bluuebunny/crossref_metadata_2025_split huggingface dataset:
Method comparison and estimation of causal effects of insomnia on health outcomes in a survey sampled population
Authors: Shahu Anja , Chung Joon , Tarraf Wassim , Ramos Alberto R. , González Hector M. , Redline Susan , Cai Jianwen , Sofer Tamar 
Published: June 2023

AbstractApplying causal inference methods, such as weighting and matching methods, to a survey sampled population requires properly incorporating the survey weights and design to obtain effect estimates that are representative of the target population and correct standard errors (SEs). With a simulation study, we compared various approaches for incorporating the survey weights and design into weighting and matching-based causal inference methods. When the models were correctly specified, most approaches performed well. However, when a variable was treated as an unmeasured confounder and the survey weights were constructed to depend on this variable, only the matching methods that used the survey weights in causal estimation and as a covariate in matching continued to perform well. If unmeasured confounders are potentially associated with the survey sample design, we recommend that investigators include the survey weights as a covariate in matching, in addition to incorporating them in causal effect estimation. Finally, we applied the various approaches to the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) and found that insomnia has a causal association with both mild cognitive impairment (MCI) and incident hypertension 6–7 years later in the US Hispanic/Latino population.
Complete genomes and comparative analyses of Streptomyces phages that influence secondary metabolism and sporulation
Authors: Kronheim Sarah , Solomon Ethan , Ho Louis , Glossop Michelle , Davidson Alan R. , Maxwell Karen L. 
Published: June 2023

AbstractBacteria in the genus Streptomyces are found ubiquitously in nature and are known for the number and diversity of specialized metabolites they produce, as well as their complex developmental lifecycle. Studies of the viruses that prey on Streptomyces, known as phages, have aided the development of tools for genetic manipulation of these bacteria, as well as contributing to a deeper understanding of Streptomyces and their behaviours in the environment. Here, we present the genomic and biological characterization of twelve Streptomyces phages. Genome analyses reveal that these phages are closely related genetically, while experimental approaches show that they have broad overlapping host ranges, infect early in the Streptomyces lifecycle, and induce secondary metabolite production and sporulation in some Streptomyces species. This work expands the group of characterized Streptomyces phages and improves our understanding of Streptomyces phage-host dynamics.
Machine-learning-based diagnosis of thyroid fine-needle aspiration biopsy synergistically by Papanicolaou staining and refractive index distribution
Authors: Lee Young Ki , Ryu Dongmin , Kim Seungwoo , Park Juyeon , Park Seog Yun , Ryu Donghun , Lee Hayoung , Lim Sungbin , Min Hyun-Seok , Park YongKeun , Lee Eun Kyung 
Published: June 2023

AbstractWe developed a machine learning algorithm (MLA) that can classify human thyroid cell clusters by exploiting both Papanicolaou staining and intrinsic refractive index (RI) as correlative imaging contrasts and evaluated the effects of this combination on diagnostic performance. Thyroid fine-needle aspiration biopsy (FNAB) specimens were analyzed using correlative optical diffraction tomography, which can simultaneously measure both, the color brightfield of Papanicolaou staining and three-dimensional RI distribution. The MLA was designed to classify benign and malignant cell clusters using color images, RI images, or both. We included 1535 thyroid cell clusters (benign: malignancy = 1128:407) from 124 patients. Accuracies of MLA classifiers using color images, RI images, and both were 98.0%, 98.0%, and 100%, respectively. As information for classification, the nucleus size was mainly used in the color image; however, detailed morphological information of the nucleus was also used in the RI image. We demonstrate that the present MLA and correlative FNAB imaging approach has the potential for diagnosing thyroid cancer, and complementary information from color and RI images can improve the performance of the MLA.
Correlation between standardized uptake value of 18F-FDG PET/CT and conductivity with pathologic prognostic factors in breast cancer
Authors: Shin Dong-Joo , Choi Hongyoon , Oh Dong Kyu , Sung Hyun Pil , Kim Jun-Hyeong , Kim Dong-Hyun , Kim Soo-Yeon 
Published: June 2023

