bluuebunny/crossref_metadata_2025 huggingface dataset:
The verification of the possibility of alkalis penetration from the surrounding environment into the concrete pavement slabs
Authors: Dohnalkova B , Grosek J , Nevosad Z
Published: September 2022

The short material service life of concrete is currently a frequently discussed topic, especially for newly constructed roadways with cement concrete pavement. This early degradation of cement concrete pavement slabs is a major problem that threatens the service life of sub-sections or the entire road. As some partial results demonstrate, a possible cause of this degradation can be seen in the surrounding road environment, namely the possibility of transferring aggressive substances to the concrete pavement slab. This paper is concerned with the verification of the possibility of the penetration of alkalis penetration from the surrounding environment into the concrete pavement slab by simulating the effect of different external conditions and environments.
Monte Carlo simulations of vehicle-mounted whole-body NaI(Tl) counter
Authors: Mo H. , Gong P. , Liang D. , Wang Z. , Zhang J. , Hu Z. , Wu R. , Tang X. , Wang J. , Ma J. , Yang X.
Published: September 2022

During a nuclear emergency, an internal exposure detection
device with on-site and rapid measurements should be developed to
assess the level of internal exposure of people in radioactively
contaminated areas. Based on MCNP simulations, this work designed a
shielding structure of a NaI(Tl) type vehicle-mounted whole-body
counter (VM-WBC) and it has good shielding performance against the
background radiation. The mass of the shielding structure was less
than 800 kg, and the minimum detectable activity (MDA) of 60Co
and 137Cs obtained by simulation for a 10 min measurement was
less than 50 Bq. And we also study its counting efficiency
calibration by simulating radiation computing phantoms with Chinese
and American reference physiological characteristics. Equations that
fit counting efficiency, body build index, and photon energy were
also developed. The relative efficiency deviation between the
equation and the MCNP simulation was less than 5%.
Flapping dynamics of an inverted flag behind a cylinder
Authors: Ojo Oluwafemi , Kohtanen Eetu , Jiang Aojia , Brody Jacob , Erturk Alper , Shoele Kourosh
Published: September 2022

The inverted flag configuration is inspired by biological structures (e.g. leaves on a tree branch), showing rich dynamics associated with instabilities at lower flow speeds than the regular flag configuration. In the biological counterpart, the arrangement of leaves and twigs on foliage creates a complex interacting environment that promotes certain dynamic fluttering modes. While enabling a large amplitude response for reduced flow speeds is advantageous in emerging fields such as energy harvesting, still, little is known about the consequence of such interactions. In this work, we numerically study the canonical bio-inspired problem of the flow-structural interaction of a 2D inverted flag behind a cylindrical bluff body, mimicking a leaf behind a tree branch, to investigate its distinct fluttering regimes. The separation distance between the cylinder and flag is gradually modified to determine the effective distance beyond which small-amplitude or large-amplitude flapping occurs for different flow velocities. It is shown that the flag exhibits a periodic large amplitude−low frequency response mode when the cylinder is placed at a sufficiently large distance in front of the flag. At smaller distances, when the flag is within the immediate wake of the cylinder, the flag undergoes a high frequency−small amplitude response. Finally, the flag’s piezoelectric power harvesting capability is investigated numerically and experimentally for varying geometrical and electrical parameters associated with these two conditions. Two separate optimal response modes with the highest energy output have also been identified.
Derivation of Euler equations from quantum and classical microscopic dynamics
Authors: Hannani Amirali , Huveneers François
Published: September 2022

We derive Euler equations from a Hamiltonian microscopic dynamics. The microscopic system is a one-dimensional disordered harmonic chain, and the dynamics is either quantum or classical. This chain is an Anderson insulator with a symmetry protected mode: thermal fluctuations are frozen while the low modes ensure the transport of elongation, momentum and mechanical energy, that evolve according to Euler equations in an hyperbolic scaling limit. In this paper, we strengthen considerably the results in Bernardin et al (2019 Commun. Math. Phys.
365 215–37); Hannani (2022 Commun. Math. Phys.
390 349–23), where we established a limit in mean starting from a local Gibbs state: we now control the second moment of the fluctuations around the average, yielding a limit in probability, and we enlarge the class of admissible initial states.
Study the physical, chemical and biological changes in Um-Hawliyah drainage polluted with oil residues in Karbala Province-Iraq
Authors: Al-Yasari W.A. K. , Abdalakhwa S. H , Al-Alwani B. A.
Published: September 2022

