bluuebunny/crossref_metadata_2025 huggingface dataset:
The Assessment of Thought Fusion Beliefs and Beliefs About Rituals
Authors: Melchior Kim , Franken Ingmar H. A. , Vuijk Richard , Peerbooms Vivian , van der Heiden Colin
Published: July 2021

Abstract. Background: According to the metacognitive model, two domains of metacognitive beliefs play a role in the development and maintenance of obsessive-compulsive disorder (OCD). The Thought Fusion Instrument (TFI) has been developed to measure metacognitive beliefs about the significance of intrusive thoughts. The Beliefs About Rituals Inventory (BARI) assesses metacognitive beliefs about the necessity of performing ritual behaviors. Studies assessing the psychometric properties of the TFI and BARI are scarce. There are no studies assessing the factor structure of the TFI and the BARI. Methods: In this study, we assessed the psychometric properties of the TFI and the BARI in nonclinical ( n = 141) and clinical populations (OCD [ n = 60], anxiety disorder [ n = 30], and autism spectrum disorder [ n = 50]). In the nonclinical population, the factor structure is also explored. Results: For both the TFI and the BARI, an explorative factor analysis revealed a one-factor solution, which now needs further exploration using confirmative approaches. The internal consistency appeared good, and they had a moderate test–retest reliability. Convergent and divergent validity of the instruments appeared sufficient, but more research is required to draw firm conclusions. The criterion validity turned out to be moderate for the BARI but low for the TFI in measuring OCD-specific metacognitions. Conclusions: Based on the explorative factor analysis, we hypothesize the TFI and the BARI to measure a single-factor construct. The current study shows that the TFI and the BARI are potentially suitable questionnaires to assess metacognitions in clinical and nonclinical populations. More research is required before clear recommendations can be made for the utility and use in clinical practice.
Constraining Plateau Uplift in Southern Africa by Combining Thermochronology, Sediment Flux, Topography, and Landscape Evolution Modeling
Authors: Stanley Jessica R. , Braun Jean , Baby Guillaume , Guillocheau François , Robin Cécile , Flowers Rebecca M. , Brown Roderick , Wildman Mark , Beucher Romain
Published: July 2021

The uplift of the southern African Plateau with its average elevations of ∼1,000 m is often attributed to mantle processes, but there are conflicting theories for the timing and drivers of topographic development. Evidence for most proposed plateau development histories is derived from continental erosion histories, marine stratigraphic architecture, or landscape morphology. Here we use a landscape evolution model to integrate a large data set of low‐temperature thermochronometry, sediment flux rates to surrounding marine basins, and current topography for southern Africa. We explore three main hypotheses for surface uplift: (a) southern Africa was already elevated by the Early Cretaceous before Gondwana breakup, (b) uplift and continental tilting occurred during the mid‐Cretaceous, or (c) uplift occurred during the mid to late Cenozoic. We test which of these three intervals of plateau development are plausible by using an inversion method to constrain the range in erosional and uplift model parameters that can best reproduce the observed data. Results indicate four regions of parameter space that fall into two families of uplift histories are most compatible with the data. Both uplift families have limited initial topography with some topographic uplift and continental tilting starting at ∼90–100 Ma. In one acceptable scenario, nearly all of the topography, >1,300 m, is created at this time with little Cenozoic uplift. In the other acceptable scenario, ∼400–800 m of uplift occurs in the mid‐Cretaceous with another ∼500–1,000 m of uplift in the mid‐Cenozoic. The two model scenarios have different geodynamic implications, which we compare to geodynamic models.
The January 11, 2018, Mw 6.0 Bago‐Yoma, Myanmar Earthquake: A Shallow Thrust Event Within the Deforming Bago‐Yoma Range
Authors: Fadil Wardah , Lindsey Eric O. , Wang Yu , Maung Phyo Maung , Luo Heng , Swe Tint Lwin , Tun Pa Pa , Wei Shengji
Published: July 2021

On January 11, 2018 (18:26 UTC), a Mw 6.0 earthquake occurred approximately 30 km west of the Sagaing Fault in the Bago‐Yoma Range (BYR). Using a local broadband seismic network and regional seismic stations, we refine the locations and moment tensors of the earthquake sequence. We relocate 98 earthquake epicenters and determine the focal mechanism and centroid depth of the mainshock and 20 aftershocks with Mw > 4. The relocated epicenters cluster in a NW‐SE direction that is consistent with the strike of the mainshock fault plane solution and the slip distribution derived from ALOS‐2 interferometric synthetic aperture radar observations. Most of the aftershocks have a pure thrust focal mechanism similar to the mainshock, except for four strike‐slip aftershocks. The refined locations and moment tensors of the thrust events clearly delineate a fault dipping ∼40° to the southwest at a depth range of 3–7 km, indicating that the earthquake sequence ruptured a previously unmapped, active fault. We interpret the earthquake sequence to be associated with pre‐existing faults within the BYR anticlinorium. This earthquake sequence and historical seismicity indicate that the upper crust of the BYR is highly stressed, resulting in ongoing distributed deformation between the oblique Rakhine megathrust and the dextral Sagaing Fault. The seismic hazard posed by these active faults has been increasing with the development of infrastructure such as dams within the BYR. Our study highlights the need for high‐resolution earthquake source parameter and strong ground motion attenuation studies for further understanding of the neotectonics of Myanmar and its related seismic hazard.
Distributed Acoustic Sensing (DAS) for Natural Microseismicity Studies: A Case Study From Antarctica
Authors: Hudson T. S. , Baird A. F. , Kendall J. M. , Kufner S. K. , Brisbourne A. M. , Smith A. M. , Butcher A. , Chalari A. , Clarke A.
Published: July 2021

