bluuebunny/crossref_metadata_2025 huggingface dataset:
Accurate medium-range global weather forecasting with 3D neural networks
Authors: Bi Kaifeng , Xie Lingxi , Zhang Hengheng , Chen Xin , Gu Xiaotao , Tian Qi
Published: July 2023

Weather forecasting is important for science and society. At present, the most accurate forecast system is the numerical weather prediction (NWP) method, which represents atmospheric states as discretized grids and numerically solves partial differential equations that describe the transition between those states1. However, this procedure is computationally expensive. Recently, artificial-intelligence-based methods2 have shown potential in accelerating weather forecasting by orders of magnitude, but the forecast accuracy is still significantly lower than that of NWP methods. Here we introduce an artificial-intelligence-based method for accurate, medium-range global weather forecasting. We show that three-dimensional deep networks equipped with Earth-specific priors are effective at dealing with complex patterns in weather data, and that a hierarchical temporal aggregation strategy reduces accumulation errors in medium-range forecasting. Trained on 39 years of global data, our program, Pangu-Weather, obtains stronger deterministic forecast results on reanalysis data in all tested variables when compared with the world’s best NWP system, the operational integrated forecasting system of the European Centre for Medium-Range Weather Forecasts (ECMWF)3. Our method also works well with extreme weather forecasts and ensemble forecasts. When initialized with reanalysis data, the accuracy of tracking tropical cyclones is also higher than that of ECMWF-HRES.
The carbon costs of global wood harvests
Authors: Peng Liqing , Searchinger Timothy D. , Zionts Jessica , Waite Richard
Published: July 2023

After agriculture, wood harvest is the human activity that has most reduced the storage of carbon in vegetation and soils1,2. Although felled wood releases carbon to the atmosphere in various steps, the fact that growing trees absorb carbon has led to different carbon-accounting approaches for wood use, producing widely varying estimates of carbon costs. Many approaches give the impression of low, zero or even negative greenhouse gas emissions from wood harvests because, in different ways, they offset carbon losses from new harvests with carbon sequestration from growth of broad forest areas3,4. Attributing this sequestration to new harvests is inappropriate because this other forest growth would occur regardless of new harvests and typically results from agricultural abandonment, recovery from previous harvests and climate change itself. Nevertheless some papers count gross emissions annually, which assigns no value to the capacity of newly harvested forests to regrow and approach the carbon stocks of unharvested forests. Here we present results of a new model that uses time discounting to estimate the present and future carbon costs of global wood harvests under different scenarios. We find that forest harvests between 2010 and 2050 will probably have annualized carbon costs of 3.5–4.2 Gt CO2e yr−1, which approach common estimates of annual emissions from land-use change due to agricultural expansion. Our study suggests an underappreciated option to address climate change by reducing these costs.
Martian dunes indicative of wind regime shift in line with end of ice age
Authors: Liu Jianjun , Qin Xiaoguang , Ren Xin , Wang Xu , Sun Yong , Zeng Xingguo , Wu Haibin , Chen Zhaopeng , Chen Wangli , Chen Yuan , Wang Cheng , Sun Zezhou , Zhang Rongqiao , Ouyang Ziyuan , Guo Zhengtang , Head James W. , Li Chunlai
Published: July 2023

Orbital observations suggest that Mars underwent a recent ‘ice age’ (roughly 0.4–2.1 million years ago), during which a latitude-dependent ice-dust mantle (LDM)1,2was emplaced. A subsequent decrease in obliquity amplitude resulted in the emergence of an ‘interglacial period’1,3during which the lowermost latitude LDM ice4–6was etched and removed, returning it to the polar cap. These observations are consistent with polar cap stratigraphy1,7, but lower- to mid-latitude in situ surface observations in support of a glacial–interglacial transition that can be reconciled with mesoscale and global atmospheric circulation models8is lacking. Here we present a suite of measurements obtained by the Zhurong rover during its traverse across the southern LDM region in Utopia Planitia, Mars. We find evidence for a stratigraphic sequence involving initial barchan dune formation, indicative of north-easterly winds, cementation of dune sediments, followed by their erosion by north-westerly winds, eroding the barchan dunes and producing distinctive longitudinal dunes, with the transition in wind regime consistent with the end of the ice age. The results are compatible with the Martian polar stratigraphic record and will help improve our understanding of the ancient climate history of Mars9.
Cooperation between bHLH transcription factors and histones for DNA access
Authors: Michael Alicia K. , Stoos Lisa , Crosby Priya , Eggers Nikolas , Nie Xinyu Y. , Makasheva Kristina , Minnich Martina , Healy Kelly L. , Weiss Joscha , Kempf Georg , Cavadini Simone , Kater Lukas , Seebacher Jan , Vecchia Luca , Chakraborty Deyasini , Isbel Luke , Grand Ralph S. , Andersch Florian , Fribourgh Jennifer L. , Schübeler Dirk , Zuber Johannes , Liu Andrew C. , Becker Peter B. , Fierz Beat , Partch Carrie L. , Menet Jerome S. , Thomä Nicolas H.
Published: July 2023

