.36 ± 0.68 mg/g after subtracting all impurity masses from the sample mass. The result can be traced to SI units.
Taste, smell and food-related nausea and vomiting responses in hyperemesis gravidarum: A case-controlled study
Authors: Tan Peng Chiong , Kartik Balaraman , Thanendran Panjaratnam , Zakaria Rozita , Win Sandar Tin , Omar Siti Zawiah
Published: March 2020

A case-controlled study was performed to evaluate taste and smell impairment, nausea or vomiting (NV) response to taste and smell and toleration to food texture, item and cooking method in hyperemesis gravidarum patients (HG) compared to gestation-matched controls from a university hospital and primary care clinic in Malaysia. Taste strips (4 base tastes), sniff sticks (16 selected smells) and a food-related questionnaire were used. 124 participants were recruited. Taste impairment was found in 13%(8/62) vs. 0%(0/62) P = 0.003 and the median for correct smell identification was 5[4–6] vs. 9[7–9] P < 0.001 in HG vs. controls. In HG, bitter was most likely (32%) and sweet taste least likely (5%) to provoke NV. In both arms, fish smell was most likely to provoke NV, 77% vs. 32% P < 0.001 and peppermint smell least likely 10% vs. 0% P = 0.012; NV response was significantly more likely for HG arm in 10/16 smells. In HG, worst and best NV responses to food-texture were pasty 69% and crunchy 26%; food-item, plain rice 71% and apple 16% and cooking-style, deep-frying 71% and steaming 55%. HG demonstrated taste and smell impairment and increased NV responses to many tastes and smells. Crunchy sweet uncooked food (apple or watermelon) maybe best tolerated in HG.
Machine learning for characterizing risk of type 2 diabetes mellitus in a rural Chinese population: the Henan Rural Cohort Study
Authors: Zhang Liying , Wang Yikang , Niu Miaomiao , Wang Chongjian , Wang Zhenfei
Published: March 2020

With the development of data mining, machine learning offers opportunities to improve discrimination by analyzing complex interactions among massive variables. To test the ability of machine learning algorithms for predicting risk of type 2 diabetes mellitus (T2DM) in a rural Chinese population, we focus on a total of 36,652 eligible participants from the Henan Rural Cohort Study. Risk assessment models for T2DM were developed using six machine learning algorithms, including logistic regression (LR), classification and regression tree (CART), artificial neural networks (ANN), support vector machine (SVM), random forest (RF) and gradient boosting machine (GBM). The model performance was measured in an area under the receiver operating characteristic curve, sensitivity, specificity, positive predictive value, negative predictive value and area under precision recall curve. The importance of variables was identified based on each classifier and the shapley additive explanations approach. Using all available variables, all models for predicting risk of T2DM demonstrated strong predictive performance, with AUCs ranging between 0.811 and 0.872 using laboratory data and from 0.767 to 0.817 without laboratory data. Among them, the GBM model performed best (AUC: 0.872 with laboratory data and 0.817 without laboratory data). Performance of models plateaued when introduced 30 variables to each model except CART model. Among the top-10 variables across all methods were sweet flavor, urine glucose, age, heart rate, creatinine, waist circumference, uric acid, pulse pressure, insulin, and hypertension. New important risk factors (urinary indicators, sweet flavor) were not found in previous risk prediction methods, but determined by machine learning in our study. Through the results, machine learning methods showed competence in predicting risk of T2DM, leading to greater insights on disease risk factors with no priori assumption of causality.
Radiative MHD Casson Nanofluid Flow with Activation energy and chemical reaction over past nonlinearly stretching surface through Entropy generation
Authors: Shah Zahir , Kumam Poom , Deebani Wejdan
Published: March 2020

