bluuebunny/crossref_metadata_2025_split huggingface dataset:
Active and stable alcohol dehydrogenase-assembled hydrogels via synergistic bridging of triazoles and metal ions
Authors: Chen Qiang , Qu Ge , Li Xu , Feng Mingjian , Yang Fan , Li Yanjie , Li Jincheng , Tong Feifei , Song Shiyi , Wang Yujun , Sun Zhoutong , Luo Guangsheng 
Published: April 2023

AbstractBiocatalysis is increasingly replacing traditional methods of manufacturing fine chemicals due to its green, mild, and highly selective nature, but biocatalysts, such as enzymes, are generally costly, fragile, and difficult to recycle. Immobilization provides protection for the enzyme and enables its convenient reuse, which makes immobilized enzymes promising heterogeneous biocatalysts; however, their industrial applications are limited by the low specific activity and poor stability. Herein, we report a feasible strategy utilizing the synergistic bridging of triazoles and metal ions to induce the formation of porous enzyme-assembled hydrogels with increased activity. The catalytic efficiency of the prepared enzyme-assembled hydrogels toward acetophenone reduction is 6.3 times higher than that of the free enzyme, and the reusability is confirmed by the high residual catalytic activity after 12 cycles of use. A near-atomic resolution (2.1 Å) structure of the hydrogel enzyme is successfully analyzed via cryogenic electron microscopy, which indicates a structure–property relationship for the enhanced performance. In addition, the possible mechanism of gel formation is elucidated, revealing the indispensability of triazoles and metal ions, which guides the use of two other enzymes to prepare enzyme-assembled hydrogels capable of good reusability. The described strategy can pave the way for the development of practical catalytic biomaterials and immobilized biocatalysts.
Babesia duncani multi-omics identifies virulence factors and drug targets
Authors: Singh Pallavi , Lonardi Stefano , Liang Qihua , Vydyam Pratap , Khabirova Eleonora , Fang Tiffany , Gihaz Shalev , Thekkiniath Jose , Munshi Muhammad , Abel Steven , Ciampossin Loic , Batugedara Gayani , Gupta Mohit , Lu Xueqing Maggie , Lenz Todd , Chakravarty Sakshar , Cornillot Emmanuel , Hu Yangyang , Ma Wenxiu , Gonzalez Luis Miguel , Sánchez Sergio , Estrada Karel , Sánchez-Flores Alejandro , Montero Estrella , Harb Omar S. , Le Roch Karine G. , Mamoun Choukri Ben 
Published: April 2023

AbstractBabesiosis is a malaria-like disease in humans and animals that is caused by Babesia species, which are tick-transmitted apicomplexan pathogens. Babesia duncani causes severe to lethal infection in humans, but despite the risk that this parasite poses as an emerging pathogen, little is known about its biology, metabolic requirements or pathogenesis. Unlike other apicomplexan parasites that infect red blood cells, B. duncani can be continuously cultured in vitro in human erythrocytes and can infect mice resulting in fulminant babesiosis and death. We report comprehensive, detailed molecular, genomic, transcriptomic and epigenetic analyses to gain insights into the biology of B. duncani. We completed the assembly, 3D structure and annotation of its nuclear genome, and analysed its transcriptomic and epigenetics profiles during its asexual life cycle stages in human erythrocytes. We used RNA-seq data to produce an atlas of parasite metabolism during its intraerythrocytic life cycle. Characterization of the B. duncani genome, epigenome and transcriptome identified classes of candidate virulence factors, antigens for diagnosis of active infection and several attractive drug targets. Furthermore, metabolic reconstitutions from genome annotation and in vitro efficacy studies identified antifolates, pyrimethamine and WR-99210 as potent inhibitors of B. duncani to establish a pipeline of small molecules that could be developed as effective therapies for the treatment of human babesiosis.
A dataset of global ocean alkaline phosphatase activity
Authors: Su Bei , Song Xianrui , Duhamel Solange , Mahaffey Claire , Davis Clare , Ivančić Ingrid , Liu Jihua 
Published: April 2023