The basic helix–loop–helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members1. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. 2,3). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry–exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A–H2B acidic patch4, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes5–7 at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors.
A harmonized resource of integrated prostate cancer clinical, -omic, and signature features
Authors: Laajala Teemu D. , Sreekanth Varsha , Soupir Alex C. , Creed Jordan H. , Halkola Anni S. , Calboli Federico C. F. , Singaravelu Kalaimathy , Orman Michael V. , Colin-Leitzinger Christelle , Gerke Travis , Fridley Brooke L. , Tyekucheva Svitlana , Costello James C.
Published: July 2023

Genomic and transcriptomic data have been generated across a wide range of prostate cancer (PCa) study cohorts. These data can be used to better characterize the molecular features associated with clinical outcomes and to test hypotheses across multiple, independent patient cohorts. In addition, derived features, such as estimates of cell composition, risk scores, and androgen receptor (AR) scores, can be used to develop novel hypotheses leveraging existing multi-omic datasets. The full potential of such data is yet to be realized as independent datasets exist in different repositories, have been processed using different pipelines, and derived and clinical features are often not provided or  not standardized. Here, we present the curatedPCaData R package, a harmonized data resource representing >2900 primary tumor, >200 normal tissue, and >500 metastatic PCa samples across 19 datasets processed using standardized pipelines with updated gene annotations. We show that meta-analysis across harmonized studies has great potential for robust and clinically meaningful insights. curatedPCaData is an open and accessible community resource with code made available for reproducibility.
Influence of particle size in supercritical carbon dioxide extraction of roselle (Hibiscus sabdariffa) on bioactive compound recovery, extraction rate, diffusivity, and solubility
Authors: Putra Nicky Rahmana , Rizkiyah Dwila Nur , Aziz Ahmad Hazim Abdul , Mamat Hasmadi , Jusoh Wan Muhammad Syahir Wan , Idham Zuhaili , Yunus Mohd Azizi Che , Irianto Irianto
Published: July 2023

The purpose of this work was to establish the best particle size for recovering high yields of total phenolic compounds (TPC), total anthocyanin compounds(TAC) and total flavonoid compounds (TFC) from roselle (Hibiscus sabdariffa) by applying supercritical carbon dioxide (ScCO2). The extraction rate, diffusivity and solubility of yield in ScCO2 were also studied and calculated utilizing models. Pressure (10 and 30 MPa), temperature (40 and 60 °C), and particle size (250 µm < dp < 355 µm, 355 µm < dp < 425 µm and 425 µm < dp < 500 µm) were employed as variables in this experiment. The greatest recovery was 11.96% yield, 7.16 mg/100 g TAC, 42.93 mg/100 g TPC and 239.36 mg/100 g TFC under the conditions of 30 MPA, 40 °C and 250 µm < dp < 355 µm, respectively. The extraction rate of supercritical carbon dioxide in roselle extraction ranged from 5.19 E−03 to 1.35 E−03 mg/s fitted using the Esquivel model. The diffusivity coefficient of ScCO2 ranged from 2.17E−12 to 3.72E−11 mg/s2, as fitted by a single sphere model. The greatest solubility of global yield, TAC, TPC and TFC in ScCO2 was 1.50 g/L, 0.3 mg/L, 1.69 mg/L and 9.97 mg/L, respectively, with a particle size of 250 µm < dp < 355 µm. The smaller particle size of roselle provides the maximum bioactive compound recovery and solubility. Furthermore, the diffusivity and extraction of ScCO2 are increased by decreasing the particle size. Therefore, a smaller particle size is appropriate for roselle extraction by ScCO2 based on the experimental and modelling data.
Influence of microbial cell morphology and composition on radio frequency heating of simple media at different frequencies
Authors: Espitia Julian , Verheyen Davy , Kozak Dmytro S. , Van Impe Jan F. M.
Published: July 2023

The effect of Listeria monocytogenes, Salmonella Typhimurium, and Saccharomyces cerevisiae on RF heating was studied in sterilized Milli-Q water and saline solution during treatments at 27.0 ± 0.6 MHz and 3.0 ± 0.02 MHz for 30 min. The presence of microorganisms caused a significant increase in temperature (maximum to 54.9 °C), with no significant decrease in cell numbers being observed for any conditions. For both media and frequencies, heating rates followed the order S. Typhimurium ≤ L. monocytogenes ≤ S. cerevisiae, except for heating at 3.0 ± 0.02 MHz in saline solution, where heating rates for S. cerevisiae and S. Typhimurium were equal. Generally, heating rates for microorganisms were significantly higher at 27.0 ± 0.6 MHz than at 3.0 ± 0.02 MHz, except for the S. cerevisiae case. Observed phenomena were probably caused by differences in the cell lipid and peptidoglycan content, with interaction effects with salt being present. This study was the first to investigate the influence of the presence of microorganisms on heating behavior of simple media. On the long term, more research on this topic could lead to finding specific RF frequencies more suitable for the heating of specific media and products for various applications.
Remote sensing imagery detects hydromorphic soils hidden under agriculture system
Authors: Mello Fellipe A. O. , Demattê José A. M. , Bellinaso Henrique , Poppiel Raul R. , Rizzo Rodnei , de Mello Danilo C. , Rosin Nícolas Augusto , Rosas Jorge T. F. , Silvero Nélida E. Q. , Rodríguez-Albarracín Heidy S.
Published: July 2023

