bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental Investigation of Shale Rock Properties Altering In-Situ Gas Density and Storage
Authors: Lou Xuanqing , Chakraborty Nirjhor , Karpyn Zuleima
Published: April 2022

Shale gas reservoir has become a crucial resource for the past decade to sustain growing energy needs while reducing the carbon intensity of energy systems relative to other fossil fuels. However, these reservoirs are geologically complex in their chemical composition and dominance of nano-scale pores, resulting in limited predictability of their effective storage capacity. To predict gas storage and estimate volumetric gas-in-place, in-situ gas properties need to be defined. However, only a few direct experimental measurements on in-situ gas properties are available in the literature, and the interactions between gas and the surrounding surface area of the medium remain poorly understood. In this study, gas invasion experiments were conducted in conjunction with 3D X-ray micro-CT imaging on three different shales, i.e., Bakken, Haynesville and Marcellus. Results show evidence of increased storage capacity in all cases, with different degrees of gas densification across the three shale specimens. The average of measured in-situ xenon density within the Bakken, Haynesville and Marcellus shale samples were found to be 171.53 kg/m3, 326.05 kg/m3 and 947 kg/m3, respectively. These measured densities are higher than their corresponding theoretical free gas density, though lower than the xenon density at boiling point, indicating that current practices of estimating adsorbed gas and gas in place, using boiling point liquid density, may be overestimated. The xenon densification factor in the Marcellus sample was found to be 7.4, indicating the most significant degree of localized densification. This densification factor drops to 2.6, and to 1.4, in the Haynesville and the Bakken sample, respectively. Characterization of shale composition and pore structure are presented, in order to assess the shale properties controlling in-situ gas density and storage capacity. Results indicate that the observed degree of gas densification in shales can be attributed to surface area and pore size. The findings in this work provide valuable reference for simulation to much more accurately predict gas storage in shales. More importantly, the contribution of this work lay a foundation to evaluate excess storage capacity of various gases in ranging tight formations.
Possible Impact of Boreal Winter Siberian High on ENSO Development in the Following Year
Authors: Fu Jiayu , Liu Minghong , Wang Run , Wang Yuwen , Zhao Shuo
Published: April 2022

Siberian High (SH) is the dominant pressure system located in the mid-high latitudes of Eurasia during boreal wintertime. This study reveals a triggering impact of SH variation in preceding winter on the following ENSO events, and gives a possible explanation via diagnosing the SH-associated air-sea response over the tropical Pacific and North Pacific. When SH is anomalously enhanced (suppressed) during boreal winter, an Aleutian Low enhanced (suppressed) response will occur over the downstream North Pacific. The Aleutian Low response gradually evolves into a meridional dipole structure similar to the negative (positive) phase of the North Pacific Oscillation (NPO) during the following spring and early summer. Correspondingly, the oceanic response in the North Pacific features a pattern similar to the negative (positive) phase of the Victoria mode. These SH-associated air-sea responses over the subtropical North Pacific will be maintained and further delivered into the tropical Pacific through the so-called seasonal footprinting mechanism, which favors the Bjerknes feedback established around boreal summer and finally grows into a La Niña (El Niño).
PACAP/GCGa Is an Important Modulator of the Amphioxus CNS-Hatschek’s Pit Axis, the Homolog of the Vertebrate Hypothalamic-Pituitary Axis in the Basal Chordates
Authors: On Jason S. W. , Su Liuru , Shen Hong , Arokiaraj Aloysius W. R. , Cardoso João C. R. , Li Guang , Chow Billy K. C.
Published: April 2022

The Hatschek’s pit in the cephalochordate amphioxus, an invertebrate deuterostome basal to chordates is suggested to be the functional homolog structure of the vertebrate adenohypophysis based on anatomy and expression of homologous neuroendocrine genes. However, the endocrine potential of the cephalochordate Hatschek’s pit remains to be demonstrated as well as the physiological actions of the secreted neuropeptides. In this study, we have explored the distribution and characterize the potential function of the amphioxus PACAP/GCG precursor, which is the ortholog of the hypothalamic PACAP neuropeptide in vertebrates. In amphioxi, two PACAP/GCG transcripts PACAP/GCGa and PACAP/GCGbc that are alternative isoforms of a single gene with different peptide coding potentials were isolated. Immunofluorescence staining detected their expression around the nucleus of Rohde, supporting that this structure may be homologous of the neurosecretory cells of the vertebrate hypothalamus where abundant PACAP is found. PACAP/GCGa was also detected in the infundibulum‐like downgrowth approaching the Hatschek’s pit, indicating diffusion of PACAP/GCGa from the CNS to the pit via the infundibulum‐like downgrowth. Under a high salinity challenge, PACAP/GCGa was upregulated in amphioxi head and PACAP/GCGa treatment increased expression of GHl in Hatschek’s pit in a dose-dependent manner, suggesting that PACAP/GCGa may be involved in the regulation of GHl via hypothalamic-pituitary (HP)-like axis similar as in the vertebrates. Our results support that the amphioxus Hatschek’s pit is likely to be the functional homolog of pituitary gland in vertebrates.
Maternal Urinary Cotinine Concentrations During Pregnancy Predict Infant BMI Trajectory After Birth: Analysis of 89617 Mother-Infant Pairs in the Japan Environment and Children’s Study
Authors: Hirai Hiroyuki , Okamoto Shiki , Masuzaki Hiroaki , Murata Tsuyoshi , Ogata Yuka , Sato Akiko , Horiuchi Sayaka , Shinohara Ryoji , Shinoki Kosei , Nishigori Hidekazu , Fujimori Keiya , Hosoya Mitsuaki , Yasumura Seiji , Hashimoto Koichi , Yamagata Zentaro , Shimabukuro Michio ,   the JECS Group
Published: April 2022

