bluuebunny/crossref_metadata_2025 huggingface dataset:
Association between methylation of BIN1 promoter in peripheral blood and preclinical Alzheimer’s disease
Authors: Hu Hao , Tan Lan , Bi Yan-Lin , Xu Wei , Tan Lin , Shen Xue-Ning , Hou Xiao-He , Ma Ya-Hui , Dong Qiang , Yu Jin-Tai
Published: February 2021

The bridging integrator 1 (BIN1) gene is the second most important susceptibility gene for late-onset Alzheimer’s disease (LOAD) after apolipoprotein E (APOE) gene. To explore whether the BIN1 methylation in peripheral blood changed in the early stage of LOAD, we included 814 participants (484 cognitively normal participants [CN] and 330 participants with subjective cognitive decline [SCD]) from the Chinese Alzheimer’s Biomarker and LifestylE (CABLE) database. Then we tested associations of methylation of BIN1 promoter in peripheral blood with the susceptibility for preclinical AD or early changes of cerebrospinal fluid (CSF) AD-related biomarkers. Results showed that SCD participants with significant AD biological characteristics had lower methylation levels of BIN1 promoter, even after correcting for covariates. Hypomethylation of BIN1 promoter were associated with decreased CSF Aβ42 (p = 0.0008), as well as increased p-tau/Aβ42 (p = 0.0001) and t-tau/Aβ42 (p < 0.0001) in total participants. Subgroup analysis showed that the above associations only remained in the SCD subgroup. In addition, hypomethylation of BIN1 promoter was also accompanied by increased CSF p-tau (p = 0.0028) and t-tau (p = 0.0130) in the SCD subgroup, which was independent of CSF Aβ42. Finally, above associations were still significant after correcting single nucleotide polymorphic sites (SNPs) and interaction of APOE ɛ4 status. Our study is the first to find a robust association between hypomethylation of BIN1 promoter in peripheral blood and preclinical AD. This provides new evidence for the involvement of BIN1 in AD, and may contribute to the discovery of new therapeutic targets for AD.
Host immunity modulates the efficacy of microbiota transplantation for treatment of Clostridioides difficile infection
Authors: Littmann Eric R. , Lee Jung-Jin , Denny Joshua E. , Alam Zahidul , Maslanka Jeffrey R. , Zarin Isma , Matsuda Rina , Carter Rebecca A. , Susac Bože , Saffern Miriam S. , Fett Bryton , Mattei Lisa M. , Bittinger Kyle , Abt Michael C.
Published: February 2021

Fecal microbiota transplantation (FMT) is a successful therapeutic strategy for treating recurrent Clostridioides difficile infection. Despite remarkable efficacy, implementation of FMT therapy is limited and the mechanism of action remains poorly understood. Here, we demonstrate a critical role for the immune system in supporting FMT using a murine C. difficile infection system. Following FMT, Rag1 heterozygote mice resolve C. difficile while littermate Rag1−/− mice fail to clear the infection. Targeted ablation of adaptive immune cell subsets reveal a necessary role for CD4+ Foxp3+ T-regulatory cells, but not B cells or CD8+ T cells, in FMT-mediated resolution of C. difficile infection. FMT non-responsive mice exhibit exacerbated inflammation, impaired engraftment of the FMT bacterial community and failed restoration of commensal bacteria-derived secondary bile acid metabolites in the large intestine. These data demonstrate that the host’s inflammatory immune status can limit the efficacy of microbiota-based therapeutics to treat C. difficile infection.
Extreme temperatures compromise male and female fertility in a large desert bird
Authors: Schou Mads F. , Bonato Maud , Engelbrecht Anel , Brand Zanell , Svensson Erik I. , Melgar Julian , Muvhali Pfunzo T. , Cloete Schalk W. P. , Cornwallis Charlie K.
Published: February 2021

Temperature has a crucial influence on the places where species can survive and reproduce. Past research has primarily focused on survival, making it unclear if temperature fluctuations constrain reproductive success, and if so whether populations harbour the potential to respond to climatic shifts. Here, using two decades of data from a large experimental breeding programme of the iconic ostrich (Struthio camelus) in South Africa, we show that the number of eggs females laid and the number of sperm males produced were highly sensitive to natural temperature extremes (ranging from −5 °C to 45 °C). This resulted in reductions in reproductive success of up to 44% with 5 °C deviations from their thermal optimum. In contrast, gamete quality was largely unaffected by temperature. Extreme temperatures also did not expose trade-offs between gametic traits. Instead, some females appeared to invest more in reproducing at high temperatures, which may facilitate responses to climate change. These results show that the robustness of fertility to temperature fluctuations, and not just temperature increases, is a critical aspect of species persistence in regions predicted to undergo the greatest change in climate volatility.
Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism
Authors: Wang Gang , Zhang Xingtan , Herre Edward Allen , McKey Doyle , Machado Carlos A. , Yu Wen-Bin , Cannon Charles H. , Arnold Michael L. , Pereira Rodrigo A. S. , Ming Ray , Liu Yi-Fei , Wang Yibin , Ma Dongna , Chen Jin
Published: February 2021