AbstractUtilisation of dissolved organic phosphorus (DOP) by marine microbes as an alternative phosphorus (P) source when phosphate is scarce can help sustain non-Redfieldian carbon:nitrogen:phosphorus ratios and efficient ocean carbon export. However, global spatial patterns and rates of microbial DOP utilisation are poorly investigated. Alkaline phosphatase (AP) is an important enzyme group that facilitates the remineralisation of DOP to phosphate and thus its activity is a good proxy for DOP-utilisation, particularly in P-stressed regions. We present a Global Alkaline Phosphatase Activity Dataset (GAPAD) with 4083 measurements collected from 79 published manuscripts and one database. Measurements are organised into four groups based on substrate and further subdivided into seven size fractions based on filtration pore size. The dataset is globally distributed and covers major oceanic regions, with most measurements collected in the upper 20 m of low-latitude oceanic regions during summer since 1997. This dataset can help support future studies assessing global ocean P supply from DOP utilisation and provide a useful data reference for both field investigations and modelling activities.
Dichotomous versus 5-scale grading system for the interpretation of the point-of-care immunoassay for tear matrix metalloproteinase-9 in dry eye
Authors: Oh Ja Young , Chun Yeoun Sook , Kim Kyoung Woo 
Published: April 2023

AbstractIn this study, we compared the dichotomous and 5-scale grading systems for point-of-care immunoassay of tear matrix metalloproteinase (MMP)-9 in dry eye disease (DED) patients and identified the optimal dichotomous system to correlate with DED parameters. We included 167 DED patients without primary Sjogren's syndrome (pSS) (Non-SS DED) and 70 DED patients with pSS (SS DED). We graded MMP-9 expression in InflammaDry® (Quidel, San Diego, CA, USA) using a 5-scale grading system and dichotomous grading systems with four different cut-off grades (D1 to D4 systems). The only DED parameter that showed a significant correlation with the 5-scale grading method was tear osmolarity (Tosm). In both groups, subjects with positive MMP-9 had lower tear secretion and higher Tosm than those with negative MMP-9 according to the D2 dichotomous system. Tosm determined D2 positivity at cutoffs > 340.5 and > 317.5 mOsm/L in the Non-SS DED and SS DED groups, respectively. Tear secretion < 10.5 mm or tear break-up time < 5.5 s stratified D2 positivity in the Non-SS DED group. In conclusion, the dichotomous grading system of InflammaDry reflects ocular surface indices better than the 5-scale grading system and may be more practical in real clinical circumstances.
Neural networks determination of material elastic constants and structures in nematic complex fluids
Authors: Zaplotnik Jaka , Pišljar Jaka , Škarabot Miha , Ravnik Miha 
Published: April 2023

AbstractSupervised machine learning and artificial neural network approaches can allow for the determination of selected material parameters or structures from a measurable signal without knowing the exact mathematical relationship between them. Here, we demonstrate that material nematic elastic constants and the initial structural material configuration can be found using sequential neural networks applied to the transmmited time-dependent light intensity through the nematic liquid crystal (NLC) sample under crossed polarizers. Specifically, we simulate multiple times the relaxation of the NLC from a random (qeunched) initial state to the equilibirum for random values of elastic constants and, simultaneously, the transmittance of the sample for monochromatic polarized light. The obtained time-dependent light transmittances and the corresponding elastic constants form a training data set on which the neural network is trained, which allows for the determination of the elastic constants, as well as the initial state of the director. Finally, we demonstrate that the neural network trained on numerically generated examples can also be used to determine elastic constants from experimentally measured data, finding good agreement between experiments and neural network predictions.
Sex and age affect acute and persisting COVID-19 illness
Authors: Vasilevskaya Anna , Mushtaque Asma , Tsang Michelle Y. , Alwazan Batoul , Herridge Margaret , Cheung Angela M. , Tartaglia Maria Carmela 
Published: April 2023

AbstractLong COVID is associated with neurological and neuropsychiatric manifestations. We conducted an observational study on 97 patients with prior SARS-CoV-2 infection and persisting cognitive complaints that presented to the University Health Network Memory Clinic between October 2020 and December 2021. We assessed the main effects of sex, age, and their interaction on COVID-19 symptoms and outcomes. We also examined the relative contribution of demographics and acute COVID-19 presentation (assessed retrospectively) on persistent neurological symptoms and cognition. Among our cohort, males had higher hospitalization rates than females during the acute COVID-19 illness (18/35 (51%) vs. 15/62 (24%); P = .009). Abnormal scores on cognitive assessments post-COVID were associated with older age (AOR = 0.84; 95% CI 0.74–0.93) and brain fog during initial illness (AOR = 8.80; 95% CI 1.76–65.13). Female sex (ARR = 1.42; 95% CI 1.09–1.87) and acute shortness of breath (ARR = 1.41; 95% CI 1.09–1.84) were associated with a higher risk of experiencing more persistent short-term memory symptoms. Female sex was the only predictor associated with persistent executive dysfunction (ARR = 1.39; 95% CI 1.12–1.76) and neurological symptoms (ARR = 1.66; 95% CI 1.19–2.36). Sex differences were evident in presentations and cognitive outcomes in patients with long COVID.
Pan-cancer investigation of psoriasis-related BUB1B gene: genetical alteration and oncogenic immunology
Authors: Li Xiaobin , Wang Wenwen , Ding Xiaoxia 
Published: April 2023