Icequakes, microseismic earthquakes at glaciers, offer insights into the dynamics of ice sheets. For the first time in the Antarctic, we explore the use of fiber optic cables as Distributed Acoustic Sensors (DAS) as a new approach for monitoring basal icequakes. We present the use of DAS for studying icequakes as a case study for the application of DAS to microseismic datasets in other geological settings. Fiber was deployed on the ice surface at Rutford Ice Stream in two different configurations. We compare the performance of DAS with a conventional geophone network for: microseismic detection and location; resolving source and noise spectra; source mechanism inversion; and measuring anisotropic shear‐wave splitting parameters. Both DAS array geometries detect fewer events than the geophone array. However, DAS is superior to geophones for recording the microseism signal, suggesting the applicability of DAS for ambient noise interferometry. We also present the first full‐waveform source mechanism inversions using DAS anywhere, successfully showing the horizontal stick‐slip nature of the icequakes. In addition, we develop an approach to use a 2D DAS array geometry as an effective multi‐component sensor capable of accurately characterizing shear‐wave splitting due to the anisotropic ice fabric. Although our observations originate from a glacial environment, the methodology and implications of this work are relevant for employing DAS in other microseismic environments.
Precambrian Crystalline Basement Properties From Pressure History Matching and Implications for Induced Seismicity in the US Midcontinent
Authors: Ansari Esmail , Bidgoli Tandis S.
Published: July 2021

Injection‐induced seismicity across the US midcontinent has almost exclusively occurred in the crystalline basement that underlies the Arbuckle Group aquifer and its equivalents, the primary wastewater disposal zone in this region. However, the properties of the basement are not well known. Newly compiled data, from Class I wells in Kansas, provide a unique record of pressures in the Arbuckle and an opportunity to constrain the reservoir‐scale properties of the basement such as permeability, diffusivity, and specific storage. Constraints on these parameters are critical for modeling fluid flow and pressures across the entire Arbuckle‐basement system, and are necessary for accurate evaluation and prediction of injection‐induced earthquakes. Here, we present a detailed, three‐dimensional geological and pressure history‐matched numerical model for the Arbuckle and basement, based on data from >400 wells covering a large region in south‐central Kansas, where injection‐induced seismicity has been concentrated since 2014. Simulations of dynamic data from 319 wells indicate that Arbuckle pressures have increased by 1.1 MPa in high injection rate areas and an overpressure of <0.1 MPa may be the cause of seismicity in the basement. Pressure‐history matching also yields the likely range in porosity (0.3%–7%), permeability (0.1–0.7 mD), and diffusivity (0.004–0.07 m2/s) for the basement. The resulting estimates suggest reservoir‐scale properties of the basement are enhanced by faults and fractures. Importantly, the diffusivities determined in this study are lower than estimates derived from Kansas earthquake triggering fronts, and suggest that such seismicity‐based techniques may have limitations, particularly where space‐time patterns between injection and seismicity are complex.
Estimation of Absolute Stress in the Hypocentral Region of the 2019 Ridgecrest, California, Earthquakes
Authors: Fialko Y.
Published: July 2021

Strength of the upper brittle part of the Earth's lithosphere controls deformation styles in tectonically active regions, surface topography, seismicity, and the occurrence of plate tectonics, yet it remains one of the most debated quantities in geophysics. Direct measurements of stresses acting at seismogenic depths are largely lacking. Seismic data (in particular, earthquake focal mechanisms) have been used to infer orientation of the principal stress axes. I show that the focal mechanism data can be combined with information from precise earthquake locations to place constraints not only on the orientation, but also on the magnitude of absolute stress at depth. The proposed method uses relative attitudes of conjugate faults to evaluate the amplitude and spatial heterogeneity of the deviatoric stress and frictional strength in the seismogenic zone. Relative fault orientations (dihedral angles) and sense of slip are determined using quasi‐planar clusters of seismicity and their composite focal mechanisms. The observed distribution of dihedral angles between active conjugate faults in the area of Ridgecrest (California, USA) that hosted a recent sequence of strong earthquakes suggests in situ coefficient of friction of 0.4–0.6, and depth‐averaged shear stress on the order of 25–40 MPa, intermediate between predictions of the “strong” and “weak” fault theories.
Predicting traffic noise using land-use regression—a scalable approach
Authors: Staab Jeroen , Schady Arthur , Weigand Matthias , Lakes Tobia , Taubenböck Hannes
Published: July 2021

Background

In modern societies, noise is ubiquitous. It is an annoyance and can have a negative impact on human health as well as on the environment. Despite increasing evidence of its negative impacts, spatial knowledge about noise distribution remains limited. Up to now, noise mapping is frequently inhibited by the necessary resources and therefore limited to selected areas.

Objective

Based on the assumption, that prevalent noise is determined by the arrangement of sources and the surrounding environment in which the sound propagates, we build a geostatistical model representing these parameters. Aiming for a large-scale noise mapping approach, we utilize publicly available data, context-aware feature engineering and a linear land-use regression (LUR) model.

Methods

Compliant to the European Noise Directive 2002/49/EG, we work at a high spatial granularity of 10 × 10-m resolution. As reference, we use the day–evening–night noise level indicatorLden. Therewith, we carry out 2000 virtual field campaigns simulating different sampling schemes and introduce spatial cross-validation concepts to test the transferability to new areas.

