bluuebunny/crossref_metadata_2025_split huggingface dataset:
Song recordings suggest feeding ground sharing in Southern Hemisphere humpback whales
Authors: Schall Elena , Djokic Divna , Ross-Marsh Erin C. , Oña Javier , Denkinger Judith , Ernesto Baumgarten Julio , Rodrigues Padovese Linilson , Rossi-Santos Marcos R. , Carvalho Gonçalves Maria Isabel , Sousa-Lima Renata , Hucke-Gaete Rodrigo , Elwen Simon , Buchan Susannah , Gridley Tess , Van Opzeeland Ilse 
Published: August 2022

AbstractThe Atlantic sector of the Southern Ocean (ASSO) has one of the highest densities of Antarctic krill (Euphausia superba) compared to other polar and subpolar regions, which attracts migratory baleen whale species to aggregate in this area for feeding. Humpback whales (Megaptera novaeangliae) also sing extensively while on the Southern Ocean feeding grounds which allows for the exploration of song similarity between feeding grounds and breeding populations which helps to understand population mixing. The results of comparative song analyses between the ASSO and the Ecuadorian and Brazilian breeding populations and recordings from the Chilean, South African and Namibian migration routes/mid-latitude feeding grounds revealed that individuals from at least three humpback whale breeding populations most likely migrate to shared feeding grounds in the ASSO. Humpback whales from different populations potentially mix at different times (i.e., years) at feeding hotspots in variable locations. The ASSO seems to provide sufficient prey resources and seems to present an important area for both cultural and maybe even genetic exchange between populations supporting the maintenance of large gene pools. Assuming that multi-population feeding hotspots are also suitable habitat for krill and other krill-dependent predators, these areas in the ASSO should be carefully managed integrating population, ecosystem and fisheries management.
Cell death responses to acute high light mediated by non-photochemical quenching in the dinoflagellate Karenia brevis
Authors: Gao Yida , Erdner Deana L. 
Published: August 2022

AbstractProgrammed cell death (PCD) can be induced in microalgae by many abiotic challenges via generation of reactive oxygen species (ROS). Marine phytoplankton live in a highly variable light environment, yet the potential for excess photosynthetically available radiation to trigger PCD has not been examined. On the other hand, photoprotective non-photochemical quenching (NPQ) is hypothesized to counteract intracellular ROS, potentially preventing cell death. The main objective of this study is to investigate high-light-induced death processes and their relationship with photosynthesis in bloom-forming dinoflagellate Karenia brevis. Here, we characterized the prevalence of ROS, caspase-like enzyme activity and cell death as well as photosynthetic status under acute irradiance of 500, 750 or 1000 µmol m−2 s−1. PCD only occurred at the largest light shift. Although depressed photosynthetic capacities and oxidative stress were apparent across the stress gradient, they did not necessarily lead to cell death. NPQ exhibited dose-dependent activation with increasing light stress, which enabled cells to resist or delay PCD. These results highlight the important role of the balance between ROS generation and NPQ activation on determining cell fates in Karenia under acute irradiance stress. This research also provides insights into potential survival strategies and mechanisms of cell loss under a changeable light environment.
Jitter noise modeling and its removal using recursive least squares in shape from focus systems
Authors: Mutahira Husna , Shin Vladimir , Park Unsang , Muhammad Mannan Saeed 
Published: August 2022

AbstractThree-dimensional shape recovery from the set of 2D images has many applications in computer vision and related fields. Passive techniques of 3D shape recovery utilize a single view point and one of these techniques is Shape from Focus or SFF. In SFF systems, a stack of images is taken with a single camera by manipulating its focus settings. During the image acquisition, the inter-frame distance or the sampling step size is predetermined and assumed constant. However, in a practical situation, this step size cannot remain constant due to mechanical vibrations of the translational stage, causing jitter. This jitter produces Jitter noise in the resulting focus curves. Jitter noise is invisible in every image, because all images in the stack are exposed to the same error in focus; thus, limiting the use of traditional noise removal techniques. This manuscript formulates a model of Jitter noise based on Quadratic function and the Taylor series. The proposed method, then, solves the jittering problem for SFF systems through recursive least squares (RLS) filtering. Different noise levels were considered during experiments performed on both real as well as simulated objects. A new metric measure is also proposed, referred to as depth distortion (DD), which calculates the number of pixels contributing to the RMSE in percentage. The proposed measure is used along with the RMSE and correlation, to compute and test the reconstructed shape quality. The results confirm the effectiveness of the proposed scheme.
A lignan from Alnus japonica inhibits glioblastoma tumorspheres by suppression of FOXM1
Authors: Shim Jin-Kyoung , Lim Seung Hoon , Jeong Ji Hye , Choi Ran Joo , Oh Yoojung , Park Junseong , Choi Sunghee , Hong Junpyo , Kim Seo Jin , Moon Ju Hyung , Kim Eui Hyun , Teo Wan-Yee , Park Bong Jin , Chang Jong Hee , Ryu Jae-Ha , Kang Seok-Gu 
Published: August 2022