In the present research analysis we have addressed comparative investigation of radiative electrically conducting Casson nanofluid. Nanofluid Flow is assumed over a nonlinearly stretching sheet. Heat transport analysis is carried via joule dissipation, thermal behavior and convective boundary condition. To employ the radiative effect radiation was involved to show the diverse states of nanoparticles. Furthermore entropy optimization with activation energy and chemical reaction are considered. Thermodynamics 2nd law is applied to explore entropy generation rate. Nonlinear expression is simplified through similarity variables. The reduced ordinary system is tackled through optimal approach. Flow pattern was reported for wide range of scrutinized parameters. Computational consequences of velocity drag force, heat flux and concentration gradient are analyzed numerically in tables. Results verify that conduction mode augments with enhance of magnetic parameter.Increasing radiation boosts the temperature and entropy. Activation energy corresponds to augmented concentration. Heat transmission rate augments with the consideration of radiation source term.
The Global Flood Protection Benefits of Mangroves
Authors: Menéndez Pelayo , Losada Iñigo J. , Torres-Ortega Saul , Narayan Siddharth , Beck Michael W.
Published: March 2020

Coastal flood risks are rising rapidly. We provide high resolution estimates of the economic value of mangroves forests for flood risk reduction every 20 km worldwide. We develop a probabilistic, process-based valuation of the effects of mangroves on averting damages to people and property. We couple spatially-explicit 2-D hydrodynamic analyses with economic models, and find that mangroves provide flood protection benefits exceeding $US 65 billion per year. If mangroves were lost, 15 million more people would be flooded annually across the world. Some of the nations that receive the greatest economic benefits include the USA, China, India and Mexico. Vietnam, India and Bangladesh receive the greatest benefits in terms of people protected. Many (>45) 20-km coastal stretches particularly those near cities receive more than $US 250 million annually in flood protection benefits from mangroves. These results demonstrate the value of mangroves as natural coastal defenses at global, national and local scales, which can inform incentives for mangrove conservation and restoration in development, climate adaptation, disaster risk reduction and insurance.
Rapid detection of CITES-listed shark fin species by loop-mediated isothermal amplification assay with potential for field use
Authors: But Grace Wing-Chiu , Wu Hoi-Yan , Shao Kwang-Tsao , Shaw Pang-Chui
Published: March 2020

Shark fin is a delicacy in many Asian countries. Overexploitation of sharks for shark fin trading has led to a drastic reduction in shark population. To monitor international trade of shark fin products and protect the endangered species from further population decline, we present rapid, user-friendly and sensitive diagnostic loop-mediated isothermal amplification (LAMP) and effective polymerase chain reaction (PCR) assays for all twelve CITES-listed shark species. Species-specific LAMP and PCR primers were designed based on cytochrome oxidase I (COI) and NADH2 regions. Our LAMP and PCR assays have been tested on 291 samples from 93 shark and related species. Target shark species could be differentiated from non-target species within three hours from DNA extraction to LAMP assay. The LAMP assay reported here is a simple and robust solution for on-site detection of CITES-listed shark species with shark fin products.
Genetic and physical mapping of loci for resistance to blackleg disease in canola (Brassica napus L.)
Authors: Raman Rosy , Diffey Simon , Barbulescu Denise M. , Coombes Neil , Luckett David , Salisbury Phil , Cowley Raymond , Marcroft Steve , Raman Harsh
Published: March 2020

