bluuebunny/crossref_metadata_2025 huggingface dataset:
Mining and validation of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for the estimation of the genetic diversity and population structure of coconuts (Cocos nucifera L.) in Thailand
Authors: Riangwong Kanamon , Wanchana Samart , Aesomnuk Wanchana , Saensuk Chatree , Nubankoh Phakchana , Ruanjaichon Vinitchan , Kraithong Tippaya , Toojinda Theerayut , Vanavichit Apichart , Arikit Siwaret
Published: October 2020

Coconut (Cocos nucifera L.) is an important economic crop in tropical countries. However, the lack of a complete reference genome and the limitations of usable DNA markers hinder genomic studies and the molecular breeding of coconut. Here, we present the results of simple sequence repeat (SSR) mining from a high-throughput genotyping-by-sequencing (GBS) study of a collection of 38 coconut accessions. A total of 22,748 SSRs with di-, tri-, tetra-, penta- and hexanucleotide repeats of five or more were identified, 2451 of which were defined as polymorphic loci based on locus clustering in 38 coconut accessions, and 315 loci were suitable for the development of SSR markers. One hundred loci were selected, and primer pairs for each SSR locus were designed and validated in 40 coconut accessions. The analysis of 74 polymorphic markers identified between 2 and 9 alleles per locus, with an average of 3.01 alleles. The assessment of the genetic diversity and genetic relationships among the 40 coconut varieties based on the analysis of population structure, principal coordinate analysis (PCoA), and phylogenetic tree analysis using the 74 polymorphic SSR markers revealed three main groups of coconuts in Thailand. The identified SSR loci and SSR markers developed in this study will be useful for the study of coconut diversity and molecular breeding. The SSR mining approach used in this study could be applied to other plant species with a complex genome regardless of the availability of reference genome.
From landrace to modern hybrid broccoli: the genomic and morphological domestication syndrome within a diverse B. oleracea collection
Authors: Stansell Zachary , Björkman Thomas
Published: October 2020

Worldwide, broccoli (Brassica oleracea var. italica) is among the most economically important, nutritionally rich, and widely-grown vegetable crops. To explore the genomic basis of the dramatic changes in broccoli morphology in the last century, we evaluated 109 broccoli or broccoli/cauliflower intermediates for 24 horticultural traits. Genotype-by-sequencing markers were used to determine four subpopulations within italica: Calabrese broccoli landraces and hybrids, sprouting broccoli, and violet cauliflower, and to evaluate between and within group relatedness and diversity. While overall horticultural quality and harvest index of improved hybrid broccoli germplasm has increased by year of cultivar release, this improvement has been accompanied by a considerable reduction in allelic diversity when compared to the larger pool of germplasm. Two landraces are the most likely founding source of modern broccoli hybrids, and within these modern hybrids, we identified 13 reduction-in-diversity genomic regions, 53 selective sweeps, and 30 (>1 Mbp) runs of homozygosity. Landrace accessions collected in southern Italy contained 4.8-fold greater unique alleles per accessions compared to modern hybrids and provide a valuable resource in subsequent improvement efforts. This work broadens the understanding of broccoli germplasm, informs conservation efforts, and enables breeding for complex quality traits and regionally adapted cultivars.
Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper
Authors: Feng Shijing , Liu Zhenshan , Hu Yang , Tian Jieyun , Yang Tuxi , Wei Anzhi
Published: October 2020

Chinese pepper, mainly includingZanthoxylum bungeanumandZanthoxylum armatum, is an economically important crop popular in Asian countries due to its unique taste characteristics and potential medical uses. Numerous cultivars of Chinese pepper have been developed in China through long-term domestication. To better understand the population structure, demographic history, and speciation of Chinese pepper, we performed a comprehensive analysis at a genome-wide level by analyzing 38,395 genomic SNPs that were identified in 112 cultivated and wild accessions using a high-throughput genome-wide genotyping-by-sequencing (GBS) approach. Our analysis provides genetic evidence of multiple splitting events occurring between and within species, resulting in at least four clades inZ. bungeanumand two clades inZ. armatum. Despite no evidence of recent admixture between species, we detected substantial gene flow within species. Estimates of demographic dynamics and species distribution modeling suggest that climatic oscillations during the Pleistocene (including the Penultimate Glaciation and the Last Glacial Maximum) and recent domestication events together shaped the demography and evolution of Chinese pepper. Our analyses also suggest that southeastern Gansu province is the most likely origin ofZ. bungeanumin China. These findings provide comprehensive insights into genetic diversity, population structure, demography, and adaptation inZanthoxylum.
Coexpression network analysis reveals an MYB transcriptional activator involved in capsaicinoid biosynthesis in hot peppers
Authors: Sun Binmei , Zhou Xin , Chen Changming , Chen Chengjie , Chen Kunhao , Chen Muxi , Liu Shaoqun , Chen Guoju , Cao Bihao , Cao Fanrong , Lei Jianjun , Zhu Zhangsheng
Published: October 2020