AbstractForkhead Box M1 (FOXM1) is known to regulate cell proliferation, apoptosis and tumorigenesis. The lignan, (−)-(2R,3R)-1,4-O-diferuloylsecoisolariciresinol (DFS), from Alnus japonica has shown anti-cancer effects against colon cancer cells by suppressing FOXM1. The present study hypothesized that DFS can have anti-cancer effects against glioblastoma (GBM) tumorspheres (TSs). Immunoprecipitation and luciferase reporter assays were performed to evaluate the ability of DFS to suppress nuclear translocation of β-catenin through β-catenin/FOXM1 binding. DFS-pretreated GBM TSs were evaluated to assess the ability of DFS to inhibit GBM TSs and their transcriptional profiles. The in vivo efficacy was examined in orthotopic xenograft models of GBM. Expression of FOXM1 was higher in GBM than in normal tissues. DFS-induced FOXM1 protein degradation blocked β-catenin translocation into the nucleus and consequently suppressed downstream target genes of FOXM1 pathways. DFS inhibited cell viability and ATP levels, while increasing apoptosis, and it reduced tumorsphere formation and the invasiveness of GBM TSs. And DFS reduced the activities of transcription factors related to tumorigenesis, stemness, and invasiveness. DFS significantly inhibited tumor growth and prolonged the survival rate of mice in orthotopic xenograft models of GBM. It suggests that DFS inhibits the proliferation of GBM TSs by suppressing FOXM1. DFS may be a potential therapeutic agent to treat GBM.
New fossils from Kromdraai and Drimolen, South Africa, and their distinctiveness among Paranthropus robustus
Authors: Braga José , Chinamatira G. , Zipfel B. , Zimmer V. 
Published: August 2022

AbstractMost fossil hominin species are sampled with spatial, temporal or anatomical biases that can hinder assessments of their paleodiversity, and may not yield genuine evolutionary signals. We use new fossils from the Kromdraai (Unit P) and Drimolen sites (South Africa) to provide insights into the paleodiversity of the Lower Pleistocene robust australopith, Paranthropus robustus. Our focus is the morphology of the temporal bone and the relationships between size and shape (allometry) of the semi-circular canals (SCC), an aspect that has not yet been investigated among southern African australopiths. We find significant size and shape SCC differences between P. robustus from Kromdraai, Drimolen and Swartkrans. This site-related variation is consistent with other differences observed on the temporal bone. P. robustus from Kromdraai Unit P is distinctive because of its smaller temporal bone and SCC, and its proportionally less developed posterior SCC, independently of age and sex. We emphasize the importance of allometry to interpret paleodiversity in P. robustus as either the consequence of differences in body size, or as yet unknown factors. Some features of the inner ear of P. robustus represent directional selection soon after its origin, whereas the size and shape variations described here may result from evolutionary changes.
Preliminary study of thermal density distribution and entropy analysis during cycling exercise stress test using infrared thermography
Authors: Bogomilsky S. , Hoffer O. , Shalmon G. , Scheinowitz M. 
Published: August 2022