The pressure for food production has expanded agriculture frontiers worldwide, posing a threat to water resources. For instance, placing crop systems over hydromorphic soils (HS), have a direct impact on groundwater and influence the recharge of riverine ecosystems. Environmental regulations improved over the past decades, but it is difficult to detect and protect these soils. To overcome this issue, we applied a temporal remote sensing strategy to generate a synthetic soil image (SYSI) associated with random forest (RF) to map HS in an 735,953.8 km2 area in Brazil. HS presented different spectral patterns from other soils, allowing the detection by satellite sensors. Slope and SYSI contributed the most for the prediction model using RF with cross validation (accuracy of 0.92). The assessments showed that 14.5% of the study area represented HS, mostly located inside agricultural areas. Soybean and pasture areas had up to 14.9% while sugar cane had just 3%. Here we present an advanced remote sensing technique that may improve the identification of HS under agriculture and assist public policies for their conservation.
Monitoring and risk analysis of residual pesticides drifted by unmanned aerial spraying
Authors: Kim Chang Jo , Yuan Xiu , Kim Min , Kyung Kee Sung , Noh Hyun Ho
Published: July 2023

This study aimed to investigate the residual characteristics of pesticides drifted by unmanned aerial spray according to buffer strip, windbreak, and morphological characteristics of non-target crops, suggest prevention for drift reduction, and finally conduct a risk analysis on pesticides exceeding the maximum residue limit (MRL) or uniform level (0.01 mg/kg) of the positive list system (PLS). Non-target crops were collected around the aerial sprayed area (paddy rice) in Boryeong, Seocheon, and Pyeongtaek after UAV spray. When pesticides were detected in more than three samples, Duncan’s multiple range test was performed. In cases where pesticides were detected in only two samples, an independent sample t-test was conducted (p < 0.05). The drift rate of pesticides tends to decrease by up to 100% as the buffer distance from aerial sprayed area increases or when a windbreak, such as maize, is present between two locations. Thus, the reduction of drifted pesticides could be effective if both factors were applied near the UAV spray area. Moreover, the residue of drifted pesticides was found to be the highest in leafy vegetables such as perilla leaves or leaf and stem vegetables such as Welsh onion, followed by fruit vegetables and cucurbits, owing to the morphological characteristics of crops. Therefore, selecting pulse or cereal such as soybean or maize as a farm product near the UAV spray area can be considered to minimize the drift. For pesticides that exceed the MRL or PLS uniform level, %acceptable dietary intake is 0–0.81% with no risk. Additionally, employing pesticides approved for both paddy rice and farm products in UAV spraying can effectively minimize instances where MRL or PLS are exceeded. Therefore, this study aims to provide farmers with effective guidelines for mitigating drift. Furthermore, we strive to promote stable and uninterrupted food production while facilitating the utilization of agricultural technologies such as UAV spraying to address labor shortages and ensure sustainable food security.
Comparison of translucency, thickness, and gap width of thermoformed and 3D-printed clear aligners using micro-CT and spectrophotometer
Authors: Park So Yeon , Choi Sung-Hwan , Yu Hyung-Seog , Kim Su-Jung , Kim Hoon , Kim Ki Beom , Cha Jung-Yul
Published: July 2023

The present study compared the thickness and gap width of thermoformed and 3D-printed clear aligners (CAs) using micro-computed tomography (micro-CT) and evaluated their translucency using spectrophotometer. Four groups of CAs were tested: thermoformed with polyethylene terephthalate glycol (TS) or copolyester-elastomer combination (TM), and 3D-printed TC-85 cleaned with alcohol (PA) or with centrifuge (PC). CIELab coordinates were measured (n = 10) to evaluate translucency. CAs (n = 10) were fitted onto respective models and micro-CT was performed to evaluate the thickness and gap width. Thickness and gap width were measured for different tooth type and location in sagittal sections on all sides. The PC group showed significantly higher translucency than the PA group, which was similar to the TS and TM groups (p < 0.01). After the manufacturing process, thickness reduction was observed in the thermoformed groups, whereas thickness increase was observed in the 3D printed-groups. The TM group showed the least gap width amongst the groups (p < 0.01). Thermoformed and 3D-printed CAs had significantly varied thicknesses and regions of best fit depending on the tooth type and location. Differences in the translucency and thickness of the 3D-printed CAs were observed depending on the cleaning methods.
Transient regulatory-T-cell interruption promotes skin-resident memory T cells mediated tumor protection
Authors: Zhao Shushu , Wu Shuting , Jiang Sheng , Zhou Xiaoyu , Zhao Gan , Wang Bin
Published: July 2023