Ficus(figs) and their agaonid wasp pollinators present an ecologically important mutualism that also provides a rich comparative system for studying functional co-diversification throughout its coevolutionary history (~75 million years). We obtained entire nuclear, mitochondrial, and chloroplast genomes for 15 species representing all major clades ofFicus. Multiple analyses of these genomic data suggest that hybridization events have occurred throughoutFicusevolutionary history. Furthermore, cophylogenetic reconciliation analyses detect significant incongruence among all nuclear, chloroplast, and mitochondrial-based phylogenies, none of which correspond with any published phylogenies of the associated pollinator wasps. These findings are most consistent with frequent host-switching by the pollinators, leading to fig hybridization, even between distantly related clades. Here, we suggest that these pollinator host-switches and fig hybridization events are a dominant feature of fig/wasp coevolutionary history, and by generating novel genomic combinations in the figs have likely contributed to the remarkable diversity exhibited by this mutualism.
Plasma membrane H+-ATPase overexpression increases rice yield via simultaneous enhancement of nutrient uptake and photosynthesis
Authors: Zhang Maoxing , Wang Yin , Chen Xi , Xu Feiyun , Ding Ming , Ye Wenxiu , Kawai Yuya , Toda Yosuke , Hayashi Yuki , Suzuki Takamasa , Zeng Houqing , Xiao Liang , Xiao Xin , Xu Jin , Guo Shiwei , Yan Feng , Shen Qirong , Xu Guohua , Kinoshita Toshinori , Zhu Yiyong
Published: February 2021

Nitrogen (N) and carbon (C) are essential elements for plant growth and crop yield. Thus, improved N and C utilisation contributes to agricultural productivity and reduces the need for fertilisation. In the present study, we find that overexpression of a single rice gene, Oryza sativa plasma membrane (PM) H+-ATPase 1 (OSA1), facilitates ammonium absorption and assimilation in roots and enhanced light-induced stomatal opening with higher photosynthesis rate in leaves. As a result, OSA1 overexpression in rice plants causes a 33% increase in grain yield and a 46% increase in N use efficiency overall. As PM H+-ATPase is highly conserved in plants, these findings indicate that the manipulation of PM H+-ATPase could cooperatively improve N and C utilisation, potentially providing a vital tool for food security and sustainable agriculture.
Intelligent driving intelligence test for autonomous vehicles with naturalistic and adversarial environment
Authors: Feng Shuo , Yan Xintao , Sun Haowei , Feng Yiheng , Liu Henry X.
Published: February 2021

Driving intelligence tests are critical to the development and deployment of autonomous vehicles. The prevailing approach tests autonomous vehicles in life-like simulations of the naturalistic driving environment. However, due to the high dimensionality of the environment and the rareness of safety-critical events, hundreds of millions of miles would be required to demonstrate the safety performance of autonomous vehicles, which is severely inefficient. We discover that sparse but adversarial adjustments to the naturalistic driving environment, resulting in the naturalistic and adversarial driving environment, can significantly reduce the required test miles without loss of evaluation unbiasedness. By training the background vehicles to learn when to execute what adversarial maneuver, the proposed environment becomes an intelligent environment for driving intelligence testing. We demonstrate the effectiveness of the proposed environment in a highway-driving simulation. Comparing with the naturalistic driving environment, the proposed environment can accelerate the evaluation process by multiple orders of magnitude.
Nucleic acid binding by SAMHD1 contributes to the antiretroviral activity and is enhanced by the GpsN modification
Authors: Yu Corey H. , Bhattacharya Akash , Persaud Mirjana , Taylor Alexander B. , Wang Zhonghua , Bulnes-Ramos Angel , Xu Joella , Selyutina Anastasia , Martinez-Lopez Alicia , Cano Kristin , Demeler Borries , Kim Baek , Hardies Stephen C. , Diaz-Griffero Felipe , Ivanov Dmitri N.
Published: February 2021

SAMHD1 impedes infection of myeloid cells and resting T lymphocytes by retroviruses, and the enzymatic activity of the protein—dephosphorylation of deoxynucleotide triphosphates (dNTPs)—implicates enzymatic dNTP depletion in innate antiviral immunity. Here we show that the allosteric binding sites of the enzyme are plastic and can accommodate oligonucleotides in place of the allosteric activators, GTP and dNTP. SAMHD1 displays a preference for oligonucleotides containing phosphorothioate bonds in the Rp configuration located 3’ to G nucleotides (GpsN), the modification pattern that occurs in a mechanism of antiviral defense in prokaryotes. In the presence of GTP and dNTPs, binding of GpsN-containing oligonucleotides promotes formation of a distinct tetramer with mixed occupancy of the allosteric sites. Mutations that impair formation of the mixed-occupancy complex abolish the antiretroviral activity of SAMHD1, but not its ability to deplete dNTPs. The findings link nucleic acid binding to the antiretroviral activity of SAMHD1, shed light on the immunomodulatory effects of synthetic phosphorothioated oligonucleotides and raise questions about the role of nucleic acid phosphorothioation in human innate immunity.
Cryo-EM of mammalian PA28αβ-iCP immunoproteasome reveals a distinct mechanism of proteasome activation by PA28αβ
Authors: Chen Jinhuan , Wang Yifan , Xu Cong , Chen Kaijian , Zhao Qiaoyu , Wang Shutian , Yin Yue , Peng Chao , Ding Zhanyu , Cong Yao
Published: February 2021

The proteasome activator PA28αβ affects MHC class I antigen presentation by associating with immunoproteasome core particles (iCPs). However, due to the lack of a mammalian PA28αβ-iCP structure, how PA28αβ regulates proteasome remains elusive. Here we present the complete architectures of the mammalian PA28αβ-iCP immunoproteasome and free iCP at near atomic-resolution by cryo-EM, and determine the spatial arrangement between PA28αβ and iCP through XL-MS. Our structures reveal a slight leaning of PA28αβ towards the α3-α4 side of iCP, disturbing the allosteric network of the gatekeeper α2/3/4 subunits, resulting in a partial open iCP gate. We find that the binding and activation mechanism of iCP by PA28αβ is distinct from those of constitutive CP by the homoheptameric TbPA26 or PfPA28. Our study sheds lights on the mechanism of enzymatic activity stimulation of immunoproteasome and suggests that PA28αβ-iCP has experienced profound remodeling during evolution to achieve its current level of function in immune response.
Flux periodic oscillations and phase-coherent transport in GeTe nanowire-based devices
Authors: Zhang Jinzhong , Tse Pok-Lam , Jalil Abdur-Rehman , Kölzer Jonas , Rosenbach Daniel , Luysberg Martina , Panaitov Gregory , Lüth Hans , Hu Zhigao , Grützmacher Detlev , Lu Jia Grace , Schäpers Thomas
Published: February 2021