This experiment was conducted to investigate the physical, chemical and biological parameters in Um-Hawliyah drainage which is contaminated with oil residues in the governorate of Karbala during the period from November,2015 to February,2016 in three stations. It was found that all physical and chemical properties were clearly affected by these wastes. During November and December, as the study stations varied in the proportions of physical, chemical and biological parameters, as observed in the variability in the number and types of bacteria and algae during the period and stations of study, as well as observed a clear increase in the effectiveness of enzymes superoxide dismutase (SOD) and Catalase (CAT) for Phragmites spp. plant during November at the second station. Each treatment with three replications, and all data were analyzed according SPSS statistics 17.0 software by (L.S.D 0.05).
Primary Productivity of Iraqi lakes: A Review
Authors: Wahhab Taibat A. , Hassan Fikrat M
Published: September 2022

Lentic ecosystems are important for fish production and are a critical habitat for waterfowl and numerous migratory birds. In this study we have gathered data on primary productivity of lakes across Iraq to provide updated information to strategize conservation and management. Tigris and Euphrates rivers are the primary sources of filling up major lakes in Iraq the overall assessment shows that the primary productivity is dependent on the algal composition and environmental factors with coincident role of macrophytes. An average of 37 to 637 mg carbon/m3/day of primary productivity was calculated for most of the lakes comprised of Bacillariophyceae and followed by Cyanophyceae, Chlorophyceae, Euglenophyceae, and Pyrrophyceae. It is hoped that this study can be an input to fill knowledge gaps and help to build long term maintainability of water quality and conservation of lake ecosystem across Iraq.
A Study of Some Aquatic Oligochaetes Community in Shatt Al-Hillah/ Middle of Iraq
Authors: Obaid Zahraa Hussein
Published: September 2022

The current study discusses the spatial distribution of Oligochaete communities on Shatt Al-Hillah. Monthly samples of Oligochaete worms were gathered from four locations along the Shatt Al-Hillah in the middle of Iraq, between September 2019 and May 2020. show the study for the existence of521Individual aquatic Oligochaeta belong to 7 species from the Naididae and Lumriculdae subfamilies, as well as the Pristinae subfamily, and in Site S3 had the largest number of worms, with 180 worms from 7 species being detected, while in Site S2 had the least number of worms, 107 from 5 species. The largest individual numbers were registered in February, while the lowest were recorded in April. The species, Prisma aequiseta, was first recorded, in the Shatt Al-Hillah rive. Show tubificid worms, Branchuira sowerbyi, and Limnodrilus hoffmeisteri were the most abundant species in the Shatt Al-Hillah.
Heavy metals pollution profiles in Tigris River within Baghdad city
Authors: Aljanabi Zahraa Zahraw , Hassan Fikrat M. , Jawad Al-Obaidy Abdul-Hameed M.
Published: September 2022

The Tigris River is a major source of Iraq’s drinking and agricultural water supply. An increase in pollution by heavy metals can be a great threat to human and aquatic life. In this study, the pollution index (PI) and metal index (MI) were used to evaluate the status of the Tigris River in Baghdad City. Five stations were chosen to conduct the study. Five heavy metals were analyzed: iron (Fe), lead (Pb), nickel (Ni), zinc (Zn), and chromium (Cr). The result of PI was ranked between “No effect to moderately affected for Fe; Slightly Affected to Seriously Affected for Pb; no effect to moderately affected for Ni, and no effect to strongly affected for Cr; only Zn was in the No effect class. While the Metal Index (MI) exceeded the warning threshold on all sites, its results ranged between 2.85 and 5.89. Pb was the most significant element that caused the rise of both indices where their values exceeded the allowable limits all the time, followed by Fe and Ni. increasing the concentration of heavy metals in the Tigris River, which returns to effluents of waste from many industrial facilities located on its bank, and the direct discharge of public sewage.
Water decolourisation using a phytoremediation method: Ocimum basilicum as model
Authors: Al-Saffar Abdulkareem K. I. , Attaee Muammar H. , kadhum Zainab Akeel , Abood Emad Salaam , Samaka Isra’a S. , Al-Sareji Osamah J.
Published: September 2022