Most cancer immunotherapy approaches aim to stimulate cytotoxic CD8+ T lymphocytes to reject tumor cells. Due to the tumor-mediated suppressive micro-environment, of which the major contributor is regulatory T cells (Tregs), promising preclinical approaches were disappointing in clinical settings. Our recent study demonstrated that transient interruption of Tregs could induce CD8+ T cell responses to reject tumors in an animal model. The long-term tumor protective effect has yet not to be investigated. In this study, mice with Treg depletion rejected tumors and were rechallenged to study anti-tumor memory immune responses. The effects of major immune cell subsets on tumor protection were explored. Finally, we demonstrate that transient depletion of Tregs during primary tumor challenge can result in long-lasting protection against the tumor rechallenge. Skin-resident memory T cells (sTRM) were major factors in rejecting rechallenged tumors even when peripheral T cells were deficient. These findings highlight a promising strategy for empowering tissue-resident memory T cells for cancer prevention and immunotherapy in humans by interrupting Tregs.
Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species
Authors: Singh Jagveer , Sharma Ankush , Sharma Vishal , Gaikwad Popat Nanaso , Sidhu Gurupkar Singh , Kaur Gurwinder , Kaur Nimarpreet , Jindal Taveena , Chhuneja Parveen , Rattanpal H. S.
Published: July 2023

Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species.
Multi-landmark alignment of genomic signals reveals conserved expression patterns across transcription start sites
Authors: Vilar Jose M. G. , Saiz Leonor
Published: July 2023

The prevalent one-dimensional alignment of genomic signals to a reference landmark is a cornerstone of current methods to study transcription and its DNA-dependent processes but it is prone to mask potential relations among multiple DNA elements. We developed a systematic approach to align genomic signals to multiple locations simultaneously by expanding the dimensionality of the genomic-coordinate space. We analyzed transcription in human and uncovered a complex dependence on the relative position of neighboring transcription start sites (TSSs) that is consistently conserved among cell types. The dependence ranges from enhancement to suppression of transcription depending on the relative distances to the TSSs, their intragenic position, and the transcriptional activity of the gene. Our results reveal a conserved hierarchy of alternative TSS usage within a previously unrecognized level of genomic organization and provide a general methodology to analyze complex functional relationships among multiple types of DNA elements.
Probiotic properties and antimicrobial evaluation of silymarin-enriched Lactobacillus bacteria isolated from traditional curd
Authors: Haghshenas Babak , Kiani Amir , Mansoori Saeideh , Mohammadi-noori Ehsan , Nami Yousef
Published: July 2023

Nowadays, the increasing use of medicinal plants in the treatment and prevention of diseases has attracted the attention of researchers. The aim of this work was to investigate the probiotic properties and antibacterial and antifungal activity of silymarin-enriched Lactobacillus bacteria against several important pathogenic bacteria and also Aspergillus flavus as one of the harmful molds in the food and health industries. For this purpose, 52 g-positive and catalase-negative bacteria were isolated from 60 traditional curd samples from Ilam province. Five of the 52 bacterial strains had more than 90% viability in high bile salt and acidic conditions and were selected for further investigation. The five strains with positive results showed good hydrophobicity (≥ 50.30%), auto-aggregation (≥ 53.70%), coaggregation (≥ 28.20%), and high cholesterol removal ability (from 09.20 to 67.20%) and therefore can be considered potential probiotics. The tested strains displayed acceptable antibacterial and antifungal activity against all 12 pathogenic bacteria and A. flavus. Also, the results of the simultaneous antifungal activity of probiotic strains and silymarin showed that the combination of silymarin and probiotics has a significantly better (P < 0.05) antifungal effect than the control group or the probiotic groups alone. Interestingly, in addition to the Limosilactobacillus fermentum C3 strain, the Limosilactobacillus fermentum C18 and Lactiplantibacillus pentosus C20 strains also had significant inhibitory effects against A. flavus when used with silymarin extract in methanol. Meanwhile, silymarin extract in DMSO and PEG increased the antagonistic activity of all five potential probiotic strains.
Long-term in vivo vitamin D3 supplementation modulates bovine IL-1 and chemokine responses
Authors: Reid Cian , Flores-Villalva Susana , Remot Aude , Kennedy Emer , O’Farrelly Cliona , Meade Kieran G.
Published: July 2023

Vitamin D deficiency at birth, followed by prolonged insufficiency in early life may predispose bovine calves to infection and disease. However, the effects of vitamin D levels on innate immunity are unclear due to the lack of long-term supplementation trials in vivo and reliable approaches for reproducibly assessing immune function. Here, a standardized whole blood immunophenotyping assay was used to compare innate immune responses to infection relevant ligands (LPS, Pam3CSK4 and R848) between Holstein–Friesian calves supplemented with vitamin D (n = 12) from birth until 7 months of age and control calves (n = 10) raised on an industry standard diet. Transcriptomic analysis in unstimulated whole blood cells revealed increased expression of type I interferons and chemokines in vitamin D supplemented calves, while IL-1 and inflammasome gene expression was decreased. In response to stimulation with the bacterial ligand LPS, supplemented calves had significantly increased expression of CASP1, CX3CR1, CAT, whereas STAT1 was decreased. Stimulation with the bacterial ligand Pam3CSK4 revealed increased expression of IL1A, IL1B and CAT genes; and decreased C5AR1 expression. In response to the viral ligand R848, STAT1 and S100A8 expression was significantly decreased. An increased IL-1 and inflammasome gene expression signature in vitamin D supplemented calves in response to LPS and Pam3CSK4 was also found, with ELISA confirming increased IL-1β protein production. In contrast, a decreased chemokine gene expression signature was found in response to R848 in supplemented animals, with decreased IL-8 protein expression exhibited in response to all PAMPs also found. These results demonstrated expression of several cytokine, chemokine and inflammasome genes were impacted by vitamin D supplementation in the first 7 months of life, with IL-8 expression particularly responsive to vitamin D. Overall, vitamin D supplementation induced differential innate immune responses of blood immune cells that could have important implications for disease susceptibility in cattle.
Neurophysiological mechanisms underlying the differential effect of reward prospect on response selection and inhibition
Authors: Koyun Anna Helin , Stock Ann-Kathrin , Beste Christian
Published: July 2023