AbstractConsiderable differences related to the results of temperature changes acquired during exercise exist, and in many cases, these lead to poor correlation with physiological variables. In this preliminary study we investigated the temperature changes and the temperature distribution (entropy) of the torso during a graded cycling exercise stress test using thermal imaging and studied the correlation between the increase in pulmonary ventilation (VE) and the changes in the surface temperature of the anterior torso during exercise. Thermal images of the anterior torso were captured every 30 s during the exercise, while the resistance was gradually increased every minute until exhaustion. The thermal images were processed to obtain a mean temperature in the regions of interest (ROI) (chest, forehead, and abdomen). We also developed an algorithm to calculate the distribution of temperature and texture (entropy) within each ROI. No changes were found in absolute temperatures. However, the entropy of the chest surface area increased significantly throughout the exercise test, compared with baseline temperature at rest. This increase in entropy was significantly correlated with exercise duration and intensity (p < 0.001). Furthermore, a high correlation between the increase in VE and chest entropy during exercise was detected (r = 0.9515). No correlations were found between the increase in entropy and the abdomen or the forehead compared with the VE. The non-invasive IR thermal imaging during graded exercise, combined with advanced image processing, successfully correlates surface thermography with exercise duration and pulmonary ventilation.
A comparison of reinforcement learning models of human spatial navigation
Authors: He Qiliang , Liu Jancy Ling , Eschapasse Lou , Beveridge Elizabeth H. , Brown Thackery I. 
Published: August 2022

AbstractReinforcement learning (RL) models have been influential in characterizing human learning and decision making, but few studies apply them to characterizing human spatial navigation and even fewer systematically compare RL models under different navigation requirements. Because RL can characterize one’s learning strategies quantitatively and in a continuous manner, and one’s consistency of using such strategies, it can provide a novel and important perspective for understanding the marked individual differences in human navigation and disentangle navigation strategies from navigation performance. One-hundred and fourteen participants completed wayfinding tasks in a virtual environment where different phases manipulated navigation requirements. We compared performance of five RL models (3 model-free, 1 model-based and 1 “hybrid”) at fitting navigation behaviors in different phases. Supporting implications from prior literature, the hybrid model provided the best fit regardless of navigation requirements, suggesting the majority of participants rely on a blend of model-free (route-following) and model-based (cognitive mapping) learning in such navigation scenarios. Furthermore, consistent with a key prediction, there was a correlation in the hybrid model between the weight on model-based learning (i.e., navigation strategy) and the navigator’s exploration vs. exploitation tendency (i.e., consistency of using such navigation strategy), which was modulated by navigation task requirements. Together, we not only show how computational findings from RL align with the spatial navigation literature, but also reveal how the relationship between navigation strategy and a person’s consistency using such strategies changes as navigation requirements change.
Classifying grains using behaviour-informed machine learning
Authors: Laudari Sudip , Marks Benjy , Rognon Pierre 
Published: August 2022

AbstractSorting granular materials such as ores, coffee beans, cereals, gravels and pills is essential for applications in mineral processing, agriculture and waste recycling. Existing sorting methods are based on the detection of contrast in grain properties including size, colour, density and chemical composition. However, many grain properties cannot be directly detected in-situ, which significantly impairs sorting efficacy. We show here that a simple neural network can infer contrast in a wide range of grain properties by detecting patterns in their observable kinematics. These properties include grain size, density, stiffness, friction, dissipation and adhesion. This method of classification based on behaviour can significantly widen the range of granular materials that can be sorted. It can similarly be applied to enhance the sorting of other particulate materials including cells and droplets in microfluidic devices.
Nomograms predicting cancer-specific survival for stage IV colorectal cancer with synchronous lung metastases
Authors: Cheng Pu , Chen Haipeng , Huang Fei , Li Jiyun , Liu Hengchang , Zheng Zhaoxu , Lu Zhao 
Published: August 2022

AbstractThis study aimed to establish a nomogram for the prediction of cancer-specific survival (CSS) of CRC patients with synchronous LM. The final prognostic nomogram based on prognostic factors was evaluated by concordance index (C-index), time-dependent receiver operating characteristic curves, and calibration curves. In the training and validation groups, the C-index for the nomogram was 0.648 and 0.638, and the AUC was 0.793 and 0.785, respectively. The high quality of the calibration curves in the nomogram models for CSS at 1-, 3-, and 5-year was observed. The nomogram model provided a conventional and useful tool to evaluate the 1-, 3-, and 5-year CSS of CRC patients with synchronous LM.
Clinical significance of STING expression and methylation in lung adenocarcinoma based on bioinformatics analysis
Authors: lin Ze , Liu Yu , Lin Peng , Li Jinping , Gan Jinfeng 
Published: August 2022