Phytoremediation is the utilisation of plants to remove pollutants from a polluted media, such as soils and water. This method is an eco-friendly approach because it remediates water or soil from pollutants without chemical treatments or a chemical pre-treatment. For this reason, this method was used in this study to decolourise artificial water from a textile dye (methyl orange (MO)). The phytoremediation process was done using the Ocimum basilicum plant and continued for 30 days. The Ocimum basilicum plants were placed in plastic enclosures and exposed to 5 litres of coloured water (25 mg/L and 50 mg/L of OM) for the required duration. The enclosures were kept in a greenhouse with a controlled temperature (27±2°C), and 100 mL samples were taken from the enclosures every two days. The experiments showed that 1) the Ocimum basilicum plant removed 90% of the MO after 24 days when the MO dye concentration of 25 mg and 2) the MO dye in water decreases the relative growth rate of the Ocimum basilicum plant. This study concluded that the Ocimum basilicum plant is a promising alternative to removing dyes from water and should be adopted to reduce the effects of water pollution on the environment.
A divide-and-conquer method to improve performance in quantum transport calculations: conductance in rotated graphene nanoribbons side-contact junctions
Authors: Rodríguez Mauricio J , Ramírez Carlos
Published: September 2022

We propose a divide-and-conquer algorithm to find recursively the scattering matrix of general tight-binding structures. The scattering matrix allows a direct calculation of transport properties in mesoscopic systems by using the Landauer formula. The method is exact, and by analyzing the performance of the algorithm in square, triangular and honeycomb lattices, we show a significant improvement in comparison to other state-of-the-art recursive and non-recursive methods. We utilize this algorithm to compute the conductance of a rotated graphene nanoribbon side-contact junction, revealing that for electrons with energies smaller than −2.7 eV the transmission function depends negligibly on the angle of the junction, whereas for electrons with energies greater than −2.7 eV, there exists a set of angles for the system that increase its conductance independently of the energy of the particles.
GeneNetTools: tests for Gaussian graphical models with shrinkage
Authors: Bernal Victor , Soancatl-Aguilar Venustiano , Bulthuis Jonas , Guryev Victor , Horvatovich Peter , Grzegorczyk Marco
Published: September 2022

Motivation

Gaussian graphical models (GGMs) are network representations of random variables (as nodes) and their partial correlations (as edges). GGMs overcome the challenges of high-dimensional data analysis by using shrinkage methodologies. Therefore, they have become useful to reconstruct gene regulatory networks from gene-expression profiles. However, it is often ignored that the partial correlations are ‘shrunk’ and that they cannot be compared/assessed directly. Therefore, accurate (differential) network analyses need to account for the number of variables, the sample size, and also the shrinkage value, otherwise, the analysis and its biological interpretation would turn biased. To date, there are no appropriate methods to account for these factors and address these issues.

Results

We derive the statistical properties of the partial correlation obtained with the Ledoit–Wolf shrinkage. Our result provides a toolbox for (differential) network analyses as (i) confidence intervals, (ii) a test for zero partial correlation (null-effects) and (iii) a test to compare partial correlations. Our novel (parametric) methods account for the number of variables, the sample size and the shrinkage values. Additionally, they are computationally fast, simple to implement and require only basic statistical knowledge. Our simulations show that the novel tests perform better than DiffNetFDR—a recently published alternative—in terms of the trade-off between true and false positives. The methods are demonstrated on synthetic data and two gene-expression datasets from Escherichia coli and Mus musculus.