Results

The experimental results suggest the necessity for more than 500 samples stratified over the different noise levels to produce a representative model. Eventually, using 21 selected variables, our model was able to explain large proportions of the yearly averaged road noise (Lden) variability (R2 = 0.702) with a mean absolute error of 4.24 dB(A), 3.84 dB(A) for build-up areas, respectively. In applying this best performing model for an area-wide prediction, we spatially close the blank spots in existing noise maps with continuous noise levels for the entire range from 24 to 106 dB(A).

Significance

This data is new, particular for small communities that have not been mapped sufficiently in Europe so far. In conjunction, our findings also supplement conventionally sampled studies using physical microphones and spatially blocked cross-validations.
Clonal hematopoiesis and its emerging effects on cellular therapies
Authors: von Bonin Malte , Jambor Helena Klara , Teipel Raphael , Stölzel Friedrich , Thiede Christian , Damm Frederik , Kroschinsky Frank , Schetelig Johannes , Chavakis Triantafyllos , Bornhäuser Martin
Published: July 2021

The accumulation of somatic mutations in hematopoietic stem cells during aging, leading to clonal expansion, is linked to a higher risk of cardiovascular mortality and hematologic malignancies. Clinically, clonal hematopoiesis is associated with a pro-inflammatory phenotype of hematopoietic cells and their progeny, inflammatory conditions and a poor outcome for patients with hematologic neoplasms and solid tumors. Here, we review the relevance and complications of clonal hematopoiesis for the treatment of hematologic malignancies with cell therapeutic approaches. In autologous and allogeneic hematopoietic stem cell transplantation native hematopoietic and immune effector cells of clonal origin are transferred, which may affect outcome of the procedure. In chimeric antigen receptor modified T-cell therapy, the effectiveness may be altered by preexisting somatic mutations in genetically modified effector cells or by unmodified bystander cells harboring clonal hematopoiesis. Registry studies and carefully designed prospective trials will be required to assess the relative roles of donor- and recipient-derived individual clonal events for autologous and allogeneic cell therapies and to incorporate novel insights into therapeutic strategies.
FAM64A is an androgen receptor-regulated feedback tumor promoter in prostate cancer
Authors: Zhou Yingchen , Ou Longhua , Xu Jinming , Yuan Haichao , Luo Junhua , Shi Bentao , Li Xianxin , Yang Shangqi , Wang Yan
Published: July 2021

Endocrine therapy for prostate cancer (PCa) mainly inhibits androgen receptor (AR) signaling, due to increased androgen synthesis and AR changes, PCa evolved into castration-resistant prostate cancer (CRPC). The function of Family With Sequence Similarity 64 Member A (FAM64A) and its association with prostate cancer has not been reported. In our research, we first reported that FAM64A is up-regulated and positively associated with poor prognosis of patients with prostate cancer (PCa) by TCGA database and immunohistochemistry staining. Moreover, knockdown of FAM64A significantly suppressed the proliferation, migration, invasion, and cell cycle of PCa cells in vitro. Mechanistically, FAM64A expression was increased by dihydrotestosterone (DHT) through direct binding of AR to FAM64A promoter, and notably promoted the proliferation, migration, invasion, and cell cycle of androgen-dependent cell line of PCa. In addition, abnormal expression of FAM64A affects the immune and interferon signaling pathway of PCa cells. In conclusion, FAM64A was up-regulated by AR through directly binding to its specific promoter region to promote the development of PCa, and was associated with the immune mechanism and interferon signaling pathway, which provided a better understanding and a new potential for treating PCa.
Tribbles homolog 3-mediated targeting the AKT/mTOR axis in mice with retinal degeneration
Authors: Saltykova Irina V. , Elahi Asif , Pitale Priyam M. , Gorbatyuk Oleg S. , Athar Mohammad , Gorbatyuk Marina S.
Published: July 2021

Various retinal degenerative disorders manifest in alterations of the AKT/mTOR axis. Despite this, consensus on the therapeutic targeting of mTOR in degenerating retinas has not yet been achieved. Therefore, we investigated the role of AKT/mTOR signaling inrd16retinas, in which we restored the AKT/mTOR axis by genetic ablation of pseudokinase TRB3, known to inhibit phosphorylation of AKT and mTOR. First, we found that TRB3 ablation resulted in preservation of photoreceptor function in degenerating retinas. Then, we learned that the mTOR downstream cellular pathways involved in the homeostasis of photoreceptors were also reprogrammed inrd16TRB3−/−retinas. Thus, the level of inactivated translational repressor p-4E-BP1 was significantly increased in these mice along with the restoration of translational rate. Moreover, inrd16mice manifesting decline in p-mTOR at P15, we found elevated expression of Beclin-1 and ATG5 autophagy genes. Thus, these mice showed impaired autophagy flux measured as an increase in LC3 conversion and p62 accumulation. In addition, the RFP-EGFP-LC3 transgene expression inrd16retinas resulted in statistically fewer numbers of red puncta in photoreceptors, suggesting impaired late autophagic vacuoles. In contrast, TRIB3 ablation in these mice resulted in improved autophagy flux. The restoration of translation rate and the boost in autophagosome formation occurred concomitantly with an increase in total Ub and rhodopsin protein levels and the elevation of E3 ligase Parkin1. We propose that TRB3 may retard retinal degeneration and be a promising therapeutic target to treat various retinal degenerative disorders.
HMGB2 orchestrates mitotic clonal expansion by binding to the promoter of C/EBPβ to facilitate adipogenesis
Authors: Chen Keren , Zhang Junyan , Liang Feng , Zhu Qi , Cai Shufang , Tong Xian , He Zuyong , Liu Xiaohong , Chen Yaosheng , Mo Delin
Published: July 2021

