bluuebunny/crossref_metadata_2025 huggingface dataset:
The Vertical Extent of Enhanced Densities in Cusp‐Like Regions of the Ionosphere of Mars
Authors: Golden‐Marx E. , Withers P. , Kopf A. J.
Published: May 2021

Unusually large values of peak electron density in the ionosphere of Mars are occasionally observed in cusp‐like regions of crustal magnetic field. These features are observed as atypical examples of oblique echoes in ionograms. However, the vertical extent over which electron density values are enhanced has not yet been determined. Furthermore, the physical processes responsible for these striking features are not yet understood. Here we analyze ionograms from the Mars Advanced Radar for Subsurface and Ionosphere Sounding (MARSIS) instrument on Mars Express to better constrain the spatial distribution of electron density in and around these rare ionospheric features. Data from orbits 2359, 2491, 4469, and 4513 are examined. When peak electron density is unusually large, electron density values from the peak to 165 km are increased by 30% ± 10% and the electron density at the spacecraft (∼300–400 km) is diminished. We investigate whether the central portion of an oblique echo is equivalent to a nadir echo, which would permit the reliable determination of an electron density profile in instances of unusually large peak electron densities. We find that uncertainties in the location of the center of an oblique echo render this approach unfeasible. We also report that 86.5 μs should be subtracted from travel time values reported in current MARSIS data products released prior to 2019.
Graph‐Space Optimal Transport Concept for Time‐Domain Full‐Waveform Inversion of Ocean‐Bottom Seismometer Data: Nankai Trough Velocity Structure Reconstructed From a 1D Model
Authors: Górszczyk Andrzej , Brossier Romain , Métivier Ludovic
Published: May 2021

Detailed reconstruction of deep structures with full‐waveform inversion (FWI) of wide‐angle ocean‐bottom seismometer (OBS) data remains challenging and unconventional. The complexity of the long‐offset waveforms increases the nonlinearity of the inverse problem, while the sparsity of the OBS deployments leads to a poorly constrained model reconstruction. Consequently, for such a FWI setting it is difficult to derive an initial model that satisfies the cycle‐skipping criterion. Searching for a remedy to this issue, we investigate the graph‐space optimal transport (GSOT) technique, which can potentially overcome the cycle‐skipping problem at the initial FWI stage. The key feature of the GSOT cost function is the convexity with respect to the patterns in the two seismograms, which allows for correct matching of the arrivals shifted in time for more than half of the wavelet. This in turn shall allow FWI to handle the large kinematic errors of the starting model. We test this hypothesis by applying the time‐domain acoustic FWI to the synthetic and field data from the subduction zone environment. We show that despite the complexity of the geological structure, the GSOT misfit function is able to guide the FWI toward the precise velocity model reconstruction and data fitting starting from a simple 1D model. The improved convexity of the GSOT misfit function allows FWI to converge even when mismatches between the observed and synthetic signals reach a few cycles. This ability reduces the constraint on the kinematic accuracy of the initial model and makes the FWI from the OBS data more feasible.
Contribution of Biological Effects to Carbonate‐System Variations and the Air–Water CO2 Flux in Urbanized Bays in Japan
Authors: Tokoro Tatsuki , Nakaoka Shin‐ichiro , Takao Shintaro , Kuwae Tomohiro , Kubo Atsushi , Endo Toru , Nojiri Yukihiro
Published: May 2021

We evaluated the contribution of net biological effects (photosynthesis + respiration + decomposition) to the carbonate parameters and air–water CO2 fluxes in Tokyo Bay, Ise Bay, and Osaka Bay in Japan. The carbonate parameters (fugacity of CO2, total alkalinity, and dissolved inorganic carbon) were measured mainly by cargo ships traveling between Japan and other countries. We used the measurement data from three inner bays and surrounding outer bays in Japan along with reference data from previous studies for complementary analysis. We found that (a) the inner and outer bays in this study were strong annual atmospheric CO2 sinks, (b) the annual biological effect on the air–water CO2 fluxes was about 6%–27% of the measured CO2 fluxes, and it affected the seasonal variation of the CO2 flux, and (c) the biological effect was largest in Tokyo Bay, and almost the same in Ise and Osaka Bays. The intensity of the biological effect corresponded mainly with nutrient concentrations, which seemed to be controlled by the wastewater treatment in urbanized areas around the bays. Our results suggest that labile carbon/nutrient ratio of wastewater should be a major consideration for evaluating the biological effect on the carbon cycle in urbanized bays, which will continue to expand globally.
A Shift in the Wind Regime of the Southern End of the Canary Upwelling System at the Turn of the 20th Century
Authors: Gallego D. , García‐Herrera R. , Losada T. , Mohino E. , Rodríguez de Fonseca B.
Published: May 2021

In this study, we make use of historical wind direction observations to assemble an instrumental upwelling index (DUI) at the southern end of the Canary Current Upwelling System. The DUI covers the period between 1825 and 2014 and, unlike other upwelling indices, it does not rely neither in wind speed nor in reanalyzed data. In this sense, the DUI can be regarded as an instrumental index. Additionally, it avoids the suspected bias toward increasing wind speed of historical wind observations documented in previous research. Our results indicate that the frequency of the alongshore winds at the west coast of Africa between 10°N and 20°N measured by the DUI is significantly related with the wind stress and therefore the upwelling intensity in this region. The DUI presents a significant variability both at interannual and decadal timescales. We have not found any significant trend for the 20th century. However, when the entire length of the series is considered, a large shift toward more frequent alongshore winds is evidenced as a result of several decade‐long fluctuations which took place between the late 19th century and the beginning of the 20th century. This fact would imply that a significant change in the upwelling intensity at the southern end of the Canary Current Upwelling System should have occurred at the turn of the 20th century.
South Pole Ice Core Reveals History of Antarctic Sea Ice
Authors: Thompson Elizabeth
Published: May 2021