Availability and implementation

The R package with the methods and the R script with the analysis are available in https://github.com/V-Bernal/GeneNetTools.

Supplementary information

Supplementary data are available at Bioinformatics online.
The different brain areas occupied for integrating information of hierarchical linguistic units: a study based on EEG and TMS
Authors: Pei Changfu , Qiu Yuan , Li Fali , Huang Xunan , Si Yajing , Li Yuqin , Zhang Xiabing , Chen Chunli , Liu Qiang , Cao Zehong , Ding Nai , Gao Shan , Alho Kimmo , Yao Dezhong , Xu Peng
Published: September 2022

Human language units are hierarchical, and reading acquisition involves integrating multisensory information (typically from auditory and visual modalities) to access meaning. However, it is unclear how the brain processes and integrates language information at different linguistic units (words, phrases, and sentences) provided simultaneously in auditory and visual modalities. To address the issue, we presented participants with sequences of short Chinese sentences through auditory, visual, or combined audio-visual modalities while electroencephalographic responses were recorded. With a frequency tagging approach, we analyzed the neural representations of basic linguistic units (i.e. characters/monosyllabic words) and higher-level linguistic structures (i.e. phrases and sentences) across the 3 modalities separately. We found that audio-visual integration occurs in all linguistic units, and the brain areas involved in the integration varied across different linguistic levels. In particular, the integration of sentences activated the local left prefrontal area. Therefore, we used continuous theta-burst stimulation to verify that the left prefrontal cortex plays a vital role in the audio-visual integration of sentence information. Our findings suggest the advantage of bimodal language comprehension at hierarchical stages in language-related information processing and provide evidence for the causal role of the left prefrontal regions in processing information of audio-visual sentences.
The relevance of heterotopic callosal fibers to interhemispheric connectivity of the mammalian brain
Authors: Szczupak Diego , Iack Pamela Meneses , Rayêe Danielle , Liu Cirong , Lent Roberto , Tovar-Moll Fernanda , Silva Afonso C
Published: September 2022

The corpus callosum (CC) is the largest white matter structure and the primary pathway for interhemispheric brain communication. Investigating callosal connectivity is crucial to unraveling the brain’s anatomical and functional organization in health and disease. Classical anatomical studies have characterized the bulk of callosal axonal fibers as connecting primarily homotopic cortical areas. Whenever detected, heterotopic callosal fibers were ascribed to altered sprouting and pruning mechanisms in neurodevelopmental diseases such as CC dysgenesis (CCD). We hypothesized that these heterotopic connections had been grossly underestimated due to their complex nature and methodological limitations. We used the Allen Mouse Brain Connectivity Atlas and high-resolution diffusion-weighted imaging to identify and quantify homotopic and heterotopic callosal connections in mice, marmosets, and humans. In all 3 species, we show that ~75% of interhemispheric callosal connections are heterotopic and comprise the central core of the CC, whereas the homotopic fibers lay along its periphery. We also demonstrate that heterotopic connections have an essential role in determining the global properties of brain networks. These findings reshape our view of the corpus callosum’s role as the primary hub for interhemispheric brain communication, directly impacting multiple neuroscience fields investigating cortical connectivity, neurodevelopment, and neurodevelopmental disorders.
Parallel Analysis of Pre- and Postoperative Circulating Tumor DNA and Matched Tumor Tissues in Resectable Pancreatic Ductal Adenocarcinoma: A Prospective Cohort Study
Authors: Lee Jee-Soo , Han Youngmin , Yun Won-Gun , Kwon Wooil , Kim Hongbeom , Jeong Hyeonju , Seo Myoung-Seock , Park Yongsook , Cho Sung Im , Kim Haeryoung , Kim Ji Yeon , Seong Moon-Woo , Jang Jin-Young , Park Sung Sup
Published: September 2022

Background

Circulating tumor DNA (ctDNA) is a promising biomarker for early tumor detection and minimal residual disease (MRD) assessment in early-stage cancer, but quantifying minute amounts of ctDNA is challenging and well-designed studies on ctDNA in early-stage cancer are still lacking. Here, we adapted a sensitive next-generation sequencing (NGS) technology and performed parallel analysis of pre- and postoperative ctDNA and matched tumor tissues in a prospective cohort of patients with resectable pancreatic ductal adenocarcinoma (PDAC).