Despite the fact that GeTe is known to be a very interesting material for applications in thermoelectrics and for phase-change memories, the knowledge on its low-temperature transport properties is only limited. We report on phase-coherent phenomena in the magnetotransport of GeTe nanowires. From universal conductance fluctuations measured on GeTe nanowires with Au contacts, a phase-coherence length of about 280 nm at 0.5 K is determined. The distinct phase-coherence is confirmed by the observation of Aharonov–Bohm type oscillations for parallel magnetic fields. We interpret the occurrence of these magnetic flux-periodic oscillations by the formation of a tubular hole accumulation layer. For Nb/GeTe-nanowire/Nb Josephson junctions we obtained a critical current of 0.2 μA at 0.4 K. By applying a perpendicular magnetic field the critical current decreases monotonously with increasing field, whereas in a parallel field the critical current oscillates with a period of the magnetic flux quantum confirming the presence of a tubular hole channel.
Activatable polymer nanoagonist for second near-infrared photothermal immunotherapy of cancer
Authors: Jiang Yuyan , Huang Jiaguo , Xu Cheng , Pu Kanyi
Published: February 2021

Nanomedicine in combination with immunotherapy offers opportunities to treat cancer in a safe and effective manner; however, remote control of immune response with spatiotemporal precision remains challenging. We herein report a photothermally activatable polymeric pro-nanoagonist (APNA) that is specifically regulated by deep-tissue-penetrating second near-infrared (NIR-II) light for combinational photothermal immunotherapy. APNA is constructed from covalent conjugation of an immunostimulant onto a NIR-II semiconducting transducer through a labile thermo-responsive linker. Upon NIR-II photoirradiation, APNA mediates photothermal effect, which not only triggers tumor ablation and immunogenic cell death but also initiates the cleavage of thermolabile linker to liberate caged agonist for in-situ immune activation in deep solid tumor (8 mm). Such controlled immune regulation potentiates systemic antitumor immunity, leading to promoted cytotoxic T lymphocytes and helper T cell infiltration in distal tumor, lung and liver to inhibit cancer metastasis. Thereby, the present work illustrates a generic strategy to prepare pro-immunostimulants for spatiotemporal regulation of cancer nano-immunotherapy.
Author Correction: Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes
Authors: Wang Qingbo , Pierce-Hoffman Emma , Cummings Beryl B. , Alföldi Jessica , Francioli Laurent C. , Gauthier Laura D. , Hill Andrew J. , O’Donnell-Luria Anne H. ,   Genome Aggregation Database Production Team, Armean Irina M. , Banks Eric , Bergelson Louis , Cibulskis Kristian , Collins Ryan L. , Connolly Kristen M. , Covarrubias Miguel , Daly Mark J. , Donnelly Stacey , Farjoun Yossi , Ferriera Steven , Gabriel Stacey , Gentry Jeff , Gupta Namrata , Jeandet Thibault , Kaplan Diane , Laricchia Kristen M. , Llanwarne Christopher , Minikel Eric V. , Munshi Ruchi , Neale Benjamin M. , Novod Sam , Petrillo Nikelle , Poterba Timothy , Roazen David , Ruano-Rubio Valentin , Saltzman Andrea , Samocha Kaitlin E. , Schleicher Molly , Seed Cotton , Solomonson Matthew , Soto Jose , Tiao Grace , Tibbetts Kathleen , Tolonen Charlotte , Vittal Christopher , Wade Gordon , Wang Arcturus , Ware James S. , Watts Nicholas A. , Weisburd Ben , Whiffin Nicola ,   Genome Aggregation Database Consortium, Aguilar Salinas Carlos A. , Ahmad Tariq , Albert Christine M. , Ardissino Diego , Atzmon Gil , Barnard John , Beaugerie Laurent , Benjamin Emelia J. , Boehnke Michael , Bonnycastle Lori L. , Bottinger Erwin P. , Bowden Donald W. , Bown Matthew J. , Chambers John C. , Chan Juliana C. , Chasman Daniel , Cho Judy , Chung Mina K. , Cohen Bruce , Correa Adolfo , Dabelea Dana , Darbar Dawood , Duggirala Ravindranath , Dupuis Josée , Ellinor Patrick T. , Elosua Roberto , Erdmann Jeanette , Esko Tõnu , Färkkilä Martti , Florez Jose , Franke Andre , Getz Gad , Glaser Benjamin , Glatt Stephen J. , Goldstein David , Gonzalez Clicerio , Groop Leif , Haiman Christopher , Hanis Craig , Harms Matthew , Hiltunen Mikko , Holi Matti M. , Hultman Christina M. , Kallela Mikko , Kaprio Jaakko , Kathiresan Sekar , Kim Bong-Jo , Kim Young Jin , Kirov George , Kooner Jaspal , Koskinen Seppo , Krumholz Harlan M. , Kugathasan Subra , Kwak Soo Heon , Laakso Markku , Lehtimäki Terho , Loos Ruth J. F. , Lubitz Steven A. , Ma Ronald C. W. , Marrugat Jaume , Mattila Kari M. , McCarroll Steven , McCarthy Mark I. , McGovern Dermot , McPherson Ruth , Meigs James B. , Melander Olle , Metspalu Andres , Nilsson Peter M. , O’Donovan Michael C. , Ongur Dost , Orozco Lorena , Owen Michael J. , Palmer Colin N. A. , Palotie Aarno , Park Kyong Soo , Pato Carlos , Pulver Ann E. , Rahman Nazneen , Remes Anne M. , Rioux John D. , Ripatti Samuli , Roden Dan M. , Saleheen Danish , Salomaa Veikko , Samani Nilesh J. , Scharf Jeremiah , Schunkert Heribert , Shoemaker Moore B. , Sklar Pamela , Soininen Hilkka , Sokol Harry , Spector Tim , Sullivan Patrick F. , Suvisaari Jaana , Tai E. Shyong , Teo Yik Ying , Tiinamaija Tuomi , Tsuang Ming , Turner Dan , Tusie-Luna Teresa , Vartiainen Erkki , Watkins Hugh , Weersma Rinse K. , Wessman Maija , Wilson James G. , Xavier Ramnik J. , Vawter Marquis P. , Karczewski Konrad J. , MacArthur Daniel G.
Published: February 2021