Background

Clinical or epidemiological conclusions remain undecided on the direct effects of active and second-hand smoking during pregnancy on childhood obesity. Urinary cotinine (UC) concentration, an accurate and quantitative marker for smoking, may elucidate the dose-dependent relationship between smoking during pregnancy and childhood obesity. To analyze the relationship between UC concentration and smoking questionnaire (SQ) classes for active and second-hand smoking in pregnant mothers and trajectory of infant Kaup index (body mass index: BMI).

Methods

This multicenter prospective cohort study was conducted using a list-wise complete set of 35829 among 89617 mother-infant singleton pairs, recruited between 2011 and 2014, in the Japan Environment and Children’s Study (JECS). Pairs were categorized according to UC levels (1 to 4 classes) or SQ (0 to 4 classes).

Results

Maternal BMI at delivery was the highest in UC class 4 (highest). Maternal and paternal education of ≥16 years and annual household income were lowest in UC class 4. Infant BMI was lower at birth, but trends in BMI and ΔBMI were higher from six to 36 months step-wise in the UC classes. The above tendency was observed in the list-wise complete dataset but was emphasized after multiple imputations and corrections of cofounders. UC concentration in five SQ classes largely fluctuated, and the relationship between SQ classes and trends in BMI and ΔBMI was not statistically significant.

Conclusion

Infants from high UC mothers had a low BMI at birth, increasing from six to 36 months of age. UC concentrations, but not smoking questionnaire classes, predict infant BMI trajectory, suggesting that active and second-hand smoking affect child obesity in a dose-dependent manner.
Chaotic Oscillation Control Model of Power System Under Electromechanical Power Disturbance
Authors: Hu Qiankun
Published: April 2022

The influence of electromechanical power on the power system is controlled in order to stabilize the power system. The author establishes a fourth-order power system model with a power disturbance term based on the dissipative property; the possibility of the existence of a system chaotic attractor is analyzed using the Lyapunov exponent spectrum, bifurcation diagram, phase diagram, spectral entropy, etc., and the influence of the power disturbance term on the motion state of the system is studied. It can be seen that under the influence of the disturbance frequency, the system will exhibit sufficient dynamic behavior. The parameters of the power disturbance term are more sensitive to the influence of the system power angle, and when the disturbance amplitude reaches a certain value, the power angle will increase sharply, and eventually the system will become unstable. The experimental results show that when controller parameters c1=c2=60 are selected, thenτ = 0.01, η = 0.3, and ε = 0.001. Moreover, when two groups of different control objectives r = 1.2 + 0.1 sin(t) and r = 1.2 are chosen, it can be clearly seen that the power angle δ in the system is very unstable before the controller is connected and the fluctuations are large and irregular, whereas after the controller is added for 150 s, the power angle δ tends to become stable, the fluctuation range becomes small and regular, and the system has almost no chattering. In order to reflect the superiority of the author’s control method, under the same parameter conditions, the symbolic function θ(s)=sgn(s) is used as a switching function of the controller and the tracking control numerical simulation is carried out for the same control objectives r = 1.2 + 0.1 sin(t) and r = 1.2. The controller that adopts the relay characteristic function θ(s)=ss+|ε| as a switching function has a better control effect and the system is smooth and stable without chattering.
Comparing Decoupling and Driving Forces of CO2 Emissions in China and India
Authors: Jiao Ziheng , Xing Zhencheng , Zhang Guofeng , Ma Xiaolin , Wang Haikun
Published: April 2022

As the two largest developing countries globally, China and India have become the top 1 and 3 carbon emitters, respectively. Quantitating their CO2 emissions in terms of the characteristics and driving factors is highly significant to mitigating global climate change. This study compiled the CO2 emission inventories from 1990 to 2017 in China and India. The Tapio model and index decomposition analysis were used to analyze the impact of socio-economic factors on CO2 emissions. We found that 1) CO2 emissions of China and India reached 9526 and 2242 Mt, respectively, in 2017. CO2 emissions increased during 1990–2017 with an average annual growth rate of 5% in both countries. 2) In China, the economic development has remained weakly decoupling from emissions since 2012, reaching a strong decoupling (-0.2) in 2017. In contrast, the contribution of India’s economy to emissions continued to increase, and the decoupling status showed continuous fluctuations. 3) Economic development and population explosion were the dominant factors driving CO2 emissions in the countries. The effect of energy intensity inhibited India’s emissions growth after 2008 with an impact degree lower than China. Overall, our findings on the impact of the economy and emission development may provide references for other developing countries at different stages to achieve low-carbon development.
RETRACTED: Effect of Islamic Financial Development on Carbon Emissions: A Spatial Econometric Analysis
Authors: Al-Silefanee Rebean Ramadhan , Mamkhezri Jamal , Khezri Mohsen , Karimi Mohammad Sharif , Khan Yousaf Ali
Published: April 2022