Methods

In total, 70 consecutive patients undergoing curative resection for resectable PDAC were enrolled. We performed integrated digital error suppression-enhanced cancer personalized profiling by deep sequencing NGS of triple-matched samples (pre/postoperative plasma cell-free DNA [cfDNA], tumor tissue, and genomic DNA) targeting 77 genes.

Results

Preoperative ctDNA was detected in 37.7% of the evaluable patients, with a median variant allele frequency of 0.09%. Twelve additional oncogenic mutations were detected exclusively in preoperative ctDNA but not in tissue. When quantitative concentrations of ctDNA were estimated in haploid genome equivalents per milliliter (hGE/mL), the risk of early recurrence was high in patients with postoperative ctDNA >1 hGE/mL. cfDNA variants from 24.5% of patients had features compatible with clonal hematopoiesis.

Conclusions

An optimized NGS approach might add value beyond tissue analysis through the highly sensitive detection of minute amounts of ctDNA in resectable PDAC. Postoperative ctDNA concentration could be a tool for MRD assessment. Moreover, parallel analyses of matched tissues and leukocytes might be required to accurately detect clinically relevant ctDNA.
Resistance of Grapevine Genotypes (Vitisspp.) toDaktulosphaira vitifoliae(Hemiptera: Phylloxeridae) in Brazil: Implications for Pest Management
Authors: Andzeiewski S , Oliveira D C , Bernardi D , Botton M
Published: September 2022

The phylloxera Daktulosphaira vitifoliae (Fitch) is considered the main pest in vine crops in the world. One of the alternatives for pest management is the use of resistant rootstocks. In the present study, 14 vine genotypes comprised of 6 canopy cultivars (Bordô, Isabel, BRS Lorena, Cabernet Sauvignon, Magnólia, and Chardonnay), 4 commercial rootstocks (Paulsen 1103, SO4, IAC 766, and IAC 572), and 4 promising rootstocks for pest management (1111-21, 548-44, 548-15, and IBCA-125) were evaluated for resistance to infestation the of root form of pest. For each genotype, the number of eggs, nymphs, and adults present in the roots were evaluated at 15, 20, 25, 30, and 35 d after egg infestation. In addition, the feeding place (lignified or nonlignified root), the presence or absence of tuberosities and nodosities, and the total fecundity of females were evaluated. The highest survival rates of nymphs and adults were observed in Cabernet Sauvignon, BRS Lorena, Chardonnay, and IBCA-25 in lignified roots, with the formation of tuberosities characterizing the materials as susceptible. In contrast, SO4, Paulsen 1103, IAC 572, IAC 766, 548-44, 548-15, Magnólia, and 1111-21 provided the least nymph and adult survival over time in nonlignified roots present in the nodosities, characterizing the materials as resistant. In addition, the lowest fecundity was observed in the roots of Magnólia (16 eggs). According to the results, it was verified that the cultivar Magnolia and the selections 548-15 and 1111-21 present reduced infestation and survival of nymphs of D. vitifoliae in the roots. This fact demonstrates the potential of the materials to be used as new resistant rootstocks or sources of insect resistance.
What drives performance in machine learning models for predicting heart failure outcome?
Authors: Gutman Rom , Aronson Doron , Caspi Oren , Shalit Uri
Published: September 2022

Aims

The development of acute heart failure (AHF) is a critical decision point in the natural history of the disease and carries a dismal prognosis. The lack of appropriate risk-stratification tools at hospital discharge of AHF patients significantly limits clinical ability to precisely tailor patient-specific therapeutic regimen at this pivotal juncture. Machine learning-based strategies may improve risk stratification by incorporating analysis of high-dimensional patient data with multiple covariates and novel prediction methodologies. In the current study, we aimed at evaluating the drivers for success in prediction models and establishing an institute-tailored artificial Intelligence-based prediction model for real-time decision support.