AbstractThe role of stimulator of interferon genes [STING, also known as transmembrane protein 173 (TMEM173)] in various human cancers has begun to emerge. However, the clinical value of STING in lung adenocarcinoma (LUAD) remains elusive. This study aims to elucidate the clinical significance of STING expression and methylation in LUAD. Here, through analyzing data from public resources, we found that both the mRNA and protein expression of STING were reduced in lung cancer. Moreover, lower expression of STING was associated with a worse prognosis in LUAD, but not lung squamous cell carcinoma (LUSC). Of note, higher methylation of STING was found in LUAD and had the potential to distinguish LUAD tissues from adjacent non-tumor lung tissues and correlated with unfavorable outcomes. Furthermore, the methylation of STING could serve as an independent prognostic indicator for both the overall survival (OS) and disease-free survival (DFS) of LUAD patients. Additionally, the constructed nomogram exhibited a favorable predictive accuracy in predicting the probability of 1- and 2-year OS. Our findings suggest that the mRNA expression, and especially the DNA methylation of STING, have the potential to be prognostic indicators for LUAD patients.
High-frequency stimulation of the subthalamic nucleus induces a sustained inhibition of serotonergic system via loss of cell phenotype
Authors: Alosaimi Faisal , Temel Yasin , Hescham Sarah , Witzig Victoria S. , Almasabi Faris , Tan Sonny K. H. , Jahanshahi Ali 
Published: August 2022

AbstractDeep brain stimulation (DBS) of the subthalamic nucleus (STN) has become a standard treatment for Parkinson’s disease (PD). However, in a considerable number of patients debilitating psychiatric side-effects occur. Recent research has revealed that external stimuli can alter the neurotransmitters’ homeostasis in neurons, which is known as “neurotransmitter respecification”. Herein, we addressed if neurotransmitter respecification could be a mechanism by which DBS suppresses the serotonergic function in the dorsal raphe nucleus (DRN) leading to mood changes. We infused transgenic 5-HT-Cre (ePET-Cre) mice with AAV viruses to achieve targeted expression of eYFP and the genetically encoded calcium indicator GCaMP6s in the DRN prior to methyl-4phenyl-1,2,3,6-tetrahydropyridine (MPTP) treatment. Mice received bilateral DBS electrodes in the STN and an optic fiber in the DRN for calcium photometry. MPTP-treated mice demonstrated behavioral and histological PD phenotype, whereas all STN-DBS animals exhibited an increased immobility time in the forced swim test, reduced calcium activity, and loss of tryptophan hydroxylase-2 expression in the DRN. Given the prominent role of calcium transients in mediating neurotransmitter respecification, these results suggest a loss of serotonergic phenotype in the DRN following STN-DBS. These findings indicate that loss of serotonergic cell phenotype may underlie the unwanted depressive symptoms following STN-DBS.
Demonstration of a two-bit controlled-NOT quantum-like gate using classical acoustic qubit-analogues
Authors: Runge Keith , Hasan M. Arif , Levine Joshua A. , Deymier Pierre A. 
Published: August 2022

AbstractThe Controlled-NOT (CNOT) gate is the key to unlock the power of quantum computing as it is a fundamental component of a universal set of gates. We demonstrate the operation of a two-bit C-NOT quantum-like gate using classical qubit acoustic analogues, called herein logical phi-bits. The logical phi-bits are supported by an externally driven nonlinear acoustic metamaterial composed of a parallel array of three elastically coupled waveguides. A logical phi-bit has a two-state degree of freedom associated with the two independent relative phases of the acoustic wave in the three waveguides. A simple physical manipulation involving the detuning of the frequency of one of the external drivers is shown to operate on the complex vectors in the Hilbert space of pairs of logical phi-bits. This operation achieves a systematic and predictable C-NOT gate with unambiguously measurable input and output. The possibility of scaling the approach to more phi-bits is promising.
Binary dose level classification of tumour microvascular response to radiotherapy using artificial intelligence analysis of optical coherence tomography images
Authors: Majumdar Anamitra , Allam Nader , Zabel W. Jeffrey , Demidov Valentin , Flueraru Costel , Vitkin I. Alex 
Published: August 2022