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-21077-8.
QM7-X, a comprehensive dataset of quantum-mechanical properties spanning the chemical space of small organic molecules
Authors: Hoja Johannes , Medrano Sandonas Leonardo , Ernst Brian G. , Vazquez-Mayagoitia Alvaro , DiStasio Robert A. , Tkatchenko Alexandre
Published: February 2021

We introduce QM7-X, a comprehensive dataset of 42 physicochemical properties for ≈4.2 million equilibrium and non-equilibrium structures of small organic molecules with up to seven non-hydrogen (C, N, O, S, Cl) atoms. To span this fundamentally important region of chemical compound space (CCS), QM7-X includes an exhaustive sampling of (meta-)stable equilibrium structures—comprised of constitutional/structural isomers and stereoisomers, e.g., enantiomers and diastereomers (including cis-/trans- and conformational isomers)—as well as 100 non-equilibrium structural variations thereof to reach a total of ≈4.2 million molecular structures. Computed at the tightly converged quantum-mechanical PBE0+MBD level of theory, QM7-X contains global (molecular) and local (atom-in-a-molecule) properties ranging from ground state quantities (such as atomization energies and dipole moments) to response quantities (such as polarizability tensors and dispersion coefficients). By providing a systematic, extensive, and tightly-converged dataset of quantum-mechanically computed physicochemical properties, we expect that QM7-X will play a critical role in the development of next-generation machine-learning based models for exploring greater swaths of CCS and performing in silico design of molecules with targeted properties.
Reference carbon cycle dataset for typical Chinese forests via colocated observations and data assimilation
Authors: He Honglin , Ge Rong , Ren Xiaoli , Zhang Li , Chang Qingqing , Xu Qian , Zhou Guoyi , Xie Zongqiang , Wang Silong , Wang Huimin , Zhang Qibin , Wang Anzhi , Fan Zexin , Zhang Yiping , Shen Weijun , Yin Huajun , Lin Luxiang , Williams Mathew , Yu Guirui
Published: February 2021

Chinese forests cover most of the representative forest types in the Northern Hemisphere and function as a large carbon (C) sink in the global C cycle. The availability of long-term C dynamics observations is key to evaluating and understanding C sequestration of these forests. The Chinese Ecosystem Research Network has conducted normalized and systematic monitoring of the soil-biology-atmosphere-water cycle in Chinese forests since 2000. For the first time, a reference dataset of the decadal C cycle dynamics was produced for 10 typical Chinese forests after strict quality control, including biomass, leaf area index, litterfall, soil organic C, and the corresponding meteorological data. Based on these basic but time-discrete C-cycle elements, an assimilated dataset of key C cycle parameters and time-continuous C sequestration functions was generated via model-data fusion, including C allocation, turnover, and soil, vegetation, and ecosystem C storage. These reference data could be used as a benchmark for model development, evaluation and C cycle research under global climate change for typical forests in the Northern Hemisphere.
Corrosion protection properties of different inhibitors containing PEO/LDHs composite coating on magnesium alloy AZ31
Authors: Zhang Gen , Jiang E , Wu Liang , Ma Weigang , Yang Hong , Tang Aitao , Pan Fusheng
Published: February 2021

Corrosion inhibitors 2,5-pyridinedicarboxilate (PDC), sodium metavanadate (SMV) and 5-aminosalicylate (AS) were impregnated into porous PEO coatings respectively via vacuuming process, followed by fast sealing treatment in a Ce containing solution. After that layered double hydroxides (LDHs) based nanocontainers were respectively prepared on them via hydrothermal treatment. In frame of this work it was shown, that sealing effect for the pore was provided by formation of new phase CeO2 on the surface of PEO coatings. And, hydrothermal preparation for preparing LDHs leaded obvious changes in structure and thickness of the coatings. In addition, impregnation of inhibitors was in favor of improving LDHs content in final composite coatings. EIS result indicated that AS/Ce-HT specimen exhibited a best corrosion protection.
Genomic variations in patients with myelodysplastic syndrome and karyotypes without numerical or structural changes
Authors: Ribeiro Cristiano Luiz , Pinto Irene P. , Pereira Samara S. S. , Minasi Lysa B. , de S. M. Kluthcouski Fernanda , de M. Arantes Adriano , da Cruz Aparecido D. , de Almeida Marcio A. A. , Howard Tom E. , da Silva Cláudio C.
Published: February 2021