Methods and results

We used a cohort of all 10 868 patients AHF patients admitted to a tertiary hospital during a 12 years period. A total of 372 covariates were collected from admission to the end of the hospitalization. We assessed model performance across two axes: (i) type of prediction method and (ii) type and number of covariates. The primary outcome was 1-year survival from hospital discharge. For the model-type axis, we experimented with seven different methods: logistic regression (LR) with either L1 or L2 regularization, random forest (RF), Cox proportional hazards model (Cox), extreme gradient boosting (XGBoost), a deep neural-net (NeuralNet) and an ensemble classifier of all the above methods. We were able to achieve an area under receiver operator curve (AUROC) prediction accuracy of more than 80% with most prediction models including L1/L2-LR (80.4%/80.3%), Cox (80.2%), XGBoost (80.5%), NeuralNet (80.4%). RF was inferior to other methods (78.8%), and the ensemble model was slightly superior (81.2%). The number of covariates was a significant modifier (P < 0.001) of prediction success, the use of multiplex-covariates preformed significantly better (AUROC 80.4% for L1-LR) compared with a set of known clinical covariates (AUROC 77.8%). Demographics followed by lab-tests and administrative data resulted in the largest gain in model performance.

Conclusions

The choice of the predictive modelling method is secondary to the multiplicity and type of covariates for predicting AHF prognosis. The application of a structured data pre-processing combined with the use of multiple-covariates results in an accurate, institute-tailored risk prediction in AHF
Empirical shaking scenarios for Europe: a feasibility study
Authors: Bindi D , Zaccarelli R , Razafindrakoto H N T , Yen M-H , Cotton F
Published: September 2022

We process a large number of seismic recordings in Europe (i.e. about half a million recordings from about 19 500 earthquakes) with the aim of decomposing the Fourier amplitude spectra into source, propagation and site effects. To account for first-order, large-scale regional differences in propagation effects, the spectral decomposition simultaneously solves six different models describing the spectral attenuation within different subregions. Since the decomposition approach is affected by trade-offs that make the solution non-unique, we assume a station installed on rock in Switzerland as reference station and we invert for relative site amplifications. To propagate the reference site condition to the entire data set, we develop a procedure based on a sequence of decompositions considering increasing and overlapping data sets. The applied procedure allows for a consistent evaluation of relative site effects for about 3200 station channels using a single reference station for the whole data set. Comparisons with site amplifications obtained in previous studies at common stations in Italy and Switzerland confirm the site amplification results. The target of this work is to show that the spectral models obtained for attenuation and site effects can be used to generate empirical shaking scenarios in the Fourier domain. Therefore, we conclude our feasibility study by presenting shaking maps generated at different frequencies for hypothetical magnitude 6.5 earthquakes with a Brune-type stress drop of 10 MPa located at different positions across Europe.
Concordance and Discordance Between Patient-reported Remission, Patient-reported Outcomes, and Physician Global Assessment
Authors: Kamp Kendra J , Hawes Stephen E , Tse Chung Sang , Singh Siddharth , Dang Nhu , Oberai Ridhima , Weaver S Alandra , Melmed Gil Y , Siegel Corey A , van Deen Welmoed K ,   IBD Qorus, Younes Ziad , Mattar Mark C , Metwally Mark , Scott Frank , Ostrov Arthur , Rubin David T , Gerich Mark , Gerner Donna , Heagy Erica , Nelson Eugene , Holthoff Megan , Hudesman David , Oberai Ridhima , Almario Christopher , Bray Harry , Crate Damara , Hou Jason K , Singh Siddharth , Arrieta Rose , Banty Andrea , Betteridge John , Carron Jessica , Charabaty Aline , Danielewicz Michael , Deitch Josh , Farraye Francis , Fasanya Helen , Flynn Ann , Ha Christina , Kaufman Lia , Kaur Nirmal , Kearney Kristi , Kennedy Alice M , Kim Betty , Kwon Michelle , Le Helen , Mize Carrie , Morgan Emily , Morris-McCoy Linda , Oonk Alexis , Pashby Teresa , Rai Victoria , Reddy Swapna , Roake Kami , Shukla Richa , Syal Gaurav , Traboulsi Cindy , Turner Quin , Valentine John , Vrabie Raluca , Walker Trisha , Weatherly Julie , Williams Emmanuelle , Yun Laura , Zisman Tim
Published: September 2022

