bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sandwich-like construction of a new aminated chitosan Schiff base for efficient removal of Congo red
Authors: Abd El-Monaem Eman M. , Ayoup Mohammed Salah , Omer Ahmed M. , Hammad Eman Nasr , Eltaweil Abdelazeem S. 
Published: January 2023

AbstractHerein, a novel sandwich-like α-ketoglutaric acid Schiff base-aminated chitosan composite (α-kGl-AmCsSB) was fabricated by reacting α-ketoglutaric acid and aminated chitosan. The as-fabricated α-kGl-AmCsSB was inspected by diversified characterization tools to determine its morphology, surface charge, and chemical composition as well as define the linkage pathway between α-kGl and AmCs. The SEM images demonstrated a spongy network of AmCs with interconnected pores structure which turned to a quite rough surface due to the linkage of α-kGl to the free amine groups of AmCs. Notably, the XPS and FTIR spectra suggested the linkage of α-kGl to the amine group of AmCs. The experimental results implied the superior adsorption efficiency of Congo red (CR) onto α-kGl-AmCsSB since the maximum adsorption capacity (qmax) reached 434.78 mg/g at 25 °C and pH 3. Based on kinetics data, the adsorption of CR on α-kGl-AmCsSB followed pseudo-second-order model. Furthermore, D-R model infers that the CR adsorption onto α-kGl-AmCsSB occurred via physical interactions since the E value < 8 kJ/mol. The recyclability test was implemented for five cycles with R% > 72%. More importantly, the adsorption mechanism of CR onto α-kGl-AmCsSB was proposed and discussed. Ultimately, the novel sandwich-like α-kGl-AmCsSB exhibited advanced adsorption performance toward CR along with excellent reusability. Based on these results, we recommend more modifications on α-kGl-AmCsSB for exploiting its remarkable advantages and applying it on a large scale.
Use of expanded polystyrene (EPS) as a support media for trickling filters applied to wastewater treatment
Authors: Paixão Filho Jorge Luiz da , Portela Daniella Gonçalves , da Silva Carlos Isaque , de Oliveira Gabriel Camargo , Tonetti Adriano Luiz 
Published: January 2023

AbstractDeveloping countries demand a sewage treatment plant with low-cost processes that are viable in warm climates. The UASB (upflow anaerobic sludge blanket) associated with the trickling filter (TF) would meet this requirement. However, there is still a need for studies aimed at the use of new support media. Based on this, the use of expanded polystyrene (EPS) as a support media in TF was evaluated in this study. As a result, the TF filled with EPS presented a final effluent with quality similar to reactors filled with crushed stone or patented materials. The density of EPS (6.56 ± 0.30 kg m−3), the void ratio (61.7 ± 2.1%), and the mean surface area (201.9 ± 14.9 m2 m−3) once again demonstrate that EPS has characteristics similar to other alternative or patented materials. Therefore, we found that EPS can be another alternative material to be used in sewage treatment, and also that one could give an appropriate destination to a portion of this material, which is currently still discarded in landfills.
Cystoscopic depth estimation using gated adversarial domain adaptation
Authors: Somers Peter , Holdenried-Krafft Simon , Zahn Johannes , Schüle Johannes , Veil Carina , Harland Niklas , Walz Simon , Stenzl Arnulf , Sawodny Oliver , Tarín Cristina , Lensch Hendrik P. A. 
Published: January 2023

AbstractMonocular depth estimation from camera images is very important for surrounding scene evaluation in many technical fields from automotive to medicine. However, traditional triangulation methods using stereo cameras or multiple views with the assumption of a rigid environment are not applicable for endoscopic domains. Particularly in cystoscopies it is not possible to produce ground truth depth information to directly train machine learning algorithms for using a monocular image directly for depth prediction. This work considers first creating a synthetic cystoscopic environment for initial encoding of depth information from synthetically rendered images. Next, the task of predicting pixel-wise depth values for real images is constrained to a domain adaption between the synthetic and real image domains. This adaptation is done through added gated residual blocks in order to simplify the network task and maintain training stability during adversarial training. Training is done on an internally collected cystoscopy dataset from human patients. The results after training demonstrate the ability to predict reasonable depth estimations from actual cystoscopic videos and added stability from using gated residual blocks is shown to prevent mode collapse during adversarial training.
Impaired T-cell response to phytohemagglutinin (PHA) in tuberculosis patients is associated with high IL-6 plasma levels and normalizes early during anti-mycobacterial treatment
Authors: Vivekanandan Monika M. , Adankwah Ernest , Aniagyei Wilfred , Acheampong Isaac , Minadzi Difery , Yeboah Augustine , Arthur Joseph F. , Lamptey Millicent , Abass Mohammed K. , Kumbel Francis , Osei-Yeboah Francis , Gawusu Amidu , Debrah Linda Batsa , Owusu Dorcas O. , Debrah Alexander , Mayatepek Ertan , Seyfarth Julia , Phillips Richard O. , Jacobsen Marc 
Published: January 2023

