bluuebunny/crossref_metadata_2025 huggingface dataset:
Malaria trends in Ethiopian highlands track the 2000 ‘slowdown’ in global warming
Authors: Rodó Xavier , Martinez Pamela P. , Siraj Amir , Pascual Mercedes
Published: March 2021

A counterargument to the importance of climate change for malaria transmission has been that regions where an effect of warmer temperatures is expected, have experienced a marked decrease in seasonal epidemic size since the turn of the new century. This decline has been observed in the densely populated highlands of East Africa at the center of the earlier debate on causes of the pronounced increase in epidemic size from the 1970s to the 1990s. The turnaround of the incidence trend around 2000 is documented here with an extensive temporal record for malaria cases for both Plasmodium falciparum and Plasmodium vivax in an Ethiopian highland. With statistical analyses and a process-based transmission model, we show that this decline was driven by the transient slowdown in global warming and associated changes in climate variability, especially ENSO. Decadal changes in temperature and concurrent climate variability facilitated rather than opposed the effect of interventions.
Creation and observation of Hopfions in magnetic multilayer systems
Authors: Kent Noah , Reynolds Neal , Raftrey David , Campbell Ian T. G. , Virasawmy Selven , Dhuey Scott , Chopdekar Rajesh V. , Hierro-Rodriguez Aurelio , Sorrentino Andrea , Pereiro Eva , Ferrer Salvador , Hellman Frances , Sutcliffe Paul , Fischer Peter
Published: March 2021

Among topological solitons, magnetic skyrmions are two-dimensional particle-like objects with a continuous winding of the magnetization, and magnetic Hopfions are three-dimensional objects that can be formed from a closed loop of twisted skyrmion strings. Theoretical models suggest that magnetic Hopfions can be stabilized in frustrated or chiral magnetic systems, and target skymions can be transformed into Hopfions by adapting their perpendicular magnetic anisotropy, but their experimental verification has been elusive so far. Here, we present an experimental study of magnetic Hopfions that are created in Ir/Co/Pt multilayers shaped into nanoscale disks, known to host target skyrmions. To characterize three-dimensional spin textures that distinguish Hopfions from target skyrmions magnetic images are recorded with surface-sensitive X-ray photoemission electron microscopy and bulk-sensitive soft X-ray transmission microscopy using element-specific X-ray magnetic circular dichroism effects as magnetic contrast. These results could stimulate further investigations of Hopfions and their potential application in three-dimensional spintronics devices.
Phosphorylation regulates the binding of autophagy receptors to FIP200 Claw domain for selective autophagy initiation
Authors: Zhou Zixuan , Liu Jianping , Fu Tao , Wu Ping , Peng Chao , Gong Xinyu , Wang Yingli , Zhang Mingfang , Li Ying , Wang Yaru , Xu Xiaolong , Li Miao , Pan Lifeng
Published: March 2021

The ULK complex initiates the autophagosome formation, and has recently been implicated in selective autophagy by interacting with autophagy receptors through its FIP200 subunit. However, the structural mechanism underlying the interactions of autophagy receptors with FIP200 and the relevant regulatory mechanism remain elusive. Here, we discover that the interactions of FIP200 Claw domain with autophagy receptors CCPG1 and Optineurin can be regulated by the phosphorylation in their respective FIP200-binding regions. We determine the crystal structures of FIP200 Claw in complex with the phosphorylated CCPG1 and Optineurin, and elucidate the detailed molecular mechanism governing the interactions of FIP200 Claw with CCPG1 and Optineurin as well as their potential regulations by kinase-mediated phosphorylation. In addition, we define the consensus FIP200 Claw-binding motif, and find other autophagy receptors that contain this motif within their conventional LC3-interacting regions. In all, our findings uncover a general and phosphoregulatable binding mode shared by many autophagy receptors to interact with FIP200 Claw for autophagosome biogenesis, and are valuable for further understanding the molecular mechanism of selective autophagy.
Suppression of multiple myeloma by mitochondrial targeting
Authors: Aisen Yana , Gatt Moshe E. , Hertz Rachel , Smeir Elia , Bar-Tana Jacob
Published: March 2021

Treatment of multiple myeloma (MM) aims at inducing cell apoptosis by surpassing the limited capacity of MM cells to cope with oxidative stress. MM cell survival may further be suppressed by limiting cellular cholesterol. Long-chain fatty acid analogs of the MEDICA series promote mitochondrial stress and inhibit cholesterol biosynthesis, thus prompting us to verify their efficacy and mode-of-action in suppressing MM cell survival, in comparison to bortezomib. MEDICA analog is shown here to effectively suppress survival of MM cells, and to inhibit growth of MM xenograft. Suppression of MM cell survival by MEDICA is accompanied by inhibition of the STAT3, MAPK and the mTORC1 transduction pathways due to mitochondrial oxidative stress. MEDICA-induced oxidative stress is abrogated by added exogenous cholesterol. Suppression of MM cell survival by bortezomib is similarly driven by bortezomib-induced oxidative stress, being abrogated by added cholesterol. In line with that, the time-to-best-response of MM patients to bortezomib-based treatment protocols is shown to be positively correlated with their plasma cholesterol level. MEDICA profile may indicate novel therapeutic potential in the management of MM.
Nitrogen addition decreases methane uptake caused by methanotroph and methanogen imbalances in a Moso bamboo forest
Authors: Li Quan , Peng Changhui , Zhang Junbo , Li Yongfu , Song Xinzhang
Published: March 2021

