bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibody-dependent cell-mediated cytotoxicity (ADCC) assay with natural killer cells in malaria immunity
Authors: Feng Goaqian , Beeson James 
Published: January 2024

Abstract
Antibody-dependent cellular cytotoxicity (ADCC) by natural killer (NK) cells describes the release of cytotoxic granules against a pathogen or infected cells. This can be mediated by antibodies opsonising a pathogen or infected cell and interacting with the cell surface receptor CD16 (FcγRIIIa) on NK cells. Studies suggest that NK ADCC activity plays a role in acquired and vaccine-induced immunity to malaria. This protocol measures ADCC using CD107 as a marker for cytotoxic granule release following incubation with antigen-coated beads or malaria parasites. Briefly, antigen-coated beads or malaria parasites are opsonised by antigen-specific antibodies and incubated with PBMCs and a fluorescently tagged anti-CD107 antibody. Interactions between the Fc-region of antibodies bound in immune complexes and CD16 expressed by NK cells promotes ADCC results in activation of NK cells with granule release and surface expression of CD107. The level of ADCC is assessed by measuring CD107 expression on NK cells (defined as CD3-CD56+ lymphocytes) with flow cytometry.
Validity and reliability of a flavonoid-focused food frequency questionnaire for Chinese adults
Authors: Cheng Yu , Zhang Wanyi , Zeng Jing , Meng Chengji , Chao Hong , Liu Jinghua , Dong Zheng , Liu Jicheng 
Published: January 2024

Abstract
Background: In recent years, an increasing amount of evidence from nutritional epidemiological studies has revealed an association between flavonoid intake and noncommunicable diseases. The food frequency questionnaire (FFQ) is the most cost-effective method of assessing the dietaryflavonoidintake of both groups and individuals. However, only a few studies in China have developed tailored FFQs to describe dietary flavonoid intake. Therefore, this study aims to develop a flavonoid-focused FFQ for Chinese adults and to assess its relative validity and reproducibility.
Method: We assessed the intake of representativefoods of the Chinese diet using the flavonoid-focused FFQ, which includes 12 food categories and 147 items. We invited 100 healthy adults to complete the flavonoid-focused FFQ twice (at a one-month interval) to assess the reproducibility of the tool. To assess the validity of the questionnaire, we asked 85 adults to complete the flavonoid-focused FFQ once and to complete three 24-hour dietary recall (24HDR) questionnaires for one week.
Results: The reproducibility assessment showed that except for pelargonidin, there were no significant differences in flavonoid intakes between the two FFQ administrations. The Spearman correlation coefficients for nutrients, flavonoid subclasses, and their primary compounds ranged from 0.501 to 0.910, indicating excellent/moderate correlations. The energy-adjusted correlations were within the recommended range for all items. The ICCs ranged from 0.780 to 0.953, and the mean kappa coefficient (Kw) was 0.539. Validity assessment showed that 8 of 19 primary flavonoid compounds had higher intake levels on the FFQ than on the 24HDR. Spearman’s correlation analysis revealed that almost all flavonoid subclasses and primary flavonoid compounds had excellent/moderate correlation coefficients, with the exception of delphinidin, malvidin, pelargonidin, and apigenin. The energy-adjusted intakes showed slightly stronger agreement between the two tools, but this difference did not change the conclusions. The level of agreement (the same tertile) between the flavonoid-focused FFQ and the 24HDR ranged from 41.18% (pelargonidin and apigenin) to 77.65% (total flavonoids). Kw displayed substantial/moderate concordance of nutrients and flavonoid subclass intake and a fair to moderate concordance in almost all primary flavonoid compounds. Only malvidin, pelargonidin, and apigenin had weak concordance.
Conclusion: The flavonoid-focused FFQ developed herein exhibited satisfactory reliability and validity for assessing the intake of most flavonoid subclasses and their primary compounds among Chinese adults. It can be used as a tool to investigate the relationship of flavonoid intake with health- and disease-related outcomes.
Migration of continental arcs dictates Earth's long-term climate state
Authors: Zhang zhaochong , Zhu Jiang , Gernon Thomas , Deng Yinan 
Published: January 2024