AbstractWe investigated the correlation between standardized uptake value (SUV) of 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET)/computed tomography (CT) and conductivity parameters in breast cancer and explored the feasibility of conductivity as an imaging biomarker. Both SUV and conductivity have the potential to reflect the tumors’ heterogeneous characteristics, but their correlations have not been investigated until now. Forty four women diagnosed with breast cancer who underwent breast MRI and 18F-FDG PET/CT at the time of diagnosis were included. Among them, 17 women received neoadjuvant chemotherapy followed by surgery and 27 women underwent upfront surgery. For conductivity parameters, maximum and mean values of the tumor region-of-interests were examined. For SUV parameters, SUVmax, SUVmean, and SUVpeak of the tumor region-of-interests were examined. Correlations between conductivity and SUV were evaluated, and among them, the highest correlation was observed between mean conductivity and SUVpeak (Spearman’s correlation coefficient = 0.381). In a subgroup analysis for 27 women with upfront surgery, tumors with lymphovascular invasion (LVI) showed higher mean conductivity than those without LVI (median: 0.49 S/m vs 0.06 S/m, p < 0.001). In conclusion, our study shows a low positive correlation between SUVpeak and mean conductivity in breast cancer. Furthermore, conductivity showed a potential to noninvasively predict LVI status.
Tracking volcanic explosions using Shannon entropy at Volcán de Colima
Authors: Rey-Devesa Pablo , Prudencio Janire , Benítez Carmen , Bretón Mauricio , Plasencia Imelda , León Zoraida , Ortigosa Félix , Gutiérrez Ligdamis , Arámbula-Mendoza Raúl , Ibáñez Jesús M. 
Published: June 2023

AbstractThe main objective of this work is to show that Shannon Entropy (SE) calculated on continuous seismic signals can be used in a volcanic eruption monitoring system. We analysed three years of volcanic activity of Volcán de Colima, México, recorded between January 2015 and May 2017. This period includes two large explosions, with pyroclastic and lava flows, and intense activity of less energetic explosion, culminating with a period of quiescence. In order to confirm the success of our results, we used images of the Visual Monitoring system of Colima Volcano Observatory. Another of the objectives of this work is to show how the decrease in SE values can be used to track minor explosive activity, helping Machine Learning algorithms to work more efficiently in the complex problem of distinguishing the explosion signals in the seismograms. We show that the two big eruptions selected were forecasted successfully (6 and 2 days respectively) using the decay of SE. We conclude that SE could be used as a complementary tool in seismic volcano monitoring, showing its successful behaviour prior to energetic eruptions, giving time enough to alert the population and prepare for the consequences of an imminent and well predicted moment of the eruption.
Cannabis sativa-based oils against aluminum-induced neurotoxicity
Authors: Alves Carla , Tamagno Wagner Antonio , Vanin Ana Paula , Pompermaier Aline , Barcellos Leonardo José Gil 
Published: June 2023

AbstractThe use of terpenoid compounds in different neural-related conditions is becoming useful for several illnesses. Another possible activity of these compounds is the reduction of nervous impairment. Cannabis sativa plants are known for their concentration of two important terpenoids, the delta-9-tetrahydrocannabinol (THC) and cannabidiol (CBD). CBD and THC have central peripheral activities already described and their usage in different brain diseases, such as Alzheimer's and multiple sclerosis. Aluminum (Al) is known as an important neurotoxic compound, the physiological action of Al is not known already, and in high concentrations can lead to intoxication and cause neurotoxicity. Here we evaluated the potential effect of two different doses of CBD- and THC-rich based oils against Al-induced toxicity, in the zebrafish model. We evaluated behavioral biomarkers of the novel tank test (NTT) and social preference test (SPT), and biochemical markers: the activity of the enzyme acetylcholinesterase (AChE) and the antioxidant enzymes—catalase, superoxide dismutase, and glutathione-S-transferase. CBD- and THC-based oils were able to increase the AChE activity helping the cholinergic nervous system actuate against Al toxicity which was reflected by the behavioral biomarkers changes. We concluded that the oils have a protective effect and might be used with proposals for neurological and antioxidant impairment avoidance caused by Al intoxications.
Effects of high- and low-yield moso bamboo (Phyllostachys edulis) forests on bacterial community structure
Authors: Liu Fang , Yuan Zong-sheng , Zeng Zhi-hao , Pan Hui 
Published: June 2023