Reward and cognitive control play crucial roles in shaping goal-directed behavior. Yet, the behavioral and neural underpinnings of interactive effects of both processes in driving our actions towards a particular goal have remained rather unclear. Given the importance of inhibitory control, we investigated the effect of reward prospect on the modulatory influence of automatic versus controlled processes during response inhibition. For this, a performance-contingent monetary reward for both correct response selection and response inhibition was added to a Simon NoGo task, which manipulates the relationship of automatic and controlled processes in Go and NoGo trials. A neurophysiological approach was used by combining EEG temporal signal decomposition and source localization methods. Compared to a non-rewarded control group, rewarded participants showed faster response execution, as well as overall lower response selection and inhibition accuracy (shifted speed-accuracy tradeoff). Interestingly, the reward group displayed a larger interference of the interactive effects of automatic versus controlled processes during response inhibition (i.e., a larger Simon NoGo effect), but not during response selection. The reward-specific behavioral effect was mirrored by the P3 amplitude, underlining the importance of stimulus–response association processes in explaining variability in response inhibition performance. The selective reward-induced neurophysiological modulation was associated with lower activation differences in relevant structures spanning the inferior frontal and parietal cortex, as well as higher activation differences in the somatosensory cortex. Taken together, this study highlights relevant neuroanatomical structures underlying selective reward effects on response inhibition and extends previous reports on the possible detrimental effect of reward-triggered performance trade-offs on cognitive control processes.
Association of daily physical activity and leisure-time exercise with dysphagia risk in community-dwelling older adults: a cross-sectional study
Authors: Maehara Tomoko , Nishimura Rumi , Yoshitake Akari , Tsukamoto Mineko , Kadomatsu Yuka , Kubo Yoko , Okada Rieko , Nagayoshi Mako , Tamura Takashi , Hishida Asahi , Takeuchi Kenji , Wakai Kenji , Naito Mariko
Published: July 2023

This study aimed to clarify the association of daily physical activity and leisure-time exercise with the risk of dysphagia in community-dwelling Japanese older adults using a questionnaire-based survey. We analyzed 3070 participants (1657 men, 1413 women; age 66 ± 4 years [mean ± SD]) of the Shizuoka and Daiko studies within the Japanese Multi-Institutional Collaborative Cohort study. We used the Dysphagia Risk Assessment for the Community-dwelling Elderly questionnaire to assess dysphagia risk and the International Physical Activity Questionnaire to assess daily physical activity and leisure-time exercise. Logistic regression analyses were used to evaluate the independent association of the amount of physical activity and leisure-time exercise with dysphagia risk. The proportion of participants with dysphagia risk was 27.5% (n = 844) and the risk was significantly higher in women (29.8%, n = 421) than in men (25.5%, n = 423; P = 0.008). Daily physical activity was not associated with dysphagia risk. A greater amount of leisure-time exercise was associated with lower dysphagia risk (P for trend = 0.003) and individuals in the highest leisure-time exercise quartile had a significantly lower odds ratio (0.68, 95% CI 0.52–0.89) than those in the lowest quartile, even after adjusting for the covariates.
LAMP assay for the detection of the Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psylloidea: Psyllidae)
Authors: Agarwal Arati , Martoni Francesco , Eow Lixin , Rodoni Brendan C. , Blacket Mark J.
Published: July 2023

Diaphorina citri Kuwayama, also known as the Asian citrus psyllid (ACP), can vector the bacterium Candidatus Liberibacter asiaticus (CLas), agent of Huanglongbing (HLB): an incurable disease affecting citrus trees worldwide. In citrus growing regions where ACP and HLB are absent, such as Australia, the risk of an incursion and consequent economic damage to citrus industries make this psyllid one of the top-priority pests. Due to ACP’s small dimensions and the generally poorly studied native psylloid fauna worldwide, morphological identification of this insect to distinguish it from harmless species is challenging, especially in the field, and with immature, partial or damaged specimens. To allow rapid and efficient detection of ACP in the field, we designed and optimised a new Loop-mediated isothermal amplification (LAMP) assay for the detection of D. citri based on the mitochondrial 16S locus. The optimised ACP 16S LAMP assay produced amplification from D. citri samples within 13.3 ± 3.6 min, with an anneal derivative of ~ 78.5 °C. A synthetic gBlock gene fragment was also developed to be used as positive control for the new LAMP assay with a different anneal derivative of ~ 83 °C. An existing commercially available LAMP assay for detection of the bacterium CLas was also tested in this study on ACP DNA. The ACP 16S LAMP assay we developed and tested here provides a valuable new in-field compatible tool that can allow early detections of ACP, enabling a quick biosecurity response, and could potentially be adopted by a wide range of users, from farmers to agronomists and from researchers to industry.
Persistent homological cell tracking technology
Authors: Oda Haruhisa , Tonami Kazuo , Nakata Yoichi , Takubo Naoko , Kurihara Hiroki
Published: July 2023