Forest soils play an important role in controlling global warming by reducing atmospheric methane (CH4) concentrations. However, little attention has been paid to how nitrogen (N) deposition may alter microorganism communities that are related to the CH4cycle or CH4oxidation in subtropical forest soils. We investigated the effects of N addition (0, 30, 60, or 90 kg N ha−1 yr−1) on soil CH4flux and methanotroph and methanogen abundance, diversity, and community structure in a Moso bamboo (Phyllostachys edulis) forest in subtropical China. N addition significantly increased methanogen abundance but reduced both methanotroph and methanogen diversity. Methanotroph and methanogen community structures under the N deposition treatments were significantly different from those of the control. In N deposition treatments, the relative abundance ofMethanoculleuswas significantly lower than that in the control. Soil pH was the key factor regulating the changes in methanotroph and methanogen diversity and community structure. The CH4emission rate increased with N addition and was negatively correlated with both methanotroph and methanogen diversity but positively correlated with methanogen abundance. Overall, our results suggested that N deposition can suppress CH4uptake by altering methanotroph and methanogen abundance, diversity, and community structure in subtropical Moso bamboo forest soils.
Blocks in the pseudouridimycin pathway unlock hidden metabolites in the Streptomyces producer strain
Authors: Iorio Marianna , Davatgarbenam Sahar , Serina Stefania , Criscenzo Paolo , Zdouc Mitja M. , Simone Matteo , Maffioli Sonia I. , Ebright Richard H. , Donadio Stefano , Sosio Margherita
Published: March 2021

We report a metabolomic analysis of Streptomyces sp. ID38640, a soil isolate that produces the bacterial RNA polymerase inhibitor pseudouridimycin. The analysis was performed on the wild type, on three newly constructed and seven previously reported mutant strains disabled in different genes required for pseudouridimycin biosynthesis. The results indicate that Streptomyces sp. ID38640 is able to produce, in addition to lydicamycins and deferroxiamines, as previously reported, also the lassopeptide ulleungdin, the non-ribosomal peptide antipain and the osmoprotectant ectoine. The corresponding biosynthetic gene clusters were readily identified in the strain genome. We also detected the known compound pyridindolol, for which we propose a previously unreported biosynthetic gene cluster, as well as three families of unknown metabolites. Remarkably, the levels of most metabolites varied strongly in the different mutant strains, an observation that enabled detection of metabolites unnoticed in the wild type. Systematic investigation of the accumulated metabolites in the ten different pum mutants identified shed further light on pseudouridimycin biosynthesis. We also show that several Streptomyces strains, able to produce pseudouridimycin, have distinct genetic relationship and metabolic profile with ID38640.
Three-dimensional and two-dimensional relationships of gangliogenesis with folliculogenesis in mature mouse ovary: a Golgi–Cox staining approach
Authors: Asadi Zarch Mohammad Ebrahim , Afshar Alireza , Rahmanifar Farhad , Jafarzadeh Shirazi Mohammad Reza , Baghban Mandana , Dadpasand Mohammad , Mohammad Rezazadeh Farzad , Khoradmehr Arezoo , Baharvand Hossein , Tamadon Amin
Published: March 2021

The present study was set out to investigate two-dimensional (2D) and three-dimensional (3D) evaluations of ovarian nervous network development and the structural relationship between folliculogenesis and gangliogenesis in mouse ovaries. Adult mice ovarian tissue samples were collected from follicular and luteal phases after cardiac perfusion. Ovarian samples were stained by a Golgi–Cox protocol. Following staining, tissues were serially sectioned for imaging. Neural filaments and ganglia were present in the ovaries. In both 2D and 3D studies, an increase in the number and area of ganglia was seen during the follicular growth. The same pattern was also seen in corpora lutea development. However, in some cases such as ratio of ganglia number to follicle area, the ratio of ganglia area to follicular area, 2D findings were different compared with the 3D results. 3D analysis of ovarian gangliogenesis showed the possible direct effect of them on folliculogenesis. Golgi–Cox staining was used in this study for 3D evaluation in non-brain tissue. The results of 3D analysis of the present study showed that, in some cases, the information provided by 2D analysis does not match the reality of ovarian neuronal function. This confirmed the importance of 3D analysis for evaluation of ovarian function.
A multicenter study of interocular symmetry of corneal biometrics in Chinese myopic patients
Authors: Xu Guihua , Hu Yijun , Zhu Shanqing , Guo Yunxiang , Xiong Lu , Fang Xuejun , Liu Jia , Zhang Qingsong , Huang Na , Zhou Jin , Li Fangfang , Lei Xiaohua , Jiang Li , Wang Zheng
Published: March 2021