Abstract
Purpose
Human tuberculosis is characterized by immunopathology that affects T-cell phenotype and functions. Previous studies found impaired T-cell response to phytohemagglutinin (PHA) in patients with acute tuberculosis. However, the influence of disease severity, affected T-cell subsets, and underlying mechanisms remain elusive.

Methods
Here we investigated PHA-induced and antigen-specific T-cell effector cytokines in tuberculosis patients (n = 55) as well as in healthy asymptomatic contacts (n = 32) from Ghana. Effects of Mycobacterium (M.) tuberculosis sputum burden and treatment response were analyzed and compared during follow-up. Finally, cytokine characteristics of the aberrant plasma milieu in tuberculosis were analyzed as a potential cause for impaired PHA response.

Results
PHA-induced IFN-γ expression was significantly lower in sputum-positive tuberculosis patients as compared to both, contacts and paucibacillary cases, and efficiently discriminated the study groups. T-cell responses to PHA increased significantly early during treatment and this was more pronounced in tuberculosis patients with rapid treatment response. Analysis of alternative cytokines revealed distinct patterns and IL-22, as well as IL-10, showed comparable expression to IFN-γ in response to PHA. Finally, we found that high IL-6 plasma levels were strongly associated with impaired IFN-γ and IL-22 response to PHA.

Conclusion
We conclude that impaired T-cell response to PHA stimulation in acute tuberculosis patients (i) was potentially caused by the aberrant plasma milieu, (ii) affected differentially polarized T-cell subsets, (iii) normalized early during treatment. This study shed light on the mechanisms of impaired T-cell functions in tuberculosis and yielded promising biomarker candidates for diagnosis and monitoring of treatment response.
stAPAminer: Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies
Authors: Ji Guoli , Tang Qi , Zhu Sheng , Zhu Junyi , Ye Pengchao , Xia Shuting , Wu Xiaohui 
Published: January 2023

Abstract
Alternative polyadenylation (APA) contributes to transcriptome complexity and gene expression regulation and has been implicated in various cellular processes and diseases. Single-cell RNA sequencing (scRNA-seq) has enabled the profiling of APA at the single-cell level; however, the spatial information of cells is not preserved in scRNA-seq. Alternatively, spatial transcriptomics (ST) technologies provide opportunities to decipher the spatial context of the transcriptomic landscape. Pioneering studies have revealed potential spatially variable genes and/or splice isoforms; however, the pattern of APA usage in spatial contexts remains unappreciated. In this study, we developed a toolkit called stAPAminer for mining spatial patterns of APA from spatially barcoded ST data. APA sites were identified and quantified from the ST data. In particular, an imputation model based on the k-nearest neighbors algorithm was designed to recover APA signals, and then APA genes with spatial patterns of APA usage variation were identified. By analyzing well-established ST data of the mouse olfactory bulb (MOB), we presented a detailed view of spatial APA usage across morphological layers of the MOB. We compiled a comprehensive list of genes with spatial APA dynamics and obtained several major spatial expression patterns that represent spatial APA dynamics in different morphological layers. By extending this analysis to two additional replicates of the MOB ST data, we observed that the spatial APA patterns of several genes were reproducible among replicates. stAPAminer employs the power of ST to explore the transcriptional atlas of spatial APA patterns with spatial resolution. This toolkit is available at https://github.com/BMILAB/stAPAminer and https://ngdc.cncb.ac.cn/biocode/tools/BT007320.
Relationships between cumulative entropy/extropy, Gini mean difference and probability weighted moments
Authors: Kattumannil Sudheesh K. , Sreedevi E. P. , Balakrishnan N. 
Published: January 2023