Plant biosynthesis involves numerous specialized metabolites with diverse chemical natures and biological activities. The biosynthesis of metabolites often exclusively occurs in response to tissue-specific combinatorial developmental cues that are controlled at the transcriptional level. Capsaicinoids are a group of specialized metabolites that confer a pungent flavor to pepper fruits. Capsaicinoid biosynthesis occurs in the fruit placenta and combines its developmental cues. Although the capsaicinoid biosynthetic pathway has been largely characterized, the regulatory mechanisms that control capsaicinoid metabolism have not been fully elucidated. In this study, we combined fruit placenta transcriptome data with weighted gene coexpression network analysis (WGCNA) to generate coexpression networks. A capsaicinoid-related gene module was identified in which the MYB transcription factor CaMYB48 plays a critical role in regulating capsaicinoid in pepper. Capsaicinoid biosynthetic gene (CBG) and CaMYB48 expression primarily occurs in the placenta and is consistent with capsaicinoid biosynthesis. CaMYB48 encodes a nucleus-localized protein that primarily functions as a transcriptional activator through its C-terminal activation motif. CaMYB48 regulates capsaicinoid biosynthesis by directly regulating the expression of CBGs, including AT3a and KasIa. Taken together, the results of this study indicate ways to generate robust networks optimized for the mining of CBG-related regulators, establishing a foundation for future research elucidating capsaicinoid regulation.
Suppression of external quantum efficiency rolloff in organic light emitting diodes by scavenging triplet excitons
Authors: Karunathilaka Buddhika S. B. , Balijapalli Umamahesh , Senevirathne Chathuranganie A. M. , Yoshida Seiya , Esaki Yu , Goushi Kenichi , Matsushima Toshinori , Sandanayaka Atula S. D. , Adachi Chihaya
Published: October 2020

Large external quantum efficiency rolloff at high current densities in organic light-emitting diodes (OLEDs) is frequently caused by the quenching of radiative singlet excitons by long-lived triplet excitons [singlet–triplet annihilation (STA)]. In this study, we adopted a triplet scavenging strategy to overcome the aforementioned STA issue. To construct a model system for the triplet scavenging, we selected 2,6-dicyano-1,1-diphenyl-λ5σ4-phosphinine (DCNP) as the emitter and 4,4′-bis[(N-carbazole)styryl]biphenyl (BSBCz) as the host material by considering their singlet and triplet energy levels. In this system, the DCNP’s triplets are effectively scavenged by BSBCz while the DCNP’s singlets are intact, resulting in the suppressed STA under electrical excitation. Therefore, OLEDs with a 1 wt.%-DCNP-doped BSBCz emitting layer demonstrated the greatly suppressed efficiency rolloff even at higher current densities. This finding favourably provides the advanced light-emitting performance for OLEDs and organic semiconductor laser diodes from the aspect of the suppressed efficiency rolloff.
A biogenic secondary organic aerosol source of cirrus ice nucleating particles
Authors: Wolf Martin J. , Zhang Yue , Zawadowicz Maria A. , Goodell Megan , Froyd Karl , Freney Evelyn , Sellegri Karine , Rösch Michael , Cui Tianqu , Winter Margaux , Lacher Larissa , Axisa Duncan , DeMott Paul J. , Levin Ezra J. T. , Gute Ellen , Abbatt Jonathan , Koss Abigail , Kroll Jesse H. , Surratt Jason D. , Cziczo Daniel J.
Published: October 2020

Atmospheric ice nucleating particles (INPs) influence global climate by altering cloud formation, lifetime, and precipitation efficiency. The role of secondary organic aerosol (SOA) material as a source of INPs in the ambient atmosphere has not been well defined. Here, we demonstrate the potential for biogenic SOA to activate as depositional INPs in the upper troposphere by combining field measurements with laboratory experiments. Ambient INPs were measured in a remote mountaintop location at –46 °C and an ice supersaturation of 30% with concentrations ranging from 0.1 to 70 L–1. Concentrations of depositional INPs were positively correlated with the mass fractions and loadings of isoprene-derived secondary organic aerosols. Compositional analysis of ice residuals showed that ambient particles with isoprene-derived SOA material can act as depositional ice nuclei. Laboratory experiments further demonstrated the ability of isoprene-derived SOA to nucleate ice under a range of atmospheric conditions. We further show that ambient concentrations of isoprene-derived SOA can be competitive with other INP sources. This demonstrates that isoprene and potentially other biogenically-derived SOA materials could influence cirrus formation and properties.
Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation
Authors: Xin Jingxue , Zhang Hui , He Yaoxi , Duren Zhana , Bai Caijuan , Chen Lang , Luo Xin , Yan Dong-Sheng , Zhang Chaoyu , Zhu Xiang , Yuan Qiuyue , Feng Zhanying , Cui Chaoying , Qi Xuebin , Ouzhuluobu  , Wong Wing Hung , Wang Yong , Su Bing
Published: October 2020

High-altitude adaptation of Tibetans represents a remarkable case of natural selection during recent human evolution. Previous genome-wide scans found many non-coding variants under selection, suggesting a pressing need to understand the functional role of non-coding regulatory elements (REs). Here, we generate time courses of paired ATAC-seq and RNA-seq data on cultured HUVECs under hypoxic and normoxic conditions. We further develop a variant interpretation methodology (vPECA) to identify active selected REs (ASREs) and associated regulatory network. We discover three causal SNPs of EPAS1, the key adaptive gene for Tibetans. These SNPs decrease the accessibility of ASREs with weakened binding strength of relevant TFs, and cooperatively down-regulate EPAS1 expression. We further construct the downstream network of EPAS1, elucidating its roles in hypoxic response and angiogenesis. Collectively, we provide a systematic approach to interpret phenotype-associated noncoding variants in proper cell types and relevant dynamic conditions, to model their impact on gene regulation.
A three-order-parameter bistable magnetoelectric multiferroic metal
Authors: Urru Andrea , Ricci Francesco , Filippetti Alessio , Íñiguez Jorge , Fiorentini Vincenzo
Published: October 2020