Every summer, most of the sea ice near Antarctica melts away, but its saltiness leaves a permanent record that scientists can trace back for millennia.
A novel dual HDAC and HSP90 inhibitor, MPT0G449, downregulates oncogenic pathways in human acute leukemia in vitro and in vivo
Authors: Wu Yi-Wen , Chao Min-Wu , Tu Huang-Ju , Chen Liang-Chieh , Hsu Kai-Cheng , Liou Jing-Ping , Yang Chia-Ron , Yen Shih-Chung , HuangFu Wei-Chun , Pan Shiow-Lin
Published: May 2021

Acute leukemia is a highly heterogeneous disease; therefore, combination therapy is commonly used for patient treatment. Drug–drug interaction is a major concern of combined therapy; hence, dual/multi-target inhibitors have become a dominant approach for cancer drug development. HDACs and HSP90 are involved in the activation of various oncogenic signaling pathways, including PI3K/AKT/mTOR, JAK/STAT, and RAF/MEK/ERK, which are also highly enriched in acute leukemia gene expression profiles. Therefore, we suggest that dual HDAC and HSP90 inhibitors could represent a novel therapeutic approach for acute leukemia. MPT0G449 is a dual effect inhibitor, and it showed cytotoxic effectiveness in acute leukemia cells. Molecular docking analysis indicated that MPT0G449 possessed dual HDAC and HSP90 inhibitory abilities. Furthermore, MPT0G449 induced G2 arrest and caspase-mediated cell apoptosis in acute leukemia cells. The oncogenic signaling molecules AKT, mTOR, STAT3, STAT5, MEK, and ERK were significantly downregulated after MPT0G449 treatment in HL-60 and MOLT-4 cells. In vivo xenograft models confirmed the antitumor activity and showed the upregulation of acetyl-histone H3 and HSP70, biomarkers of pan-HDAC and HSP90 inhibition, with MPT0G449 treatment. These findings suggest that the dual inhibition of HDAC and HSP90 can suppress the expression of oncogenic pathways in acute leukemia, and MPT0G449 represents a novel therapeutic for anticancer treatment.
Dichotomy in temporal and thermal spin correlations observed in the breathing pyrochlore LiGa1−xInxCr4O8
Authors: Lee S. , Do S.-H. , Lee W. , Choi Y. S. , van Tol J. , Reyes A. P. , Gorbunov D. , Chen W.-T. , Choi K.-Y.
Published: May 2021

A breathing pyrochlore system is predicted to host a variety of quantum spin liquids. Despite tremendous experimental and theoretical efforts, such sought-after states remain elusive as perturbation terms and lattice distortions lead to magnetic order. Here, we utilize bond alternation and disorder to tune a magnetic ground state in the Cr-based breathing pyrochlore LiGa1−xInxCr4O8. By combining thermodynamic and magnetic resonance techniques, we provide experimental signatures of a spin-liquid-like state in x = 0.8, namely, a nearly T2-dependent magnetic specific heat and persistent spin dynamics by muon spin relaxation (μSR). Moreover, 7Li NMR, ZF-μSR, and ESR unveil the temporal and thermal dichotomy of spin correlations: a tetramer singlet on a slow time scale vs. a spin-liquid-like state on a fast time scale. Our results showcase that a bond disorder in the breathing pyrochlore offers a promising route to disclose exotic magnetic phases.
Distinct roles of tumor associated mutations in collective cell migration
Authors: Lee Rachel M. , Vitolo Michele I. , Losert Wolfgang , Martin Stuart S.
Published: May 2021

Recent evidence suggests that groups of cells are more likely to form clinically dangerous metastatic tumors, emphasizing the importance of understanding mechanisms underlying collective behavior. The emergent collective behavior of migrating cell sheets in vitro has been shown to be disrupted in tumorigenic cells but the connection between this behavior and in vivo tumorigenicity remains unclear. We use particle image velocimetry to measure a multidimensional migration phenotype for genetically defined human breast epithelial cell lines that range in their in vivo behavior from non-tumorigenic to aggressively metastatic. By using cells with controlled mutations, we show that PTEN deletion enhances collective migration, while Ras activation suppresses it, even when combined with PTEN deletion. These opposing effects on collective migration of two mutations that are frequently found in patient tumors could be exploited in the development of novel treatments for metastatic disease. Our methods are based on label-free phase contrast imaging, and thus could easily be applied to patient tumor cells. The short time scales of our approach do not require potentially selective growth, and thus in combination with label-free imaging would allow multidimensional collective migration phenotypes to be utilized in clinical assessments of metastatic potential.
Wild Bornean orangutans experience muscle catabolism during episodes of fruit scarcity
Authors: O’Connell Caitlin A. , DiGiorgio Andrea L. , Ugarte Alexa D. , Brittain Rebecca S. A. , Naumenko Daniel J. , Utami Atmoko Sri Suci , Vogel Erin R.
Published: May 2021