It is essential to know the normal range of the interocular symmetry of the cornea (ISC) for keratoconus diagnosis and corneal substitutes design. In the present study we investigated the interocular symmetry of corneal biometrics in 6,644 Chinese myopic patients from multiple ophthalmic centers. Corneal biometrics of both eyes were exported from the Pentacam instrument. Interocular symmetry of the corneal biometrics was analyzed by Spearman’s correlation test, intraclass correlation coefficient (ICC) analysis and Bland–Altman plot. Significantly strong interocular correlations were found in anterior and posterior corneal curvatures, corneal diameter, corneal thickness, corneal volume, corneal eccentricity, and corneal asphericity (r = 0.87–0.98, all P < 0.001). Moderate interocular correlations were observed in whole corneal astigmatism (r = 0.78) and posterior corneal astigmatism (r = 0.73). ICC between the right and left eyes was 0.94–0.98 for anterior and posterior corneal curvatures, corneal diameter, corneal thickness and corneal volume, 0.80–0.88 for corneal eccentricity and asphericity, and 0.73–0.79 for corneal astigmatism (all P < 0.001). Bland–Altman plot showed that the 95% limit of agreement between both eyes was narrow and symmetric in most of the corneal biometrics, suggesting strong interocular agreements in these corneal biometrics. In conclusion, significant interocular symmetry of corneal biometrics is observed in Chinese myopia patients. Extra attention should be paid to patients with interocular corneal asymmetry.
Performance of EasyBreath Decathlon Snorkeling mask for delivering continuous positive airway pressure
Authors: Noto Alberto , Crimi Claudia , Cortegiani Andrea , Giardina Massimiliano , Benedetto Filippo , Princi Pietro , Carlucci Annalisa , Appendini Lorenzo , Gregoretti Cesare
Published: March 2021

During the COVID-19 pandemic, the need for noninvasive respiratory support devices has dramatically increased, sometimes exceeding hospital capacity. The full-face Decathlon snorkeling mask, EasyBreath (EB mask), has been adapted to deliver continuous positive airway pressure (CPAP) as an emergency respiratory interface. We aimed to assess the performance of this modified EB mask and to test its use during different gas mixture supplies. CPAP set at 5, 10, and 15 cmH2O was delivered to 10 healthy volunteers with a high-flow system generator set at 40, 80, and 120 L min−1 and with a turbine-driven ventilator during both spontaneous and loaded (resistor) breathing. Inspiratory CO2 partial pressure (PiCO2), pressure inside the mask, breathing pattern and electrical activity of the diaphragm (EAdi) were measured at all combinations of CPAP/flows delivered, with and without the resistor. Using the high-flow generator set at 40 L min−1, the PiCO2 significantly increased and the system was unable to maintain the target CPAP of 10 and 15 cmH2O and a stable pressure within the respiratory cycle; conversely, the turbine-driven ventilator did. EAdi significantly increased with flow rates of 40 and 80 L min−1 but not at 120 L min−1 and with the turbine-driven ventilator. EB mask can be safely used to deliver CPAP only under strict constraints, using either a high-flow generator at a flow rate greater than 80 L min−1, or a high-performance turbine-driven ventilator.
Enhanced XUV harmonics generation from diatomic gases using two orthogonally polarized laser fields
Authors: Boltaev Ganjaboy S. , Iqbal Mazhar , Abbasi Naveed A. , Kim Vyacheslav V. , Ganeev Rashid A. , Alnaser Ali S.
Published: March 2021

Enhanced high repetition rate coherent extreme ultraviolet (XUV) harmonics represent efficient probe of electron dynamics in atoms, molecules and solids. In this work, we used orthogonally-polarized two-color laser field to generate strong even and odd high order harmonics from molecular gas targets. The dynamics of odd and even harmonics from O2, and N2 gases were investigated by employing single- and two-color laser fields using the fundamental radiation and second harmonic of 1030 nm, 37 fs, 50 kHz pulses. The relative efficiencies of harmonics were analyzed as a function of the thickness of the barium borate crystal used for second harmonic generation. Defocusing-assisted phase matching conditions were achieved in N2 gas for different groups of XUV harmonics.
Deep learning predicts boiling heat transfer
Authors: Suh Youngjoon , Bostanabad Ramin , Won Yoonjin
Published: March 2021

Boiling is arguably Nature’s most effective thermal management mechanism that cools submersed matter through bubble-induced advective transport. Central to the boiling process is the development of bubbles. Connecting boiling physics with bubble dynamics is an important, yet daunting challenge because of the intrinsically complex and high dimensional of bubble dynamics. Here, we introduce a data-driven learning framework that correlates high-quality imaging on dynamic bubbles with associated boiling curves. The framework leverages cutting-edge deep learning models including convolutional neural networks and object detection algorithms to automatically extract both hierarchical and physics-based features. By training on these features, our model learns physical boiling laws that statistically describe the manner in which bubbles nucleate, coalesce, and depart under boiling conditions, enabling in situ boiling curve prediction with a mean error of 6%. Our framework offers an automated, learning-based, alternative to conventional boiling heat transfer metrology.
Nano urea effects on Pleurotus ostreatus nutritional value depending on the dose and timing of application
Authors: Sassine Youssef N. , Naim Layla , El Sebaaly Zeina , Abou Fayssal Sami , Alsanad Mohammed A. , Yordanova Milena H.
Published: March 2021

The work investigated the effect of Lithovit-Urea50 on the composition of Pleurotus ostreatus (Jacq. Ex Fr.) P. Kumm. (1871) cultivated on spent oyster substrate mixed with wheat straw (1:1, w/w mixture). The product was applied in different doses (C1: 3 g kg−1 and C2: 5 g kg−1) at three distinct timings (t1: at spawning, t2: after first harvest, t3: at spawning and after first harvest). Protein and fiber contents increased respectively by 0.64 and 0.2% in C1t1 and by 0.46 and 0.8% in C2t2 compared to control (C0t0). Total carbohydrates increased by 0.48–3.76%. Sucrose and glucose contents decreased in the majority of treatments, while fructose increased in C2t1 (by 0.045%). Essential amino acids were the highest in C1t1, wherein respective improvement of 0.31, 0.10, 0.05, 0.21, 0.18, and 0.09% compared to C0t0. Similarly, C1t1 was superior in non-essential amino acids. Potassium, sodium, calcium, iron, and copper contents decreased in all treatments, with minor exceptions, zinc decreased in C1t1 and C2t1, while nickel and lead increased in all treatments. Conclusively, despite important ameliorations in the mushroom nutritional value, mostly in C1t1, the product should be further tested in lower doses (< 3 g kg−1) to counteract its effect on heavy metal bioaccumulation.
Variability of serum IgG sialylation and galactosylation degree in women with advanced endometriosis
Authors: Sołkiewicz Katarzyna , Krotkiewski Hubert , Jędryka Marcin , Kratz Ewa M.
Published: March 2021