High-mobility group box 2 (HMGB2) is an abundant, chromatin-associated protein that plays an essential role in the regulation of transcription, cell proliferation, differentiation, and tumorigenesis. However, the underlying mechanism of HMGB2 in adipogenesis remains poorly known. Here, we provide evidence that HMGB2 deficiency in preadipocytes impedes adipogenesis, while overexpression of HMGB2 increases the potential for adipogenic differentiation. Besides, depletion of HMGB2 in vivo caused the decrease in body weight, white adipose tissue (WAT) mass, and adipocyte size. Consistently, the stromal vascular fraction (SVF) of adipose tissue derived from hmgb2−/− mice presented impaired adipogenesis. When hmgb2−/− mice were fed with high-fat diet (HFD), the body size, and WAT mass were increased, but at a lower rate. Mechanistically, HMGB2 mediates adipogenesis via enhancing expression of C/EBPβ by binding to its promoter at “GGGTCTCAC” specifically during mitotic clonal expansion (MCE) stage, and exogenous expression of C/EBPβ can rescue adipogenic abilities of preadipocytes in response to HMGB2 inhibition. In general, our findings provide a novel mechanism of HMGB2-C/EBPβ axis in adipogenesis and a potential therapeutic target for obesity.
Quantifying nitrogen fixation by heterotrophic bacteria in sinking marine particles
Authors: Chakraborty Subhendu , Andersen Ken H. , Visser André W. , Inomura Keisuke , Follows Michael J. , Riemann Lasse
Published: July 2021

Nitrogen ($${{\rm{N}}}_{2}$$

N

2

) fixation by heterotrophic bacteria associated with sinking particles contributes to marine N cycling, but a mechanistic understanding of its regulation and significance are not available. Here we develop a mathematical model for unicellular heterotrophic bacteria growing on sinking marine particles. These bacteria can fix $${{\rm{N}}}_{2}$$

N

2

under suitable environmental conditions. We find that the interactive effects of polysaccharide and polypeptide concentrations, sinking speed of particles, and surrounding $${{\rm{O}}}_{2}$$

O

2

and $${{{\rm{NO}}}_{3}}^{-}$$

NO

3

−

concentrations determine the $${{\rm{N}}}_{2}$$

N

2

fixation rate inside particles. $${{\rm{N}}}_{2}$$

N

2

fixation inside sinking particles is mainly fueled by $${{{\rm{SO}}}_{4}}^{2-}$$

SO

4

2
−

respiration rather than $${{{\rm{NO}}}_{3}}^{-}$$

NO

3

−

respiration. Our model suggests that anaerobic processes, including heterotrophic $${{\rm{N}}}_{2}$$

N

2

fixation, can take place in anoxic microenvironments inside sinking particles even in fully oxygenated marine waters. The modelled $${{\rm{N}}}_{2}$$

N

2

fixation rates are similar to bulk rates measured in the aphotic ocean, and our study consequently suggests that particle-associated heterotrophic $${{\rm{N}}}_{2}$$

N

2

fixation contributes significantly to oceanic $${{\rm{N}}}_{2}$$

N

2

fixation.
Impact of cavity on interatomic Coulombic decay
Authors: Cederbaum Lorenz S. , Kuleff Alexander I.
Published: July 2021

The interatomic Coulombic decay (ICD) is an efficient electronic decay process of systems embedded in environment. In ICD, the excess energy of an excited atom A is efficiently utilized to ionize a neighboring atom B. In quantum light, an ensemble of atoms A form polaritonic states which can undergo ICD with B. Here we investigate the impact of quantum light on ICD and show that this process is strongly altered compared to classical ICD. The ICD rate depends sensitively on the atomic distribution and orientation of the ensemble. It is stressed that in contrast to superposition states formed by a laser, forming polaritons by a cavity enables to control the emergence and suppression, as well as the efficiency of ICD.
A release-and-capture mechanism generates an essential non-centrosomal microtubule array during tube budding
Authors: Gillard Ghislain , Girdler Gemma , Röper Katja
Published: July 2021

Non-centrosomal microtubule arrays serve crucial functions in cells, yet the mechanisms of their generation are poorly understood. During budding of the epithelial tubes of the salivary glands in theDrosophilaembryo, we previously demonstrated that the activity of pulsatile apical-medial actomyosin depends on a longitudinal non-centrosomal microtubule array. Here we uncover that the exit from the last embryonic division cycle of the epidermal cells of the salivary gland placode leads to one centrosome in the cells losing all microtubule-nucleation capacity. This restriction of nucleation activity to the second, Centrobin-enriched, centrosome is key for proper morphogenesis. Furthermore, the microtubule-severing protein Katanin and the minus-end-binding protein Patronin accumulate in an apical-medial position only in placodal cells. Loss of either in the placode prevents formation of the longitudinal microtubule array and leads to loss of apical-medial actomyosin and impaired apical constriction. We thus propose a mechanism whereby Katanin-severing at the single active centrosome releases microtubule minus-ends that are then anchored by apical-medial Patronin to promote formation of the longitudinal microtubule array crucial for apical constriction and tube formation.
Object representations in the human brain reflect the co-occurrence statistics of vision and language
Authors: Bonner Michael F. , Epstein Russell A.
Published: July 2021