In this paper, we develop a cell tracking method based on persistent homological figure detection technology. We apply our tracking method to 9 different time-series cell images and extract several kinds of cell movements. Being able to analyze various images with a single method allows researchers to systematically understand and compare different tracking data. Persistent homological cell tracking technology’s 9 parameters all have clear meanings. Thus, researchers can decide the parameters not by black box trial-and-error but by the purpose of their analysis. We use model data with ground truth to see our method’s performance. We compare persistent homological figure detection and cell tracking technology with Image-Pro, sure-foreground in watershed method, and cell detection methods in previous studies. We see that there are some cases where Image-Pro’s tracking stops and requires manual plots, while our method does not require manual plots. We show that our technology includes sure-foreground and has more information, and can be applied to different types of data that previously needed different methods. We also show that our technology is powerful as a detection technology by applying the technology to 5 different types of cell images.
Development and validation of a nomogram for predicting sepsis in patients with pyogenic liver abscess
Authors: Li Ji , Wang Yin , Luo Jinhong , Yin Zhikun , Huang Weifeng , Zhang Jinyan
Published: July 2023

Pyogenic liver abscess (PLA) is a severe condition that significantly increases the risk of sepsis. However, there is a notable dearth of research regarding the prediction of sepsis in PLA patients. The objective of this study was to develop and validate a prognostic nomogram for predicting sepsis in PLA patients. A total of 206 PLA patients were enrolled in our study, out of which 60 individuals (29.1%) met the Sepsis-3 criteria. Independent risk factors for sepsis were identified through univariate and multivariate logistic regression analyses. Subsequently, a nomogram was developed based on age, positive blood culture, procalcitonin, alanine aminotransferase, blood urea nitrogen, and d-dimer. The nomogram demonstrated excellent calibration and discrimination, as evidenced by the area under the receiver operating characteristic curve (AUC) values of 0.946 (95% confidence interval [CI], 0.912–0.979) and 0.980 (95%CI 0.951–1.000) in the derivation and validation cohorts, respectively. Furthermore, decision-curve analysis confirmed the clinical utility of the nomogram. This study provides valuable insights for the prevention of sepsis in PLA patients and underscores the potential application of the prognostic nomogram in clinical practice.
Optimal slice thickness for improved accuracy of quantitative analysis of fluorescent cell and microsphere distribution in cryo-images
Authors: Wuttisarnwattana Patiwet , Eck Brendan L. , Gargesha Madhusudhana , Wilson David L.
Published: July 2023

Cryo-imaging has been effectively used to study the biodistribution of fluorescent cells or microspheres in animal models. Sequential slice-by-slice fluorescent imaging enables detection of fluorescent cells or microspheres for corresponding quantification of their distribution in tissue. However, if slices are too thin, there will be data overload and excessive scan times. If slices are too thick, then cells can be missed. In this study, we developed a model for detection of fluorescent cells or microspheres to aid optimal slice thickness determination. Key factors include: section thickness (X), fluorescent cell intensity (Ifluo), effective tissue attenuation coefficient (μT), and a detection threshold (T). The model suggests an optimal slice thickness value that provides near-ideal sensitivity while minimizing scan time. The model also suggests a correction method to compensate for missed cells in the case that image data were acquired with overly large slice thickness. This approach allows cryo-imaging operators to use larger slice thickness to expedite the scan time without significant loss of cell count. We validated the model using real data from two independent studies: fluorescent microspheres in a pig heart and fluorescently labeled stem cells in a mouse model. Results show that slice thickness and detection sensitivity relationships from simulations and real data were well-matched with 99% correlation and 2% root-mean-square (RMS) error. We also discussed the detection characteristics in situations where key assumptions of the model were not met such as fluorescence intensity variation and spatial distribution. Finally, we show that with proper settings, cryo-imaging can provide accurate quantification of the fluorescent cell biodistribution with remarkably high recovery ratios (number of detections/delivery). As cryo-imaging technology has been used in many biological applications, our optimal slice thickness determination and data correction methods can play a crucial role in further advancing its usability and reliability.
Modeling interfacial tension of surfactant–hydrocarbon systems using robust tree-based machine learning algorithms
Authors: Rashidi-Khaniabadi Ali , Rashidi-Khaniabadi Elham , Amiri-Ramsheh Behnam , Mohammadi Mohammad-Reza , Hemmati-Sarapardeh Abdolhossein
Published: July 2023