Endometriosis is an inflammatory disease which diagnostics is difficult and often invasive, therefore non-invasive diagnostics methods and parameters are needed for endometriosis detection. The aim of our study was to analyse the glycosylation of native serum IgG and IgG isolated from sera of women classified as: with endometriosis, without endometriosis but with some benign ginecological disease, and control group of healthy women, in context of its utility for differentiation of advanced endometriosis from the group of healthy women. IgG sialylation and galactosylation/agalactosylation degree was determined using specific lectins: MAA and SNA detecting sialic acid α2,3- and α2,6-linked, respectively, RCA-I and GSL-II specific to terminal Gal and terminal GlcNAc, respectively. The results of ROC and cluster analysis showed that the serum IgG MAA-reactivity, sialylation and agalactosylation factor may be used as supplementary parameters for endometriosis diagnostics and could be taken into account as a useful clinical tool to elucidate women with high risk of endometriosis development. Additionally, we have shown that the analysis of native serum IgG glycosylation, without the prior time-consuming and expensive isolation of the protein, is sufficient to differentiation endometriosis from a group of healthy women.
A pilot study of scleral thickness in central serous chorioretinopathy using anterior segment optical coherence tomography
Authors: Lee Yun Ji , Lee Yeon Jeong , Lee Jae Yeon , Lee Suhwan
Published: March 2021

The aim of this study is to compare the scleral thickness of central serous chorioretinopathy (CSC) eyes with controls using anterior segment optical coherence tomography (AS OCT). This prospective case control study included 15 patients (15 eyes) with CSC and 15 age and gender matched healthy subjects. All subjects underwent spectral domain OCT with enhanced depth imaging and swept source AS OCT of temporal sclera. We investigated difference in scleral thickness between the two groups and relationship between choroidal and scleral thickness. Among the 15 eyes in the study group, 1 eye had acute CSC, 4 had recurrent CSC, 7 had inactive CSC, and 3 had chronic CSC. There was no significant difference in terms of age, gender, axial length and spherical equivalent between the two groups. The choroidal and scleral thickness of the study group were significantly greater than those of the control group (P < 0.001, P = 0.034). Choroidal thickness was positively correlated with scleral thickness (P = 0.031). A thick sclera along with a thick choroid were demonstrated in CSC eyes using AS OCT. Scleral characteristics might be involved in the pathogenesis of CSC by affecting outflow resistance of venous drainage in choroidal circulation.
A novel approach to the classification of terrestrial drainage networks based on deep learning and preliminary results on solar system bodies
Authors: Donadio Carlo , Brescia Massimo , Riccardo Alessia , Angora Giuseppe , Veneri Michele Delli , Riccio Giuseppe
Published: March 2021

Several approaches were proposed to describe the geomorphology of drainage networks and the abiotic/biotic factors determining their morphology. There is an intrinsic complexity of the explicit qualification of the morphological variations in response to various types of control factors and the difficulty of expressing the cause-effect links. Traditional methods of drainage network classification are based on the manual extraction of key characteristics, then applied as pattern recognition schemes. These approaches, however, have low predictive and uniform ability. We present a different approach, based on the data-driven supervised learning by images, extended also to extraterrestrial cases. With deep learning models, the extraction and classification phase is integrated within a more objective, analytical, and automatic framework. Despite the initial difficulties, due to the small number of training images available, and the similarity between the different shapes of the drainage samples, we obtained successful results, concluding that deep learning is a valid way for data exploration in geomorphology and related fields.
Differential normal skin transcriptomic response in total body irradiated mice exposed to scattered versus scanned proton beams
Authors: Leduc Alexandre , Chaouni Samia , Pouzoulet Frédéric , De Marzi Ludovic , Megnin-Chanet Frédérique , Corre Erwan , Stefan Dinu , Habrand Jean-Louis , Sichel François , Laurent Carine
Published: March 2021

Proton therapy allows to avoid excess radiation dose on normal tissues. However, there are some limitations. Indeed, passive delivery of proton beams results in an increase in the lateral dose upstream of the tumor and active scanning leads to strong differences in dose delivery. This study aims to assess possible differences in the transcriptomic response of skin in C57BL/6 mice after TBI irradiation by active or passive proton beams at the dose of 6 Gy compared to unirradiated mice. In that purpose, total RNA was extracted from skin samples 3 months after irradiation and RNA-Seq was performed. Results showed that active and passive delivery lead to completely different transcription profiles. Indeed, 140 and 167 genes were differentially expressed after active and passive scanning compared to unirradiated, respectively, with only one common gene corresponding to RIKEN cDNA 9930021J03. Moreover, protein–protein interactions performed by STRING analysis showed that 31 and 25 genes are functionally related after active and passive delivery, respectively, with no common gene between both types of proton delivery. Analysis showed that active scanning led to the regulation of genes involved in skin development which was not the case with passive delivery. Moreover, 14 ncRNA were differentially regulated after active scanning against none for passive delivery. Active scanning led to 49 potential mRNA-ncRNA pairs with one ncRNA mainly involved, Gm44383 which is a miRNA. The 43 genes potentially regulated by the miRNA Gm44393 confirmed an important role of active scanning on skin keratin pathway. Our results demonstrated that there are differences in skin gene expression still 3 months after proton irradiation versus unirradiated mouse skin. And strong differences do exist in late skin gene expression between scattered or scanned proton beams. Further investigations are strongly needed to understand this discrepancy and to improve treatments by proton therapy.
Seasonal to multi-year soil moisture drought forecasting
Authors: Esit Musa , Kumar Sanjiv , Pandey Ashutosh , Lawrence David M. , Rangwala Imtiaz , Yeager Stephen
Published: March 2021