Abstract

Earth has experienced multiple shifts between icehouse and greenhouse climate states over multimillion-year time scales, yet the dominant geological processes controlling these shifts remain uncertain. Continental arcs have been proposed to play a dual role in the global carbon cycle via volcanic and metamorphic degassing, as well as the chemical weathering of silicate rocks. Here we reconstructed the paleogeographic extent of active and extinct continental arcs to evaluate the global net degassing and weatherability over geological time. Our results show that prolonged glacial intervals are associated with shorter active continental arcs at mid-high latitudes and longer extinct continental arcs at low latitudes. Conversely, short-lived glacial intervals coincide with longer active continental arcs at mid-high latitudes and extinct continental arcs at low latitudes, or a reduction in the length of active continental arcs at mid-high latitudes combined with a moderate length of extinct continental arcs at low latitudes. We also observe that the length of active or extinct continental arcs at low latitudes increases during long-lived greenhouse intervals, potentially preventing a runaway greenhouse effect through increasing global weatherability. Our findings suggest that the importance of the development of continental arcs along latitudinal migration controlling Earth's climate state.
Benchmarking Machine Learning Methods for Synthetic Lethality Prediction in Cancer
Authors: Zheng Jie , Feng YiMiao , Long Yahui , Wang He , Ouyang Yang , Li Quan , Wu Min 
Published: January 2024

Abstract

Synthetic lethality (SL) is a type of genetic interaction that occurs when defects in two genes cause cell death, while a defect in a single gene does not. Targeting an SL partner of a gene mutated in cancer can selectively kill tumor cells. Traditional wet-lab experiments for SL screening are resource-intensive. Hence, many computational methods have been developed for virtual screening of SL gene pairs. This study benchmarks recent machine learning methods for SL prediction, including three matrix factorization and eight deep learning models. We scrutinize model performance using various data splitting scenarios, negative sample ratios, and negative sampling methods on both classification and ranking tasks to assess the models’ generalizability and robustness. Our benchmark analyzed performance differences among the models and emphasized the importance of data and real-world scenarios. Finally, we suggest future directions to improve machine learning methods for SL discovery in terms of predictive power and interpretability.
Molecular signatures of astrocytes and microglia maladaptive responses to acute stress are rescued by a single administration of ketamine in a rodent model of PTSD
Authors: Scuderi Caterina , Valenza Marta , Facchinetti Roberta , Torazza Carola , Ciarla Claudia , Bronzuoli Maria , Balbi Matilde , Bonanno Giambattista , Popoli Maurizio , Steardo Luca , Milanese Marco , Musazzi Laura , Bonifacino Tiziana 
Published: January 2024

Abstract

Stress affects the brain and alters its neuroarchitecture and function; these changes can be severe and lead to psychiatric disorders. Recent evidence suggests that astrocytes and microglia play an essential role in the stress response by contributing to the maintenance of cerebral homeostasis. These cells respond rapidly to all stimuli reaching the brain, including stressors. Using a recently validated rodent model of post-traumatic stress disorder that allows rats to be classified as resilient or vulnerable after acute inescapable footshock stress, we here examined the functional, molecular, and morphological determinants of stress resilience and vulnerability in the prefrontal cortex, focusing on both glial and neuronal cells. In addition, we studied the effects of a single subanesthetic dose of ketamine, a fast-acting antidepressant recently approved for use in treatment-resistant depression and proposed for other stress-related psychiatric disorders. The present results suggest a prompt glial cell response and activation of the NF-κB pathway after acute stress, with an increase in specific cytokines such as IL-18 and TNF-α. This response persists in vulnerable individuals and is associated with a significant change in the levels of critical glial proteins such as S100B, CD11b, and CX43, brain trophic factors such as BDNF and FGF2, and proteins related to dendritic arborization and synaptic architecture such as MAP2 and PSD95. Administration of ketamine 24 h after the acute stress event rescued many changes observed in vulnerable rats, possibly contributing to support brain homeostasis. Overall, our results suggest that glial reactivity, changes in brain trophic factors, and neuronal damage are critical determinants of vulnerability to acute traumatic stress and confirm the therapeutic effect of acute ketamine against the development of stress-related psychiatric disorders.
An Organic “Proton Cage” that is Ultra-Resistant to Hydroxide-Promoted Degradation
Authors: Holdcroft Steven , Radford Chase , Saatkamp Torben , Bennet Andrew 
Published: January 2024