AbstractUnknown factors contribute to psoriasis' hyperproliferative, chronic, inflammatory, and arthritic features. Psoriasis patients have been linked to an increased risk of cancer, though the underlying genetics remain unknown. Since our prior research indicated that BUB1B contributes to the development of psoriasis, we designed and carried out this investigation using bioinformatics analysis. Using the TCGA database, we investigated the oncogenic function of BUB1B in 33 tumor types. To sum up, our work sheds light on BUB1B's function in pan-cancer from various perspectives, including its pertinent signaling pathways, mutation locations, and connection to immune cell infiltration. BUB1B was shown to have a non-negligible role in pan-cancer, which is connected to immunology, cancer stemness, and genetic alterations in a variety of cancer types. BUB1B is highly expressed in a variety of cancers and may serve as a prognostic marker. This study is anticipated to offer molecular details on the elevated cancer risk that psoriasis sufferers experience.
Measuring antigen expression of cancer cell lines and circulating tumour cells
Authors: Mentink Anouk , Isebia Khrystany T. , Kraan Jaco , Terstappen Leon W. M. M. , Stevens Michiel 
Published: April 2023

AbstractWhen evaluating EpCAM-based enrichment technologies for circulating tumour cells (CTCs), the cell lines used should closely resemble real CTCs, meaning the EpCAM expression of CTCs needs to be known, but also the EpCAM expression of cell lines at different institutions and times is important. As the number of CTCs in the blood is low, we enriched CTCs through the depletion of leukocytes from diagnostic leukapheresis products of 13 prostate cancer patients and measured EpCAM expression using quantitative flow cytometry. Antigen expression was compared between multiple institutions by measuring cultures from each institution. Capture efficiency was also measured for one of the used cell lines. Results show CTCs derived from castration-sensitive prostate cancer patients have varying but relatively low EpCAM expression, with median expression per patient ranging from 35 to 89,534 (mean 24,993) molecules per cell. A large variation in the antigen expression of identical cell lines cultured at different institutions was found, resulting in recoveries when using the CellSearch system ranging from 12 up to 83% for the same cell line. We conclude that large differences in capture efficiency can occur while using the same cell line. To closely resemble real CTCs from castration-sensitive prostate cancer patients, a cell line with a relatively low EpCAM expression should be used, and its expression should be monitored frequently.
The risk of post-polio syndrome among immigrant groups in Sweden
Authors: Wändell Per , Borg Kristian , Li Xinjun , Carlsson Axel C. , Sundquist Jan , Sundquist Kristina 
Published: April 2023

AbstractTo examine the risk of post-polio syndrome (PPS) in immigrant groups using native Swedish-born individuals as referents. This is a retrospective study. The study population included all individuals aged 18 years and older registered in Sweden. PPS was defined as having at least one registered diagnosis in the Swedish National Patient Register. The incidence of post-polio in different immigrant groups, using Swedish-born individuals as referents, was assessed by Cox regression, with hazard ratios (HRs) and 99% confidence intervals (CI). The models were stratified by sex and adjusted for age, geographical residence in Sweden, educational level, marital status, co-morbidities, and neighbourhood socioeconomic status. In total 5300 post-polio cases were registered, 2413 males and 2887 females. Fully adjusted HRs (99% CI) in immigrants versus Swedish-born were 1.77 in men (1.52–2.07) and 1.39 (1.19–1.62) in women. Statistically significant excess risks of post-polio were found in the following subgroups: men and women from Africa, HRs (with 99% CI) 7.40 (5.17–10.59) and 8.39 (5.44–12.95), respectively, and Asia, HRs 6.32 (5.11–7.81) and 4.36 (3.38–5.62) respectively, and in men from Latin America, HR 3.66 (2.17–6.18). It is of importance to be aware of risks of PPS in immigrants settled in Western countries, and that it is more common in immigrants from regions of the world where polio is still prevalent. Patients with PPS need treatment and proper follow-up until polio has been eradicated through global vaccination programs.
Antiviral effect of melatonin on Japanese encephalitis virus infection involves inhibition of neuronal apoptosis and neuroinflammation in SH-SY5Y cells
Authors: Kitidee Kuntida , Samutpong Arisara , Pakpian Nattaporn , Wisitponchai Tanchanok , Govitrapong Piyarat , Reiter Russel J. , Wongchitrat Prapimpun 
Published: April 2023