In this research, data from 36 countries from 2013 to 2018 were used to examine the factors influencing CO2 emissions in Islamic countries, focusing on the impact of Islamic financial growth. The spatial econometric technique estimation findings indicate that there is no geographical association between CO2 emissions in the analyzed countries. The test findings establish the existence of the Kuznets hypothesis for the environment. Additionally, trade openness and increased energy usage have resulted in an increase in CO2 emissions. The impacts of traditional financial development factors, such as financial market and financial institution variables, were examined in this research. The findings indicate that the two variables have no direct and substantial influence on CO2 emissions and that their significant effect on CO2 emissions appears only when their nonlinear and spillover effects on energy consumption and economic growth are included. Additionally, the growth of financial institutions is inversely proportional to the intensity of carbon emissions. The results indicate that while the development of financial markets and institutions results in a significant increase in CO2 emissions, the negative coefficient of the interaction between financial development and energy consumption indicates that financial development ensures energy efficiency, which reduces the intensity of carbon emissions. The findings indicate that the expansion and depth of Islamic finance, as measured by total assets, asset quality, earnings, and efficiency of Islamic banks, can result in a nonlinear increase in CO2 emissions with a U-shaped relationship. The study of spillover effects demonstrates that in addition to their direct and positive effects on CO2 emissions, the increase in Islamic social responsibility and consumer education, and awareness about Islamic banking reduce the enhancing effects of energy consumption on greenhouse gas emissions.
The Synergistic Effect of Urban Canyon Geometries and Greenery on Outdoor Thermal Comfort in Humid Subtropical Climates
Authors: Peng Mingxi , Huang Haijing
Published: April 2022

Understanding the synergistic effect of multiple parameters is helpful to urban planners trying to design sustainable cities through a holistic approach. The objective of this research was to investigate how the street aspect ratio (HW), street orientation (AO), and greenery parameters, such as leaf area density (LAD) and aspect ratio of trees (ART), could affect the microclimate and outdoor thermal comfort of street canyons in a central business district under the local climate conditions of Chongqing city. To achieve this goal, a series of single- and multi-parameter simulations which followed an orthogonal design of experiments (ODOE) were conducted. The physiological equivalent temperature (PET) was adopted to assess the results of microclimate simulations for different urban models. The main findings are as follows: 1) The aspect ratio and orientation of urban canyons and ART play significant roles in influencing microclimate variables at the pedestrian level. 2) There is an inverse relationship between the street aspect ratio and Tmrt, and likewise for ART; the highest wind velocity was obtained when the aspect ratio of canyons was 2 and 3, which consequently developed the channeling phenomenon (when the domain wind is prevailing with street direction). 3) The East–West streets and canyons with an HW = 0.5 incur the warmest thermal conditions and longest extreme discomfort durations. 4) Results for the PET and meteorological parameters exhibit less significant variation obtained from different values of LAD than those observed in the other three parameters.
Venn Diagrams May Indicate Erroneous Statistical Reasoning in Transcriptomics
Authors: Weiner January , Obermayer Benedikt , Beule Dieter
Published: April 2022

A common application of differential expression analysis is finding genes that are differentially expressed upon treatment in only one out of several groups of samples. One of the approaches is to test for significant difference in expression between treatment and control separately in the two groups, and then select genes that show statistical significance in one group only. This approach is then often combined with a gene set enrichment analysis to find pathways and gene sets regulated by treatment in only this group. Here we show that this procedure is statistically incorrect and that the interaction between treatment and group should be tested instead. Moreover, we show that gene set enrichment analysis applied to such incorrectly defined genes group-specific genes may result in misleading artifacts. Due to the presence of false negatives, genes significant in one, but not the other group are enriched in gene sets which correspond to the overall effect of the treatment. Thus, the results appear related to the problem at hand, but do not reflect the group-specific effect of a treatment. A literature search revealed that more than a quarter of papers which used a Venn diagram to illustrate the results of separate differential analysis have also applied this incorrect reasoning.
Pleural Resident Macrophages and Pleural IRA B Cells Promote Efficient Immunity Against Pneumonia by Inducing Early Pleural Space Inflammation
Authors: Bénard Alan , Podolska Malgorzata J. , Czubayko Franziska , Kutschick Isabella , Klösch Bettina , Jacobsen Anne , Naschberger Elisabeth , Brunner Maximilian , Krautz Christian , Trufa Denis I. , Sirbu Horia , Lang Roland , Grützmann Robert , Weber Georg F.
Published: April 2022

Airway infection is a major cause of mortality worldwide. The identification of new mechanisms aiding in effective host immune response is therefore required. Here, we show that the specific depletion of the pleural immune cell compartment during bacterial pneumonia resulted in a reduced pulmonary immune response and increased mortality in mice. Bacterial airway infection provoked early pleural space (PS) inflammation characterized by innate response activator (IRA) B cell development and pleural large resident macrophage (LRM) necroptosis, the repopulation of LRMs being driven by cellular proliferationin situ. Necroptotic LRMs amplified PS inflammation by stimulating pleural Mincle-expressing macrophages whereas IRA B cells contributed partially to GM-CSF-induced PS inflammation. Upon pulmonary infection, the induction of PS inflammation resulted in reduced bacterial burden whereas the specific depletion of pleural resident macrophages led to increased mortality and bacterial burden and reduced pulmonary immunity. Moreover, mice in which B cells were unable to produce GM-CSF exhibited reduced CD103+dendritic cells and reduced CD4+T cell numbers in the draining lymph node. Altogether, our results describe a previously unrecognized mechanism of pleural space inflammation necessary for effective protection against bacterial airway infection.
Cultivation and Functional Characterization of a Deep-Sea Lentisphaerae Representative Reveals Its Unique Physiology and Ecology
Authors: Zhang Tianhang , Zheng Rikuan , Liu Rui , Li Ronggui , Sun Chaomin
Published: April 2022