Sustainable canola production is essential to meet growing human demands for vegetable oil, biodiesel, and meal for stock feed markets. Blackleg, caused by the fungal pathogen, Leptosphaeria maculans is a devastating disease that can lead to significant yield loss in many canola production regions worldwide. Breakdown of race-specific resistance to L. maculans in commercial cultivars poses a constant threat to the canola industry. To identify new alleles, especially for quantitative resistance (QR), we analyzed 177 doubled haploid (DH) lines derived from an RP04/Ag-Outback cross. DH lines were evaluated for QR under field conditions in three experiments conducted at Wagga Wagga (2013, 2014) and Lake Green (2015), and under shade house conditions using the ‘ascospore shower’ test. DH lines were also characterized for qualitative R gene-mediated resistance via cotyledon tests with two differential single spore isolates, IBCN17 and IBCN76, under glasshouse conditions. Based on 18,851 DArTseq markers, a linkage map representing 2,019 unique marker bins was constructed and then utilized for QTL detection. Marker regression analysis identified 22 significant marker associations for resistance, allowing identification of two race-specific resistance R genes, Rlm3 and Rlm4, and 21 marker associations for QR loci. At least three SNP associations for QR were repeatedly detected on chromosomes A03, A07 and C04 across phenotyping environments. Physical mapping of markers linked with these consistent QR loci on the B. napus genome assembly revealed their localization in close proximity of the candidate genes of B. napus BnaA03g26760D (A03), BnaA07g20240D (A07) and BnaC04g02040D (C04). Annotation of these candidate genes revealed their association with protein kinase and jumonji proteins implicated in defense resistance. Both Rlm3 and Rlm4 genes identified in this DH population did not show any association with resistance loci detected under either field and/or shade house conditions (ascospore shower) suggesting that both genes are ineffective in conferring resistance to L. maculans in Australian field conditions. Taken together, our study identified sequence-based molecular markers for dissecting R and QR loci to L. maculans in a canola DH population from the RP04/Ag-Outback cross.
Edaphic and temporal patterns of Tuber melanosporum fruitbody traits and effect of localised peat-based amendment
Authors: Garcia-Barreda Sergi , Marco Pedro , Martín-Santafé María , Tejedor-Calvo Eva , Sánchez Sergio
Published: March 2020

InTuber melanosporumcultivation, fruitbody traits are gaining relevance due to their increasing prominence on prices. We investigated the edaphic and temporal patterns of fruitbody traits and characterised the effect of truffle nests (localised peat-based amendment supplemented withT. melanosporumspores) on traits. We monitored fruitbody traits throughout two fruiting seasons in three blocks along a soil gradient. Each trait followed specific edaphic and temporal patterns. The number of fruitbodies per dig and spore maturity followed characteristic within-season trends, whereas fruitbody weight and infestation by truffle beetles were subject to complex interactions among edaphic and temporal variables, suggesting a relevant influence of annual environmental conditions. The application of truffle nests increased fruitbody depth, improved its shape and decreased infestation by truffle beetles. Nests increased the number of fruitbodies per dig, but only in two of the soils, suggesting a relevant role of the bulk soil/substrate interface in fruiting initiation. These results outline a complex scenario, with each trait being differently affected by environmental factors. In this scenario, nests proved to effectively modify several traits, although not always in the desired direction.
A novel accurate LC-MS/MS method for quantitative determination of Z-lumirubin
Authors: Jašprová Jana , Dvořák Aleš , Vecka Marek , Leníček Martin , Lacina Ondřej , Valášková Petra , Zapadlo Miloš , Plavka Richard , Klán Petr , Vítek Libor
Published: March 2020

Although phototherapy (PT) is a standard treatment for neonatal jaundice, no validated clinical methods for determination of bilirubin phototherapy products are available. Thus, the aim of our study was to establish a such method for clinical use. To achieve this aim, a LC-MS/MS assay for simultaneous determination of Z-lumirubin (LR) and unconjugated bilirubin (UCB) was conducted. LR was purified after irradiation of UCB at 460 nm. The assay was tested on human sera from PT-treated neonates. Samples were separated on a HPLC system with a triple quadrupole mass spectrometer detector. The instrument response was linear up to 5.8 and 23.4 mg/dL for LR and UCB, respectively, with submicromolar limits of detection and validity parameters relevant for use in clinical medicine. Exposure of newborns to PT raised serum LR concentrations three-fold (p < 0.01), but the absolute concentrations were low (0.37 ± 0.16 mg/dL), despite a dramatic decrease of serum UCB concentrations (13.6 ± 2.2 vs. 10.3 ± 3.3 mg/dL, p < 0.01). A LC-MS/MS method for the simultaneous determination of LR and UCB in human serum was established and validated for clinical use. This method should help to monitor neonates on PT, as well as to improve our understanding of both the kinetics and biology of bilirubin phototherapy products.
Gulls as Sources of Environmental Contamination by Colistin-resistant Bacteria
Authors: Franklin Alan B. , Ramey Andrew M. , Bentler Kevin T. , Barrett Nicole L. , McCurdy Loredana M. , Ahlstrom Christina A. , Bonnedahl Jonas , Shriner Susan A. , Chandler Jeffrey C.
Published: March 2020