Interfacial tension (IFT) between surfactants and hydrocarbon is one of the important parameters in petroleum engineering to have a successful enhanced oil recovery (EOR) operation. Measuring IFT in the laboratory is time-consuming and costly. Since, the accurate estimation of IFT is of paramount significance, modeling with advanced intelligent techniques has been used as a proper alternative in recent years. In this study, the IFT values between surfactants and hydrocarbon were predicted using tree-based machine learning algorithms. Decision tree (DT), extra trees (ET), and gradient boosted regression trees (GBRT) were used to predict this parameter. For this purpose, 390 experimental data collected from previous studies were used to implement intelligent models. Temperature, normal alkane molecular weight, surfactant concentration, hydrophilic–lipophilic balance (HLB), and phase inversion temperature (PIT) were selected as inputs of models and independent variables. Also, the IFT between the surfactant solution and normal alkanes was selected as the output of the models and the dependent variable. Moreover, the implemented models were evaluated using statistical analyses and applied graphical methods. The results showed that DT, ET, and GBRT could predict the data with average absolute relative error values of 4.12%, 3.52%, and 2.71%, respectively. The R-squared of all implementation models is higher than 0.98, and for the best model, GBRT, it is 0.9939. Furthermore, sensitivity analysis using the Pearson approach was utilized to detect correlation coefficients of the input parameters. Based on this technique, the results of sensitivity analysis demonstrated that PIT, surfactant concentration, and HLB had the greatest effect on IFT, respectively. Finally, GBRT was statistically credited by the Leverage approach.
Micro- and nano- bentonite to improve the strength of clayey sand as a nano soil-improvement technique
Authors: Cheraghalikhani Mohadeseh , Niroumand Hamed , Balachowski Lech
Published: July 2023

Nano-additives results in the formation of nano-cementation (NC). This process is recently used to improve the durability of various building materials. NC used to improve the strength of untreated soil materials, also known as nano soil-improvement (NSI). In few years, the role of nano-additives in various types of soils were developed. In this research, the role of micro- and nano- size of bentonite as soil stabilizer was evaluated as first few research to improve geotechnical properties of soils. Nano-additives prepared by micro- and nano- sizes of bentonite were blend with four formulations. These formulations of micro- and nano- additives at concentrations of 0, 1, 2, and 3%, namely 0% Micro-Bentonite, 1% Micro-Bentonite, 2% Micro-Bentonite, 3% Micro-Bentonite, 0% Nano-Bentonite, 1% Nano-Bentonite, 2% Nano-Bentonite, and 3% Nano-Bentonite, respectively. These formulations of micro- and nano- additives were separately added to soil. Specimens with 3% nano-bentonite showed significant improvement in unconfined compressive strength (UCS) of soil that was more than 2.3-times higher than control specimen in 7-d curing time. Also the performance of micro-bentonite resulted in improvement in UCS of soil that was more than 1.1-times higher than control specimen at 7-d curing time. The secant modulus at 50% of peak stress (E50) of the samples treated with micro- and nano- additives increased in comparison to untreated specimens. Further, X-ray fluorescence (XRF), scanning electron microscopy, and X-ray diffraction analyses characterized micro- and nano- structures of soil specimens, and showed the performance of nano-additives in improving strength of soils. Results show that nano-bentonite as a type of nano-additives is an effective means of increasing the strength of soils. This research shows the significant of nano-bentonite in soil improvement, as a NSI technique.
Atypical femur fracture associated with common anti-osteoporosis drugs in FDA adverse event reporting system
Authors: Xiao Yao , Chen Yiqian , Huang Yan , Xiao Yuan
Published: July 2023

Atypical femur fracture (AFF) is a rare but catastrophic adverse event first reported in the long-term use of alendronate, one of the most commonly used drugs for osteoporosis currently. However, further evidence is needed to learn more regarding other common anti-osteoporosis drugs and the risk for AFF. In this study, reports of AFF were identified from Food and Drug Administration Adverse Event Reporting System database. Disproportionality analyses were performed to examine the reporting odds ratio (ROR), information component (IC) and adjusted ROR (adj. ROR) signals for AFF for common anti-osteoporosis drugs. A total of 1692 unique AFF reports were identified. The disproportionality signals (the lower bound of 95% confidence interval > 1 for ROR and adjusted ROR, and > 0 for IC) were detected for alendronate, denosumab, pamidronate, risedronate, zoledronate, ibandronate, and teriparatide while no signal was detected for raloxifene, abaloparatide, and romosozumab. When restricted in patients with osteoporosis, the disproportionality signals were still detected for alendronate, pamidronate, risedronate, denosumab, and ibandronate. Our results suggest that alendronate has the largest risk signal, while the risks varied among different bisphosphonates. In addition, denosumab was found statistically associated with AFF in both the entire database and patients with osteoporosis.
Socioeconomic inequalities in type 2 diabetes comorbidities in different population subgroups: trend analyses using German health insurance data
Authors: Safieddine Batoul , Sperlich Stefanie , Beller Johannes , Lange Karin , Geyer Siegfried
Published: July 2023