Using first-principles calculations we predict that the layered-perovskite metal Bi5Mn5O17 is a ferromagnet, ferroelectric, and ferrotoroid which may realize the long sought-after goal of a room-temperature ferromagnetic single-phase multiferroic with large, strongly coupled, primary-order polarization and magnetization. Bi5Mn5O17 has two nearly energy-degenerate ground states with mutually orthogonal vector order parameters (polarization, magnetization, ferrotoroidicity), which can be rotated globally by switching between ground states. Giant cross-coupling magnetoelectric and magnetotoroidic effects, as well as optical non-reciprocity, are thus expected. Importantly, Bi5Mn5O17 should be thermodynamically stable in O-rich growth conditions, and hence experimentally accessible.
Piperacillin/tazobactam resistance in a clinical isolate of Escherichia coli due to IS26-mediated amplification of blaTEM-1B
Authors: Hubbard Alasdair T. M. , Mason Jenifer , Roberts Paul , Parry Christopher M. , Corless Caroline , van Aartsen Jon , Howard Alex , Bulgasim Issra , Fraser Alice J. , Adams Emily R. , Roberts Adam P. , Edwards Thomas
Published: October 2020

A phenotype of Escherichia coli and Klebsiella pneumoniae, resistant to piperacillin/tazobactam (TZP) but susceptible to carbapenems and 3rd generation cephalosporins, has emerged. The resistance mechanism associated with this phenotype has been identified as hyperproduction of the β-lactamase TEM. However, the mechanism of hyperproduction due to gene amplification is not well understood. Here, we report a mechanism of gene amplification due to a translocatable unit (TU) excising from an IS26-flanked pseudo-compound transposon, PTn6762, which harbours blaTEM-1B. The TU re-inserts into the chromosome adjacent to IS26 and forms a tandem array of TUs, which increases the copy number of blaTEM-1B, leading to TEM-1B hyperproduction and TZP resistance. Despite a significant increase in blaTEM-1B copy number, the TZP-resistant isolate does not incur a fitness cost compared to the TZP-susceptible ancestor. This mechanism of amplification of blaTEM-1B is an important consideration when using genomic data to predict susceptibility to TZP.
Dynamics and clinical relevance of maternal mRNA clearance during the oocyte-to-embryo transition in humans
Authors: Sha Qian-Qian , Zheng Wei , Wu Yun-Wen , Li Sen , Guo Lei , Zhang Shuoping , Lin Ge , Ou Xiang-Hong , Fan Heng-Yu
Published: October 2020

Maternal mRNA clearance is an essential process that occurs during maternal-to-zygotic transition (MZT). However, the dynamics, functional importance, and pathological relevance of maternal mRNA decay in human preimplantation embryos have not yet been analyzed. Here we report the zygotic genome activation (ZGA)-dependent and -independent maternal mRNA clearance processes during human MZT and demonstrate that subgroups of human maternal transcripts are sequentially removed by maternal (M)- and zygotic (Z)-decay pathways before and after ZGA. Key factors regulating M-decay and Z-decay pathways in mouse have similar expression pattern during human MZT, suggesting that YAP1-TEAD4 transcription activators, TUT4/7-mediated mRNA 3ʹ-oligouridylation, and BTG4/CCR4-NOT-induced mRNA deadenylation may also be involved in the regulation of human maternal mRNA stability. Decreased expression of these factors and abnormal accumulation of maternal transcripts are observed in the development-arrested embryos of patients who seek assisted reproduction. Defects of M-decay and Z-decay are detected with high incidence in embryos that are arrested at the zygote and 8-cell stages, respectively. In addition, M-decay is not found to be affected by maternal TUBB8 mutations, although these mutations cause meiotic cell division defects and zygotic arrest, which indicates that mRNA decay is regulated independent of meiotic spindle assembly. Considering the correlations between maternal mRNA decay defects and early developmental arrest of in vitro fertilized human embryos, M-decay and Z-decay pathway activities may contribute to the developmental potential of human preimplantation embryos.
Highly efficient oxygen evolution reaction via facile bubble transport realized by three-dimensionally stack-printed catalysts
Authors: Kim Ye Ji , Lim Ahyoun , Kim Jong Min , Lim Donghoon , Chae Keun Hwa , Cho Eugene N. , Han Hyeuk Jin , Jeon Ki Ung , Kim Moohyun , Lee Gun Ho , Lee Gyu Rac , Ahn Hyun S. , Park Hyun S. , Kim Hyoungsoo , Kim Jin Young , Jung Yeon Sik
Published: October 2020

Despite highly promising characteristics of three-dimensionally (3D) nanostructured catalysts for the oxygen evolution reaction (OER) in polymer electrolyte membrane water electrolyzers (PEMWEs), universal design rules for maximizing their performance have not been explored. Here we show that woodpile (WP)-structured Ir, consisting of 3D-printed, highly-ordered Ir nanowire building blocks, improve OER mass activity markedly. The WP structure secures the electrochemically active surface area (ECSA) through enhanced utilization efficiency of the extended surface area of 3D WP catalysts. Moreover, systematic control of the 3D geometry combined with theoretical calculations and various electrochemical analyses reveals that facile transport of evolved O2 gas bubbles is an important contributor to the improved ECSA-specific activity. The 3D nanostructuring-based improvement of ECSA and ECSA-specific activity enables our well-controlled geometry to afford a 30-fold higher mass activity of the OER catalyst when used in a single-cell PEMWE than conventional nanoparticle-based catalysts.
Biophysical ambiguities prevent accurate genetic prediction
Authors: Li Xianghua , Lehner Ben
Published: October 2020