In 2015, the mcr-1 gene was discovered in Escherichia coli in domestic swine in China that conferred resistance to colistin, an antibiotic of last resort used in treating multi-drug resistant bacterial infections in humans. Since then, mcr-1 was found in other human and animal populations, including wild gulls. Because gulls could disseminate the mcr-1 gene, we conducted an experiment to assess whether gulls are readily colonized with mcr-1 positive E. coli, their shedding patterns, transmission among conspecifics, and environmental deposition. Shedding of mcr-1 E. coli by small gull flocks followed a lognormal curve and gulls shed one strain >101 log10 CFU/g in their feces for 16.4 days, which persisted in the environment for 29.3 days. Because gulls are mobile and can shed antimicrobial-resistant bacteria for extended periods, gulls may facilitate transmission of mcr-1 positive E. coli to humans and livestock through fecal contamination of water, public areas and agricultural operations.
Enhanced soil quality with reduced tillage and solid manures in organic farming – a synthesis of 15 years
Authors: Krauss Maike , Berner Alfred , Perrochet Frédéric , Frei Robert , Niggli Urs , Mäder Paul
Published: March 2020

Demands upon the sustainability of farming are increasing in step with climate change and diversity loss. Organic farming offers a viable approach. To further improve organic management, three strategies with potential to enhance soil quality are being tested in a long-term trial since 2002 on a clay loam in temperate Switzerland: reduced tillage vs. ploughing, solid vs. liquid manures and biodynamic preparations. A synthesis of 15 years reveals an increase in topsoil organic carbon (SOC, +25%), microbial biomass (+32%) and activity (+34%) and a shift in microbial communities with conversion from ploughing to reduced tillage. Soils under reduced tillage are more stratified in SOC and nutrients. Additional application of composted manure has increased SOC by 6% compared to pure slurry application, with little impact on soil microbes. Biodynamic preparations have had a minor impact on soil quality. Fertilisation and biodynamic preparations did not affect yields. Both higher and lower yields were harvested in the reduced tillage system in relation to ploughing. The main yield determinants were N supply and higher weed infestation under reduced tillage. Continuously reduced tillage in organic farming has been proven to enhance soil quality at this site, while also presenting more challenges in management.
Velocity dependent up-winding scheme for node control volume finite element method for fluid flow in porous media
Authors: Abd Abdul Salam , Abushaikha Ahmad
Published: March 2020

We present a novel velocity based up-winding scheme for the node control volume finite element (NCVFE) method. The NCVFE method solves for the pressure at the vertices of elements and a control volume mesh is constructed around them; where the advection of fluids is modelled. Therefore, each element shares several control volumes, and traditionally the fluid saturations used in calculating the mobilities over each element  −  hence updating pressure  −  are arithmetically weighted. In this paper, we use the velocity vector to allocate the upstream direction of the fluid flow in each element and use the upstream fluid saturation in calculating the mobility needed for the pressure equation. We test his novel approach using triangle and tetrahedron elements, and we show that it produces more accurate fluid saturation profiles than the traditional approach. The method can easily be implemented in current NCVFE simulators.
Predicting pregnancy test results after embryo transfer by image feature extraction and analysis using machine learning
Authors: Chavez-Badiola Alejandro , Flores-Saiffe Farias Adolfo , Mendizabal-Ruiz Gerardo , Garcia-Sanchez Rodolfo , Drakeley Andrew J. , Garcia-Sandoval Juan Paulo
Published: March 2020