While socioeconomic inequalities in the prevalence and management of type 2 diabetes (T2D) are well established, little is known about whether inequalities exist in the prevalence and the temporal development of T2D comorbidities. Previous research points towards expansion of morbidity in T2D as depicted mainly by a rising trend of T2D comorbidities. Against this background, and using German claims data, this study aims to examine whether socioeconomic status (SES) inequalities exist in the rates and the temporal development of T2D comorbidities. Since previous research indicates varying risk levels for T2D prevalence in the population subgroups: working individuals, nonworking spouses and pensioners, the analyses are stratified by these three population subgroups. The study is done on a large population of statutory insured individuals with T2D in three time-periods between 2005 and 2017. Predicted probabilities of three comorbidity groups and the number of comorbidities were estimated using logistic and ordinal regression analyses among different income, education and occupation groups. Interaction analyses were applied to examine whether potential SES inequalities changed over time. The study showed that neither the cross-sectional existence, nor the temporal development of T2D comorbidities differed significantly among SES groups, ruling out SES inequalities in the prevalence and the temporal development of T2D comorbidities in Germany. In men and women of all examined population subgroups, predicted probabilities for less severe cardiovascular (CVD) comorbidities, other vascular diseases and the number of comorbidities per individual rose significantly over time regardless of SES, but little if any change took place for more severe CVD comorbidities. Another important finding is that the population subgroup of nonworking spouses had markedly higher predicted probabilities for most of the examined outcomes compared to working individuals. The study indicates that the expansion of morbidity in T2D in Germany does not appear to be SES-dependent, and applies equally to different population subgroups. Yet, the study highlights that nonworking spouses are a susceptible population subgroup that needs to be focused upon when planning and implementing T2D management interventions.
P53 status, and G2/M cell cycle arrest, are determining factors in cell-death induction mediated by ELF-EMF in glioblastoma
Authors: Mehdizadeh Romina , Madjid Ansari Alireza , Forouzesh Flora , Shahriari Fatemeh , Shariatpanahi Seyed Peyman , Salaritabar Ali , Javidi Mohammad Amin
Published: July 2023

The average survival of patients with glioblastoma is 12–15 months. Therefore, finding a new treatment method is important, especially in cases that show resistance to treatment. Extremely low-frequency electromagnetic fields (ELF-EMF) have characteristics and capabilities that can be proposed as a new cancer treatment method with low side effects. This research examines the antitumor effect of ELF-EMF on U87 and U251 glioblastoma cell lines. Flowcytometry determined the viability/apoptosis and distribution of cells in different phases of the cell cycle. The size of cells was assessed by TEM. Important cell cycle regulation genes mRNA expression levels were investigated by real-time PCR. ELF-EMF induced apoptosis in U87cells much more than U251 (15% against 2.43%) and increased G2/M cell population in U87 (2.56%, p value < 0.05), and S phase in U251 (2.4%) (data are normalized to their sham exposure). The size of U87 cells increased significantly after ELF-EMF exposure (overexpressing P53 in U251 cells increased the apoptosis induction by ELF-EMF). The expression level of P53, P21, and MDM2 increased and CCNB1 decreased in U87. Among the studied genes, MCM6 expression decreased in U251. Increasing expression of P53, P21 and decreasing CCNB1, induction of cell G2/M cycle arrest, and consequently increase in the cell size can be suggested as one of the main mechanisms of apoptosis induction by ELF-EMF; furthermore, our results demonstrate the possible footprint of P53 in the apoptosis induction by ELF-EMF, as U87 carry the wild type of P53 and U251 has the mutated form of this gene.
In vitro study on the preventive effect of children’s toothpastes on erosive tooth wear of primary bovine enamel and dentin
Authors: Chalkidis Jennifer , Barke Sarah , Rohland Bianca , Schmidt Alexandra , Kanzow Philipp , Wiegand Annette
Published: July 2023

This in vitro study aimed to analyse the effect of various children’s toothpastes on erosive tooth wear of primary bovine enamel and dentin. Enamel and dentin specimens (n = 12) were cyclically eroded (6 × 60 s/d, citric acid, pH 2.4) and brushed (2 × 15 s/d, 2 N) over 5 days. Nine fluoride toothpastes (500 to 1450 ppm) and eight toothpastes containing no fluoride or other active ingredients (hydroxyapatite and/or xylitol) were tested. Unbrushed specimens served as control. Tissue loss was quantified using widefield confocal microscopy and statistically analysed using two-way and one-way ANOVAs followed by Scheffe’s (enamel) or Tamhane’s (dentin) post-hoc tests (p < 0.05). Only one fluoride toothpaste (1400 ppm) was able to reduce erosive wear of enamel significantly by 15% compared to the control (padj. = 0.002). All fluoridated toothpastes reduced dentin surface loss significantly by 32 to 69% compared to the control (padj. ≤ 0.001), while fluoride-free toothpastes were unable to reduce dentin loss significantly (padj. ≥ 0.971). Most fluoridated toothpastes caused less erosive wear compared to fluoride-free toothpastes. Children toothpastes containing fluoride were more effective in reducing erosive wear compared to toothpastes containing no fluoride or other active ingredients.