Myelodysplastic syndrome (MDS) is an onco-hematologic disease with distinct levels of peripheral blood cytopenias, dysplasias in cell differentiation and various forms of chromosomal and cytogenomic alterations. In this study, the Chromosomal Microarray Analysis (CMA) was performed in patients with primary MDS without numerical and/or structural chromosomal alterations in karyotypes. A total of 17 patients was evaluated by GTG banding and eight patients showed no numerical and/or structural alterations. Then, the CMA was carried out and identified gains and losses CNVs and long continuous stretches of homozygosity (LCSHs). They were mapped on chromosomes 1, 2, 3, 4, 5, 6, 7, 9, 10, 12, 14, 16, 17, 18, 19, 20, 21, X, and Y. Ninety-one genes that have already been implicated in molecular pathways important for cell viability were selected and in-silico expression analyses demonstrated 28 genes differentially expressed in mesenchymal stromal cells of patients. Alterations in these genes may be related to the inactivation of suppressor genes or the activation of oncogenes contributing to the evolution and malignization of MDS. CMA provided additional information in patients without visible changes in the karyotype and our findings could contribute with additional information to improve the prognostic and personalized stratification for patients.
Author Correction: An earth system model shows self-sustained thawing of permafrost even if all man-made GHG emissions stop in 2020
Authors: Randers Jorgen , Goluke Ulrich
Published: February 2021

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Understanding learner behaviour in online courses with Bayesian modelling and time series characterisation
Authors: Peach Robert L. , Greenbury Sam F. , Johnston Iain G. , Yaliraki Sophia N. , Lefevre David J. , Barahona Mauricio
Published: February 2021

The intrinsic temporality of learning demands the adoption of methodologies capable of exploiting time-series information. In this study we leverage the sequence data framework and show how data-driven analysis of temporal sequences of task completion in online courses can be used to characterise personal and group learners’ behaviors, and to identify critical tasks and course sessions in a given course design. We also introduce a recently developed probabilistic Bayesian model to learn sequential behaviours of students and predict student performance. The application of our data-driven sequence-based analyses to data from learners undertaking an on-line Business Management course reveals distinct behaviors within the cohort of learners, identifying learners or groups of learners that deviate from the nominal order expected in the course. Using course grades a posteriori, we explore differences in behavior between high and low performing learners. We find that high performing learners follow the progression between weekly sessions more regularly than low performing learners, yet within each weekly session high performing learners are less tied to the nominal task order. We then model the sequences of high and low performance students using the probablistic Bayesian model and show that we can learn engagement behaviors associated with performance. We also show that the data sequence framework can be used for task-centric analysis; we identify critical junctures and differences among types of tasks within the course design. We find that non-rote learning tasks, such as interactive tasks or discussion posts, are correlated with higher performance. We discuss the application of such analytical techniques as an aid to course design, intervention, and student supervision.
Risk factors for suicidal tendency in people with epilepsy in China: a case–control study
Authors: Lin Mintao , Chen Jiani , Li Sisi , Qin Yingjie , Wang Xuruan , Liu Yadong , Abdulaziz Ammar Taha Abdullah , Liu Wenyu , Zhou Dong , Li Jinmei
Published: February 2021

People with epilepsy (PWE) have an increased suicide prevalence. This study aimed to identify the risk factors for suicidal tendency among PWE in West China. A nested case–control study was designed in a cohort of patients with epilepsy (n = 2087). In total, 28 variates were calculated. In the univariate analysis, unemployment, low income, seizure frequency, seizure-free time, infectious or structural etiology, levetiracetam or phenobarbital use, anxiety, depression, and stigma were associated with suicidal tendency. A multivariate analysis indicated that unemployment (odds ratio [OR] 5.74, 95% confidence interval [CI] 2.13–15.48), levetiracetam use (OR 2.80, 95%CI 1.11–7.05), depression (C-NDDI-E score ≥ 13; OR 3.21, 95%CI 1.26–8.21), and stigma (SSCI score ≥ 16; OR 6.67, 95%CI 1.80–24.69) were independently associated with suicidal tendency. Conditional inference tree analysis indicated that SSCI and C-NDDI-E scores could effectively identify patients with suicidal tendency. Thus, this study suggests that unemployment, levetiracetam use, depression, and stigma are independent risk factors for suicidal tendency in PWE in China.
Recursive dynamic functional connectivity reveals a characteristic correlation structure in human scalp EEG
Authors: Panwar Siddharth , Joshi Shiv Dutt , Gupta Anubha , Kunnatur Sandhya , Agarwal Puneet
Published: February 2021

Time-varying neurophysiological activity has been classically explored using correlation based sliding window analysis. However, this method employs only lower order statistics to track dynamic functional connectivity of the brain. We introduce recursive dynamic functional connectivity (rdFC) that incorporates higher order statistics to generate a multi-order connectivity pattern by analyzing neurophysiological data at multiple time scales. The technique builds a hierarchical graph between various temporal scales as opposed to traditional approaches that analyze each scale independently. We examined more than a million rdFC patterns obtained from morphologically diverse EEGs of 2378 subjects of varied age and neurological health. Spatiotemporal evaluation of these patterns revealed three dominant connectivity patterns that represent a universal underlying correlation structure seen across subjects and scalp locations. The three patterns are both mathematically equivalent and observed with equal prevalence in the data. The patterns were observed across a range of distances on the scalp indicating that they represent a spatially scale-invariant correlation structure. Moreover, the number of patterns representing the correlation structure has been shown to be linked with the number of nodes used to generate them. We also show evidence that temporal changes in the rdFC patterns are linked with seizure dynamics.
Micro computed tomography with and without contrast enhancement for the characterization of microcarriers in dry and wet state
Authors: de Bournonville Sébastien , Geris Liesbet , Kerckhofs Greet
Published: February 2021