AbstractThe dominant consequence of irradiating biological systems is cellular damage, yet microvascular damage begins to assume an increasingly important role as the radiation dose levels increase. This is currently becoming more relevant in radiation medicine with its pivot towards higher-dose-per-fraction/fewer fractions treatment paradigm (e.g., stereotactic body radiotherapy (SBRT)). We have thus developed a 3D preclinical imaging platform based on speckle-variance optical coherence tomography (svOCT) for longitudinal monitoring of tumour microvascular radiation responses in vivo. Here we present an artificial intelligence (AI) approach to analyze the resultant microvascular data. In this initial study, we show that AI can successfully classify SBRT-relevant clinical radiation dose levels at multiple timepoints (t = 2–4 weeks) following irradiation (10 Gy and 30 Gy cohorts) based on induced changes in the detected microvascular networks. Practicality of the obtained results, challenges associated with modest number of animals, their successful mitigation via augmented data approaches, and advantages of using 3D deep learning methodologies, are discussed. Extension of this encouraging initial study to longitudinal AI-based time-series analysis for treatment outcome predictions at finer dose level gradations is envisioned.
Bioinformatics analyses of potential ACLF biological mechanisms and identification of immune-related hub genes and vital miRNAs
Authors: Liang Jiajun , Wei Xiaoyi , Hou Weixin , Wang Hanjing , Zhang Qiuyun , Gao Yanbin , Du Yuqiong 
Published: August 2022

AbstractAcute-on-chronic liver failure (ACLF) is a critical and refractory disease and a hepatic disorder accompanied by immune dysfunction. Thus, it is essential to explore key immune-related genes of ACLF and investigate its mechanisms. We used two public datasets (GSE142255 and GSE168048) to perform various bioinformatics analyses, including WGCNA, CIBERSORT, and GSEA. We also constructed an ACLF immune-related protein–protein interaction (PPI) network to obtain hub differentially expressed genes (DEGs) and predict corresponding miRNAs. Finally, an ACLF rat model was established to verify the results. A total of 388 DEGs were identified in ACLF, including 162 upregulated and 226 downregulated genes. The enrichment analyses revealed that these DEGs were mainly involved in inflammatory-immune responses and biosynthetic metabolic pathways. Twenty-eight gene modules were obtained using WGCNA and the coral1 and darkseagreen4 modules were highly correlated with M1 macrophage polarization. As a result, 10 hub genes and 2 miRNAs were identified to be significantly altered in ACLF. The bioinformatics analyses of the two datasets presented valuable insights into the pathogenesis and screening of hub genes of ACLF. These results might contribute to a better understanding of the potential molecular mechanisms of ACLF. Finally, further studies are required to validate our current findings.
Elevated gamma-glutamyl transpeptidase level is associated with an increased risk of hip fracture in postmenopausal women
Authors: Kim Kyoung Jin , Hong Namki , Yu Min Heui , Lee Seunghyun , Shin Sungjae , Kim Sin Gon , Rhee Yumie 
Published: August 2022

AbstractThe aim of this study was to evaluate the association between gamma-glutamyl transferase (GGT) levels and the risk of hip fracture among middle-aged women by using the Korean National Health Insurance Service claims database from 2002 to 2015. After exclusion of those with any chronic liver disease, heavy alcohol consumption, any missing values required for our analysis, or GGT levels less than 1 or greater than 99 percentile, we classified subjects into three groups according to baseline GGT levels. A total of 127,141 women aged 50 years or older were included for analysis (GGT range: 8–106 U/L). During an average 12.1 years of follow-up, 2758 patients sustained hip fractures (2.17%). Compared with the group in the lowest tertile, the group in the highest tertile had the highest cumulative incidence of hip fracture. One log-unit increase in GGT was associated with a 17% increased risk of hip fracture. Subgroup analysis by BMI (≥ 25 vs. < 25 kg/m2), presence of diabetes, levels of other liver enzymes, and alcohol consumption level did not show significant effect modification. In summary, elevated baseline GGT level was associated with an increased risk of hip fracture in postmenopausal women, independent of alcohol consumption and chronic liver disease.