A goal of biology is to predict how mutations combine to alter phenotypes, fitness and disease. It is often assumed that mutations combine additively or with interactions that can be predicted. Here, we show using simulations that, even for the simple example of the lambda phage transcription factor CI repressing a gene, this assumption is incorrect and that perfect measurements of the effects of mutations on a trait and mechanistic understanding can be insufficient to predict what happens when two mutations are combined. This apparent paradox arises because mutations can have different biophysical effects to cause the same change in a phenotype and the outcome in a double mutant depends upon what these hidden biophysical changes actually are. Pleiotropy and non-monotonic functions further confound prediction of how mutations interact. Accurate prediction of phenotypes and disease will sometimes not be possible unless these biophysical ambiguities can be resolved using additional measurements.
Oxepinamide F biosynthesis involves enzymatic d-aminoacyl epimerization, 3H-oxepin formation, and hydroxylation induced double bond migration
Authors: Zheng Liujuan , Wang Haowen , Fan Aili , Li Shu-Ming
Published: October 2020

Oxepinamides are derivatives of anthranilyl-containing tripeptides and share an oxepin ring and a fused pyrimidinone moiety. To the best of our knowledge, no studies have been reported on the elucidation of an oxepinamide biosynthetic pathway and conversion of a quinazolinone to a pyrimidinone-fused 1H-oxepin framework by a cytochrome P450 enzyme in fungal natural product biosynthesis. Here we report the isolation of oxepinamide F from Aspergillus ustus and identification of its biosynthetic pathway by gene deletion, heterologous expression, feeding experiments, and enzyme assays. The nonribosomal peptide synthase (NRPS) OpaA assembles the quinazolinone core with d-Phe incorporation. The cytochrome P450 enzyme OpaB catalyzes alone the oxepin ring formation. The flavoenzyme OpaC installs subsequently one hydroxyl group at the oxepin ring, accompanied by double bond migration. The epimerase OpaE changes the d-Phe residue back to l-form, which is essential for the final methylation by OpaF.
PINCH-1 regulates mitochondrial dynamics to promote proline synthesis and tumor growth
Authors: Guo Ling , Cui Chunhong , Wang Jiaxin , Yuan Jifan , Yang Qingyang , Zhang Ping , Su Wen , Bao Ruolu , Ran Jingchao , Wu Chuanyue
Published: October 2020

Reprograming of proline metabolism is critical for tumor growth. Here we show that PINCH-1 is highly expressed in lung adenocarcinoma and promotes proline synthesis through regulation of mitochondrial dynamics. Knockout (KO) of PINCH-1 increases dynamin-related protein 1 (DRP1) expression and mitochondrial fragmentation, which suppresses kindlin-2 mitochondrial translocation and interaction with pyrroline-5-carboxylate reductase 1 (PYCR1), resulting in inhibition of proline synthesis and cell proliferation. Depletion of DRP1 reverses PINCH-1 deficiency-induced defects on mitochondrial dynamics, proline synthesis and cell proliferation. Furthermore, overexpression of PYCR1 in PINCH-1 KO cells restores proline synthesis and cell proliferation, and suppresses DRP1 expression and mitochondrial fragmentation. Finally, ablation of PINCH-1 from lung adenocarcinoma in mouse increases DRP1 expression and inhibits PYCR1 expression, proline synthesis, fibrosis and tumor growth. Our results identify a signaling axis consisting of PINCH-1, DRP1 and PYCR1 that regulates mitochondrial dynamics and proline synthesis, and suggest an attractive strategy for alleviation of tumor growth.
Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California
Authors: Sailani M. Reza , Metwally Ahmed A. , Zhou Wenyu , Rose Sophia Miryam Schüssler-Fiorenza , Ahadi Sara , Contrepois Kevin , Mishra Tejaswini , Zhang Martin Jinye , Kidziński Łukasz , Chu Theodore J. , Snyder Michael P.
Published: October 2020

The influence of seasons on biological processes is poorly understood. In order to identify biological seasonal patterns based on diverse molecular data, rather than calendar dates, we performed a deep longitudinal multiomics profiling of 105 individuals over 4 years. Here, we report more than 1000 seasonal variations in omics analytes and clinical measures. The different molecules group into two major seasonal patterns which correlate with peaks in late spring and late fall/early winter in California. The two patterns are enriched for molecules involved in human biological processes such as inflammation, immunity, cardiovascular health, as well as neurological and psychiatric conditions. Lastly, we identify molecules and microbes that demonstrate different seasonal patterns in insulin sensitive and insulin resistant individuals. The results of our study have important implications in healthcare and highlight the value of considering seasonality when assessing population wide health risk and management.
Author Correction: Modelling of free-form conformal metasurfaces
Authors: Wu Kedi , Coquet Philippe , Wang Qi Jie , Genevet Patrice
Published: October 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: NEMF mutations that impair ribosome-associated quality control are associated with neuromuscular disease
Authors: Martin Paige B. , Kigoshi-Tansho Yu , Sher Roger B. , Ravenscroft Gianina , Stauffer Jennifer E. , Kumar Rajesh , Yonashiro Ryo , Müller Tina , Griffith Christopher , Allen William , Pehlivan Davut , Harel Tamar , Zenker Martin , Howting Denise , Schanze Denny , Faqeih Eissa A. , Almontashiri Naif A. M. , Maroofian Reza , Houlden Henry , Mazaheri Neda , Galehdari Hamid , Douglas Ganka , Posey Jennifer E. , Ryan Monique , Lupski James R. , Laing Nigel G. , Joazeiro Claudio A. P. , Cox Gregory A.
Published: October 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Multiyear in-situ L-band microwave radiometry of land surface processes on the Tibetan Plateau
Authors: Su Z. , Wen J. , Zeng Y. , Zhao H. , Lv S. , van der Velde R. , Zheng D. , Wang X. , Wang Z. , Schwank M. , Kerr Y. , Yueh S. , Colliander A. , Qian H. , Drusch M. , Mecklenburg S.
Published: September 2020