AbstractIn this work, we establish a connection between the cumulative residual entropy and the Gini mean difference (GMD). Some relationships between the extropy and the GMD, and the truncated GMD and dynamic versions of the cumulative past extropy are also established. We then show that several entropy and extropy measures discussed here can be brought into the framework of probability weighted moments, which would facilitate finding estimators of these measures.
Second language acquisition of grammatical rules: The effects of learning condition, rule difficulty, and executive function
Authors: Rivera Marta , Paolieri Daniela , Iniesta Antonio , Pérez Ana I , Bajo Teresa 
Published: January 2023

AbstractLearning a new language is an important goal that many individuals find difficult to achieve, particularly during adulthood. Several factors have related this variability to different extrinsic (learning condition, difficulty of the materials) and intrinsic (cognitive abilities) factors, but the interaction between them is barely known. In two experiments, participants learned English grammar rules in intentional (Experiment 1) or explicit (Experiment 2), and incidental learning-contexts. Overall, results of this study indicated that intentional-explicit conditions benefitted rule-learning, as compared to incidental conditions. This benefit was mainly present when participants were learning an easy-rule; explicit and incidental learning did not differ in the case of participants learning a difficult rule (Experiment 2). Moreover, individual differences in executive functioning predicted successful learning in interaction with difficulty. When learning an easy-rule, proactive control facilitated intentional learning. In contrast, when participants were learning a complex-rule, incidental learning was enhanced by lower involvement of proactive control.
The formation of Supersonically Induced Gas Objects (SIGOs) with H2 cooling
Authors: Nakazato Yurina , Chiaki Gen , Yoshida Naoki , Naoz Smadar , Lake William , Yeou Chiou 
Published: January 2023

AbstractDuring the recombination of the universe, supersonic relative motion between baryons and dark matter (DM) generally existed. In the presence of such streaming motions, gas clumps can collapse outside of virial radii of their closest dark matter halos. Such baryon dominant objects are thought to be self-gravitating and are called supersonically induced gas objects; SIGOs. We perform three-dimensional hydrodynamical simulations by including H2 chemical reactions and stream velocity and follow SIGO’s formation from z = 200 to z = 25. SIGOs can be formed under the influence of stream velocity, and cooling is effective in contracting gas clouds. We follow its further evolution with higher resolution. We find that there are SIGOs which become Jeans unstable outside of the virial radius of the closest DM halos. Those SIGOs are gravitationally unstable and trigger star formation.
The predictive power of numerical simulations to study accretion and outflow in T Tauri Stars
Authors: de Castro Ana I. Gómez 
Published: January 2023

AbstractT Tauri Stars (TTSs) offer a unique chance to study the physics of non-relativistic accretion engines. In this invited talk, the current status of the field is presented with special emphasis on the predictive power of the numerical simulation of magnetospheric accretion and close binary systems and its impact on astronomical observations.
The Effect of Non-Gaussian Primordial Perturbations on Large-Scale Structure
Authors: Peña G. A. , Candlish G. N. 
Published: January 2023

AbstractThe late-time effect of primordial non-Gaussianity offers a window into the physics of inflation and the very early Universe. In this work we study the consequences of a particular class of primordial non-Gaussianity that is fully characterized by initial density fluctuations drawn from a non-Gaussian probability density function, rather than by construction of a particular form for the primordial bispectrum. We numerically generate multiple realisations of cosmological structure and use the late-time matter polyspectra to determine the effect of these modified initial conditions. In this non-Gaussianity has only a small imprint on the first polyspectra, when compared to a standard Gaussian cosmology. Furthermore, some of our models present an interesting scale-dependent deviation from the Gaussian case in the bispectrum and trispectrum, although the signal is at most at the percent level.
Infrared appearance of wind-blown bubbles around young massive stars
Authors: Kirsanova Maria S. , Pavlyuchenkov Yaroslav N. 
Published: January 2023

AbstractThousands of ring-like bubbles appear on infrared images of the Galaxy plane. Most of these infrared bubbles form during expansion of Hii regions around massive stars. However, the physical effects that determine their morphology are still under debate. Namely, the absence of the infrared emission toward the centres of the bubbles can be explained by pushing the dust grains by stellar radiation pressure. At the same time, small graphite grains and PAHs are not strongly affected by the radiation pressure and must be removed by another process. Stellar ultraviolet emission can destroy the smallest PAHs but the photodestruction is ineffective for the large PAHs. Meanwhile, the stellar wind can evacuate all types of grains from Hii regions. In the frame of our chemo-dynamical model we vary parameters of the stellar wind and illustrate their influence on the morphology and synthetic infrared images of the bubbles.
Modeling Stellar Jitter for the Detection of Earth-Mass Exoplanets via Precision Radial Velocity Measurements
Authors: Granovsky Samuel , Kitiashvili Irina N. , Wray Alan A. 
Published: January 2023