As a member of Planctomycetes–Verrucomicrobia–Chlamydia (PVC) superphylum, the phylum Lentisphaerae is broadly distributed in various environments. Lentisphaerae members have been recognized as being typically difficult to isolate in pure culture—only five strains belonging to this phylum were cultured up to now—and therefore their major physiology and ecology are largely unknown. Here, using a polysaccharide degradation-driven strategy, we successfully cultured a representative of Lentisphaerae bacteria (Candidatus Coldseepensis marina zth2) from the deep-sea cold seep. Based on physiological and phylogenetic analyses, strain zth2 is identified as a type strain of a novel family. Notably, strain zth2 divides by a budding manner and a unique feature seen in ultrathin-section electron microscopic observation is the occurrence of narrow protrusions, namely, both cell wall and cytoplasm on the surface of strain zth2. Through growth assays and transcriptomic analyses, strain zth2 was verified to efficiently utilize polysaccharides, phosphate, and iron for growth. Strikingly, the utilization of polysaccharide, phosphate, and iron is correlative and jointly contributes to carbon, phosphorus, and iron metabolisms and thereby facilitating the production of energy. By mimicking the ocean environment and using operational taxonomic units (OTUs) analysis, we demonstrated that strain zth2 significantly enrich the microbial diversity by metabolizing polysaccharides or other substances. Overall, we propose that Lentisphaerae members are potential contributors to the cycling of nutrient, carbon, phosphorus, and other elements in the deep biosphere.
Behavioural Responses of a Large, Benthic Elasmobranch to Catch-and-Release Angling
Authors: Lavender Edward , Aleynik Dmitry , Dodd Jane , Illian Janine , James Mark , Wright Peter J. , Smout Sophie , Thorburn James
Published: April 2022

Catch-and-release angling is widespread, but the impacts of this practice for captured individuals are understudied, especially among elasmobranchs. Studies on sub-lethal behavioural impacts are particularly sparse, despite their importance for the interpretation of biologging data and for assessments of species’ tolerance to capture. In this study, the behavioural responses of flapper skate (Dipturus intermedius) to catch-and-release angling were described for the first time, using archival observations (depth and temperature) for 21 tag deployment/retrieval events and five recreational angling events that occurred during tagged individuals’ time at liberty from charter vessels off the west coast of Scotland in 2016–17. During capture (8–50 minutes), the changes in depth and temperature experienced by individuals typically exceeded natural variability. Post-release, behavioural change was apparent from visual inspection, regression and functional data analysis of the time series. Immediately following release, movements into deeper water and short periods of low vertical activity (usually 1–2 hours in duration) were common. However, overall average vertical activity was typically around 38% higher in the 12 hours following release than in undisturbed activity. A small number of individuals (n = 3, 14%) exhibited irregular post-release behaviour in the form of rapid, transient re-ascents towards the surface following release. Collectively, the evidence for limited, short-term behavioural changes suggests that flapper skate behaviour is relatively resilient to catch-and-release angling from charter vessels, but irregular post-release behaviour in 14% of individuals is sufficiently notable to indicate that further research is required on the impacts of this practice. This study clearly demonstrates the value of biologging data and behavioural analyses for examining the impacts of disturbance and separating ‘disturbed’ and ‘undisturbed’ behaviours in studies of animal movement.
Risk Factors and Prognosis of Early Recurrence in Stage I–II Endometrial Cancer: A Large-Scale, Multi-Center, and Retrospective Study
Authors: Dou Yingyu , Song Kun , Fu Yu , Shen Yuanming , Zhang Chuyao , Yao Shuzhong , Xu Congjian , Xia Min , Lou Ge , Liu Jihong , Lin Bei , Wang Jianliu , Zhao Weidong , Zhang Jieqing , Cheng Wenjun , Guo Hongyan , Guo Ruixia , Xue Fengxia , Wang Xipeng , Han Lili , Zhao Xia , Li Xiaomao , Zhang Ping , Zhao Jianguo , Ma Jiezhi , Li Wenting , Yang Xiaohang , Wang Zizhuo , Liu Jingbo , Fang Yong , Li Kezhen , Chen Gang , Sun Chaoyang , Cheng Xiaodong , Jiang Jie , Wang Beibei , Luo Danfeng , Kong Beihua ,   The Chinese Endometrial Carcinoma Consortium (CECC)
Published: April 2022

Objective

The aim of the present study was to determine overall survival (OS) and risk factors associated with early recurrence in patients with FIGO I–II stage endometrial carcinoma (EC).

Methods

Clinical features were retrospectively extracted from the database of China Endometrial Cancer Consortium from January 2000 to December 2019. A total of 2,974 patients with Federation International of Gynecology and Obstetrics (FIGO) I–II stage endometrial cancer were included. Kaplan-Meier survival analysis was used to assess OS and disease-specific survival. Cox proportional hazard model and Fine-Gray model were used to determine the factors related to OS. Binary logistic regression model was used to determine independent predictors of early relapse patients.