In the field of regenerative medicine, microcarriers are used as support matrix for the growth of adherent cells. They are increasingly recognised as promising biomaterials for large scale, cost-effective cell expansion bioreactor processes. However, their individual morphologies can be highly heterogeneous which increases bioprocesses’ variability. Additionally, only limited information is available on the microcarriers’ 3D morphology and how it affects cell proliferation. Most imaging modalities do not provide sufficient 3D information or have a too limited field of view to appropriately study the 3D morphology. While microfocus X-ray computed tomography (microCT) could be appropriate, many microcarriers are hydrated before in-vitro use. This wet state makes them swell, changing considerably their morphology and making them indistinguishable from the culture solution in regular microCT images due to their physical density close to water. The use of contrast-enhanced microCT (CE-CT) has been recently reported for 3D imaging of soft materials. In this study, we selected a range of commercially available microcarrier types and used a combination of microCT and CE-CT for full 3D morphological characterization of large numbers of microcarriers, both in their dry and wet state. With in-house developed image processing and analysis tools, morphometrics of individual microcarriers were collected. Also, the morphology in wet state was assessed and related to accessible attachment surface area as a function of cell size. The morphological information on all microcarriers was collected in a publicly available database. This work provides a quantitative basis for optimization and modelling of microcarrier based cell expansion processes.
Detection of hydroacoustic signals on a fiber-optic submarine cable
Authors: Matsumoto Hiroyuki , Araki Eiichiro , Kimura Toshinori , Fujie Gou , Shiraishi Kazuya , Tonegawa Takashi , Obana Koichiro , Arai Ryuta , Kaiho Yuka , Nakamura Yasuyuki , Yokobiki Takashi , Kodaira Shuichi , Takahashi Narumi , Ellwood Robert , Yartsev Victor , Karrenbach Martin
Published: February 2021

A ship-based seismic survey was conducted close to a fiber-optic submarine cable, and 50 km-long distributed acoustic sensing (DAS) recordings with air-gun shots were obtained for the first time. We examine the acquired DAS dataset together with the co-located hydrophones to investigate the detection capability of underwater acoustic (hydroacoustic) signals. Here, we show the hydroacoustic signals identified by the DAS measurement characterizing in frequency-time space. The DAS measurement can be sensitive for hydroacoustic signals in a frequency range from $$10^{-1}\,\text {Hz}$$

10

-
1

Hz

to a few tens of Hz which is similar to the hydrophones. The observed phases of hydroacoustic signals are coherent within a few kilometers along the submarine cable, suggesting the DAS is suitable for applying correlation analysis using hydroacoustic signals. Although our study suggests that virtual sensor’s self-noise of the present DAS measurement is relatively high compared to the conventional in-situ hydroacoustic sensors above a few Hz, the DAS identifies the ocean microseismic background noise along the entire submarine cable except for some cable sections de-coupled from the seafloor.
Wavefront shaping assisted design of spectral splitters and solar concentrators
Authors: Gün Berk N. , Yüce Emre
Published: February 2021

Spectral splitters, as well as solar concentrators, are commonly designed and optimized using numerical methods. Here, we present an experimental method to spectrally split and concentrate broadband light (420–875 nm) via wavefront shaping. We manage to spatially control white light using a phase-only spatial light modulator. As a result, we are able to split and concentrate three frequency bands, namely red (560–875 nm), green (425–620 nm), and blue (420–535 nm), to two target spots with a total enhancement factor of 715%. Despite the significant overlap between the color channels, we obtain spectral splitting ratios as 52%, 57%, and 66% for red, green, and blue channels, respectively. We show that a higher number of adjustable superpixels ensures higher spectral splitting and concentration. We provide the methods to convert an optimized phase pattern into a diffractive optical element that can be fabricated at large scale and low cost. The experimental method that we introduce, for the first time, enables the optimization and design of SpliCons, which is $$\sim 300$$

∼
300

times faster compared to the computational methods.
Cerebrum, liver, and muscle regulatory networks uncover maternal nutrition effects in developmental programming of beef cattle during early pregnancy
Authors: Diniz Wellison J. S. , Crouse Matthew S. , Cushman Robert A. , McLean Kyle J. , Caton Joel S. , Dahlen Carl R. , Reynolds Lawrence P. , Ward Alison K.
Published: February 2021

The molecular basis underlying fetal programming in response to maternal nutrition remains unclear. Herein, we investigated the regulatory relationships between genes in fetal cerebrum, liver, and muscle tissues to shed light on the putative mechanisms that underlie the effects of early maternal nutrient restriction on bovine developmental programming. To this end, cerebrum, liver, and muscle gene expression were measured with RNA-Seq in 14 fetuses collected on day 50 of gestation from dams fed a diet initiated at breeding to either achieve 60% (RES, n = 7) or 100% (CON, n = 7) of energy requirements. To build a tissue-to-tissue gene network, we prioritized tissue-specific genes, transcription factors, and differentially expressed genes. Furthermore, we built condition-specific networks to identify differentially co-expressed or connected genes. Nutrient restriction led to differential tissue regulation between the treatments. Myogenic factors differentially regulated by ZBTB33 and ZNF131 may negatively affect myogenesis. Additionally, nutrient-sensing pathways, such as mTOR and PI3K/Akt, were affected by gene expression changes in response to nutrient restriction. By unveiling the network properties, we identified major regulators driving gene expression. However, further research is still needed to determine the impact of early maternal nutrition and strategic supplementation on pre- and post-natal performance.
Gas-phase amination of aromatic hydrocarbons by corona discharge-assisted nitrogen fixation
Authors: Shen Shanshan , Chai Yunfeng , Shen Qirong , Jiang You , Fang Xiang , Pan Yuanjiang
Published: February 2021