AbstractTo study the characteristics of bacterial community structure in high-yield and low-yield moso bamboo (Phyllostachys edulis) forests, we collected bamboo rhizome, rhizome root, stem, leaf, rhizosphere soil, and non-rhizosphere soil from high- and low-yield forests in Yong'an City and Jiangle County of Fujian Province, China. The genomic DNA of the samples was extracted, sequenced and analyzed. The results show that: the common differences between the high-yield and low-yield P. edulis forest samples in the two regions were mainly in bacterial community compositions in the bamboo rhizome, rhizome root, and soil samples. Differences in the bacterial community compositions in the stem and leaf samples were insignificant. The bacterial species and diversity in rhizome root and rhizosphere soil of high-yield P. edulis forests were less than those of low-yield forests. The relative abundance of Actinobacteria and Acidobacteria in rhizome root samples of high-yield forests was higher than that in low-yield forests. The relative abundance of Rhizobiales and Burkholderiales in bamboo rhizome samples in high-yield forests was higher than that in low-yield forests. The relative abundance of Bradyrhizobium in bamboo rhizome samples in high-yield forests was higher than that in low-yield forests in the two regions. The change of bacterial community composition in P. edulis stems and leaves showed little correlation with high- or low-yields of P. edulis forests. Notably, the bacterial community composition of the rhizome root system was correlated with the high yield of bamboo. This study provides a theoretical basis for using of microbes to enhance the yields of P. edulis forests.
To infer the probability of cervical ossification of the posterior longitudinal ligament and explore its impact on cervical surgery
Authors: Zhu Jichong , Lu Qing , Zhan Xinli , Huang Shengsheng , Zhou Chenxing , Wu Shaofeng , Chen Tianyou , Yao Yuanlin , Liao Shian , Yu Chaojie , Fan Binguang , Yang Zhenwei , Gu Wenfei , Wang Yihan , Wei Wendi , Liu Chong 
Published: June 2023

AbstractThe ossification of the posterior longitudinal ligament (OPLL) in the cervical spine is commonly observed in degenerative changes of the cervical spine. Early detection of cervical OPLL and prevention of postoperative complications are of utmost importance. We gathered data from 775 patients who underwent cervical spine surgery at the First Affiliated Hospital of Guangxi Medical University, collecting a total of 84 variables. Among these patients, 144 had cervical OPLL, while 631 did not. They were randomly divided into a training cohort and a validation cohort. Multiple machine learning (ML) methods were employed to screen the variables and ultimately develop a diagnostic model. Subsequently, we compared the postoperative outcomes of patients with positive and negative cervical OPLL. Initially, we compared the advantages and disadvantages of various ML methods. Seven variables, namely Age, Gender, OPLL, AST, UA, BMI, and CHD, exhibited significant differences and were used to construct a diagnostic nomogram model. The area under the curve (AUC) values of this model in the training and validation groups were 0.76 and 0.728, respectively. Our findings revealed that 69.2% of patients who underwent cervical OPLL surgery eventually required elective anterior surgery, in contrast to 86.8% of patients who did not have cervical OPLL. Patients with cervical OPLL had significantly longer operation times and higher postoperative drainage volumes compared to those without cervical OPLL. Interestingly, preoperative cervical OPLL patients demonstrated significant increases in mean UA, age, and BMI. Furthermore, 27.1% of patients with cervical anterior longitudinal ligament ossification (OALL) also exhibited cervical OPLL, whereas this occurrence was only observed in 6.9% of patients without cervical OALL. We developed a diagnostic model for cervical OPLL using the ML method. Our findings indicate that patients with cervical OPLL are more likely to undergo posterior cervical surgery, and they exhibit elevated UA levels, higher BMI, and increased age. The prevalence of cervical anterior longitudinal ligament ossification was also significantly higher among patients with cervical OPLL.
Metabolic benefits of 17α-estradiol in liver are partially mediated by ERβ in male mice
Authors: Mondal Samim Ali , Mann Shivani N. , van der Linden Carl , Sathiaseelan Roshini , Kamal Maria , Das Snehasis , Bubak Matthew P. , Logan Sreemathi , Miller Benjamin F. , Stout Michael B. 
Published: June 2023