Pronounced temporal and spatial variation in the availability of food resources can produce energetic deficits in organisms. Fruit-dependent Bornean orangutans face extreme variation in fruit availability and experience negative energy and protein balance during episodes of fruit scarcity. We evaluate the possibility that orangutans of different sexes and ages catabolize muscle tissue when the availability of fruit is low. We assess variation in muscle mass by examining the relationship between urinary creatinine and specific gravity and use the residuals as a non-invasive measure of estimated lean body mass (ELBM). Despite orangutans having a suite of adaptations to buffer them from fruit scarcity and associated caloric deficits, ELBM was lower during low fruit periods in all age-sex classes. As predicted, adult male orangutans had higher ELBM than adult females and immatures. Contrary to expectation, flanged and unflanged males did not differ significantly in ELBM. These findings highlight the precarity of orangutan health in the face of rapid environmental change and add to a growing body of evidence that orangutans are characterized by unique metabolic traits shaped by their unpredictable forest environment.
DOM degradation by light and microbes along the Yukon River-coastal ocean continuum
Authors: Grunert Brice K. , Tzortziou Maria , Neale Patrick , Menendez Alana , Hernes Peter
Published: May 2021

The Arctic is experiencing rapid warming, resulting in fundamental shifts in hydrologic connectivity and carbon cycling. Dissolved organic matter (DOM) is a significant component of the Arctic and global carbon cycle, and significant perturbations to DOM cycling are expected with Arctic warming. The impact of photochemical and microbial degradation, and their interactive effects, on DOM composition and remineralization have been documented in Arctic soils and rivers. However, the role of microbes, sunlight and their interactions on Arctic DOM alteration and remineralization in the coastal ocean has not been considered, particularly during the spring freshet when DOM loads are high, photoexposure can be quite limited and residence time within river networks is low. Here, we collected DOM samples along a salinity gradient in the Yukon River delta, plume and coastal ocean during peak river discharge immediately after spring freshet and explored the role of UV exposure, microbial transformations and interactive effects on DOM quantity and composition. Our results show: (1) photochemical alteration of DOM significantly shifts processing pathways of terrestrial DOM, including increasing relative humification of DOM by microbes by > 10%; (2) microbes produce humic-like material that is not optically distinguishable from terrestrial humics; and (3) size-fractionation of the microbial community indicates a size-dependent role for DOM remineralization and humification of DOM observed through modeled PARAFAC components of fluorescent DOM, either through direct or community effects. Field observations indicate apparent conservative mixing along the salinity gradient; however, changing photochemical and microbial alteration of DOM with increasing salinity indicate changing DOM composition likely due to microbial activity. Finally, our findings show potential for rapid transformation of DOM in the coastal ocean from photochemical and microbial alteration, with microbes responsible for the majority of dissolved organic matter remineralization.
Distribution of estimated glomerular filtration rate and determinants of its age dependent loss in a German population-based study
Authors: Waas Thomas , Schulz Andreas , Lotz Johannes , Rossmann Heidi , Pfeiffer Norbert , Beutel Manfred E. , Schmidtmann Irene , Münzel Thomas , Wild Philipp S. , Lackner Karl J.
Published: May 2021

Glomerular filtration rate (GFR) declines with age by approx. 1 ml/min/m2 per year beginning in the third decade of life. At 70 years of age > 40 ml/min/m2 of GFR will be lost. Thus, factors affecting loss of GFR have significant public health implications. Furthermore, the definition of chronic kidney disease based on GFR may not be appropriate for the elderly. We analyzed factors affecting absolute and relative change of eGFR over a 5 year period in 12,381 participants of the Gutenberg Health Study. We estimated GFR at baseline and after 5 years of follow-up by two different equations. Association with the decline of estimated GFR (eGFR) was assessed by multivariable regression analysis. We confirmed a median loss of eGFR per year of approx. 1 ml/min/m2. Aside from albuminuria systolic blood pressure was most strongly associated with faster decline of eGFR followed by echocardiographic evidence of left ventricular diastolic dysfunction and reduced ejection fraction. White blood cell count showed a moderate association with eGFR loss. Diastolic blood pressure, serum uric acid and serum albumin were associated with slower GFR decline in multivariable analysis. Sensitivity analysis with exclusion of individuals taking diuretics, antihypertensive, antidiabetic, or lipid lowering drugs confirmed these associations.
A predictive in vitro risk assessment platform for pro-arrhythmic toxicity using human 3D cardiac microtissues
Authors: Kofron Celinda M. , Kim Tae Yun , Munarin Fabiola , Soepriatna Arvin H. , Kant Rajeev J. , Mende Ulrike , Choi Bum-Rak , Coulombe Kareen L. K.
Published: May 2021

Cardiotoxicity of pharmaceutical drugs, industrial chemicals, and environmental toxicants can be severe, even life threatening, which necessitates a thorough evaluation of the human response to chemical compounds. Predicting risks for arrhythmia and sudden cardiac death accurately is critical for defining safety profiles. Currently available approaches have limitations including a focus on single select ion channels, the use of non-human species in vitro and in vivo, and limited direct physiological translation. We have advanced the robustness and reproducibility of in vitro platforms for assessing pro-arrhythmic cardiotoxicity using human induced pluripotent stem cell-derived cardiomyocytes and human cardiac fibroblasts in 3-dimensional microtissues. Using automated algorithms and statistical analyses of eight comprehensive evaluation metrics of cardiac action potentials, we demonstrate that tissue-engineered human cardiac microtissues respond appropriately to physiological stimuli and effectively differentiate between high-risk and low-risk compounds exhibiting blockade of the hERG channel (E4031 and ranolazine, respectively). Further, we show that the environmental endocrine disrupting chemical bisphenol-A (BPA) causes acute and sensitive disruption of human action potentials in the nanomolar range. Thus, this novel human 3D in vitro pro-arrhythmic risk assessment platform addresses critical needs in cardiotoxicity testing for both environmental and pharmaceutical compounds and can be leveraged to establish safe human exposure levels.
Spiral sound-diffusing metasurfaces based on holographic vortices
Authors: Jiménez Noé , Groby Jean-Philippe , Romero-García Vicent
Published: May 2021