Soil moisture predictability on seasonal to decadal (S2D) continuum timescales over North America is examined from the Community Earth System Modeling (CESM) experiments. The effects of ocean and land initializations are disentangled using two large ensemble datasets—initialized and uninitialized experiments from the CESM. We find that soil moisture has significant predictability on S2D timescales despite limited predictability in precipitation. On sub-seasonal to seasonal timescales, precipitation variability is an order of magnitude greater than soil moisture, suggesting land surface processes, including soil moisture memory, reemergence, land–atmosphere interactions, transform a less predictable precipitation signal into a more predictable soil moisture signal.
Water orientation and dynamics in the closed and open influenza B virus M2 proton channels
Authors: Gelenter Martin D. , Mandala Venkata S. , Niesen Michiel J. M. , Sharon Dina A. , Dregni Aurelio J. , Willard Adam P. , Hong Mei
Published: March 2021

The influenza B M2 protein forms a water-filled tetrameric channel to conduct protons across the lipid membrane. To understand how channel water mediates proton transport, we have investigated the water orientation and dynamics using solid-state NMR spectroscopy and molecular dynamics (MD) simulations. 13C-detected water 1H NMR relaxation times indicate that water has faster rotational motion in the low-pH open channel than in the high-pH closed channel. Despite this faster dynamics, the open-channel water shows higher orientational order, as manifested by larger motionally-averaged 1H chemical shift anisotropies. MD simulations indicate that this order is induced by the cationic proton-selective histidine at low pH. Furthermore, the water network has fewer hydrogen-bonding bottlenecks in the open state than in the closed state. Thus, faster dynamics and higher orientational order of water molecules in the open channel establish the water network structure that is necessary for proton hopping.
Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome
Authors: Pandey Krishan K. , Bera Sibes , Shi Ke , Rau Michael J. , Oleru Amarachi V. , Fitzpatrick James A. J. , Engelman Alan N. , Aihara Hideki , Grandgenett Duane P.
Published: March 2021

Despite conserved catalytic integration mechanisms, retroviral intasomes composed of integrase (IN) and viral DNA possess diverse structures with variable numbers of IN subunits. To investigate intasome assembly mechanisms, we employed the Rous sarcoma virus (RSV) IN dimer that assembles a precursor tetrameric structure in transit to the mature octameric intasome. We determined the structure of RSV octameric intasome stabilized by a HIV-1 IN strand transfer inhibitor using single particle cryo-electron microscopy. The structure revealed significant flexibility of the two non-catalytic distal IN dimers along with previously unrecognized movement of the conserved intasome core, suggesting ordered conformational transitions between intermediates that may be important to capture the target DNA. Single amino acid substitutions within the IN C-terminal domain affected intasome assembly and function in vitro and infectivity of pseudotyped RSV virions. Unexpectedly, 17 C-terminal amino acids of IN were dispensable for virus infection despite regulating the transition of the tetrameric intasome to the octameric form in vitro. We speculate that this region may regulate the binding of highly flexible distal IN dimers to the intasome core to form the octameric complex. Our studies reveal key steps in the assembly of RSV intasomes.
Creb5 establishes the competence for Prg4 expression in articular cartilage
Authors: Zhang Cheng-Hai , Gao Yao , Jadhav Unmesh , Hung Han-Hwa , Holton Kristina M. , Grodzinsky Alan J. , Shivdasani Ramesh A. , Lassar Andrew B.
Published: March 2021

A hallmark of cells comprising the superficial zone of articular cartilage is their expression of lubricin, encoded by the Prg4 gene, that lubricates the joint and protects against the development of arthritis. Here, we identify Creb5 as a transcription factor that is specifically expressed in superficial zone articular chondrocytes and is required for TGF-β and EGFR signaling to induce Prg4 expression. Notably, forced expression of Creb5 in chondrocytes derived from the deep zone of the articular cartilage confers the competence for TGF-β and EGFR signals to induce Prg4 expression. Chromatin-IP and ATAC-Seq analyses have revealed that Creb5 directly binds to two Prg4 promoter-proximal regulatory elements, that display an open chromatin conformation specifically in superficial zone articular chondrocytes; and which work in combination with a more distal regulatory element to drive induction of Prg4 by TGF-β. Our results indicate that Creb5 is a critical regulator of Prg4/lubricin expression in the articular cartilage.
A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology
Authors: Calhoun Sara , Bell Tisza Ann Szeremy , Dahlin Lukas R. , Kunde Yuliya , LaButti Kurt , Louie Katherine B. , Kuftin Andrea , Treen Daniel , Dilworth David , Mihaltcheva Sirma , Daum Christopher , Bowen Benjamin P. , Northen Trent R. , Guarnieri Michael T. , Starkenburg Shawn R. , Grigoriev Igor V.
Published: March 2021

