bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting traffic noise using land-use regression—a scalable approach
Authors: Staab Jeroen , Schady Arthur , Weigand Matthias , Lakes Tobia , Taubenböck Hannes 
Published: July 2021

AbstractBackgroundIn 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.ObjectiveBased 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.MethodsCompliant 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.ResultsThe 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).SignificanceThis 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

AbstractThe 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

AbstractEndocrine 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

AbstractVarious 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

AbstractHigh-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

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

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

AbstractThe 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

AbstractNon-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

AbstractA 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

AbstractCoupling 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

AbstractUrea 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

AbstractAryl 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

AbstractFlowering 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

AbstractGiven 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.