Results

Of these 2,974 ECs, 189 patients were confirmed to have relapse. The 5-year OS was significantly different between the recurrence and non-recurrence patients (p < 0.001). Three quarters of the relapse patients were reported in 36 months. The 5-year OS for early recurrence patients was shorter than late recurrence [relapse beyond 36 months, p < 0.001]. The grade 3 [odds ratio (OR) = 1.55, 95%CI 1.17–2.05, p = 0.002], lymphatic vascular infiltration (LVSI; OR = 3.36; 95%CI 1.50–7.54, p = 0.003), and myometrial infiltration (OR = 2.07, 95%CI 1.17—3.65, p = 0.012) were independent risk factors of early relapse. The protective factor of that is progesterone receptor (PR)-positive (OR = 0.50, 95%CI 0.27–0.92, p = 0.02). Bilateral ovariectomy could reduce recurrence risk rate (OR = 0.26, 95%CI 0.14–0.51, p < 0.001).

Conclusion

The OS of early relapse EC is worse. Grade 3, LVSI, and myometrial infiltration are independent risk factors for early relapse EC. In addition, the protective factor is PR-positive for those people and bilateral salpingo-oophorectomy could reduce the risk of recurrence.
Influence of Metabolic Risk Factors on the Risk of Bacterial Infections in Hepatitis B-Related Cirrhosis: A 10-Year Cohort Study
Authors: Yang Qiao , Tong Yifan , Pi Borui , Yu Hong , Lv Fangfang
Published: April 2022

Aim

The effect of metabolic factors on the risk of bacterial infections (BIs) in patients with hepatitis B virus (HBV)-related cirrhosis has not been demonstrated. This study aimed to explore specific metabolic factors associated with the BIs in these patients.

Methods

A population-based cohort of 471 patients with HBV-related cirrhosis was retrospectively enrolled between 2009 and 2019. The primary end point was the incidence of BIs during hospitalization, which were compared according to the metabolism-related indicators, namely, presence of diabetes, level of high-density lipoprotein cholesterol (HDLC) and triglyceride, and body mass index (BMI). The propensity score matching (PSM) was adopted to eliminate baseline discrepancies.

Results

Compared with the non-diabetic group, the incidences of BIs were higher in the diabetic group before and after PSM (p = 0.029 and p = 0.027). Similar results were found in the low HDLC group as compared with the normal HDLC group before and after PSM (p < 0.001 and p = 0.025). Further analysis showed that the incidences of BIs in patients with low HDLC alone were lower than patients with both low HDLC and diabetes before and after PSM (p = 0.003 and p = 0.022). Similarly, the incidence of BIs in patients with diabetes alone was lower than those in patients with both low HDLC and diabetes both before and after PSM (p = 0.002 and p = 0.018). However, neither triglyceride nor BMI level was related to BIs in our cohort.

Conclusion

In patients with HBV-related cirrhosis, the presence of diabetes and low level of HDLC were risk factors of BIs, showing a synergistic effect.
Identifying Recall Under Sedation by a Novel EEG Based Index of Attention—A Pilot Study
Authors: Baron Shahaf Dana , Weissman Avi , Priven Leonid , Shahaf Goded
Published: April 2022

Overview

Recall is an accepted consequence of sedation. But due to the very low prevalence of the more devastating awareness under anesthesia (AUA), it might be of value to assess first the efficacy of new markers for AUA by their efficacy in discovering the more prevalent recall under sedation (RUS). In this pilot study we assessed whether a novel index for attentional effort, the cognitive effort index (CEI), derived in real-time from one forehead EEG channel, could differentiate between patients with or without RUS.

Methods

EEG was sampled from 2 groups: (1) Patients who underwent deep sedation (n = 25) (using drugs according to the anesthesiologist preference, but generally combining either Midazolam or Propofol together with either Fentanyl or Remifentanil). (2) Patients who underwent general anesthesia (GA, n = 13, a negative control for recall). In recovery, recall was assessed using the BRICE questionnaire.

Results

Of the 25 sedated patients, 11 experienced recall. The CEI marker was high during significantly longer periods in patients with recall, compared to sedated patients, or patients under GA, without recall. Moreover, the increase in CEI was evident mainly toward the end of the procedure.

Conclusion

RUS seems to associate with higher level of attention, which is identified in real-time by the easy-to-extract CEI marker.
The Genome of the Acid Soil-Adapted Strain Rhizobium favelukesii OR191 Encodes Determinants for Effective Symbiotic Interaction With Both an Inverted Repeat Lacking Clade and a Phaseoloid Legume Host
Authors: Eardly Bertrand , Meor Osman Wan Adnawani , Ardley Julie , Zandberg Jaco , Gollagher Margaret , van Berkum Peter , Elia Patrick , Marinova Dora , Seshadri Rekha , Reddy T. B. K. , Ivanova Natalia , Pati Amrita , Woyke Tanja , Kyrpides Nikos , Loedolff Matthys , Laird Damian W. , Reeve Wayne
Published: April 2022