In this work, we show that scattered acoustic vortices generated by metasurfaces with chiral symmetry present broadband unusual properties in the far-field. These metasurfaces are designed to encode the holographic field of an acoustical vortex, resulting in structures with spiral geometry. In the near field, phase dislocations with tuned topological charge emerge when the scattered waves interference destructively along the axis of the spiral metasurface. In the far field, metasurfaces based on holographic vortices inhibit specular reflections because all scattered waves also interfere destructively in the normal direction. In addition, the scattering function in the far field is unusually uniform because the reflected waves diverge spherically from the holographic focal point. In this way, by triggering vorticity, energy can be evenly reflected in all directions except to the normal. As a consequence, the designed metasurface presents a mean correlation-scattering coefficient of 0.99 (0.98 in experiments) and a mean normalized diffusion coefficient of 0.73 (0.76 in experiments) over a 4 octave frequency band. The singular features of the resulting metasurfaces with chiral geometry allow the simultaneous generation of broadband, diffuse and non-specular scattering. These three exceptional features make spiral metasurfaces extraordinary candidates for controlling acoustic scattering and generating diffuse sound reflections in several applications and branches of wave physics as underwater acoustics, biomedical ultrasound, particle manipulation devices or room acoustics.
Screening of core filter layer for the development of respiratory mask to combat COVID-19
Authors: Pandey Lokesh K. , Singh Virendra V. , Sharma Pushpendra K. , Meher Damayanti , Biswas Utpal , Sathe Manisha , Ganesan Kumaran , Thakare Vikas B. , Agarwal Kavita
Published: May 2021

The severe outbreak of respiratory coronavirus disease 2019 has increased the significant demand of respiratory mask and its use become ubiquitous worldwide to control this unprecedented respiratory pandemic. The performance of a respiratory mask depends on the efficiency of the filter layer which is mostly made of polypropylene melt blown non-woven (PP-MB-NW). So far, very limited characterization data are available for the PPE-MB-NW in terms to achieve desired particulate filtration efficiency (PFE) against 0.3 µm size, which are imperative in order to facilitate the right selection of PP-MB-NW fabric for the development of mask. In present study, eight different kinds of PP-MB-NW fabrics (Sample A–H) of varied structural morphology are chosen. The different PP-MB-NW were characterized for its pore size and distribution by mercury porosimeter and BET surface area analyzer was explored first time to understand the importance of blind pore in PFE. The PP-MB-NW samples were characterized using scanning electron microscopy so as to know the surface morphology. The filtration efficiency, pressure drop and breathing resistance of various PP-MB-NW fabric samples are investigated in single and double layers combination against the particle size of 0.3, 0.5 and 1 µm. The samples which are having low pore dia, high solid fraction volume, and low air permeability has high filtration efficiency (> 90%) against 0.3 µm particle with high pressure drop (16.3–21.3 mm WC) and breathing resistance (1.42–1.92 mbar) when compared to rest of the samples. This study will pave the way for the judicial selection of right kind of filter layer i.e., PP-MB-NW fabric for the development of mask and it will be greatly helpful in manufacturing of mask in this present pandemic with desired PFE indicating considerable promise for defense against respiratory pandemic.
Kernel machine SNP set analysis finds the association of BUD13, ZPR1, and APOA5 variants with metabolic syndrome in Tehran Cardio-metabolic Genetics Study
Authors: Masjoudi Sajedeh , Sedaghati-khayat Bahareh , Givi Niloufar Javanrouh , Bonab Leila Najd Hassan , Azizi Fereidoun , Daneshpour Maryam S.
Published: May 2021

Metabolic syndrome (MetS) is one of the most important risk factors for cardiovascular disease. The 11p23.3 chromosomal region plays a potential role in the pathogenesis of MetS. The present study aimed to assess the association between 18 single nucleotide polymorphisms (SNPs) located at the BUD13, ZPR1, and APOA5 genes with MetS in the Tehran Cardio-metabolic Genetics Study (TCGS). In 5421 MetS affected and non-affected participants, we analyzed the data using two models. The first model (MetS model) examined SNPs' association with MetS. The second model (HTg-MetS Model) examined the association of SNPs with MetS affection participants who had a high plasma triglyceride (TG). The four-gamete rules were used to make SNP sets from correlated nearby SNPs. The kernel machine regression models and single SNP regression evaluated the association between SNP sets and MetS. The kernel machine results showed two sets over three sets of correlated SNPs have a significant joint effect on both models (p < 0.0001). Also, single SNP regression results showed that the odds ratios (ORs) for both models are almost similar; however, the p-values had slightly higher significance levels in the HTg-MetS model. The strongest ORs in the HTg-MetS model belonged to the G allele in rs2266788 (MetS: OR = 1.3, p = 3.6 × 10–7; HTg-MetS: OR = 1.4, p = 2.3 × 10–11) and the T allele in rs651821 (MetS: OR = 1.3, p = 2.8 × 10–7; HTg-MetS: OR = 1.4, p = 3.6 × 10–11). In the present study, the kernel machine regression models could help assess the association between the BUD13, ZPR1, and APOA5 gene variants (11p23.3 region) with lipid-related traits in MetS and MetS affected with high TG.
Prediction of functional outcomes of schizophrenia with genetic biomarkers using a bagging ensemble machine learning method with feature selection
Authors: Lin Eugene , Lin Chieh-Hsin , Lane Hsien-Yuan
Published: May 2021