Assessing the viability of a blastosyst is still empirical and non-reproducible nowadays. We developed an algorithm based on artificial vision and machine learning (and other classifiers) that predicts pregnancy using the beta human chorionic gonadotropin (b-hCG) test from both the morphology of an embryo and the age of the patients. We employed two high-quality databases with known pregnancy outcomes (n = 221). We created a system consisting of different classifiers that is feed with novel morphometric features extracted from the digital micrographs, along with other non-morphometric data to predict pregnancy. It was evaluated using five different classifiers: probabilistic bayesian, Support Vector Machines (SVM), deep neural network, decision tree, and Random Forest (RF), using a k-fold cross validation to assess the model’s generalization capabilities. In the database A, the SVM classifier achieved an F1 score of 0.74, and AUC of 0.77. In the database B the RF classifier obtained a F1 score of 0.71, and AUC of 0.75. Our results suggest that the system is able to predict a positive pregnancy test from a single digital image, offering a novel approach with the advantages of using a small database, being highly adaptable to different laboratory settings, and easy integration into clinical practice.
Developing the Ternary ZnO Doped MoS2 Nanostructures Grafted on CNT and Reduced Graphene Oxide (RGO) for Photocatalytic Degradation of Aniline
Authors: Ghasemipour Parisa , Fattahi Moslem , Rasekh Behnam , Yazdian Fatemeh
Published: March 2020

Transition metal sulfide semiconductors have achieved significant attention in the field of photocatalysis and degradation of pollutants. MoS2 with a two dimensional (2D) layered structure, a narrow bandgap and the ability of getting excited while being exposed to visible light, has demonstrated great potential in visible-light-driven photocatalysts. However, it possesses fast-paced recombination of charges. In this study, the coupled MoS2 nanosheets were synthesized with ZnO nanorods to develop the heterojunctions photocatalyst in order to obtain superior photoactivity. The charge transfer in this composite is not adequate to achieve desirable activity. Therefore, heterojunction was modified by reduced graphene oxide (RGO) nanosheets and carbon nanotubes (CNTs) to develop the RGO/ZnO/MoS2 and CNTs/ZnO/MoS2 ternary nanocomposites. The structure, morphology, composition, optical and photocatalytic properties of the as-fabricated samples were characterized through X-ray diffraction (XRD), Fourier Transform Infrared (FTIR), Field Emission Scanning Electron Microscopy (FESEM), Transmission Electron Microscopy (TEM), Energy-Dispersive X-ray (EDX), elemental mapping, Photoluminescence (PL), Ultraviolet–Visible spectroscopy (UV-VIS), and Brunauer-Emmett-Teller (BET) techniques. The photo-catalytic performance of all samples was evaluated through photodegradation of aniline in aqueous solution. The combination of RGO or CNTs into the ZnO/MoS2 greatly promoted the catalytic activity. However, the resulting RGO/ZnO/MoS2 ternary nanocomposites showed appreciably increased catalytic performance, faster than that of CNTs/ZnO/MoS2. Charge carrier transfer studies, the BET surface area analysis, and the optical studies confirmed this superiority. The role of operational variables namely, solution pH, catalyst dosage amount, and initial concentration of aniline was then investigated for obtaining maximum degradation. Complete degradation was observed, in the case of pH = 4, catalyst dosage of 0.7 g/L and aniline concentration of 80 ppm, and light intensity of 100 W. According to the results of trapping experiments, hydroxyl radical was found to be the main active species in the photocatalytic reaction. Meanwhile, a plausible mechanism was proposed for describing the degradation of aniline upon ternary composite. Moreover, the catalyst showed excellent reusability and stability after five consecutive cycles due to the synergistic effect between its components. Total-Organic-Carbon concentration (TOC) results suggested that complete mineralization of aniline occurred after 210 min of irradiation. Finally, a real petrochemical wastewater sample was evaluated for testing the catalytic ability of the as-fabricated composites in real case studies and it was observed that the process successfully quenched 100% and 93% of Chemical Oxygen Demand (COD) and TOC in the wastewater, respectively.
Laser microdissection-based microproteomics of the hippocampus of a rat epilepsy model reveals regional differences in protein abundances
Authors: do Canto Amanda M. , Vieira André S. , H.B. Matos Alexandre , Carvalho Benilton S. , Henning Barbara , Norwood Braxton A. , Bauer Sebastian , Rosenow Felix , Gilioli Rovilson , Cendes Fernando , Lopes-Cendes Iscia
Published: March 2020