Abstract
We report 1,6-diazabicyclo[4.4.4]tetradecan-1,6-ium (in-DBD), a cationic “proton cage”, that is orders of magnitude more resistant to hydroxide-promoted degradation than state-of-the-art organic cations under ultra-dry conditions and elevated temperature, and the first organic cation-hydroxide to persist at critically low hydration levels (<10% RH at 80 °C). This unprecedented stability against hydroxide-promoted degradation is due to the unique combination of endohedral protection and intra-bridgehead hydrogen bonding that prevents the removal of the inter-cavity proton and lowers the susceptibility to Hofmann elimination. We anticipate this discovery will facilitate a step-change in the advancement of materials and electrochemical devices utilizing anion-exchange membranes based on in-DBD that will enable stable operation under extreme alkaline conditions.
Accurate Fine-Grained Segmentation of Human Anatomy in Radiographs via Volumetric Pseudo-Labeling
Authors: Seibold Constantin , Jaus Alexander , Fink Matthias , Kim Moon , Reiß Simon , Herrmann Ken , Kleesiek Jens , Stiefelhagen Rainer 
Published: January 2024

Abstract
Purpose: Interpreting chest radiographs (CXR) remains challenging due to the ambiguity of overlapping structures such as the lungs, heart, and bones. To address this issue, we propose a novel method for extracting fine-grained anatom- ical structures in CXR using pseudo-labeling of three-dimensional computed tomography (CT) scans.
Methods: We created a large-scale dataset of 10,021 thoracic CTs with 157 labels and applied an ensemble of 3D anatomy segmentation models to extract anatomical pseudo-labels. These labels were projected onto a two-dimensional plane, similar to the CXR, allowing the training of detailed semantic segmentation models for CXR without any manual annotation effort.
Results: Our resulting segmentation models demonstrated remarkable performance on CXR, with a high average model-annotator agreement between two radiologists with mIoU scores of 0.93 and 0.85 for frontal and lateral anatomy, while inter-annotator agreement remained at 0.95 and 0.83 mIoU. Our anatom- ical segmentations allowed for the accurate extraction of relevant explainable medical features such as the cardio-thoracic-ratio.
Conclusion: Our method of volumetric pseudo-labeling paired with CT projection offers a promising approach for detailed anatomical segmentation of CXR with a high agreement with human annotators. This technique may have important clinical implications, particularly in the analysis of various thoracic pathologies.
Image Captioning by Using Bidirectional LSTM Neural Network
Authors: Hoseini Farnaz , Notash Anaram Yaghoobi 
Published: January 2024

Abstract

Putting captions on images is an important phase in image processing and machine vision which divides an image into different regions. In the related captioning operation, similar attributes are extracted from each region and a single caption is opted for the title of the input for the relevant image. In the developed world, due to the considerable volume of images that have been available on the Internet, it is complicated to choose a suitable method for captioning images automatically and determining concepts correctly. In this study, a method based on a Bidirectional LSTM neural network with 14 layers is used for automatic captioning. The dataset is trained on ImageNet by MobileNet architecture. Due to the high volume of the data set consequently with the huge calculations that are required for captioning, MobileNet architecture has been applied to decrease the computational load and to boost the performance of the proposed method. in this study, the data set is flickr8k with a volume of data of more than 1.04 GB which was selected as one of the challenging data sets for captioning images through the Kaggle site. The proposed method is implemented with Python language by artificial intelligence package TensorFlow and Cross on Google Colab. The proposed Bidirectional LSTM neural network has been compared with five other models based on the LSTM neural network. So, the results of these comparisons have been evaluated for Precision, Accuracy, Recall, F score, and Loss Function. According to the hardware's limitations and the huge volume of calculations, the proposed model was able to show convincing performance compared to other models. The obtained results with an accuracy of 75.90% indicate the improvement of the accuracy as well as the reduction of the cost in the captioning process for the proposed model.
Activated Factor X delivered by Adeno-Associated virus significantly inhibited bleeding and alleviated hemophilia A/B arthropathy in hemophilia mice
Authors: Wu Xia , Zhang Feixu , Zhou Xinyue , Hua Baolai , He Xinyi , Li Zhanao , Xiao Xiao 
Published: January 2024