This paper reports on the gas-phase amination reaction of aromatic hydrocarbons occurring under corona discharge conditions with N2 gas as the nitrogen source. The corona discharge device within an atmospheric pressure chemical ionization source was employed to achieve the plasma-assisted N2 fixation, and the coupled ion trap mass spectrometer (IT-MS) was used to detect positively charged product ions. In the model case, under APCI conditions, unusual product ions, [M + 16]+ and [M + 14]+, were observed. Based on the high resolution MS data and tandem mass spectrometric information, [M + 16]+ was confirmed to be protonated p-toluidine and [M + 14]+ was confirmed to be p-methylphenylnitrenium ion. According to the experimental results of the isotopic labelling and substituent effect, one feasible mechanism is proposed as follows. Firstly, N2 is activated by plasma caused via the corona discharge and then electrophilically attacks toluene, yielding the key intermediate, p-methylphenylnitrenium; secondly, the intermediate undergoes double-hydrogen transfer reaction to give rise to the final product ion, protonated p-toluidine. This study may provide a novel idea to explore new and green method for the synthesis of anilines.
Theoretical and experimental revision of surface acoustic waves on the (100) plane of silicon
Authors: Tarasenko Alexander , Čtvrtlík Radim , Kudělka Radim
Published: February 2021

The phase velocity dispersion of the surface acoustic waves on a basal plane of Si(100) has been calculated in the whole range of the azimuthal angle of propagation. We present a detailed description of the calculations. These calculations are compared with the experimental data obtained by a laser acoustic method. Our data convincingly demonstrate the existence of a gap in the spectrum of the phase velocities. The gap means that in a definite range of the phase velocities the SAWs are absent in the whole interval of the azimuthal angles. There is an excellent coincidence between the numerical and experimental data.
Greater liver PNPLA3 protein abundance in vivo and in vitro supports lower triglyceride accumulation in dairy cows
Authors: Pralle Ryan S. , Erb Sophia J. , Holdorf Henry T. , White Heather M.
Published: February 2021

Fatty liver syndrome is a prevalent metabolic disorder in peripartum dairy cows that unfavorably impacts lactation performance and health. Patatin-like phospholipase domain-containing protein 3 (PNPLA3) is a lipase that plays a central role in human non-alcoholic fatty liver disease etiology but has received limited attention in bovine fatty liver research. Thus, we investigated the relationship between tissue PNPLA3 expression and liver triglyceride accumulation in vivo via a ketosis induction protocol in multiparous dairy cows peripartum, as well as in vitro via small interfering RNA knockdown of PNPLA3 mRNA expression in bovine primary hepatocytes. Results demonstrated a negative association (P = 0.04) between liver PNPLA3 protein abundance and liver triglyceride content in peripartum dairy cows, while adipose PNPLA3 protein abundance was not associated with liver triglyceride content or blood fatty acid concentration. Knockdown of PNPLA3 mRNA resulted in reduced PNPLA3 protein abundance (P < 0.01) and greater liver triglyceride content (P < 0.01). Together, these results suggest greater liver PNPLA3 protein abundance may directly limit liver triglyceride accumulation peripartum, potentially preventing bovine fatty liver or accelerating recovery from fatty liver syndrome.
Comparison of plant growth and remediation potential of pyrochar and thermal desorption for crude oil-contaminated soils
Authors: Ilyas Noshin , Shoukat Uzma , Saeed Maimona , Akhtar Nosheen , Yasmin Humaira , Khan Wajiha , Iqbal Sumera
Published: February 2021

Crude oil contamination is a serious environmental threat for soil and plants growing in it. This study provides the first experimental evidence for comparison of the efficacy of pyrochar (slow pyrolysis biochar), thermal desorption and their combined application for degradation of crude oil contaminated soil (0%, 10%, and 20%), and growth of lettuce under glasshouse conditions. Pyrochar was produced by pyrolysis of sawdust at 350 °C, whereas thermal desorption was done by soil pyrolysis at 500 °C. Soil incubations were done for 120 days. The results of soil analysis showed that the crude oil degradation efficiency for the combined application was highest (40%), whereas pyrochar and thermal desorption was 25% and 19.6%, respectively. The maximum degradation products of crude oil were manifested by the detection of low molecular weight hydrocarbons (ranged between 173 and 422) in the soil with combined application treatment using Gas Chromatography-Mass Spectrometry (GC–MS) analysis. Crude oil contamination significantly reduced the germination and growth of the lettuce plants. Similarly, the combined application also improved plant growth by an increase of 24% in germination percentage, 35.5% in seedling vigor index, and 27% in promptness index under 20% crude oil contamination. Remediation caused a significant increase in fresh and dry biomass (40%), leaf area (30%), total chlorophyll (21%), water potential (23.6%), osmotic potential (27%), and membrane stability index (40%). Moreover, there was an increase in the contents of proline (32%), total amino acids (29%), soluble sugars (37%), proteins (27%), and antioxidant enzymes such as superoxide dismutase (19%), catalase (33%) and peroxidase (38%). This study confirmed the efficacy of pyrochar (slow pyrolysis biochar), thermal desorption, and their combined application for crude oil decontamination of soil at laboratory scale and also in improving soil usability by improved germination and growth of lettuce.
Second primary malignancies in colorectal cancer patients
Authors: Halamkova Jana , Kazda Tomas , Pehalova Lucie , Gonec Roman , Kozakova Sarka , Bohovicova Lucia , Krakorova Dagmar Adamkova , Slaby Ondrej , Demlova Regina , Svoboda Marek , Kiss Igor
Published: February 2021