AbstractMetabolic dysfunction underlies several chronic diseases. Dietary interventions can reverse metabolic declines and slow aging but remaining compliant is difficult. 17α-estradiol (17α-E2) treatment improves metabolic parameters and slows aging in male mice without inducing significant feminization. We recently reported that estrogen receptor α is required for the majority of 17α-E2-mediated benefits in male mice, but that 17α-E2 also attenuates fibrogenesis in liver, which is regulated by estrogen receptor β (ERβ)-expressing hepatic stellate cells (HSC). The current studies sought to determine if 17α-E2-mediated benefits on systemic and hepatic metabolism are ERβ-dependent. We found that 17α-E2 treatment reversed obesity and related systemic metabolic sequela in both male and female mice, but this was partially blocked in female, but not male, ERβKO mice. ERβ ablation in male mice attenuated 17α-E2-mediated benefits on hepatic stearoyl-coenyzme A desaturase 1 (SCD1) and transforming growth factor β1 (TGF-β1) production, which play critical roles in HSC activation and liver fibrosis. We also found that 17α-E2 treatment suppresses SCD1 production in cultured hepatocytes and hepatic stellate cells, indicating that 17α-E2 directly signals in both cell-types to suppress drivers of steatosis and fibrosis. We conclude that ERβ partially controls 17α-E2-mediated benefits on systemic metabolic regulation in female, but not male, mice, and that 17α-E2 likely signals through ERβ in HSCs to attenuate pro-fibrotic mechanisms.
Common juniper, an overlooked conifer with high invasion potential in protected areas of Patagonia
Authors: Franzese Jorgelina , Ripa Ramiro Rubén 
Published: June 2023

AbstractThe benefits of early detection of biological invasions are widely recognized, especially for protected areas (PAs). However, research on incipient invasive plant species is scarce compared to species with a recognized history of invasion. Here, we characterized the invasion status of the non-native conifer Juniperus communis in PAs and interface areas of Andean Patagonia, Argentina. We mapped its distribution and described both the invasion and the environments this species inhabits through field studies, a literature review, and a citizen science initiative. We also modeled the species’ potential distribution by comparing the climatic characteristics of its native range with those of the introduced ranges studied. The results show that J. communis is now widely distributed in the region, occurring naturally in diverse habitats, and frequently within and close to PAs. This species can be considered an incipient invader with a high potential for expansion in its regional distribution range, largely due to its high reproductive potential and the high habitat suitability of this environment. Early detection of a plant invasion affords a valuable opportunity to inform citizens of the potential risks to high conservation value ecosystems before the invader is perceived as a natural component of the landscape.
A hybrid multifunctional physicochemical sensor suite for continuous monitoring of crop health
Authors: Hossain Nafize Ishtiaque , Tabassum Shawana 
Published: June 2023

AbstractThis work reports a first-of-its-kind hybrid wearable physicochemical sensor suite that we call PlantFit for simultaneous measurement of two key phytohormones, salicylic acid, and ethylene, along with vapor pressure deficit and radial growth of stem in live plants. The sensors are developed using a low-cost and roll-to-roll screen printing technology. A single integrated flexible patch that contains temperature, humidity, salicylic acid, and ethylene sensors, is installed on the leaves of live plants. The strain sensor with in-built pressure correction capability is wrapped around the plant stem to provide pressure-compensated stem diameter measurements. The sensors provide real-time information on plant health under different amounts of water stress conditions. The sensor suite is installed on bell pepper plants for 40 days and measurements of salicylic acid, ethylene, temperature, humidity, and stem diameter are recorded daily. In addition, sensors are installed on different parts of the same plant to investigate the spatiotemporal dynamics of water transport and phytohormone responses. Subsequent correlation and principal component analyses demonstrate the strong association between hormone levels, vapor pressure deficit, and water transport in the plant. Our findings suggest that the mass deployment of PlantFit in agricultural settings will aid growers in detecting water stress/deficiency early and in implementing early intervention measures to reduce stress-induced yield decline.
Characterization of bacteriophage vB_KleM_KB2 possessing high control ability to pathogenic Klebsiella pneumoniae
Authors: Peng Qin , Ma Zimeng , Han Qing , Xiang Fangfang , Wang Lushuang , Zhang Yibin , Zhao Yuting , Li Jianing , Xian Yaxin , Yuan Yihui 
Published: June 2023