Although Medicago sativa forms highly effective symbioses with the comparatively acid-sensitive genus Ensifer, its introduction into acid soils appears to have selected for symbiotic interactions with acid-tolerant R. favelukesii strains. Rhizobium favelukesii has the unusual ability of being able to nodulate and fix nitrogen, albeit sub-optimally, not only with M. sativa but also with the promiscuous host Phaseolus vulgaris. Here we describe the genome of R. favelukesii OR191 and genomic features important for the symbiotic interaction with both of these hosts. The OR191 draft genome contained acid adaptation loci, including the highly acid-inducible lpiA/acvB operon and olsC, required for production of lysine- and ornithine-containing membrane lipids, respectively. The olsC gene was also present in other acid-tolerant Rhizobium strains but absent from the more acid-sensitive Ensifer microsymbionts. The OR191 symbiotic genes were in general more closely related to those found in Medicago microsymbionts. OR191 contained the nodA, nodEF, nodHPQ, and nodL genes for synthesis of polyunsaturated, sulfated and acetylated Nod factors that are important for symbiosis with Medicago, but contained a truncated nodG, which may decrease nodulation efficiency with M. sativa. OR191 contained an E. meliloti type BacA, which has been shown to specifically protect Ensifer microsymbionts from Medicago nodule-specific cysteine-rich peptides. The nitrogen fixation genes nifQWZS were present in OR191 and P. vulgaris microsymbionts but absent from E. meliloti-Medicago microsymbionts. The ability of OR191 to nodulate and fix nitrogen symbiotically with P. vulgaris indicates that this host has less stringent requirements for nodulation than M. sativa but may need rhizobial strains that possess nifQWZS for N2-fixation to occur. OR191 possessed the exo genes required for the biosynthesis of succinoglycan, which is required for the Ensifer-Medicago symbiosis. However, 1H-NMR spectra revealed that, in the conditions tested, OR191 exopolysaccharide did not contain a succinyl substituent but instead contained a 3-hydroxybutyrate moiety, which may affect its symbiotic performance with Medicago hosts. These findings provide a foundation for the genetic basis of nodulation requirements and symbiotic effectiveness with different hosts.
Updating the Phylodynamics of Yellow Fever Virus 2016–2019 Brazilian Outbreak With New 2018 and 2019 São Paulo Genomes
Authors: Moreira Salles Ana Paula , de Seixas Santos Nastri Ana Catharina , Ho Yeh-Li , Vilas Boas Casadio Luciana , Emanuel Amgarten Deyvid , Justo Arévalo Santiago , Soares Gomes-Gouvea Michele , Jose Carrilho Flair , de Mello Malta Fernanda , Rebello Pinho João Renato
Published: April 2022

The recent outbreak of yellow fever (YF) in São Paulo during 2016–2019 has been one of the most severe in the last decades, spreading to areas with low vaccine coverage. The aim of this study was to assess the genetic diversity of the yellow fever virus (YFV) from São Paulo 2016–2019 outbreak, integrating the available genomic data with new genomes from patients from the Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP). Using phylodynamics, we proposed the existence of new IE subclades, described their sequence signatures, and determined their locations and time of origin. Plasma or urine samples from acute severe YF cases (n = 56) with polymerase chain reaction (PCR) positive to YFV were submitted to viral genome amplification using 12 sets of primers. Thirty-nine amplified genomes were subsequently sequenced using next-generation sequencing (NGS). These 39 sequences, together with all the complete genomes publicly available, were aligned and used to determine nucleotide/amino acids substitutions and perform phylogenetic and phylodynamic analysis. All YFV genomes generated in this study belonged to the genotype South American I subgroup E. Twenty-one non-synonymous substitutions were identified among the new generated genomes. We analyzed two major clades of the genotypes IE, IE1, and IE2 and proposed the existence of subclades based on their sequence signatures. Also, we described the location and time of origin of these subclades. Overall, our findings provide an overview of YFV genomic characterization and phylodynamics of the 2016–2019 outbreak contributing to future virological and epidemiological studies.
Phylogenetic Distribution and Evolution of Type VI Secretion System in the Genus Xanthomonas
Authors: Liyanapathiranage Prabha , Wagner Naama , Avram Oren , Pupko Tal , Potnis Neha
Published: April 2022

The type VI secretion system (T6SS) present in many Gram-negative bacteria is a contact-dependent apparatus that can directly deliver secreted effectors or toxins into diverse neighboring cellular targets including both prokaryotic and eukaryotic organisms. Recent reverse genetics studies with T6 core gene loci have indicated the importance of functional T6SS toward overall competitive fitness in various pathogenic Xanthomonas spp. To understand the contribution of T6SS toward ecology and evolution of Xanthomonas spp., we explored the distribution of the three distinguishable T6SS clusters, i3*, i3***, and i4, in approximately 1,740 Xanthomonas genomes, along with their conservation, genetic organization, and their evolutionary patterns in this genus. Screening genomes for core genes of each T6 cluster indicated that 40% of the sequenced strains possess two T6 clusters, with combinations of i3*** and i3* or i3*** and i4. A few strains of Xanthomonas citri, Xanthomonas phaseoli, and Xanthomonas cissicola were the exception, possessing a unique combination of i3* and i4. The findings also indicated clade-specific distribution of T6SS clusters. Phylogenetic analysis demonstrated that T6SS clusters i3* and i3*** were probably acquired by the ancestor of the genus Xanthomonas, followed by gain or loss of individual clusters upon diversification into subsequent clades. T6 i4 cluster has been acquired in recent independent events by group 2 xanthomonads followed by its spread via horizontal dissemination across distinct clades across groups 1 and 2 xanthomonads. We also noted reshuffling of the entire core T6 loci, as well as T6SS spike complex components, hcp and vgrG, among different species. Our findings indicate that gain or loss events of specific T6SS clusters across Xanthomonas phylogeny have not been random.
The Acetyltransferase RibT From Bacillus subtilis Affects in vivo Dynamics of the Multimeric Heavy Riboflavin Synthase Complex
Authors: Rotter Daniel Andreas Orlando , Heger Christoph , Kühm Christian , Schmidt Nina , Schäfer Antje , Heimerl Thomas , Mack Matthias , Graumann Peter L.
Published: April 2022