The prevalence of second primary malignancies (SPMs) in the western world is continually increasing with the risk of a new primary cancer in patients with previously diagnosed carcinoma at about 20%. The aim of this retrospective analysis is to identify SPMs in colorectal cancer patients in a single-institution cohort, describe the most frequent SPMs in colorectal cancer patients, and discover the time period to occurrence of second primary tumors. We identified 1174 patients diagnosed with colorectal cancer in the period 2003–2013, with follow-up till 31.12.2018, and median follow-up of 10.1 years, (median age 63 years, 724 men). A second primary neoplasm was diagnosed in 234 patients (19.9%). Older age patients, those with early-stage disease and those with no relapse have a higher risk of secondary cancer development. The median time from cancer diagnosis to development of CRC was 8.9 years for breast cancer and 3.4 years for prostate cancer. For the most common cancer diagnosis after primary CRC, the median time to development was 0–5.2 years, depending on the type of malignancy. Patients with a diagnosis of breast, prostate, or kidney cancer, or melanoma should be regularly screened for CRC. CRC patients should also be screened for additional CRC as well as cancers of the breast, prostate, kidney, and bladder. The screening of cancer patients for the most frequent malignancies along with systematic patient education in this field should be the standard of surveillance for colorectal cancer patients.
Evaluation of balance functions using temporo-spatial gait analysis parameters in patients with brain lesions
Authors: Lee Byung Joo , Joo Na-Young , Kim Sung Hyun , Kim Chung Reen , Yang Dongseok , Park Donghwi
Published: February 2021

This study aimed to compare gait analysis and balance function measurements, such as the Berg balance scale (BBS) score to seek specific measurements that can represent the balance functions of patients with brain lesions. Additionally, we also compared other different gait function scale scores with gait analysis measurements. This study included 77 patients with brain lesions admitted to our institution between January 2017 and August 2020. Their gait analysis parameters and clinical data, including personal data; clinical diagnosis; duration of the disease; cognition, ambulation, and stair-climbing sub-scores of the modified Barthel index (MBI); manual muscle test (MMT) findings of both lower extremities; functional ambulation category (FAC); and BBS score, were retrospectively analyzed. A multiple linear regression analysis was performed to identify the gait analysis parameters that would significantly correlate with the balance function and other physical performances. In the results, the BBS scores were significantly correlated with the gait speed and step width/height2. However, the other gait function measurements, such as the FAC and ambulation and stair-climbing sub-scores of the MBI, were correlated only with the gait speed. Additionally, both the summations of the lower extremity MMT findings and anti-gravity lower extremity MMT findings were correlated with the average swing phase time. Therefore, in the gait analysis, the gait speed may be an important factor in determining the balance and gait functions of the patients with brain lesions. Moreover, the step width/height2 may be a significant factor in determining their balance function. However, further studies with larger sample sizes should be performed to confirm this relationship.
Marker-assisted selection complements phenotypic screening at seedling stage to identify cassava mosaic disease-resistant genotypes in African cassava populations
Authors: Olasanmi Bunmi , Kyallo Martina , Yao Nasser
Published: February 2021

Cassava mosaic disease (CMD) is a serious threat to cassava production in sub-Saharan Africa. The use of genomic-assisted selection at the seedling trial stage would help to reduce the time for release, breeding cost, and resources used, hence increase selection efficiency in cassava breeding programs. Five cassava populations were screened for resistance to CMD during the seedling evaluation trial at 1, 3, and 5 months after planting using a scale of 1–5. The genotypes in the five populations were also screened using six molecular markers linked to the CMD2 gene. The correlation between the phenotypic and marker data was estimated. Based on Cassava Mosaic Disease Severity Score (CMDSS), between 53 and 82% of the progenies were resistant across the populations with an average of 70.5%. About 70% of the progenies were identified to be resistant to the disease across the populations with a range of 62–80% using the marker data. With both marker data and CMDSS combined, 40–60% of the progenies in each population, with an average of 52%, were identified to be resistant to CMD. There was a fairly significant correlation between the marker data and CMDSS in each cassava population with correlation coefficients ranging from 0.2024 to 0.3460 suggesting that novel genes not associated to the markers used might be involved in the resistance to CMD. The resistant genotypes identified in this study with potential for other desirable traits were selected for evaluation at the advanced trial stage thereby shortening the period required for the breeding program.
Estrogen induces shift in abundances of specific groups of the coral microbiome
Authors: Vilela Caren L. S. , Villela Helena D. M. , Duarte Gustavo A. S. , Santoro Erika P. , Rachid Caio T. C. C. , Peixoto Raquel S.
Published: February 2021

Synthetic estrogens such as ethinylestradiol (EE2) are persistent micropollutants that are not effectively removed from wastewater by conventional treatments. These contaminants are released into waterbodies, where they disrupt endocrine systems of organisms and cause harmful effects such as feminization, infertility, reproduction problems and genital malformations. The consequences of this pollution for key marine ecosystems such as coral reefs and their associated microbiomes are underexplored. We evaluated the effects of EE2 concentrations of 100 ng L−1 and 100 µg L−1 on the coral metaorganism Mussismilia harttii. The results indicated no effects on visible bleaching or Fv/Fm ratios in the corals during a 17-day microcosm experiment. However, next-generation sequencing of 16S rDNA revealed a statistically significant effect of high EE2 concentrations on OTU richness, and shifts in specific microbial groups after treatments with or without EE2. These groups might be bioindicators of early shifts in the metaorganism composition caused by EE2 contamination.