Microalgae efficiently convert sunlight into lipids and carbohydrates, offering bio-based alternatives for energy and chemical production. Improving algal productivity and robustness against abiotic stress requires a systems level characterization enabled by functional genomics. Here, we characterize a halotolerant microalgaScenedesmussp. NREL 46B-D3 demonstrating peak growth near 25 °C that reaches 30 g/m2/day and the highest biomass accumulation capacity post cell division reported to date for a halotolerant strain. Functional genomics analysis revealed that genes involved in lipid production, ion channels and antiporters are expanded and expressed. Exposure to temperature stress shifts fatty acid metabolism and increases amino acids synthesis. Co-expression analysis shows that many fatty acid biosynthesis genes are overexpressed with specific transcription factors under cold stress. These and other genes involved in the metabolic and regulatory response to temperature stress can be further explored for strain improvement.
Pocket MUSE: an affordable, versatile and high-performance fluorescence microscope using a smartphone
Authors: Liu Yehe , Rollins Andrew M. , Levenson Richard M. , Fereidouni Farzad , Jenkins Michael W.
Published: March 2021

Smartphone microscopes can be useful tools for a broad range of imaging applications. This manuscript demonstrates the first practical implementation of Microscopy with Ultraviolet Surface Excitation (MUSE) in a compact smartphone microscope called Pocket MUSE, resulting in a remarkably effective design. Fabricated with parts from consumer electronics that are readily available at low cost, the small optical module attaches directly over the rear lens in a smartphone. It enables high-quality multichannel fluorescence microscopy with submicron resolution over a 10× equivalent field of view. In addition to the novel optical configuration, Pocket MUSE is compatible with a series of simple, portable, and user-friendly sample preparation strategies that can be directly implemented for various microscopy applications for point-of-care diagnostics, at-home health monitoring, plant biology, STEM education, environmental studies, etc.
Controlled creation and decay of singly-quantized vortices in a polar magnetic phase
Authors: Xiao Y. , Borgh M. O. , Weiss L. S. , Blinova A. A. , Ruostekoski J. , Hall D. S.
Published: March 2021

Quantized vortices appear in physical systems from superfluids and superconductors to liquid crystals and high energy physics. Unlike their scalar cousins, superfluids with complex internal structure can exhibit rich dynamics of decay and even fractional vorticity. Here, we experimentally and theoretically explore the creation and time evolution of vortex lines in the polar magnetic phase of a trapped spin-1 87Rb Bose–Einstein condensate. A process of phase-imprinting a nonsingular vortex, its decay into a pair of singular spinor vortices, and a rapid exchange of magnetic phases creates a pair of three-dimensional, singular singly-quantized vortex lines with core regions that are filled with atoms in the ferromagnetic phase. Atomic interactions guide the subsequent vortex dynamics, leading to core structures that suggest the decay of the singly-quantized vortices into half-quantum vortices.
Experimental investigations into the irregular synthesis of iron(iii) terephthalate metal–organic frameworks MOF-235 and MIL-101
Authors: Simonsson Isabelle , Gärdhagen Philip , Andrén Moira , Tam Pui Lam , Abbas Zareen
Published: March 2021

This study investigates the role of reagent ratio, solvent composition and temperature on the solvothermal synthesis of MOF-235(Fe) and MIL-101(Fe).
Fermented blueberry and black rice containing Lactobacillus plantarum MG4221: a novel functional food for particulate matter (PM2.5)/dinitrochlorobenzene (DNCB)-induced atopic dermatitis
Authors: Hong Seong Min , Kang Min Cheol , Jin Mirim , Lee Taek Hwan , Lim Beong Ou , Kim Sun Yeou
Published: March 2021

Particulate matter (PM2.5) is a risk factor for the deterioration of atopic dermatitis (AD) and certain constituents of PM2.5 can induce inflammation via oxidative stress.
Biomass- and calcium carbide-based recyclable polymers
Authors: Metlyaeva Svetlana A. , Rodygin Konstantin S. , Lotsman Kristina A. , Samoylenko Dmitriy E. , Ananikov Valentine P.
Published: March 2021

A series of biomass-derived alcohols were successfully vinylated with calcium carbide followed by the polymerization. The polymers were tested as materials and disassembled back to monomers through pyrolysis.
Inverse vulcanization of octenyl succinate-modified corn starch as a route to biopolymer–sulfur composites
Authors: Lauer Moira K. , Tennyson Andrew G. , Smith Rhett C.
Published: March 2021

Herein we report a route to sulfur–starch composites by the modification of corn starch with octenyl succinic anhydride (OSA) and its subsequent reaction with elemental sulfur to generate OSSx (where x = wt% sulfur, either 90 or 95).
Environmental investigation of pollutants in coal mine operation and waste dump area monitored in Ordos Region, China
Authors: Li Ang , Chen Changkun , Chen Jie , Lei Peng
Published: March 2021

The increasingly severe emissions of greenhouse and poisonous gases from environmentally unsafe stockpiled coal mine waste dumps have urged people from the academia as well as the industry to focus on environmental impact assessment.
Prolongation of the singlet exciton lifetime of nonfullerene acceptor films by the replacement of the central benzene core with naphthalene
Authors: Umeyama Tomokazu , Igarashi Kensho , Tamai Yasunari , Wada Tatsuho , Takeyama Taiki , Sasada Daiki , Ishida Keiichi , Koganezawa Tomoyuki , Ohtani Shunsuke , Tanaka Kazuo , Ohkita Hideo , Imahori Hiroshi
Published: March 2021