We report a unique multiyear L-band microwave radiometry dataset collected at the Maqu site on the eastern Tibetan Plateau and demonstrate its utilities in advancing our understandings of microwave observations of land surface processes. The presented dataset contains measurements of L-band brightness temperature by an ELBARA-III microwave radiometer in horizontal and vertical polarization, profile soil moisture and soil temperature, turbulent heat fluxes, and meteorological data from the beginning of 2016 till August 2019, while the experiment is still continuing. Auxiliary vegetation and soil texture information collected in dedicated campaigns are also reported. This dataset can be used to validate the Soil Moisture and Ocean Salinity (SMOS) and Soil Moisture Active Passive (SMAP) satellite based observations and retrievals, verify radiative transfer model assumptions and validate land surface model and reanalysis outputs, retrieve soil properties, as well as to quantify land-atmosphere exchanges of energy, water and carbon and help to reduce discrepancies and uncertainties in current Earth System Models (ESM) parameterizations. Measurement cases in winter, pre-monsoon, monsoon and post-monsoon periods are presented.
Comparing preference of ankle–foot stiffness in below-knee amputees and prosthetists
Authors: Shepherd Max K. , Rouse Elliott J.
Published: September 2020

When fitting prosthetic feet, prosthetists fuse information from their visual assessment of patient gait with the patient’s communicated perceptions and preferences. In this study, we sought to simultaneously and independently assess patient and prosthetist preference for prosthetic foot stiffness using a custom variable-stiffness prosthesis. In the first part of the experiment, seven subjects with below-knee amputation walked on the variable-stiffness prosthetic foot set to a randomized stiffness, while several prosthetist subjects simultaneously observed their gait. After each trial, the amputee subjects and prosthetist subjects indicated the change to stiffness that they would prefer (increase or decrease). This paradigm allowed us to simultaneously measure amputee subject and prosthetist subject preferences, and provided a reliability index indicating the consistency of their preferences. In the second part of the experiment, amputee subjects were instructed to communicate verbally with one prosthetist subject to arrive at a mutually preferred stiffness. On average, prosthetist subjects preferred a 26% higher stiffness than amputee subjects (p < 0.001), though this depended on the amputee subject (p < 0.001). Prosthetist subjects were also considerably less consistent than amputee subjects in their preferences (CV of 5.6% for amputee subjects, CV of 23% for prosthetist subjects; p = 0.014). Mutual preference seemed to be dictated by the specific patient-prosthetist dynamic, and no clear trends emerged.
Imaging atmospheric aerosol particles from a UAV with digital holography
Authors: Kemppinen Osku , Laning Jesse C. , Mersmann Ryan D. , Videen Gorden , Berg Matthew J.
Published: September 2020

The lack of quantitative characterization of aerosol particles and their loading in the atmosphere is one of the greatest uncertainties in climate-change science. Improved instrumentation capable of determining the size and shape of aerosol particles is needed in efforts to reduce this uncertainty. We describe a new instrument carried by an unmanned aerial vehicle (UAV) that images free-floating aerosol particles in the atmosphere. Using digital holography, the instrument obtains the images in a non-contact manner, resolving particles larger than ten micrometers in size in a sensing volume of approximately three cubic centimeters. The instrument, called the holographic aerosol particle imager (HAPI), has the unique ability to image multiple particles freely entering its sensing volume from any direction via a single measurement. The construction of HAPI consists of 3D printed polymer structures that enable a sufficiently low size and weight that it may be flown on a commercial-grade UAV. Examples from field trials of HAPI show images of freshly emitted tree pollen and mineral dust.
Persistent fire foci in all biomes undermine the Paris Agreement in Brazil
Authors: da Silva Junior Carlos Antonio , Teodoro Paulo Eduardo , Delgado Rafael Coll , Teodoro Larissa Pereira Ribeiro , Lima Mendelson , de Andréa Pantaleão Ariane , Baio Fabio Henrique Rojo , de Azevedo Gileno Brito , de Oliveira Sousa Azevedo Glauce Taís , Capristo-Silva Guilherme Fernando , Arvor Damien , Facco Cassiele Uliana
Published: October 2020

Brazil is one of the world’s biggest emitters of greenhouse gases (GHGs). Fire foci across the country contributes to these emissions and compromises emission reduction targets pledged by Brazil under the Paris Agreement. In this paper, we quantify fire foci, burned areas, and carbon emissions in all Brazilian biomes (i.e., Amazon, Cerrado, Caatinga, Atlantic Forest, Pantanal and Pampa). We analyzed these variables using cluster analysis and non-parametric statistics to predict carbon and CO2 emissions for the next decade. Our results showed no increase in the number of fire foci and carbon emissions for the evaluated time series, whereby the highest emissions occur and will persist in the Amazon and Cerrado biomes. The Atlantic Forest, Pantanal, Caatinga and Pampa biomes had low emissions compared to the Amazon and Cerrado. Based on 2030 projections, the sum of emissions from fire foci in the six Brazilian biomes will exceed 5.7 Gt CO2, compromising the national GHG reduction targets. To reduce GHG emissions, Brazil will need to control deforestation induced by the expansion of the agricultural frontier in the Amazon and Cerrado biomes. This can only be achieved through significant political effort involving the government, entrepreneurs and society as a collective.
Biological sex does not predict glymphatic influx in healthy young, middle aged or old mice
Authors: Giannetto Michael , Xia Maosheng , Stæger Frederik Filip , Metcalfe Tanner , Vinitsky Hanna S. , Dang Juliana A. M. L. , Xavier Anna L. R. , Kress Benjamin T. , Nedergaard Maiken , Hablitz Lauren M.
Published: September 2020