Genetic variants such as single nucleotide polymorphisms (SNPs) have been suggested as potential molecular biomarkers to predict the functional outcome of psychiatric disorders. To assess the schizophrenia’ functional outcomes such as Quality of Life Scale (QLS) and the Global Assessment of Functioning (GAF), we leveraged a bagging ensemble machine learning method with a feature selection algorithm resulting from the analysis of 11 SNPs (AKT1rs1130233,COMTrs4680,DISC1rs821616,DRD3rs6280,G72rs1421292,G72rs2391191,5-HT2Ars6311,METrs2237717,METrs41735,METrs42336, andTPH2rs4570625) of 302 schizophrenia patients in the Taiwanese population. We compared our bagging ensemble machine learning algorithm with other state-of-the-art models such as linear regression, support vector machine, multilayer feedforward neural networks, and random forests. The analysis reported that the bagging ensemble algorithm with feature selection outperformed other predictive algorithms to forecast the QLS functional outcome of schizophrenia by using theG72rs2391191 andMETrs2237717 SNPs. Furthermore, the bagging ensemble algorithm with feature selection surpassed other predictive algorithms to forecast the GAF functional outcome of schizophrenia by using theAKT1rs1130233 SNP. The study suggests that the bagging ensemble machine learning algorithm with feature selection might present an applicable approach to provide software tools for forecasting the functional outcomes of schizophrenia using molecular biomarkers.
A retrospective cohort study of 12,306 pediatric COVID-19 patients in the United States
Authors: Parcha Vibhu , Booker Katherine S. , Kalra Rajat , Kuranz Seth , Berra Lorenzo , Arora Garima , Arora Pankaj
Published: May 2021

Children and adolescents account for ~ 13% of total COVID-19 cases in the United States. However, little is known about the nature of the illness in children. The reopening of schools underlines the importance of understanding the epidemiology of pediatric COVID-19 infections. We sought to assess the clinical characteristics and outcomes in pediatric COVID-19 patients. We conducted a retrospective cross-sectional analysis of pediatric patients diagnosed with COVID-19 from healthcare organizations in the United States. The study outcomes (hospitalization, mechanical ventilation, critical care) were assessed using logistic regression. The subgroups of sex and race were compared after propensity score matching. Among 12,306 children with lab-confirmed COVID-19, 16.5% presented with respiratory symptoms (cough, dyspnea), 13.9% had gastrointestinal symptoms (nausea, vomiting, diarrhea, abdominal pain), 8.1% had dermatological symptoms (rash), 4.8% had neurological (headache), and 18.8% had other non-specific symptoms (fever, malaise, myalgia, arthralgia and disturbances of smell or taste). In the study cohort, the hospitalization frequency was 5.3%, with 17.6% needing critical care services and 4.1% requiring mechanical ventilation. Following propensity score matching, the risk of all outcomes was similar between males and females. Following propensity score matching, the risk of hospitalization was greater in non-Hispanic Black (RR 1.97 [95% CI 1.49–2.61]) and Hispanic children (RR 1.31 [95% CI 1.03–1.78]) compared with non-Hispanic Whites. In the pediatric population infected with COVID-19, a substantial proportion were hospitalized due to the illness and developed adverse clinical outcomes.
Functional regulation of an outer retina hyporeflective band on optical coherence tomography images
Authors: Gao Shasha , Li Yichao , Bissig David , Cohen Ethan D. , Podolsky Robert H. , Childers Karen Lins , Vernon Gregory , Chen Sonia , Berkowitz Bruce A. , Qian Haohua
Published: May 2021

Human and animal retinal optical coherence tomography (OCT) images show a hyporeflective band (HB) between the photoreceptor tip and retinal pigment epithelium layers whose mechanisms are unclear. In mice, HB magnitude and the external limiting membrane-retinal pigment epithelium (ELM-RPE) thickness appear to be dependent on light exposure, which is known to alter photoreceptor mitochondria respiration. Here, we test the hypothesis that these two OCT biomarkers are linked to metabolic activity of the retina. Acetazolamide, which acidifies the subretinal space, had no significant impact on HB magnitude but produced ELM-RPE thinning. Mitochondrial stimulation with 2,4-dinitrophenol reduced both HB magnitude and ELM-RPE thickness in parallel, and also reduced F-actin expression in the same retinal region, but without altering ERG responses. For mice strains with relatively lower (C57BL/6J) or higher (129S6/ev) rod mitochondrial efficacy, light-induced changes in HB magnitude and ELM-RPE thickness were correlated. Humans, analyzed from published data captured with a different protocol, showed a similar light–dark change pattern in HB magnitude as in the mice. Our results indicate that mitochondrial respiration underlies changes in HB magnitude upstream of the pH-sensitive ELM-RPE thickness response. These two distinct OCT biomarkers could be useful indices for non-invasively evaluating photoreceptor mitochondrial metabolic activity.
Transcriptome profiling of Capsicum annuum using Illumina- and PacBio SMRT-based RNA-Seq for in-depth understanding of genes involved in trichome formation
Authors: Gao Shenghua , Li Ning , Niran Juntawong , Wang Fei , Yin Yanxu , Yu Chuying , Jiao Chunhai , Yang Changxian , Yao Minghua
Published: May 2021