Mesial temporal lobe epilepsy (MTLE) is a chronic neurological disorder affecting almost 40% of adult patients with epilepsy. Hippocampal sclerosis (HS) is a common histopathological abnormality found in patients with MTLE. HS is characterised by extensive neuronal loss in different hippocampus sub-regions. In this study, we used laser microdissection-based microproteomics to determine the protein abundances in different regions and layers of the hippocampus dentate gyrus (DG) in an electric stimulation rodent model which displays classical HS damage similar to that found in patients with MTLE. Our results indicate that there are differences in the proteomic profiles of different layers (granule cell and molecular), as well as different regions, of the DG (ventral and dorsal). We have identified new signalling pathways and proteins present in specific layers and regions of the DG, such as PARK7, RACK1, and connexin 31/gap junction. We also found two major signalling pathways that are common to all layers and regions: inflammation and energy metabolism. Finally, our results highlight the utility of high-throughput microproteomics and spatial-limited isolation of tissues in the study of complex disorders to fully appreciate the large biological heterogeneity present in different cell populations within the central nervous system.
Effects of enrofloxacin treatment on the bacterial microbiota of milk from goats with persistent mastitis
Authors: Polveiro Richard Costa , Vidigal Pedro Marcus Pereira , Mendes Tiago Antônio de Oliveira , Yamatogi Ricardo Seiti , Lima Magna Coroa , Moreira Maria Aparecida Scatamburlo
Published: March 2020

Antibiotic resistance has become a major concern for human and animal health. As fluoroquinolones have been extensively used in human and veterinary medicine, there has also been the rapid emergence and spread of antimicrobial resistance around the world. Here, we analysed the microbiome of goat milk using samples from healthy goats and those diagnosed with persistent mastitis and treated using the antibiotic enrofloxacin with 16S rRNA amplicon sequencing. We selected a group of 11 goats and 22 samples of milk that did not respond clinically to enrofloxacin treatment. Milk samples were evaluated before and after treatment to verify changes of the microbiota; the three first lactating goats were selected from the healthy control group. The milk samples from the healthy control animals presented a larger abundance of different species of bacteria of the Staphylococcus genus, but a smaller number of different genera, which indicated a more specific niche of resident bacteria. The Firmicutes phylum was predominantly different between the studied groups. Samples from before-treatment animals had a higher number of new species than those from the control group, and after being treated again. These microbiota received new bacteria, increasing the differences in bacteria even more in relation to the control group. Genotypes such as Trueperella and Mannheimia, between other genera, had a high abundance in the samples from animals with persistent mastitis. The dysbiosis in this study, with marked evidence of a complex microbiota in activity in cases of the failure of antimicrobial treatment for persistent chronic mastitis, demonstrates a need to improve the accuracy of pathogen identification and increases concern regarding antibiotic treatments in milk production herds.
Bare Earth’s Surface Spectra as a Proxy for Soil Resource Monitoring
Authors: Demattê José A. M. , Safanelli José Lucas , Poppiel Raul Roberto , Rizzo Rodnei , Silvero Nélida Elizabet Quiñonez , Mendes Wanderson de Sousa , Bonfatti Benito Roberto , Dotto André Carnieletto , Salazar Diego Fernando Urbina , Mello Fellipe Alcântara de Oliveira , Paiva Ariane Francine da Silveira , Souza Arnaldo Barros , Santos Natasha Valadares dos , Maria Nascimento Cláudia , Mello Danilo Cesar de , Bellinaso Henrique , Gonzaga Neto Luiz , Amorim Merilyn Taynara Accorsi , Resende Maria Eduarda Bispo de , Vieira Julia da Souza , Queiroz Louise Gunter de , Gallo Bruna Cristina , Sayão Veridiana Maria , Lisboa Caroline Jardim da Silva
Published: March 2020