The replacement of benzene with naphthalene in the central core of an acceptor achieved a longer singlet lifetime and a higher power conversion efficiency.
Bacterial activity hinders particle sedimentation
Authors: Singh Jaspreet , Patteson Alison E. , Torres Maldonado Bryan O. , Purohit Prashant K. , Arratia Paulo E.
Published: March 2021

Swimming bacteria significantly reduce the speed of the sedimentation front and increase the dispersion of passive particles even in the dilute regime.
Novel cobalt-doped molybdenum oxynitride quantum dot@N-doped carbon nanosheets with abundant oxygen vacancies for long-life rechargeable zinc–air batteries
Authors: Nguyen Thanh Tuan , Balamurugan Jayaraman , Lau Kin-Tak , Kim Nam Hoon , Lee Joong Hee
Published: March 2021

A novel cobalt-doped molybdenum oxynitride quantum dot@N-doped carbon nanosheets with abundant oxygen vacancies have been established. The optimal VO-CMON@NCN air-cathode achieved tremendous peak power density and ultralong cycle life for 500 h.
Auxiliary ligand-modulated trisimidazole-based coordination polymers: syntheses, structures and photoluminescence properties
Authors: Tseng Tien-Wen , Luo Tzuoo-Tsair , Kan Shou-Ju , Nguyen Doan Duy-An
Published: March 2021

Five coordination polymers having 1,3,5-tris(1-imidazolyl)benzene and the varied O-donor auxiliary ligands were designed and synthesized. Further, the auxiliary ligands modulated these complexes with structural diversities and novel topologies.
Wheat bran fermented by mixed fungal strains improves the digestibility of crude fiber and may benefit the gut health without impacting the growth performance in weaned pigs
Authors: Luo Yuheng , He Jun , Li Hua , Lan Cong , Cai Jingyi , Chen Hong , Tian Gang , Wang Huifen , Wang Quyuan , He Jun , Chen Daiwen , Yu Bing , Huang Zhiqing , Zheng Ping , Mao Xiangbing , Yu Jie , Luo Junqiu , Wu Aimin , Yan Hui
Published: March 2021

This study was conducted to compare the effect of raw (WB) or mixed fungi-fermented wheat bran (FWB) on the growth, nutrient digestibility and intestinal health in weaned piglets.
Nanorod bundle-like silver cyanamide nanocrystals for the high-efficiency photocatalytic degradation of tetracycline
Authors: Li Yulin , Cao Chencong , Zhang Qing , Lu Ying , Zhao Yanxi , Li Qin , Li Xianghong , Huang Tao
Published: March 2021

Ag2NCN nanoparticles with nanorod bundle-like assemblies and a narrower bandgap were synthesized and demonstrated a high photocatalytic activity towards TC degradation.
A novel 3-methylthiophene additive to boost the performance and stability of perovskite solar cells
Authors: Majeed Sadeer M. , Ahmed Duha S. , Mohammed Mustafa K. A.
Published: March 2021

Perovskite solar cells (PSCs) have emerged as a practical candidate for new-generation photovoltaic devices to meet global energy demands.
Carbazole sulfonamide-based macrocyclic receptors capable of selective complexation of fluoride ion
Authors: Luo Na , Li Junhong , Sun Tao , Wan Suran , Li Peijia , Wu Nan , Yan Ya , Bao Xiaoping
Published: March 2021

Two carbazole sulfonamide-based macrocycles 1 and 2 were facilely synthesized and carefully evaluated for their anion recognition properties.
Acyl metalloids: conformity and deviation from carbonyl reactivity
Authors: Holownia Aleksandra , Apte Chirag N. , Yudin Andrei K.
Published: March 2021

Originally considered as fundamental curiosities, acyl metalloids have proven to be useful tools in synthesis. This perspective aims to highlight the modes of reactivity accessible to boron, silicon, germanium and tellurium species.
Highly foldable and flexible films of PEDOT:PSS/Xuan paper composites for thermoelectric applications
Authors: Deng Liang , Zhang Yichuan , Wei Shasha , Lv Haicai , Chen Guangming
Published: March 2021

We report flexible composite films of PEDOT:PSS with Chinese traditional Xuan paper, showing excellent foldability and decent thermoelectric performance.
Responses to Auditory Feedback Manipulations in Speech May Be Affected by Previous Exposure to Auditory Errors
Authors: Niziolek Caroline A. , Parrell Benjamin
Published: March 2021

Purpose

Speakers use auditory feedback to guide their speech output, although individuals differ in the magnitude of their compensatory response to perceived errors in feedback. Little is known about the factors that contribute to the compensatory response or how fixed or flexible they are within an individual. Here, we test whether manipulating the perceived reliability of auditory feedback modulates speakers' compensation to auditory perturbations, as predicted by optimal models of sensorimotor control.

Method

Forty participants produced monosyllabic words in two separate sessions, which differed in the auditory feedback given during an initial exposure phase. In the
veridical
session exposure phase, feedback was normal. In the
noisy
session exposure phase, small, random formant perturbations were applied, reducing reliability of auditory feedback. In each session, a subsequent test phase introduced larger unpredictable formant perturbations. We assessed whether the magnitude of within-trial compensation for these larger perturbations differed across the two sessions.