Trichomes, specialized epidermal cells located in aerial parts of plants, play indispensable roles in resisting abiotic and biotic stresses. However, the regulatory genes essential for multicellular trichrome development in Capsicum annuum L. (pepper) remain unclear. In this study, the transcript profiles of peppers GZZY-23 (hairy) and PI246331 (hairless) were investigated to gain insights into the genes responsible for the formation of multicellular trichomes. A total of 40,079 genes, including 4743 novel genes and 13,568 differentially expressed genes (DEGs), were obtained. Functional enrichment analysis revealed that the most noticeable pathways were transcription factor activity, sequence-specific DNA binding, and plant hormone signal transduction, which might be critical for multicellular trichome formation in hairy plants. We screened 11 DEGs related to trichome development; 151 DEGs involved in plant hormone signal transduction; 312 DEGs belonging to the MYB, bHLH, HD-Zip, and zinc finger transcription factor families; and 1629 DEGs predicted as plant resistance genes (PRGs). Most of these DEGs were highly expressed in GZZY-23 or trichomes. Several homologs of trichome regulators, such as SlCycB2, SlCycB3, and H, were considerably upregulated in GZZY-23, especially in the trichomes. The transcriptomic data generated in this study provide a basis for future characterization of trichome formation in pepper.
Detecting the pulmonary trunk in CT scout views using deep learning
Authors: Demircioğlu Aydin , Stein Magdalena Charis , Kim Moon-Sung , Geske Henrike , Quinsten Anton S. , Blex Sebastian , Umutlu Lale , Nassenstein Kai
Published: May 2021

For CT pulmonary angiograms, a scout view obtained in anterior–posterior projection is usually used for planning. For bolus tracking the radiographer manually locates a position in the CT scout view where the pulmonary trunk will be visible in an axial CT pre-scan. We automate the task of localizing the pulmonary trunk in CT scout views by deep learning methods. In 620 eligible CT scout views of 563 patients between March 2003 and February 2020 the region of the pulmonary trunk as well as an optimal slice (“reference standard”) for bolus tracking, in which the pulmonary trunk was clearly visible, was annotated and used to train a U-Net predicting the region of the pulmonary trunk in the CT scout view. The networks’ performance was subsequently evaluated on 239 CT scout views from 213 patients and was compared with the annotations of three radiographers. The network was able to localize the region of the pulmonary trunk with high accuracy, yielding an accuracy of 97.5% of localizing a slice in the region of the pulmonary trunk on the validation cohort. On average, the selected position had a distance of 5.3 mm from the reference standard. Compared to radiographers, using a non-inferiority test (one-sided, paired Wilcoxon rank-sum test) the network performed as well as each radiographer (P < 0.001 in all cases). Automated localization of the region of the pulmonary trunk in CT scout views is possible with high accuracy and is non-inferior to three radiographers.
The features of the coastal fronts in the Eastern Guangdong coastal waters during the downwelling-favorable wind period
Authors: Yang Chaoyu , Ye Haibin
Published: May 2021

A coastal front was detected in the eastern Guangdong (EGD) coastal waters during a downwelling-favorable wind period by using the diffuse attenuation coefficient at 490 nm (Kd(490)). Long-term satellite data, meteorological data and hydrographic data collected from 2003 to 2017 were jointly utilized to analyze the environmental factors affecting coastal fronts. The intensities of the coastal fronts were found to be associated with the downwelling intensity. The monthly mean Kd(490) anomalies in shallow coastal waters less than 25 m deep along the EGD coast and the monthly mean Ekman pumping velocities retrieved by the ERA5 dataset were negatively correlated, with a Pearson correlation of − 0.71. The fronts started in October, became weaker and gradually disappeared after January, extending southwestward from the southeastern coast of Guangdong Province to the Wanshan Archipelago in the South China Sea (SCS). The cross-frontal differences in the mean Kd(490) values could reach 3.7 m−1. Noticeable peaks were found in the meridional distribution of the mean Kd(490) values at 22.5°N and 22.2°N and in the zonal distribution of the mean Kd(490) values at 114.7°E and 114.4°E. The peaks tended to narrow as the latitude increased. The average coastal surface currents obtained from the global Hybrid Coordinate Ocean Model (HYCOM) showed that waters with high nutrient and sediment contents in the Fujian and Zhejiang coastal areas in the southern part of the East China Sea could flow into the SCS. The directions and lengths of the fronts were found to be associated with the flow advection.
Different land-use types equally impoverish but differentially preserve grassland species and functional traits of spider assemblages
Authors: Pinto Carolina M. , Pairo Pamela E. , Bellocq M. Isabel , Filloy Julieta
Published: May 2021