AbstractThe detection of Earth-size exoplanets is a technological and data analysis challenge. Future progress in Earth-mass exoplanet detection is expected from the development of extreme precision radial velocity measurements. Increasing radial velocity precision requires developing a new physics-based data analysis methodology to discriminate planetary signals from host-star-related effects, taking stellar variability and instrumental uncertainties into account. In this work, we investigate and quantify stellar disturbances of the planet-hosting solar-type star HD121504 (G2V spectral type) from 3D radiative modeling obtained with the StellarBox code. The model has been used for determining statistical properties of the turbulent plasma and obtaining synthetic spectroscopic observations for several Fe I lines at different locations on the stellar disk to mimic high-resolution spectroscopic observations.
Spring Regional Sea Surface Temperatures as a Precursor of European Summer Heatwaves
Authors: Beobide‐Arsuaga Goratz , Düsterhus André , Müller Wolfgang A. , Barnes Elizabeth A. , Baehr Johanna 
Published: January 2023

AbstractDifferent spring and early summer North Atlantic sea surface temperature anomalies (SSTAs) have been shown to precede recent European summer heatwaves (EuSHWs). So far, the limited number of observed events associated with several physical mechanisms has prevented a robust identification of SSTAs as precursors. Here, we extend beyond previous studies by combining 100 historical simulations (1850–2005) of the MPI Grand‐Ensemble with an explainable neural‐network method. We find that the spring tripolar North Atlantic pattern with positive SSTAs in the Subtropical Gyre is a precursor of EuSHWs. In addition, positive SSTAs west of the Iberian Peninsula, and in the North Sea, the Baltic Sea and the Mediterranean Sea relate to distinct early summer soil moisture anomaly patterns and are precursors of western and southeastern EuSHWs, respectively. While the phase of the tripolar North Atlantic pattern indicates whether a EuSHW might emerge, regional SSTAs indicate the spatial characteristics of EuSHWs.
Description and Evaluation of a New Deep Convective Cloud Model Considering In‐Cloud Inhomogeneity
Authors: Chu Wenchao , Lin Yanluan 
Published: January 2023

AbstractConvections still need to be parameterized in general circulation models (GCMs) in the coming decades. Performances of GCMs are significantly influenced by the convection schemes used. In contrast to most conventional cloud models that ignore in‐cloud inhomogeneities, a new convective cloud model explicitly considering in‐cloud inhomogeneities is developed. The new model adopts a single bulk plume approach, but divides the plume into a series of interacting sub‐plumes in order to mimic the transition from the plume core to its edges. We implemented the new cloud model in NCAR Community Atmosphere Model version 5.0 (CAM5) and evaluated its performance. Single‐column tests show a stronger mass flux profile and low‐level detrainment with the new model. In global simulations, the long‐lasting wet bias in the tropical free troposphere of CAM5 is alleviated. Spatial pattern and intensity distribution of precipitation is improved, but the global hydrological cycle is over‐enhanced. The diurnal cycle of tropical precipitation is also better captured though the precipitation peak still occurs earlier than the observations and the amplitude of the cycle tends to weaken. MJO simulation is slightly improved with the new scheme. In addition, the new cloud model generated more tropical cyclones, in better agreement with observations.
Moving Aircraft River Velocimetry (MARV): Framework and Proof‐of‐Concept on the Tanana River
Authors: Legleiter Carl J. , Kinzel Paul J. , Laker Mark , Conaway Jeffrey S. 
Published: January 2023