A central regularity of visual perception is the co-occurrence of objects in the natural environment. Here we use machine learning and fMRI to test the hypothesis that object co-occurrence statistics are encoded in the human visual system and elicited by the perception of individual objects. We identified low-dimensional representations that capture the latent statistical structure of object co-occurrence in real-world scenes, and we mapped these statistical representations onto voxel-wise fMRI responses during object viewing. We found that cortical responses to single objects were predicted by the statistical ensembles in which they typically occur, and that this link between objects and their visual contexts was made most strongly in parahippocampal cortex, overlapping with the anterior portion of scene-selective parahippocampal place area. In contrast, a language-based statistical model of the co-occurrence of object names in written text predicted responses in neighboring regions of object-selective visual cortex. Together, these findings show that the sensory coding of objects in the human brain reflects the latent statistics of object context in visual and linguistic experience.
Evanescent waves modulate energy efficiency of photocatalysis within TiO2 coated optical fibers illuminated using LEDs
Authors: Song Yinghao , Ling Li , Westerhoff Paul , Shang Chii
Published: July 2021

Coupling photocatalyst-coated optical fibers (P-OFs) with LEDs shows potential in environmental applications. Here we report a strategy to maximize P-OF light usage and quantify interactions between two forms of light energy (refracted light and evanescent waves) and surface-coated photocatalysts. Different TiO2-coated quartz optical fibers (TiO2-QOFs) are synthesized and characterized. An energy balance model is then developed by correlating different nano-size TiO2 coating structures with light propagation modes in TiO2-QOFs. By reducing TiO2 patchiness on optical fibers to 0.034 cm2/cm2 and increasing the average interspace distance between fiber surfaces and TiO2 coating layers to 114.3 nm, refraction is largely reduced when light is launched into TiO2-QOFs, and 91% of light propagated on the fiber surface is evanescent waves. 24% of the generated evanescent waves are not absorbed by nano-TiO2 and returned to optical fibers, thus increasing the quantum yield during degradation of a refractory pollutant (carbamazepine) in water by 32%. Our model also predicts that extending the TiO2-QOF length could fully use the returned light to double the carbamazepine degradation and quantum yield. Therefore, maximizing evanescent waves to activate photocatalysts by controlling photocatalyst coating structures emerges as an effective strategy to improve light usage in photocatalysis.
Electrochemical synthesis of urea on MBenes
Authors: Zhu Xiaorong , Zhou Xiaocheng , Jing Yu , Li Yafei
Published: July 2021

Urea is an important raw material in the chemical industry and is widely used as a nitrogen source in chemical fertilizers. The current industrial urea synthesis not only requires harsh reaction conditions, but also consumes most of the NH3 obtained through artificial synthesis. The conversion of N2 and CO2 into urea through electrochemical reactions under ambient conditions represents a novel green urea synthesis method. However, the large-scale promotion of this method is limited by the lack of suitable electrocatalysts. Here, by means of density functional theory computations, we systematically study the catalytic activity of three experimentally available two-dimensional metal borides (MBenes), Mo2B2, Ti2B2, and Cr2B2 toward simultaneous electrocatalytic coupling of N2 and CO2 to produce urea under ambient conditions. According to our results, these three MBenes not only have superior intrinsic basal activity for urea formation, with limiting potentials ranging from −0.49 to −0.65 eV, but also can significantly suppress the competitive reaction of N2 reduction to NH3. In particular, 2D Mo2B2 and Cr2B2 possess superior capacity to suppress surface oxidation and self-corrosion under electrochemical reaction conditions, rendering them relatively promising electrocatalysts for urea production. Our work paves the way for the electrochemical synthesis of urea.
Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation
Authors: Johnston Isabel , Osborn Lucas J. , Markley Rachel L. , McManus Elizabeth A. , Kadam Anagha , Schultz Karlee B. , Nagajothi Nagashreyaa , Ahern Philip P. , Brown J. Mark , Claesen Jan
Published: July 2021

Aryl polyenes (APEs) are specialized polyunsaturated carboxylic acids that were identified in silico as the product of the most widespread family of bacterial biosynthetic gene clusters (BGCs). They are present in several Gram-negative host-associated bacteria, including multidrug-resistant human pathogens. Here, we characterize a biological function of APEs, focusing on the BGC from a uropathogenic Escherichia coli (UPEC) strain. We first perform a genetic deletion analysis to identify the essential genes required for APE biosynthesis. Next, we show that APEs function as fitness factors that increase protection from oxidative stress and contribute to biofilm formation. Together, our study highlights key steps in the APE biosynthesis pathway that can be explored as potential drug targets for complementary strategies to reduce fitness and prevent biofilm formation of multi-drug resistant pathogens.
Linkage mapping and QTL analysis of flowering time in faba bean
Authors: Aguilar-Benitez David , Casimiro-Soriguer Inés , Maalouf Fouad , Torres Ana M.
Published: July 2021