Abstract

In hemophilia, deficient factor VIII or IX in hemophilia prevents activation of the common coagulation pathway, inhibiting conversion of FX to activated FXa required for thrombin generation. We hypothesized that delivering FXa could activate the common pathway and restore coagulation in hemophilia patients. In this study, we tried to deliver FXa by adeno-associated virus (AAV) for treating hemophilia and hemophilic arthropathy. The cassettes that expressed FXa, FXa (FXaop) and FXa-FVII was constructed and were packaged into an engineered AAV capsid, AAV843. Delivered AAVs into hemophilia A and B mice by intravenous injection. We evaluated the therapeutic efficacy by tail clip bleeding assay and D-Dimer test. Further, FXa was transduced into hemophilia A mice with FVIII inhibitor or hemophilic arthropathy for evaluating its efficacy. AAV-FXa could stably express in vivo, and AAV-FXaop showed the best immediate and prolonged hemostatic effects that was similar to the positive drug groups (Xyntha and Benefix). Compared to other two AAVs, AAV-FXaop could significantly inhibit bleeding of hemophilia A mice with inhibitor. In addition, long-term expression of FXa in vivo significantly alleviated the occurrence of hemophilia arthropathy. AAV-delivered FXa may be a novel target to treating hemophilia A/B and hemophilia arthropathy.
Testicular sperm aspiration (TESA) outcome in Middle Eastern patients with non-obstructive azoospermia: A Retrospective cohort study
Authors: Alquobaili Manal , Hamsho Shahd , Alhalabi Marwan 
Published: January 2024

Abstract

Background: Infertility is an important health problem, affecting couples worldwide. Non -obstructive azoospermia is the most severe form of azoospermia, which is almost idiopathic or caused by different causes such as chemotherapy and genetic disorders. Testicular Fine needle aspiration (or Testicular sperm aspiration (TESA)) is a simple, cost-effective and less invasive than testicular sperm extraction.
Materials and Methods: 320 Middle Eastern patients with NOA were recruited in this study. The patients underwent routine infertility assessment including medical, surgical and reproductive history, physical examination, semen analysis and hormonal profile including FSH, Testosterone and inhibin B in addition to Genetic assessment including karyotype and Y-chromosome micro-deletion
Results: Testicular sperm aspiration was positive in 70 patients (22.18%). Serum FSH levels were clearly elevated in the patients with negative sperm retrieval (mean = 20.6IU/L), while they were reduced in the positive result (mean = 15.2IU/L). Testosterone value did not clearly affect the results of Testicular sperm aspiration in the two groups of patients, and testicular volume was normal for most of the patients in the two groups. Patients with Y-chromosome micro-deletion represented 11.22% and they had negative TESA result, while 13.12% of patients had Klinefelter Syndrome and their TESA results were negative.
Conclusion: we confirmed that there are many factors negatively affect Testicular sperm aspiration results: high FSH and low inhibin B levels, smoking and genetic disorders .Despite the absence of sperms in the semen, some NOA patients have a chance to have children by using this technique.
Coffee Leaf Plant Disease Identification through Image Processing and Machine-Learning Techniques in Ethiopia.
Authors: Taye Bayile Getu , Goel Neeraj 
Published: January 2024

Abstract
Abstract—Coffee plants are woody evergreens that can reach a height of up to ten meter’s in the wild with the fruit of coffee beans, which are the seeds that produce the majority of the world’s coffee. This study focuses on a variety of Arabica Coffee leaf diseases that occurs frequently in Ethiopia. The diseases which occurred primarily are Miner coffee leaf disease (MCLD), Rust coffee leaf disease (RCLD), Cercospora coffee leaf disease (CCLD), and Phoma coffee leaf disease (PCLD). The study focuses on the identification of those four a variety of diseases through image processing as well as machine learning mechanisms through Transfer learning and convolution neural network (CNN) architectures through the feed-forward model, resnet50 model, inceptionV3 model, and deep learning model through tenser flow, which are the most popular models to detect various plant diseases with high Accuracy. All the pictures used for this study were captured from the whole state of Ethiopia in every place where coffee plant exists. The total number of data sets currently used is 58,546 with 80 percent being put to use for training, while the rest 20 percent were employed for testing, with a 99.9%, 98.5%, 99%, and 99% respectively with a total success rate in classification accuracy and 99.8%, 98%, 99% and 99.7% respectively with total success rate in confusion matrix accuracy. So there is excellent performance in inferences.
Study on properties of AgCuInTi filler metal for active bonding of alumina ceramic
Authors: Yuan Linlin , Huang Xiaomeng , Qi Yuefeng , Liu Xu 
Published: January 2024