AbstractInformation on velocity fields in rivers is critical for designing infrastructure, modeling contaminant transport, and assessing habitat. Although non‐contact approaches to measuring flow velocity are well established, these methods assume a stationary imaging platform. This study eliminates this constraint by introducing a framework for moving aircraft river velocimetry (MARV). The workflow takes as input images acquired from an airplane and involves orthorectification, frame overlap analysis, image enhancement, particle image velocimetry (PIV), and aggregation of the resulting velocity vectors onto a prediction grid. We also use new metrics to quantify the agreement between image‐derived and field‐measured velocity vectors in terms of both orientation and magnitude. The potential of MARV was evaluated using data from two Alaskan rivers: a large, highly turbid channel and its smaller, clearer tributary. Sediment boil vortices on the mainstem provided natural features trackable via PIV and estimated velocities corresponded closely with field measurements (R2 up to 0.911). We compared an exhaustive approach that evaluates overlap for all frame combinations to a simpler rolling window implementation and found that the more efficient algorithm did not compromise accuracy. Sensitivity analysis suggested that the method was robust to window parameterization. Comparing PIV output from different flying heights and imaging systems indicated that larger pixels led to higher accuracy and that a more advanced dual‐camera system provided superior performance. Results from the tributary were less encouraging, presumably due to a lack of trackable features in visible images. Testing across a range of rivers is needed to assess the generality of MARV.
Revealing the tissue-level complexity of endogenous glucagon-like peptide-1 receptor expression and signaling
Authors: Ast Julia , Nasteska Daniela , Fine Nicholas H. F. , Nieves Daniel J. , Koszegi Zsombor , Lanoiselée Yann , Cuozzo Federica , Viloria Katrina , Bacon Andrea , Luu Nguyet T. , Newsome Philip N. , Calebiro Davide , Owen Dylan M. , Broichhagen Johannes , Hodson David J. 
Published: January 2023

AbstractThe glucagon-like peptide-1 receptor (GLP1R) is a class B G protein-coupled receptor (GPCR) involved in glucose homeostasis and food intake. GLP1R agonists (GLP1RA) are widely used in the treatment of diabetes and obesity, yet visualizing the endogenous localization, organization and dynamics of a GPCR has so far remained out of reach. In the present study, we generate mice harboring an enzyme self-label genome-edited into the endogenous Glp1r locus. We also rationally design and test various fluorescent dyes, spanning cyan to far-red wavelengths, for labeling performance in tissue. By combining these technologies, we show that endogenous GLP1R can be specifically and sensitively detected in primary tissue using multiple colors. Longitudinal analysis of GLP1R dynamics reveals heterogeneous recruitment of neighboring cell subpopulations into signaling and trafficking, with differences observed between GLP1RA classes and dual agonists. At the nanoscopic level, GLP1Rs are found to possess higher organization, undergoing GLP1RA-dependent membrane diffusion. Together, these results show the utility of enzyme self-labels for visualization and interrogation of endogenous proteins, and provide insight into the biology of a class B GPCR in primary cells and tissue.
Smarcd3 is an epigenetic modulator of the metabolic landscape in pancreatic ductal adenocarcinoma
Authors: Ferguson L. Paige , Gatchalian Jovylyn , McDermott Matthew L. , Nakamura Mari , Chambers Kendall , Rajbhandari Nirakar , Lytle Nikki K. , Rosenthal Sara Brin , Hamilton Michael , Albini Sonia , Wartenberg Martin , Zlobec Inti , Galván José A. , Karamitopoulou Eva , Vavinskaya Vera , Wascher Alexis , Lowy Andrew M. , Schürch Christian M. , Puri Pier Lorenzo , Bruneau Benoit G. , Hargreaves Diana C. , Reya Tannishtha 
Published: January 2023

AbstractPancreatic cancer is characterized by extensive resistance to conventional therapies, making clinical management a challenge. Here we map the epigenetic dependencies of cancer stem cells, cells that preferentially evade therapy and drive progression, and identify SWI/SNF complex member SMARCD3 as a regulator of pancreatic cancer cells. Although SWI/SNF subunits often act as tumor suppressors, we show that SMARCD3 is amplified in cancer, enriched in pancreatic cancer stem cells and upregulated in the human disease. Diverse genetic mouse models of pancreatic cancer and stage-specific Smarcd3 deletion reveal that Smarcd3 loss preferentially impacts established tumors, improving survival especially in context of chemotherapy. Mechanistically, SMARCD3 acts with FOXA1 to control lipid and fatty acid metabolism, programs associated with therapy resistance and poor prognosis in cancer. These data identify SMARCD3 as an epigenetic modulator responsible for establishing the metabolic landscape in aggressive pancreatic cancer cells and a potential target for new therapies.