The Earth’s surface dynamics provide essential information for guiding environmental and agricultural policies. Uncovered and unprotected surfaces experience several undesirable effects, which can affect soil ecosystem functions. We developed a technique to identify global bare surface areas and their dynamics based on multitemporal remote sensing images to aid the spatiotemporal evaluation of anthropic and natural phenomena. The bare Earth’s surface and its changes were recognized by Landsat image processing over a time range of 30 years using the Google Earth Engine platform. Two additional products were obtained with a similar technique: a) Earth’s bare surface frequency, which represents where and how many times a single pixel was detected as bare surface, based on Landsat series, and b) Earth’s bare soil tendency, which represents the tendency of bare surface to increase or decrease. This technique enabled the retrieval of bare surfaces on 32% of Earth’s total land area and on 95% of land when considering only agricultural areas. From a multitemporal perspective, the technique found a 2.8% increase in bare surfaces during the period on a global scale. However, the rate of soil exposure decreased by ~4.8% in the same period. The increase in bare surfaces shows that agricultural areas are increasing worldwide. The decreasing rate of soil exposure indicates that, unlike popular opinion, more soils have been covered due to the adoption of conservation agriculture practices, which may reduce soil degradation.
MHCA with SACP versus DHCA in Pediatric Aortic Arch Surgery: A Comparative Study
Authors: Xie Ling , Xu Yan , Huang Guijin , Ye Mao , Hu Xiao , Shu Shiyu , Lynn Harness
Published: March 2020

The safety and efficacy of selective antegrade cerebral perfusion (SACP) in children undergoing aortic arch surgery are unclear. In this retrospective analysis, we compared moderate hypothermic circulatory arrest (MHCA; n = 61) plus SACP vs deep hypothermic circulatory arrest (DHCA; n = 53) in children undergoing aortic arch surgery during a period from January 2008 to December 2017. Demographic characteristics and the underlying anomalies were comparable between the two groups. The MHCA + SACP group had shorter cardiopulmonary bypass (CPB) time (146.9 ± 40.6 vs 189.6 ± 41.2 min for DHCA; p < 0.05) and higher nasopharyngeal temperature (26.0 ± 2.1 vs 18.9 ± 1.6 °C; p < 0.01). The MHCA + SACP group had lower rate of neurologic complications (3/61 vs 10/53 for DHCA; p < 0.05) but not complications in other organ systems. The MHCA + SACP group also had less 24-hour chest drainage (median, interquartile rage: 28.9, 12.6–150.0 vs 47.4, 15.2–145.0 ml/kg for DHCA; p < 0.05), shorter duration of postoperative mechanical ventilation (35.0, 15.4–80.3 vs 94.0, 42.0–144.0 h; p < 0.01), and shorter stay in intensive care unit (3.9, 3.0–7.0 vs 7.7, 5.0–15.0 d; p < 0.05). In regression analysis, in-hospital mortality was associated with longer CPB time. In conclusion, MHCA + SACP is associated with better short-term outcomes in children receiving aortic arch surgery under CPB.