Flavins are ubiquitous molecules in life as they serve as important enzyme cofactors. In the Gram-positive, soil-dwelling bacterium Bacillus subtilis, four well-characterized gene products (the enzymes RibDG, RibE, RibAB, and RibH) catalyze the biosynthesis of riboflavin (RF) from guanosine-triphosphate (GTP) and ribulose-5-phosphate (R5P). The corresponding genes form an operon together with the gene ribT (ribDG-E-AB-H-T), wherein the function of this terminal gene remained enigmatic. RibT has been structurally characterized as a GCN5-like acetyltransferase (GNAT), however, with unidentified target molecules. Bacterial two-hybrid system revealed interactions between RibT, RibH, and RibE, forming the heavy RF synthase complex. Applying single particle tracking (SPT), we found that confined (sub)diffusion of RibT is largely dependent on interacting RibE and, to a lesser degree, on interacting RibH. By induced expression of otherwise low-expressed ribT from an ectopic locus, we observed a decrease in the subpopulation considered to represent capsids of the heavy RF synthase and an increase in the subpopulation thought to represent pentamers of RibH, pointing to a putative role for RibT in capsid disassembly. Complementarily, either deletion of ribT or mutation of a key residue from RibH (K29) suspected to be the substrate of RibT for acetylation leads to increased levels of subpopulations considered as capsids of RibH-mVenus (RibH-mV) in comparison to wild-type (wt)-like cells. Thus, we provide evidence for an indirect involvement of RibT in RF biosynthesis by a putative capsid disassembling mechanism considered to involve acetylation of RibH residue K29 at the three-fold symmetry axis of 60-mer capsids.
Performance of Severe Acute Respiratory Syndrome Coronavirus 2 Serological Diagnostic Tests and Antibody Kinetics in Coronavirus Disease 2019 Patients
Authors: Choi Hyun-Woo , Jeon Chae-Hyeon , Won Eun Jeong , Kang Seung-Ji , Lee Seung Yeob , Kee Seung-Jung
Published: April 2022

Serological testing is recommended to support the detection of undiagnosed coronavirus disease 2019 (COVID-19) cases. However, the performance of serological assays has not been sufficiently evaluated. Hence, the performance of six severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binding antibody assays [three chemiluminescence (CLIAs) and three lateral flow immunoassays (LFIAs)] and a surrogate virus neutralization test (sVNT) was analyzed in a total of 988 serum samples comprising 389 COVID-19-positives and 599 COVID-19-negatives. The overall diagnostic sensitivities of CLIAs and LFIAs ranged from 54.2 to 56.6% and from 56.3 to 64.3%, respectively. The overall diagnostic specificities of CLIAs and LFIAs ranged from 98.2 to 99.8% and from 97.3 to 99.0%, respectively. In the symptomatic group (n = 321), the positivity rate increased by over 80% in all assays > 14 days after symptom onset. In the asymptomatic group (n = 68), the positivity rate increased by over 80% in all assays > 21 days after initial RT-PCR detection. In LFIAs, negatively interpreted trace bands accounted for the changes in test performance. Most false-positive results were weak or trace reactions and showed negative results in additional sVNT. For six binding antibody assays, the overall agreement percentages ranged from 91.0 to 97.8%. The median inhibition activity of sVNT was significantly higher in the symptomatic group than in the asymptomatic group (50.0% vs. 29.2%; p < 0.0001). The median times to seropositivity in the symptomatic group were 9.7 days for CLIA-IgG, 9.2 and 9.8 days for two CLIAs-Total (IgM + IgG), 7.7 days for LFIA-IgM, 9.2 days for LFIA-IgG, and 8.8 days for sVNT-IgG, respectively. There was a strong positive correlation between the quantitative results of the four binding antibody assays and sVNT with Spearman ρ-values ranging from 0.746 to 0.854. In particular, when using LFIAs, we recommend using more objective interpretable assays or establishing a band interpretation system for each laboratory, accompanied by observer training. We also anticipate that sVNT will play an essential role in SARS-CoV-2 antibody testing and become the practical routine neutralizing antibody assay.
Transcranial Direct Current Stimulation Alleviates Neurovascular Unit Dysfunction in Mice With Preclinical Alzheimer’s Disease
Authors: Luo Yinpei , Yang Hong , Yan Xiaojing , Wu Yaran , Wei Guoliang , Wu Xiaoying , Tian Xuelong , Xiong Ying , Wu Guangyan , Wen Huizhong
Published: April 2022