AbstractJapanese encephalitis virus (JEV), a mosquito-borne flavivirus, causes high mortality rates in humans and it is the most clinically important and common cause of viral encephalitis in Asia. To date, there is no specific treatment for JEV infection. Melatonin, a neurotropic hormone, is reported to be effective in combating various bacterial and viral infections. However, the effects of melatonin on JEV infection have not yet been studied. The investigation tested the antiviral effects of melatonin against JEV infection and elucidated the possible molecular mechanisms of inhibition. Melatonin inhibited the viral production in JEV-infected SH-SY5Y cells in a time- and dose-dependent manner. Time-of-addition assays demonstrated a potent inhibitory effect of melatonin at the post-entry stage of viral replication. Molecular docking analysis revealed that melatonin negatively affected viral replication by interfering with physiological function and/or enzymatic activity of both JEV nonstructural 3 (NS3) and NS5 protein, suggesting a possible underlying mechanism of JEV replication inhibition. Moreover, treatment with melatonin reduced neuronal apoptosis and inhibited neuroinflammation induced by JEV infection. The present findings reveal a new property of melatonin as a potential molecule for the further development of anti-JEV agents and treatment of JEV infection.
Deep learning synthesis of cone-beam computed tomography from zero echo time magnetic resonance imaging
Authors: Choi Hyeyeon , Yun Jong Pil , Lee Ari , Han Sang-Sun , Kim Sang Woo , Lee Chena 
Published: April 2023

AbstractCone-beam computed tomography (CBCT) produces high-resolution of hard tissue even in small voxel size, but the process is associated with radiation exposure and poor soft tissue imaging. Thus, we synthesized a CBCT image from the magnetic resonance imaging (MRI), using deep learning and to assess its clinical accuracy. We collected patients who underwent both CBCT and MRI simultaneously in our institution (Seoul). MRI data were registered with CBCT data, and both data were prepared into 512 slices of axial, sagittal, and coronal sections. A deep learning-based synthesis model was trained and the output data were evaluated by comparing the original and synthetic CBCT (syCBCT). According to expert evaluation, syCBCT images showed better performance in terms of artifacts and noise criteria but had poor resolution compared to the original CBCT images. In syCBCT, hard tissue showed better clarity with significantly different MAE and SSIM. This study result would be a basis for replacing CBCT with non-radiation imaging that would be helpful for patients planning to undergo both MRI and CBCT.
Synthetic symbiosis between a cyanobacterium and a ciliate toward novel chloroplast-like endosymbiosis
Authors: Azuma Yuki , Tsuru Saburo , Habuchi Masumi , Takami Risa , Takano Sotaro , Yamamoto Kayo , Hosoda Kazufumi 
Published: April 2023

AbstractChloroplasts are thought to have co-evolved through endosymbiosis, after a cyanobacterial-like prokaryote was engulfed by a eukaryotic cell; however, it is impossible to observe the process toward chloroplasts. In this study, we constructed an experimental symbiosis model to observe the initial stage in the process from independent organisms to a chloroplast-like organelle. Our system of synthetic symbiosis is capable of long-term coculture of two model organisms: a cyanobacterium (Synechocystis sp. PCC6803) as a symbiont and a ciliate (Tetrahymena thermophila) as a host with endocytic ability. The experimental system was clearly defined, because we used a synthetic medium and the cultures were shaken to avoid spatial complexity. We determined the experimental conditions for sustainable coculture, by analyzing population dynamics using a mathematical model. We experimentally demonstrated that the coculture was sustainable for at least 100 generations, through serial transfers. Moreover, we found that cells isolated after the serial transfer improved the probability of coexistence of both species without extinction in re-coculture. The constructed system will be useful for understanding the initial stage of primary endosymbiosis from cyanobacteria to chloroplasts, i.e., the origin of algae and plants.
Application and limitation of a biological clock-based method for estimating time of death in forensic practices
Authors: Kimura Akihiko , Ishida Yuko , Nosaka Mizuho , Ishigami Akiko , Yamamoto Hiroki , Kuninaka Yumi , Hata Satoshi , Ozaki Mitsunori , Kondo Toshikazu 
Published: April 2023