Land-use change is one of the major drivers of biodiversity loss by introducing environmental modifications, which excludes native species unable to adapt to the novel conditions. Grasslands are among the most threatened biomes; understanding the influence of different land-use types on native species is crucial to achieving sustainable management policies. We hypothesized that land-use types that partially conserve the original vegetation cover would show higher taxonomic and functional diversity and similarity with native assemblages than land-use types that replace the original vegetation cover. We compared the taxonomic and functional alpha and beta diversity of spider assemblages between soybean crops, eucalypt plantations, and cattle fields with seminatural grasslands. Through null models, we assessed the standardized effect sizes to test differences in the strength of environmental filtering among land-use types. Environmental changes introduced by different land-use types resulted in assemblages differentiated in species and trait composition, taxonomically and functionally impoverished with respect to seminatural grasslands. All land-use types drove species replacement and trait loss and replacement of grassland spiders. Each land-use showed a characteristic species and trait composition. Most of the grassland traits were not lost but were under or over-represented according to the land-use type. Only in soybean crops the formation of spider communities would be mainly driven by environmental filtering. Changes in land-use decreased species diversity and modified the composition of spider species and functional traits leading to differentiated spider assemblages. As spider species and traits varied among land-uses, a mitigation measure against grasslands biodiversity loss could be the development of productive landscapes with a mosaic of land-use types, as each of them would provide microhabitats for species with different requirements. Because land-use types mainly led to the rearrangement of grassland functional trait values, most of spider functions might be conserved in mosaics of land-use types.
Survey of electron density changes in the daytime ionosphere over the Arecibo Observatory due to lightning and solar flares
Authors: da Silva Caitano L. , Salazar Sophia D. , Brum Christiano G. M. , Terra Pedrina
Published: May 2021

Optical observations of transient luminous events and remote-sensing of the lower ionosphere with low-frequency radio waves have demonstrated that thunderstorms and lightning can have substantial impacts in the nighttime ionospheric D region. However, it remains a challenge to quantify such effects in the daytime lower ionosphere. The wealth of electron density data acquired over the years by the Arecibo Observatory incoherent scatter radar (ISR) with high vertical spatial resolution (300-m in the present study), combined with its tropical location in a region of high lightning activity, indicate a potentially transformative pathway to address this issue. Through a systematic survey, we show that daytime sudden electron density changes registered by Arecibo’s ISR during thunderstorm times are on average different than the ones happening during fair weather conditions (driven by other external factors). These changes typically correspond to electron density depletions in the D and E region. The survey also shows that these disturbances are different than the ones associated with solar flares, which tend to have longer duration and most often correspond to an increase in the local electron density content.
An open-source semi-automated robotics pipeline for embryo immunohistochemistry
Authors: Fuqua Timothy , Jordan Jeff , Halavatyi Aliaksandr , Tischer Christian , Richter Kerstin , Crocker Justin
Published: May 2021

A significant challenge for developmental systems biology is balancing throughput with controlled conditions that minimize experimental artifacts. Large-scale developmental screens such as unbiased mutagenesis surveys have been limited in their applicability to embryonic systems, as the technologies for quantifying precise expression patterns in whole animals has not kept pace with other sequencing-based technologies. Here, we outline an open-source semi-automated pipeline to chemically fixate, stain, and 3D-image Drosophila embryos. Central to this pipeline is a liquid handling robot, Flyspresso, which automates the steps of classical embryo fixation and staining. We provide the schematics and an overview of the technology for an engineer or someone equivalently trained to reproduce and further improve upon Flyspresso, and highlight the Drosophila embryo fixation and colorimetric or antibody staining protocols. Additionally, we provide a detailed overview and stepwise protocol for our adaptive-feedback pipeline for automated embryo imaging on confocal microscopes. We demonstrate the efficiency of this pipeline compared to classical techniques, and how it can be repurposed or scaled to other protocols and biological systems. We hope our pipeline will serve as a platform for future research, allowing a broader community of users to build, execute, and share similar experiments.
Lung function decline is associated with serum uric acid in Korean health screening individuals
Authors: Ahn Kyung-Min , Lee Suh-Young , Lee So-Hee , Kim Sun-Sin , Park Heung-Woo
Published: May 2021

We performed a retrospective cohort study of 19,237 individuals who underwent at least three health screenings with follow-up periods of over 5 years to find a routinely checked serum marker that predicts lung function decline. Using linear regression models to analyze associations between the rate of decline in the forced expiratory volume in 1 s (FEV1) and the level of 10 serum markers (calcium, phosphorus, uric acid, total cholesterol, total protein, total bilirubin, alkaline phosphatase, aspartate aminotransferase, creatinine, and C-reactive protein) measured at two different times (at the first and third health screenings), we found that an increased uric acid level was significantly associated with an accelerated FEV1 decline (P = 0.0014 and P = 0.037, respectively) and reduced FEV1 predicted % (P = 0.0074 and P = 8.64 × 10–7, respectively) at both visits only in non-smoking individuals. In addition, we confirmed that accelerated forced vital capacity (FVC) and FEV1/FVC ratio declines were observed in non-smoking individuals with increased serum uric acid levels using linear mixed models. The serum uric acid level thus potentially predicts an acceleration in lung function decline in a non-smoking general population.
Airglow-imager based observation of possible influences of subtropical mesospheric gravity waves on F-region ionosphere over Jammu & Kashmir, India
Authors: Ramkumar T. K. , Malik Manzoor Ahmad , Ganaie Bilal Ahmad , Bhat Aashiq Hussain
Published: May 2021