Sexual dimorphism is evident in brain structure, size, and function throughout multiple species. Here, we tested whether cerebrospinal fluid entry into the glymphatic system, a network of perivascular fluid transport that clears metabolic waste from the brain, was altered between male and female mice. We analyze glymphatic influx in 244 young reproductive age (2–4 months) C57BL/6 mice. We found no male/female differences in total influx under anesthesia, or across the anterior/posterior axis of the brain. Circadian-dependent changes in glymphatic influx under ketamine/xylazine anesthesia were not altered by sex. This was not true for diurnal rhythms under pentobarbital and avertin, but both still showed daily oscillations independent of biological sex. Finally, although glymphatic influx decreases with age there was no sex difference in total influx or subregion-dependent tracer distribution in 17 middle aged (9–10 months) and 36 old (22–24 months) mice. Overall, in healthy adult C57BL/6 mice we could not detect male/female differences in glymphatic influx. This finding contrasts the gender differences in common neurodegenerative diseases. We propose that additional sex-dependent co-morbidities, such as chronic stress, protein misfolding, traumatic brain injury or other pathological mechanisms may explain the increased risk for developing proteinopathies rather than pre-existing suppression of glymphatic influx.
The impact of musical pleasure and musical hedonia on verbal episodic memory
Authors: Cardona Gemma , Rodriguez-Fornells Antoni , Nye Harry , Rifà-Ros Xavier , Ferreri Laura
Published: September 2020

Music listening is one of the most pleasurable activities in our life. As a rewarding stimulus, pleasant music could induce long-term memory improvements for the items encoded in close temporal proximity. In the present study, we behaviourally investigated (1) whether musical pleasure and musical hedonia enhance verbal episodic memory, and (2) whether such enhancement takes place even when the pleasant stimulus is not present during the encoding. Participants (N = 100) were asked to encode words presented in different auditory contexts (highly and lowly pleasant classical music, and control white noise), played before and during (N = 49), or only before (N = 51) the encoding. The Barcelona Music Reward Questionnaire was used to measure participants’ sensitivity to musical reward. 24 h later, participants’ verbal episodic memory was tested (old/new recognition and remember/know paradigm). Results revealed that participants with a high musical reward sensitivity present an increased recollection performance, especially for words encoded in a highly pleasant musical context. Furthermore, this effect persists even when the auditory stimulus is not concurrently present during the encoding of target items. Taken together, these findings suggest that musical pleasure might constitute a helpful encoding context able to drive memory improvements via reward mechanisms.
Homocysteine level, body mass index and clinical correlates in Chinese Han patients with schizophrenia
Authors: Huang Yuanyuan , Wu Kai , Li Hehua , Zhou Jing , Xiong Dongsheng , Huang Xia , Li Jiahui , Liu Ya , Pan Zhilin , Mitchell David T. , Wu Fengchun , Zhang Xiang Yang
Published: September 2020

Obesity is common comorbidity in patients with schizophrenia. Previous studies have reported that homocysteine (Hcy) is increased in schizophrenia. However, no study has reported the association between BMI and Hcy levels in schizophrenia. This cross-sectional naturalistic study aimed to evaluate the relationship between BMI, Hcy and clinical symptoms in Chinese Han patients with chronic schizophrenia. Clinical and anthropometric data as well as plasma Hcy level and glycolipid parameters were collected. Psychopathology was measured with the Positive and Negative Syndrome Scale (PANSS). Our results showed that compared with the low BMI group, the high BMI group had a higher PANSS general psychopathology subscore, higher levels of blood glucose, total cholesterol and high-density lipoprotein (HDL) cholesterol (all p < 0.05). Hcy levels were negatively associated with BMI in patients (p < 0.001). Hcy level, the PANSS general psychopathology subscale, total cholesterol and education (all p < 0.05) were the influencing factors of high BMI. Our study suggest that Hcy level may be associated with BMI in patients with schizophrenia. Moreover, patients with high BMI show more severe clinical symptoms and higher glucose and lipid levels.
Development of droplet digital PCR for the detection of Tilletia laevis, which causes common bunt of wheat, based on the SCAR marker derived from ISSR and real-time PCR
Authors: Xu Tongshuo , Yao Zhaoqun , Liu Jianjian , Zhang Han , Din Ghulam Muhae Ud , Zhao Sifeng , Chen Wanquan , Liu Taiguo , Gao Li
Published: September 2020