Neurons, glial cells and blood vessels are collectively referred to as the neurovascular unit (NVU). In the Alzheimer’s disease (AD) brain, the main components of the NVU undergo pathological changes. Transcranial direct current stimulation (tDCS) can protect neurons, induce changes in glial cells, regulate cerebral blood flow, and exert long-term neuroprotection. However, the mechanism by which tDCS improves NVU function is unclear. In this study, we explored the effect of tDCS on the NVU in mice with preclinical AD and the related mechanisms. 10 sessions of tDCS were given to six-month-old male APP/PS1 mice in the preclinical stage. The model group, sham stimulation group, and control group were made up of APP/PS1 mice and C57 mice of the same age. All mice were histologically evaluated two months after receiving tDCS. Protein content was measured using Western blotting and an enzyme-linked immunosorbent assay (ELISA). The link between glial cells and blood vessels was studied using immunofluorescence staining and lectin staining. The results showed that tDCS affected the metabolism of Aβ; the levels of Aβ, amyloid precursor protein (APP) and BACE1 were significantly reduced, and the levels of ADAM10 were significantly increased in the frontal cortex and hippocampus in the stimulation group. In the stimulation group, tDCS reduced the protein levels of Iba1 and GFAP and increased the protein levels of NeuN, LRP1 and PDGRFβ. This suggests that tDCS can improve NVU function in APP/PS1 mice in the preclinical stage. Increased blood vessel density and blood vessel length, decreased IgG extravasation, and increased the protein levels of occludin and coverage of astrocyte foot processes with blood vessels suggested that tDCS had a protective effect on the blood-brain barrier. Furthermore, the increased numbers of Vimentin, S100 expression and blood vessels (lectin-positive) around Aβ indicated that the effect of tDCS was mediated by astrocytes and blood vessels. There was no significant difference in these parameters between the model group and the sham stimulation group. In conclusion, our results show that tDCS can improve NVU function in APP/PS1 mice in the preclinical stage, providing further support for the use of tDCS as a treatment for AD.
Improving Depressive Symptoms of Post-stroke Depression Using the Shugan Jieyu Capsule: A Resting-State Functional Magnetic Resonance Imaging Study
Authors: Yao Guanqun , Zhang Xiaoqian , Li Jing , Liu Sha , Li Xinrong , Liu Pozi , Xu Yong
Published: April 2022

Regional homogeneity (ReHo) and fractional amplitude of low-frequency fluctuation (fALFF) were used to detect the neuroimaging mechanism of Shugan Jieyu Capsule (SG) in ameliorating depression of post-stroke depression (PSD) patients. Fifteen PSD patients took SG for 8 weeks, completed the 24-item Hamilton Depression Scale (HAMD) assessment at the baseline and 8 weeks later, and underwent functional magnetic resonance imaging (fMRI) scanning. Twenty-one healthy controls (HCs) underwent these assessments at the baseline. We found that SG improved depression of PSD patients, in which ReHo values decreased in the left calcarine sulcus (CAL.L) and increased in the left superior frontal gyrus (SFG.L) of PSD patients at the baseline. The fALFF values of the left inferior parietal cortex (IPL.L) decreased in PSD patients at the baseline. Abnormal functional activities in the brain regions were reversed to normal levels after the administration of SG for 8 weeks. Receiver operating characteristic (ROC) analysis found that the changes in three altered brain regions could be used to differentiate PSD patients at the baseline and HCs. Average signal values of altered regions were related to depression in all subjects at the baseline. Our results suggest that SG may ameliorate depression of PSD patients by affecting brain region activity and local synchronization.
General and Specific Dimensions of Mood Symptoms Are Associated With Impairments in Common Executive Function in Adolescence and Young Adulthood
Authors: Peterson Elena C. , Snyder Hannah R. , Neilson Chiara , Rosenberg Benjamin M. , Hough Christina M. , Sandman Christina F. , Ohanian Leoneh , Garcia Samantha , Kotz Juliana , Finegan Jamie , Ryan Caitlin A. , Gyimah Abena , Sileo Sophia , Miklowitz David J. , Friedman Naomi P. , Kaiser Roselinde H.
Published: April 2022

Both unipolar and bipolar depression have been linked with impairments in executive functioning (EF). In particular, mood symptom severity is associated with differences in common EF, a latent measure of general EF abilities. The relationship between mood disorders and EF is particularly salient in adolescence and young adulthood when the ongoing development of EF intersects with a higher risk of mood disorder onset. However, it remains unclear if common EF impairments have associations with specific symptom dimensions of mood pathology such as blunted positive affect, mood instability, or physiological arousal, or if differences in common EF more broadly relate to what is shared across various symptom domains, such as general negative affect or distress. To address this question, bifactor models can be applied to simultaneously examine the shared and unique contributions of particular mood symptom dimensions. However, no studies to our knowledge have examined bifactor models of mood symptoms in relation to measures of common EF. This study examined associations between common EF and general vs. specific symptom dimensions (anhedonia, physiological arousal, and mania) using structural equation modeling in adolescents and young adults with varying severity of mood symptoms (n = 495, ages = 13–25 years, 68.69% female). A General Depression factor capturing shared variance across symptoms statistically predicted lower Common EF. Additionally, a factor specific to physiological arousal was associated with lower Common EF. Anhedonia-specific and Mania-specific factors were not significantly related to Common EF. Altogether, these results indicate that deficits in common EF are driven by, or reflect, general features of mood pathology that are shared across symptom dimensions but are also specifically associated with physiological arousal.