Flowering time marks the transition from vegetative to reproductive growth and is key for optimal yield in any crop. The molecular mechanisms controlling this trait have been extensively studied in model plants such asArabidopsis thalianaand rice. While knowledge on the molecular regulation of this trait is rapidly increasing in sequenced galegoid legume crops, understanding in faba bean remains limited. Here we exploited translational genomics from model legume crops to identify and fine map QTLs linked to flowering time in faba bean. Among the 31 candidate genes relevant for flowering control inA. thalianaandCicer arietinumassayed, 25 could be mapped in a segregating faba bean RIL population. While most of the genes showed conserved synteny among related legume species, none of them co-localized with the 9 significant QTL regions identified. TheFTgene, previously implicated in the control of flowering time in numerous members of the temperate legume clade, mapped close to the most relevant stable and conserved QTL in chromosome V. Interestingly, QTL analysis suggests an important role of epigenetic modifications in faba bean flowering control. The new QTLs and candidate genes assayed here provide a robust framework for further genetic studies and will contribute to the elucidation of the molecular mechanisms controlling this trait.
Livelayer: a semi-automatic software program for segmentation of layers and diabetic macular edema in optical coherence tomography images
Authors: Montazerin Mansooreh , Sajjadifar Zahra , Khalili Pour Elias , Riazi-Esfahani Hamid , Mahmoudi Tahereh , Rabbani Hossein , Movahedian Hossein , Dehghani Alireza , Akhlaghi Mohammadreza , Kafieh Rahele
Published: July 2021

Given the capacity of Optical Coherence Tomography (OCT) imaging to display structural changes in a wide variety of eye diseases and neurological disorders, the need for OCT image segmentation and the corresponding data interpretation is latterly felt more than ever before. In this paper, we wish to address this need by designing a semi-automatic software program for applying reliable segmentation of 8 different macular layers as well as outlining retinal pathologies such as diabetic macular edema. The software accommodates a novel graph-based semi-automatic method, called “Livelayer” which is designed for straightforward segmentation of retinal layers and fluids. This method is chiefly based on Dijkstra’s Shortest Path First (SPF) algorithm and the Live-wire function together with some preprocessing operations on the to-be-segmented images. The software is indeed suitable for obtaining detailed segmentation of layers, exact localization of clear or unclear fluid objects and the ground truth, demanding far less endeavor in comparison to a common manual segmentation method. It is also valuable as a tool for calculating the irregularity index in deformed OCT images. The amount of time (seconds) that Livelayer required for segmentation of Inner Limiting Membrane, Inner Plexiform Layer–Inner Nuclear Layer, Outer Plexiform Layer–Outer Nuclear Layer was much less than that for the manual segmentation, 5 s for the ILM (minimum) and 15.57 s for the OPL–ONL (maximum). The unsigned errors (pixels) between the semi-automatically labeled and gold standard data was on average 2.7, 1.9, 2.1 for ILM, IPL–INL, OPL–ONL, respectively. The Bland–Altman plots indicated perfect concordance between the Livelayer and the manual algorithm and that they could be used interchangeably. The repeatability error was around one pixel for the OPL–ONL and < 1 for the other two. The unsigned errors between the Livelayer and the manual algorithm was 1.33 for ILM and 1.53 for Nerve Fiber Layer–Ganglion Cell Layer in peripapillary B-Scans. The Dice scores for comparing the two algorithms and for obtaining the repeatability on segmentation of fluid objects were at acceptable levels.
Towards laser printing of magnetocaloric structures by inducing a magnetic phase transition in iron-rhodium nanoparticles
Authors: Nadarajah Ruksan , Landers Joachim , Salamon Soma , Koch David , Tahir Shabbir , Doñate-Buendía Carlos , Zingsem Benjamin , Dunin-Borkowski Rafal E. , Donner Wolfgang , Farle Michael , Wende Heiko , Gökce Bilal
Published: July 2021

The development of magnetocaloric materials represents an approach to enable efficient and environmentally friendly refrigeration. It is envisioned as a key technology to reduce CO2 emissions of air conditioning and cooling systems. Fe-Rh has been shown to be one of the best-suited materials in terms of heat exchange per material volume. However, the Fe-Rh magnetocaloric response depends on its composition. Hence, the adaptation of material processing routes that preserve the Fe-Rh magnetocaloric response in the generated structures is a fundamental step towards the industrial development of this cooling technology. To address this challenge, the temperature-dependent properties of laser synthesized Fe-Rh nanoparticles and the laser printing of Fe-Rh nanoparticle inks are studied to generate 2D magnetocaloric structures that are potentially interesting for applications such as waste heat management of compact electrical appliances or thermal diodes, switches, and printable magnetocaloric media. The magnetization and temperature dependence of the ink’s γ-FeRh to B2-FeRh magnetic transition is analyzed throughout the complete process, finding a linear increase of the magnetization M (0.8 T, 300 K) up to 96 Am2/kg with ca. 90% of the γ-FeRh being transformed permanently into the B2-phase. In 2D structures, magnetization values of M (0.8 T, 300 K) ≈ 11 Am2/kg could be reached by laser sintering, yielding partial conversion to the B2-phase equivalent to long-time heating temperature of app. 600 K, via this treatment. Thus, the proposed procedure constitutes a robust route to achieve the generation of magnetocaloric structures.
Single dose of multi-clade virus-like particle vaccine protects chickens against clade 2.3.2.1 and clade 2.3.4.4 highly pathogenic avian influenza viruses
Authors: Kang Yong-Myung , Cho Hyun-Kyu , Kim Ju Hun , Lee Su Jin , Park Seo-Jeong , Kim Do-Young , Kim Seong Yup , Park Jung-won , Lee Myoung-Heon , Kim Min-Chul , Kang Hyun-Mi
Published: July 2021