AbstractEstimating time of death is one of the most important problems in forensics. Here, we evaluated the applicability, limitations and reliability of the developed biological clock-based method. We analyzed the expression of the clock genes, BMAL1 and NR1D1, in 318 dead hearts with defined time of death by real-time RT-PCR. For estimating the time of death, we chose two parameters, the NR1D1/BMAL1 ratio and BMAL1/NR1D1 ratio for morning and evening deaths, respectively. The NR1D1/BMAL1 ratio was significantly higher in morning deaths and the BMAL1/NR1D1 ratio was significantly higher in evening deaths. Sex, age, postmortem interval, and most causes of death had no significant effect on the two parameters, except for infants and the elderly, and severe brain injury. Although our method may not work in all cases, our method is useful for forensic practice in that it complements classical methods that are strongly influenced by the environment in which the corpse is placed. However, this method should be applied with caution in infants, the elderly, and patients with severe brain injury.
Modelling and simulation of waste tire pyrolysis process for recovery of energy and production of valuable chemicals (BTEX)
Authors: Cao Yan , Taghvaie Nakhjiri Ali , Sarkar Shahin 
Published: April 2023

AbstractThe pyrolysis oil fraction is highly attractive for pyrolysis products. A simulated flowsheet model of a waste tire pyrolysis process is presented in this paper. A kinetic rate-based reaction model and equilibrium separation model are created in the Aspen Plus simulation package. The simulation model is effectively proven against experimental data of literature at temperatures of 400, 450, 500, 600 and 700 °C. Also, the developed model was employed to investigate the impact of temperature on the pyrolysis procedure and demonstrated that there is an optimum temperature for chain fractions. The optimum temperature to have the highest amount of limonene (as a precious chemical product of waste tire pyrolysis process) was found 500 °C. The findings indicated that the pyrolysis process is ecologically benign, although there is still space for development. In addition, a sensitivity analysis was carried out to see how altering the heating fuel in the process would affect the non-condensable gases produced in the process. Reactors and distillation columns in the Aspen Plus® simulation model was developed to assess the technical functioning of the process (e.g., upgrading the waste tires into limonene). Furthermore, this work focuses on the optimization of the operating and structure parameters of the distillation columns in the product separation unit. The PR-BM, as well as NRTL property models, were applied in the simulation model. The calculation of non-conventional components in the model was determined using HCOALGEN and DCOALIGT property models.
Generalization of vision pre-trained models for histopathology
Authors: Sikaroudi Milad , Hosseini Maryam , Gonzalez Ricardo , Rahnamayan Shahryar , Tizhoosh H. R. 
Published: April 2023

AbstractOut-of-distribution (OOD) generalization, especially for medical setups, is a key challenge in modern machine learning which has only recently received much attention. We investigate how different convolutional pre-trained models perform on OOD test data—that is data from domains that have not been seen during training—on histopathology repositories attributed to different trial sites. Different trial site repositories, pre-trained models, and image transformations are examined as specific aspects of pre-trained models. A comparison is also performed among models trained entirely from scratch (i.e., without pre-training) and models already pre-trained. The OOD performance of pre-trained models on natural images, i.e., (1) vanilla pre-trained ImageNet, (2) semi-supervised learning (SSL), and (3) semi-weakly-supervised learning (SWSL) models pre-trained on IG-1B-Targeted are examined in this study. In addition, the performance of a histopathology model (i.e., KimiaNet) trained on the most comprehensive histopathology dataset, i.e., TCGA, has also been studied. Although the performance of SSL and SWSL pre-trained models are conducive to better OOD performance in comparison to the vanilla ImageNet pre-trained model, the histopathology pre-trained model is still the best in overall. In terms of top-1 accuracy, we demonstrate that diversifying the images in the training using reasonable image transformations is effective to avoid learning shortcuts when the distribution shift is significant. In addition, XAI techniques—which aim to achieve high-quality human-understandable explanations of AI decisions—are leveraged for further investigations.