Abstract
In this paper, a novel AgCuInTi20-20-4.5 active filler paste for Al2O3 bonding was prepared using the route of vacuum smelting and centrifugal atomizing powder production. The aim of the research was to characterize the AgCuInTi filler paste, and to study the direct brazing of Al2O3 ceramics and copper. The microstructure and melting properties of AgCuInTi powder was analyzed using scanning electron microscopy (SEM) and differential scanning calorimeter (DSC). The brazing process was carried out on vacuum brazing furnace at 700°C for 10 min. The joint microstructures were studied by means of SEM and EDS. The results show that Ti reacted with Al2O3 as the active element at the interface between ceramic and filler metal and finally realizing the metallurgical combination. In participated in the reaction with Ag and Cu. The main products in the brazing seam are TiO2, Cu3TiO4, Cu4Ti, Ag3In and Cu4In based on XRD. The mean value of tensile strength of the brazed joints is approximately 89 MPa. The studied AgCuInTi possesses excellent joining characteristics with several metallic and ceramic materials.
Shaping the Future of Lighting Design: a Perspective of Architecture and Interior Architecture Students
Authors: Ozenen Gurkan 
Published: January 2024

Abstract
With the increasing sophistication of global illumination algorithms, lighting design software has become an accessible tool for architects and interior designers. Despite the potential benefits of these tools for teaching and learning lighting design, the use of lighting design software is not widely integrated into architecture and interior architecture education. This paper presents the results of an online survey of architecture and interior architecture students at two universities in Istanbul, Turkey, aiming to determine the extent of use of lighting design software in learning lighting at the undergraduate level and to assess student’s attitudes towards their usefulness in design education. The findings reveal that although lighting design software is acknowledged as an important tool for teaching and learning lighting design, it is not commonly used due to a lack of knowledge, training, and resources. The results of this study also suggest that there is a need for greater integration of lighting design software into architecture and interior architecture education. The paper concludes by proposing recommendations for integrating lighting design software into architecture and interior architecture education, including incorporating software training into the curriculum, promoting interdisciplinary collaboration between lighting designers and architects, and providing access to software and resources.
Determination of 17 β-estradiol residues in fish: A case study of using hormone for sex- reversal in Anabas testudineus (Bloch, 1792) in small farm in Thailand
Authors: Pianjing P. , Thammakhet-Buranachai C. , Deki D , Kaewklapanyacharoen L. , Payanan T. P. 
Published: January 2024

Abstract
Several small farms in Thailand mix the 17β-estradiol with fish feed and rear the Anabas testudineus fries for 21–28 days in order to obtain the female mono-sex. However, it is important to monitoring the residues of 17β-estradiol in A. testudineus that derived from real farm. This study determined the residues of 17β-estradiol in A. testudineus fries that rearing in cement tanks in a small farm in Thailand for 3 times including, April, June and November. The 3 tanks were set as the control groups (AC) and the 3 tanks were set as hormonal treatment group (AH). The fish samples were collected at the last day of hormone treatments in each month which were at day 21st except in November, the fish samples were collected at the day 28th. After 24 hours of hormone withdrawal, the fish sample were collected to investigate the hormone residues. The result showed that the residual hormone levels in fish sample collected at the last days of AH groups showed high variation among rearing tanks and the hormone levels ranged from undetectable (ND) – 1575 ng/g while the AC group cannot be detected. The highest hormone residue in fish sample was observed in November. After hormone withdrawal for 24 hours, the residual hormone cannot be detected in all treatments indicating that there was no accumulation of 17β-estradiol in A. testudineus that expose to the hormone via feeding. The A. testudineus fries can be brought to rear further and the hormone residues should be inattentive.