Common bunt of wheat caused by Tilletia laevis and/or T. caries (syn. T. tritici), is a major disease in wheat-growing regions worldwide that could lead to 80% or even total loss of production. Even though T. laevis can be distinguished from T. caries on the bases of morphology of teliospores using microscopy technique. However, molecular methods could serve as an additional method to quantify the pathogen. To develop a rapid diagnostic and quantify method, we employed the ISSR molecular marker for T. laevis in this study. The primer ISSR857 generated a polymorphic pattern displaying a 1385 bp T. laevis-specific DNA fragment. A pair of specific primers (L57F/L57R) was designed to amplify a sequence-characterized amplified region (SCAR) (763 bp) for the PCR detection assay. The primers amplified the DNA fragment in the tested isolates of T. laevis but failed in the related species, including T. caries. The detection limit of the primer set (L57F/L57R) was 5 ng/µl of DNA extracted from T. laevis teliospores. A SYBR Green I real-time PCR method for detecting T. laevis with a 100 fg/µl detection limit and droplet digital PCR with a high sensitivity (30 fg/µl detection limit) were developed; this technique showed the most sensitive detection compared to the SCAR marker and SYBR Green I real-time PCR. Additionally, this is the first study related the detection of T. laevis with the droplet digital PCR method.
A fine-scale multi-step approach to understand fish recruitment variability
Authors: Brosset Pablo , Smith Andrew Douglas , Plourde Stéphane , Castonguay Martin , Lehoux Caroline , Van Beveren Elisabeth
Published: September 2020

Recruitment is one of the dominant processes regulating fish population productivity. It is, however, notoriously difficult to predict, as it is the result of a complex multi-step process. Various fine-scale drivers might act on the pathway from adult population characteristics to spawning behaviour and egg production, and then to recruitment. Here, we provide a holistic analysis of the Northwest Atlantic mackerel recruitment process from 1982 to 2017 and exemplify why broad-scale recruitment–environment relationships could become unstable over time. Various demographic and environmental drivers had a synergetic effect on recruitment, but larval survival through a spatio-temporal match with prey was shown to be the key process. Recruitment was also mediated by maternal effects and a parent–offspring fitness trade-off due to the different feeding regimes of adults and larvae. A mismatch curtails the effects of high larval prey densities, so that despite the abundance of food in recent years, recruitment was relatively low and the pre-existing relationship with overall prey abundance broke down. Our results reaffirm major recruitment hypotheses and demonstrate the importance of fine-scale processes along the recruitment pathway, helping to improve recruitment predictions and potentially fisheries management.
Rat pancreatectomy combined with isoprenaline or uninephrectomy as models of diabetic cardiomyopathy or nephropathy
Authors: Thisted Louise , Østergaard Mette V. , Pedersen Annemarie A. , Pedersen Philip J. , Lindsay Ross T. , Murray Andrew J. , Fink Lisbeth N. , Pedersen Tanja X. , Secher Thomas , Johansen Thea T. , Thrane Sebastian T. , Skarsfeldt Torben , Jelsing Jacob , Thomsen Morten B. , Zois Nora E.
Published: September 2020

Cardiovascular and renal complications are the predominant causes of morbidity and mortality amongst patients with diabetes. Development of novel treatments have been hampered by the lack of available animal models recapitulating the human disease. We hypothesized that experimental diabetes in rats combined with a cardiac or renal stressor, would mimic diabetic cardiomyopathy and nephropathy, respectively. Diabetes was surgically induced in male Sprague Dawley rats by 90% pancreatectomy (Px). Isoprenaline (Iso, 1 mg/kg, sc., 10 days) was administered 5 weeks after Px with the aim of inducing cardiomyopathy, and cardiac function and remodeling was assessed by echocardiography 10 weeks after surgery. Left ventricular (LV) fibrosis was quantified by Picro Sirius Red and gene expression analysis. Nephropathy was induced by Px combined with uninephrectomy (Px-UNx). Kidney function was assessed by measurement of glomerular filtration rate (GFR) and urine albumin excretion, and kidney injury was evaluated by histopathology and gene expression analysis. Px resulted in stable hyperglycemia, hypoinsulinemia, decreased C-peptide, and increased glycated hemoglobin (HbA1c) compared with sham-operated controls. Moreover, Px increased heart and LV weights and dimensions and caused a shift from α-myosin heavy chain (MHC) to β-MHC gene expression. Isoprenaline treatment, but not Px, decreased ejection fraction and induced LV fibrosis. There was no apparent interaction between Px and Iso treatment. The superimposition of Px and UNx increased GFR, indicating hyperfiltration. Compared with sham-operated controls, Px-UNx induced albuminuria and increased urine markers of kidney injury, including neutrophil gelatinase-associated lipocalin (NGAL) and podocalyxin, concomitant with upregulated renal gene expression of NGAL and kidney injury molecule 1 (KIM-1). Whereas Px and isoprenaline separately produced clinical endpoints related to diabetic cardiomyopathy, the combination of the two did not accentuate disease development. Conversely, Px in combination with UNx resulted in several clinical hallmarks of diabetic nephropathy indicative of early disease development.
An on-chip wound healing assay fabricated by xurography for evaluation of dermal fibroblast cell migration and wound closure
Authors: Shabestani Monfared Ghazal , Ertl Peter , Rothbauer Mario
Published: October 2020

Dermal fibroblast cell migration is a key process in a physiological wound healing. Therefore, the analysis of cell migration is crucial for wound healing research. In this study, lab-on-a-chip technology was used to investigate the effects of basic fibroblast growth factor (bFGF), mitomycin C (MMC), MEK1/2 inhibitor (U0126) and fetal calf serum (FCS) on human dermal fibroblast cell migration. The microdevice was fabricated consisting of microchannels, pneumatic lines and pneumatically-activated actuators by xurographic rapid prototyping. In contrast to current approaches in in vitro wound healing such as scratch assays and silicone inserts in wellplate format, which show high variability and poor reproducibility, the current system aims to automate the wounding procedure at high precision and reproducibility using lab-on-a-chip. Traumatic wounding was simulated on-chip on fibroblast cell monolayers by applying air pressure on the flexible circular membrane actuator. Wound closure was monitored using light microscopy and cell migration was evaluated using image analysis. The pneumatically controlled system generates highly reproducible wound sizes compared to the conventional wound healing assay. As proof-of-principle study wound healing was investigated in the presence of several stimulatory and inhibitory substances and culture including bFGF, MMC, U0126 MEK1/2 inhibitor as well as serum starvation to demonstrate the broad applicability of the proposed miniaturized culture microsystem.
Automatic classification of healthy and disease conditions from images or digital standard 12-lead electrocardiograms
Authors: Gliner Vadim , Keidar Noam , Makarov Vladimir , Avetisyan Arutyun I. , Schuster Assaf , Yaniv Yael
Published: October 2020