As a joint research collaboration between the National Atmospheric Research Laboratory (NARL), and the University of Kashmir (KU), NARL installed an all-sky airglow CCD imager (with centre wavelengths of 630 nm, 557.7 nm [2 nm band widths] and 840 nm [150 nm wide band with blocking notch at 866 nm to avoid the contamination of molecular oxygen emissions]) in the University campus in Srinagar (75°E, 34°N, geographic), Jammu and Kashmir, India (western Himalayan region). To understand the upper atmospheric dynamics and ionospheric electrodynamics and their associated physical coupling mechanisms, the imager observes airglow emissions of OH molecules (~ 85 km height; 840 nm) and atomic oxygen occurring at the heights of ~ 97 km (557.7 nm) and ~ 250 km (630 nm). Airglow observations in Kashmir commenced in the night of August 11, 2017 and the present work reports on the characteristics of first-time observation of Medium Scale Travelling Ionospheric Disturbances (MSTIDs with horizontal wavelengths of ~ 100–300 km) over Kashmir region during 20:30—22:30 IST (Indian standard time) on August 15, 2017 (India independence day). Initially, the phase front of MSTIDs was aligned along the north-west and south-east direction and moved at ~ 57 m/s towards the south-west direction and finally the westward direction by aligning along the meridian before they disappeared. Along with SAMI-3 ionospheric model simulations, simultaneous multiwavelength airglow observations indicate that secondary gravity waves generated due to dissipation of upward propagating mesospheric gravity waves in the heights of ~ 85–95 km would have contributed to the generation of MSTIDs in the F region ionospheric plasma through electrodynamical coupling between the E and F region (Perkins instability) ionosphere.
Using past interglacial temperature maxima to explore transgressions in modern Maldivian coral and Amphistegina bleaching thresholds
Authors: Stainbank Stephanie , Kroon Dick , de Leau Erica S. , Spezzaferri Silvia
Published: May 2021

Tropical corals and Amphistegina, an example genus of symbiont-bearing larger benthic foraminifera, are presently living close to their thermal bleaching thresholds. As such, these essential reef-building organisms are vulnerable to the future prospect of more frequent sea surface temperature (SST) extremes. Exploring the earth’s paleo-climatic record, including interglacials warmer than present, may provide insights into future oceanographic conditions. We analyse foraminiferal shell geochemical compositions, from Recent surface sediments and Marine Isotope stage (MIS) 9e and MIS11c aged sediments, from the International Ocean Discovery Program Expedition 359 Site U1467 drilled in the Inner Sea of the Maldives. We illustrate through traditional (pooled) geochemical analysis (δ18O, Mg/Ca) that tropical temperatures were indeed marginally warmer during MIS9e and MIS11c in comparison to the modern ocean. Individual foraminiferal analysis (IFA) from the Recent (representing the last few hundred years) and MIS9e samples shows SSTs occasionally breached the coral bleaching threshold similarly to the modern-day. Significantly, the number of transgressions was four times higher during MIS11c, a recognised analogue for a warmer modern world. This new knowledge and novel IFA insight and application is invaluable given thermal stress is already obvious today with an increasing number of bleaching events over the last few decades.
Maternal control of visceral asymmetry evolution in Astyanax cavefish
Authors: Ma Li , Ng Mandy , Shi Janet , Gore Aniket V. , Castranova Daniel , Weinstein Brant M. , Jeffery William R.
Published: May 2021

The direction of visceral organ asymmetry is highly conserved during vertebrate evolution with heart development biased to the left and pancreas and liver development restricted to opposing sides of the midline. Here we show that reversals in visceral organ asymmetry have evolved inAstyanax mexicanus, a teleost species with interfertile surface-dwelling (surface fish) and cave-dwelling (cavefish) forms. Visceral organ asymmetry is conventional in surface fish but some cavefish have evolved reversals in heart, liver, and pancreas development. Corresponding changes in the normally left-sided expression of the Nodal-Pitx2/Lefty signaling system are also present in the cavefish lateral plate mesoderm (LPM). The Nodal antagonistslefty1(lft1) andlefty2(lft2), which confine Nodal signaling to the left LPM, are expressed in most surface fish, however,lft2,but notlft1,expression is absent during somitogenesis of most cavefish. Despite this difference, multiple lines of evidence suggested that evolutionary changes in L-R patterning are controlled upstream of Nodal-Pitx2/Lefty signaling. Accordingly, reciprocal hybridization of cavefish and surface fish showed that modifications of heart asymmetry are present in hybrids derived from cavefish mothers but not from surface fish mothers. The results indicate that changes in visceral asymmetry during cavefish evolution are influenced by maternal genetic effects.
Exploitation of blood non-Newtonian properties for ultrasonic measurement of hematocrit
Authors: Pialot B. , Gachelin J. , Provost J. , Couture O.
Published: May 2021

New processing techniques for manipulating blood and its components at a microfluidic scale are currently implemented. As for extracorporeal circulation, the in-line evaluation and monitoring of blood properties during these microfluidic techniques is a challenging task. Here, we show that the blood hematocrit can be measured non-invasively in a sub-millimeter medical tube using the non-Newtonian behavior of blood velocity profile. This hematocrit measurement is demonstrated on human blood with a simple Doppler ultrasound system. Results show a mean measurement error of 4.6 ± 1.3%Hct for hematocrit up to 52% and for 5 s-long ultrasonic signals. The simplicity and the measurement scale of the approach make it highly valuable for measuring hematocrit in new blood separation techniques. The approach may have an impact on in-vitro blood processing in general.