Virus-like particles (VLPs) are recognized as an alternative vaccine platform that provide effective protection against various highly pathogenic avian influenza viruses (HPAIVs). Here, we developed multi-clade VLPs expressing two HAs (a chimera of clade 2.3.2.1c and clade 2.3.4.4c HA) within a single vector. We then compared its protective efficacy with that of a monovalent VLP and evaluated its potency against each homologous strain. Chickens vaccinated with the multi-clade VLP shed less virus and were better protected against challenge than birds receiving monovalent vaccines. Single vaccination with a multi-clade VLP resulted in 100% survival, with no clinical symptoms and high levels of pre-challenge protective immunity (7.6–8.5 log2). Moreover, the multi-clade VLP showed high productivity (128–256 HAU) both in the laboratory and on a large scale, making it cheaper than whole inactivated vaccines produced in eggs. However, the PD50 (protective dose 50%) of the multi-clade VLP against clades 2.3.2.1c and 2.3.4.4c was < 50 PD50 (28 and 42 PD50, respectively), and effective antibody response was maintained for 2–3 months. This multi-clade VLP protects against both clades of HPAI viruses and can be produced in high amounts at low cost. Thus, the vaccine has potential as a pandemic preparedness vaccine.
Genomic regions associated with heat stress tolerance in tropical maize (Zea mays L.)
Authors: Seetharam Kaliyamoorthy , Kuchanur Prakash H. , Koirala K. B. , Tripathi Mahendra Prasad , Patil Ayyanagouda , Sudarsanam Viswanadh , Das Reshmi Rani , Chaurasia Ramesh , Pandey Kamal , Vemuri Hindu , Vinayan Madhumal Thayil , Nair Sudha K. , Babu Raman , Zaidi P. H.
Published: July 2021

With progressive climate change and the associated increase in mean temperature, heat stress tolerance has emerged as one of the key traits in the product profile of the maize breeding pipeline for lowland tropics. The present study aims to identify the genomic regions associated with heat stress tolerance in tropical maize. An association mapping panel, called the heat tolerant association mapping (HTAM) panel, was constituted by involving a total of 543 tropical maize inbred lines from diverse genetic backgrounds, test-crossed and phenotyped across nine locations in South Asia under natural heat stress. The panel was genotyped using a genotyping-by-sequencing (GBS) platform. Considering the large variations in vapor pressure deficit (VPD) at high temperature (Tmax) across different phenotyping locations, genome-wide association study (GWAS) was conducted separately for each location. The individual location GWAS identified a total of 269 novel significant single nucleotide polymorphisms (SNPs) for grain yield under heat stress at a p value of < 10–5. A total of 175 SNPs were found in 140 unique gene models implicated in various biological pathway responses to different abiotic stresses. Haplotype trend regression (HTR) analysis of the significant SNPs identified 26 haplotype blocks and 96 single SNP variants significant across one to five locations. The genomic regions identified based on GWAS and HTR analysis considering genomic region x environment interactions are useful for breeding efforts aimed at developing heat stress resilient maize cultivars for current and future climatic conditions through marker-assisted introgression into elite genetic backgrounds and/or genome-wide selection.
An efficient and secure protocol for checking remote data integrity in multi-cloud environment
Authors: Anwarbasha H. , Sasi Kumar S. , Dhanasekaran D.
Published: July 2021

In cloud environment, huge quantity of data has been generated at each and every second. In order to manage the data, cloud service provider makes use of multi-cloud platform to fulfill the requirement. The service provider cooperatively operates altogether for the accessibility of resources and are improvised by implementing the dynamic operation that can run at a time through the Multi-cloud environment. This paper presents a Dynamic Level Based Integrity Checking Protocol (DA-ICP) for storing data in multicloud environment. The proposed method introduces Provable Data Possession (PDP) approach which enables a user who outsources the data at an untrusted multi-cloud for ensuring that the server possesses the original data without downloading it. This model creates a probabilistic proof of possession by sampling an arbitrary collection of blocks from server that considerably minimizes the cost. The effective and secured outsourced data has been resolved using public key cryptography and undergo encryption using Efficient-PDP (EPDP). During experimentation, the presented DA-ICP shows a maximum accuracy of 96.78%. The proposed method uses Multi-cloud in DA-ICP which produces an efficient output than other existing techniques.
Loss of FYCO1 leads to cataract formation
Authors: Satoh Kiyotoshi , Takemura Yukitoshi , Satoh Motohiko , Ozaki Kiyokazu , Kubota Shunichiro
Published: July 2021

Autophagy is a degradation process of cytoplasmic proteins and organelles trafficked to degradation vesicles known as autophagosomes. The conversion of LC3-I to LC3-II is an essential step of autophagosome formation, and FYCO1 is a LC3-binding protein that mediates autophagosome transport. The p62 protein also directly binds to LC3 and is degraded by autophagy. In the present study, we demonstrated that disrupting the FYCO1 gene in mice resulted in cataract formation. LC3 conversion decreased in eyes from FYCO1 knockout mice. Further, FYCO1 interacted with αA- and αB-crystallin, as demonstrated by yeast two-hybrid screening and immunoprecipitation analyses. In eyes from knockout mice, the soluble forms of αA- and αB-crystallin, the lens’s major protein components, decreased. In addition, p62 accumulated in eyes from FYCO1 knockout mice. Collectively, these findings suggested that FYCO1 recruited damaged α-crystallin into autophagosomes to protect lens cells from cataract formation.
Statistical and machine learning methods for analysis of multiplex protein data from a novel proximity extension assay in patients with ST-elevation myocardial infarction
Authors: Maag Emil , Kulasingam Archana , Grove Erik Lerkevang , Pedersen Kamilla Sofie , Kristensen Steen Dalby , Hvas Anne-Mette
Published: July 2021