Results

Compensatory responses to downward (though not upward) formant perturbations were larger in the veridical session than the noisy session. However, in post hoc testing, we found the magnitude of this effect is highly dependent on the choice of analysis procedures. Compensation magnitude was not predicted by other production measures, such as formant variability, and was not reliably correlated across sessions.

Conclusions

Our results, though mixed, provide tentative support that the feedback control system monitors the reliability of sensory feedback. These results must be interpreted cautiously given the potentially limited stability of auditory feedback compensation measures across analysis choices and across sessions.

Supplemental Material

https://doi.org/10.23641/asha.14167136
Performance of Forced-Alignment Algorithms on Children's Speech
Authors: Mahr Tristan J. , Berisha Visar , Kawabata Kan , Liss Julie , Hustad Katherine C.
Published: March 2021

Purpose

Acoustic measurement of speech sounds requires first segmenting the speech signal into relevant units (words, phones, etc.). Manual segmentation is cumbersome and time consuming. Forced-alignment algorithms automate this process by aligning a transcript and a speech sample. We compared the phoneme-level alignment performance of five available forced-alignment algorithms on a corpus of child speech. Our goal was to document aligner performance for child speech researchers.

Method

The child speech sample included 42 children between 3 and 6 years of age. The corpus was force-aligned using the Montreal Forced Aligner with and without speaker adaptive training, triphone alignment from the Kaldi speech recognition engine, the Prosodylab-Aligner, and the Penn Phonetics Lab Forced Aligner. The sample was also manually aligned to create gold-standard alignments. We evaluated alignment algorithms in terms of accuracy (whether the interval covers the midpoint of the manual alignment) and difference in phone-onset times between the automatic and manual intervals.

Results

The Montreal Forced Aligner with speaker adaptive training showed the highest accuracy and smallest timing differences. Vowels were consistently the most accurately aligned class of sounds across all the aligners, and alignment accuracy increased with age for fricative sounds across the aligners too.

Conclusion

The best-performing aligner fell just short of human-level reliability for forced alignment. Researchers can use forced alignment with child speech for certain classes of sounds (vowels, fricatives for older children), especially as part of a semi-automated workflow where alignments are later inspected for gross errors.

Supplemental Material

https://doi.org/10.23641/asha.14167058
Short-Term Test–Retest Reliability of Contralateral Suppression of Click-Evoked Otoacoustic Emissions in Normal-Hearing Subjects
Authors: Keppler Hannah , Degeest Sofie , Vinck Bart
Published: March 2021

Purpose

The objective of the current study was to investigate the short-term test–retest reliability of contralateral suppression (CS) of click-evoked otoacoustic emissions (CEOAEs) using commercially available otoacoustic emission equipment.

Method

Twenty-three young normal-hearing subjects were tested. An otoscopic evaluation, admittance measures, pure-tone audiometry, measurements of CEOAEs without and with contralateral acoustic stimulation (CAS) to determine CS were performed at baseline (n= 23), an immediate retest without and with refitting of the probe (only CS of CEOAEs;n= 11), and a retest after 1 week (n= 23) were performed. Test–retest reliability parameters were determined on CEOAE response amplitudes without and with CAS, and on raw and normalized CS indices between baseline and the other test moments.

Results

Repeated-measures analysis of variance indicated no random or systematic changes in CEOAE response amplitudes without and with CAS, and in raw and normalized CS indices between the test moments. Moderate-to-high intraclass correlation coefficients with mostly high significant between-subjects variability between baseline and each consecutive test moment were found for CEOAE response amplitude without and with CAS, and for the raw and normalized CS indices. Other reliability parameters deteriorated between CEOAE response amplitudes with CAS as compared to without CAS, between baseline and retest with probe refitting, and after 1 week, as well as for frequency-specific raw and normalized CS indices as compared to global CS indices.

Conclusions

There was considerable variability in raw and normalized CS indices as measured using CEOAEs with CAS using commercially available otoacoustic emission equipment. More research is needed to optimize the measurement of CS of CEOAEs and to reduce influencing factors, as well as to make generalization of test–retest reliability data possible.
A time‐sensitive networking‐enabled synchronized three‐phase and phasor measurement‐based monitoring system for microgrids
Authors: Agarwal Tanushree , Niknejad Payam , Rahmani Fatemeh , Barzegaran Mohammadreza , Vanfretti Luigi
Published: March 2021

This paper presents the design and implementation of a Time‐Sensitive Networking (TSN) protocol‐enabled synchronized measurement‐based monitoring system for microgrids. The proposed approach synchronizes and prioritizes the communication nodes, allowing it to transfer ultra‐high three‐phase sampled data and phasors. TSN is achieved by Quality of Service (QoS) profile software library. This allows control, monitoring, traffic scheduling, and prioritization. Some buses in a microgrid may have priority over others; and this can be prioritized at the data level too, where a part of the information is more critical than the others. The advantages of utilizing the TSN protocol on a microgrid with the approach proposed are: it is an alternative to GPS technology, three‐phase data can be exchanged at much faster rate and data traffic in the network can be shaped with low packet loss, and low latency, in addition to providing interoperability through Data Distribution Services (DDS). These enhancements improve the communication reliability and enable distributed control, resulting in avoidance of any bottlenecks in the communications network. This proposed approach is implemented and demonstrated in a laboratory‐scale microgrid. The results obtained, verify low latency and high throughput of the entire system while meeting the TSN and QoS requirements.