Standard 12-lead electrocardiography (ECG) is used as the primary clinical tool to diagnose changes in heart function. The value of automated 12-lead ECG diagnostic approaches lies in their ability to screen the general population and to provide a second opinion for doctors. Yet, the clinical utility of automated ECG interpretations remains limited. We introduce a two-way approach to an automated cardiac disease identification system using standard digital or image 12-lead ECG recordings. Two different network architectures, one trained using digital signals (CNN-dig) and one trained using images (CNN-ima), were generated. An open-source dataset of 41,830 classified standard ECG recordings from patients and volunteers was generated. CNN-ima was trained to identify atrial fibrillation (AF) using 12-lead ECG digital signals and images that were also transformed to mimic mobile device camera-acquired ECG plot snapshots. CNN-dig accurately (92.9–100%) identified every possible combination of the eight most-common cardiac conditions. Both CNN-dig and CNN-ima accurately (98%) detected AF from standard 12-lead ECG digital signals and images, respectively. Similar classification accuracy was achieved with images containing smartphone camera acquisition artifacts. Automated detection of cardiac conditions in standard digital or image 12-lead ECG signals is feasible and may improve current diagnostic methods.
Evolutionary and ontogenetic changes of the anatomical organization and modularity in the skull of archosaurs
Authors: Lee Hiu Wai , Esteve-Altava Borja , Abzhanov Arhat
Published: September 2020

Comparative anatomy studies of the skull of archosaurs provide insights on the mechanisms of evolution for the morphologically and functionally diverse species of crocodiles and birds. One of the key attributes of skull evolution is the anatomical changes associated with the physical arrangement of cranial bones. Here, we compare the changes in anatomical organization and modularity of the skull of extinct and extant archosaurs using an Anatomical Network Analysis approach. We show that the number of bones, their topological arrangement, and modular organization can discriminate birds from non-avian dinosaurs, and crurotarsans. We could also discriminate extant taxa from extinct species when adult birds were included. By comparing within the same framework, juveniles and adults for crown birds and alligator (Alligator mississippiensis), we find that adult and juvenile alligator skulls are topologically similar, whereas juvenile bird skulls have a morphological complexity and anisomerism more similar to those of non-avian dinosaurs and crurotarsans than of their own adult forms. Clade-specific ontogenetic differences in skull organization, such as extensive postnatal fusion of cranial bones in crown birds, can explain this pattern. The fact that juvenile and adult skulls in birds do share a similar anatomical integration suggests the presence of a specific constraint to their ontogenetic growth.
Evidence for the intrinsically nonlinear nature of receptive fields in vision
Authors: Bertalmío Marcelo , Gomez-Villa Alex , Martín Adrián , Vazquez-Corral Javier , Kane David , Malo Jesús
Published: October 2020

The responses of visual neurons, as well as visual perception phenomena in general, are highly nonlinear functions of the visual input, while most vision models are grounded on the notion of a linear receptive field (RF). The linear RF has a number of inherent problems: it changes with the input, it presupposes a set of basis functions for the visual system, and it conflicts with recent studies on dendritic computations. Here we propose to model the RF in a nonlinear manner, introducing the intrinsically nonlinear receptive field (INRF). Apart from being more physiologically plausible and embodying the efficient representation principle, the INRF has a key property of wide-ranging implications: for several vision science phenomena where a linear RF must vary with the input in order to predict responses, the INRF can remain constant under different stimuli. We also prove that Artificial Neural Networks with INRF modules instead of linear filters have a remarkably improved performance and better emulate basic human perception. Our results suggest a change of paradigm for vision science as well as for artificial intelligence.
Transcutaneous fluorescence spectroscopy as a tool for non-invasive monitoring of gut function: first clinical experiences
Authors: Maurice James , Lett Aaron M. , Skinner Charlotte , Lim Alexandra , Richardson Matthew , Thomas Ajesh Painadath , Summers Peter A. , Vyas Khushi , Tadbier Abdul Wadood , Vilar Ramon , Kuimova Marina K. , Miodragovic Serge , Vergis Nikhil , Kelly Paul , Cordeiro Maria Francesca , Hoare Jonathan , Darzi Ara , Goldin Robert , Thursz Mark , Thompson Alex J.
Published: September 2020

Gastro-intestinal function plays a vital role in conditions ranging from inflammatory bowel disease and HIV through to sepsis and malnutrition. However, the techniques that are currently used to assess gut function are either highly invasive or unreliable. Here we present an alternative, non-invasive sensing modality for assessment of gut function based on fluorescence spectroscopy. In this approach, patients receive an oral dose of a fluorescent contrast agent and a fibre-optic probe is used to make fluorescence measurements through the skin. This provides a readout of the degree to which fluorescent dyes have permeated from the gut into the blood stream. We present preliminary results from our first measurements in human volunteers demonstrating the potential of the technique for non-invasive monitoring of multiple aspects of gastro-intestinal health.