Using data from patients with ST-elevation myocardial infarction (STEMI), we explored how machine learning methods can be used for analysing multiplex protein data obtained from proximity extension assays. Blood samples were obtained from 48 STEMI-patients at admission and after three months. A subset of patients also had blood samples obtained at four and 12 h after admission. Multiplex protein data were obtained using a proximity extension assay. A random forest model was used to assess the predictive power and importance of biomarkers to distinguish between the acute and the stable phase. The similarity of response profiles was investigated using K-means clustering. Out of 92 proteins, 26 proteins were found to significantly distinguish the acute and the stable phase following STEMI. The five proteins tissue factor pathway inhibitor, azurocidin, spondin-1, myeloperoxidase and myoglobin were found to be highly important for differentiating between the acute and the stable phase. Four of these proteins shared response profiles over the four time-points. Machine learning methods can be used to identify and assess novel predictive biomarkers as showcased in the present study population of patients with STEMI.
High prevalence of blaCTX-M and blaSHV among ESBL producing E. coli isolates from beef cattle in China’s Sichuan-Chongqing Circle
Authors: Zhang Yu-Long , Huang Fang-Yuan , Gan Lin-Li , Yu Xin , Cai Dong-Jie , Fang Jing , Zhong Zhi-jun , Guo Hong-rui , Xie Yue , Yi Jun , Wang Zhi-sheng , Zuo Zhi-Cai
Published: July 2021

Enterobacteria that produce extended-spectrum β-lactamase (ESBL) such as Escherichia coli (E. coli) are common in our environment and known to cause serious health implications in humans and animals. β-lactam antibiotics such as penicillins, cephalosporins and monobactams are the most commonly used anti-bacterials in both humans and animals, however, Gram negative bacteria (such as E. coli) that produces extended-spectrum β-lactamases (ESBLs) have the ability to hydrolyze most β-lactams therefore making them resistant to β-lactam antibiotics. Recent extensive researches on the epidemiology and genetic characteristics of extended-spectrum β-lactamase (ESBL)-producing E. coli reported the existence of ESBL-producing E. coli in humans, companion animals and poultry. Therefore, this experiment was performed to investigate the prevalence and genetic characteristics of β-lactamase producing E. coli isolated from beef cattle farms in the Sichuan-Chongqing circle of China. Phenotypic confirmation of ESBL-producing E. coli was performed using the double disk synergy test. Polymerase Chain Reaction (PCR) was used to detect blaCTX-M, blaSHV and blaTEM gene codes, then after, isolates were divided into different phylogenetic groups and multi-locus sequence typing (MLST). The results showed that out of the 222 E. coli strains isolated from the beef cattle, 102 strains showed ESBL phenotypes. The PCR results showed that blaCTX-M was the predominant ESBL gene identified among the E. coli strains with 21 (9.5%) isolates having this gene, followed by blaSHV which was found in 18 (8.1%) isolates. The majority of these ESBL positive isolates were assigned to phylogroup A (19.8%) followed by phylogroup B1 (13.5%). In addition, from the MLST results on ESBL positive isolates (n = 30) we identified 19 STs, ST398 (ST398cplx) and ST7130 which were the prevalent population (20%). In conclusion, the high prevalence of CTX-M, and SHV in the study confirmed its association with E. coli infection; therefore, this calls for health concerns on ESBL-producing E. coli. As far as we know, this is the first comprehensive research report relating to ESBL-producing E. coli incidence in Chinese beef cattle.
Distinct roles of androgen receptor, estrogen receptor alpha, and BCL6 in the establishment of sex-biased DNA methylation in mouse liver
Authors: AlOgayil Najla , Bauermeister Klara , Galvez Jose Hector , Venkatesh Varun S. , Zhuang Qinwei Kim-wee , Chang Matthew L. , Davey Rachel A. , Zajac Jeffrey D. , Ida Kinuyo , Kamiya Akihide , Taketo Teruko , Bourque Guillaume , Naumova Anna K.
Published: July 2021

Sexual dimorphism in gene regulation, including DNA methylation, is the main driver of sexual dimorphism in phenotypes. However, the questions of how and when sex shapes DNA methylation remain unresolved. Recently, using mice with different combinations of genetic and phenotypic sex, we identified sex-associated differentially methylated regions (sDMRs) that depended on the sex phenotype. Focusing on a panel of validated sex-phenotype dependent male- and female-biased sDMRs, we tested the developmental dynamics of sex bias in liver methylation and the impacts of mutations in the androgen receptor, estrogen receptor alpha, or the transcriptional repressor Bcl6 gene. True hermaphrodites that carry both unilateral ovaries and contralateral testes were also tested. Our data show that sex bias in methylation either coincides with or follows sex bias in the expression of sDMR-proximal genes, suggesting that sex bias in gene expression may be required for demethylation at certain sDMRs. Global ablation of AR, ESR1, or a liver-specific loss of BCL6, all alter sDMR methylation, whereas presence of both an ovary and a testis delays the establishment of male-type methylation levels in hermaphrodites. Moreover, the Bcl6-LKO shows dissociation between expression and methylation, suggesting a distinct role of BCL6 in demethylation of intragenic sDMRs.