AbstractKlebsiella pneumoniae is a widespread pathogen of several human diseases. The emergence of multidrug-resistant K. pneumoniae makes the treatment of these diseases a significant challenge. The application of bacteriophages is a potential approach for dealing with the emergence of multidrug-resistant pathogenic bacteria. This study isolates a novel bacteriophage vB_KleM_KB2 that infects the multidrug-resistant clinical isolates of K. pneumoniae. The bacteriophage exhibits a short latent period of 10 min, and can effectively lyse the bacterium within 60 min. Notably, the bacteriophage can completely inhibit the growth of the host bacterium at the initial concentration of 107 CFU/mL with a low multiplicity of infection of 0.001, which proves its high lytic activity. Furthermore, the bacteriophage shows high environmental tolerances, which can facilitate the practical application of the bacteriophage. Analysis of the bacteriophage genome shows that the bacteriophage possesses a novel genome sequence and can represent a new bacteriophage genus. Considering the high lytic activity, short latent period, high stability, and novel genetic background, bacteriophage vB_KleM_KB2 enriches the bacteriophage library and provides a new alternative for controlling the diseases caused by multidrug-resistant pathogenic K. pneumoniae.
Evolution of cooperation in multiplex networks through asymmetry between interaction and replacement
Authors: Inaba Masaaki , Akiyama Eizo 
Published: June 2023

AbstractCooperation is the foundation of society and has been the subject of numerous studies over the past three decades. However, the mechanisms underlying the spread of cooperation within a group are not yet fully comprehended. We analyze cooperation in multiplex networks, a model that has recently gained attention for successfully capturing certain aspects of human social connections. Previous studies on the evolution of cooperation in multiplex networks have shown that cooperative behavior is promoted when the two key processes in evolution, interaction and strategy replacement, are performed with the same partner as much as possible, that is, symmetrically, in a variety of network structures. We focus on a particular type of symmetry, namely, symmetry in the scope of communication, to investigate whether cooperation is promoted or hindered when interactions and strategy replacements have different scopes. Through multiagent simulations, we found some cases where asymmetry can promote cooperation, contrasting with previous studies. These results hint toward the potential effectiveness of not only symmetrical but also asymmetrical approaches in fostering cooperation within particular groups under certain social conditions.
Many-body correlations in one-dimensional optical lattices with alkaline-earth(-like) atoms
Authors: Bilokon Valeriia , Bilokon Elvira , Bañuls Mari Carmen , Cichy Agnieszka , Sotnikov Andrii 
Published: June 2023

AbstractWe explore the rich nature of correlations in the ground state of ultracold atoms trapped in state-dependent optical lattices. In particular, we consider interacting fermionic ytterbium or strontium atoms, realizing a two-orbital Hubbard model with two spin components. We analyze the model in one-dimensional setting with the experimentally relevant hierarchy of tunneling and interaction amplitudes by means of exact diagonalization and matrix product states approaches, and study the correlation functions in density, spin, and orbital sectors as functions of variable densities of atoms in the ground and metastable excited states. We show that in certain ranges of densities these atomic systems demonstrate strong density-wave, ferro- and antiferromagnetic, as well as antiferroorbital correlations.
Effects of PmDOME and PmSTAT knockdown on white spot syndrome virus infection in Penaeus monodon
Authors: Laohawutthichai Pasunee , Jatuyosporn Thapanan , Supungul Premruethai , Tassanakajon Anchalee , Krusong Kuakarun 
Published: June 2023

AbstractJanus kinase/signal transducers and activators of transcription (JAK/STAT) signaling pathway plays an important role in antiviral immunity. This research reports the full-length DOME receptor gene in Penaeus monodon (PmDOME) and examines the effects of PmDOME and PmSTAT silencing on immune-related gene expressions in shrimp hemocytes during white spot syndrome virus (WSSV) infection. PmDOME and PmSTAT were up-regulated in shrimp hemocytes upon WSSV infection. Suppression of PmDOME and PmSTAT showed significant impacts on the expression levels of ProPO2 (melanization), Vago5 (interferon-like protein) and several antimicrobial peptides, including ALFPm3, Penaeidin3, CrustinPm1 and CrustinPm7. Silencing of PmDOME and PmSTAT reduced WSSV copy numbers and delayed the cumulative mortality caused by WSSV. We postulated that suppression of the JAK/STAT signaling pathway may activate the proPO, IFN-like antiviral cytokine and AMP production, resulting in a delay of WSSV-related mortality.