Background

Although validated patient-reported outcome (PRO) measurements can categorize patients with inflammatory bowel disease (IBD) into clinical remission or active disease, patients may have different definitions of remission. The purpose of this study was to compare patient-defined remission to remission based on PRO measures and physician global assessment (PGA) and to understand the clinical and demographic factors associated with disagreements.

Methods

We retrospectively analyzed 3257 de-identified surveys from 2004 IBD patients who consented to participate in the Crohn’s and Colitis Foundation’s IBD Qorus Learning Health System between September 2019 and February 2021. We used logistic regression models with generalized estimating equations to analyze the clinical and demographic factors (eg, age, disease duration, health confidence) associated with discordance between patient-defined remission (yes/no) and PRO-defined remission for ulcerative colitis (UC; PRO2: stool frequency, rectal bleeding) and Crohn’s disease (CD; PRO-3: average number of liquid stools, abdominal pain, well-being).

Results

Among patients with UC, overall concordance was 79% between patient self-report and PRO2-defined remission and 49% between patient self-report and PGA-defined remission. Among patients with CD, overall concordance was 69% between patient self-report and PRO3-defined remission and 54% between patient self-report and PGA-defined remission. Patients in PRO-defined remission were more likely to report active disease if they had IBD <5 years and low health confidence. Patients with PRO-defined active disease were more likely to report remission if they were not using prednisone and had high health confidence.

Conclusion

Discordance exists between how remission is defined by patients, PRO measures, and PGA.
A retrospective study of Enterococcus faecalis infective endocarditis: comparison of clinical characteristics and outcomes associated with treatment
Authors: Vigneswaran N , McKew G
Published: September 2022

Introduction

A synergistic antibiotic combination of a penicillin and gentamicin (AG) or ceftriaxone (AC) is used in the management of Enterococcus faecalis infective endocarditis (EFIE). We compare the treatment outcomes between AG and AC, including low and high dose ceftriaxone (1 and 2 g 12 hourly).

Methods

A retrospective cohort study of patients treated for EFIE at single tertiary centre (2012–2019). Outcome measures examined were 90- and 180-day mortality, treatment associated adverse events and relapse of bacteraemia (within 1 year).

Results

39 patients were enrolled [61.6% given (AC) (n = 24), 24% received ACL (n = 10) and 34% received ACN (n = 14)], 38.4% received AG (n = 15). We noted a difference in the mortality outcomes at 90 and 180 days between those treated with AG and AC overall (6.7% and 33.3%, respectively) although this did not reach statistical significance (P = 0.114, P = 0.061). No significant difference was noted between these groups in incidence of relapsed bacteraemia with two cases noted in the AC cohort (8.3%, 2/24) and none observed (0/15) in the AG cohort (P = 0.662, P = 0.414). A greater number of adverse events was observed in the AG group (11/15, 73.3%) compared to the overall AC group (6/24, 25.0%) (P = 0.009), with no difference between the high and low dose ceftriaxone groups (P = 0.05).

Conclusion

Combination treatment of EFIE with AC is associated with a reduced number of adverse events in comparison to AG groups. Although increased mortality was observed in the AC group, this did not reach statistical significance, and reflects the greater comorbidities and reduced capacity for surgical source control in this cohort.
Sediment processing by two estuarine crabs in Bangladesh: small efficient consumers alongside big inefficient ones
Authors: Kumari Gayatri , Phillott Andrea D , Cruz-Rivera Edwin
Published: September 2022

Due to their foraging and burrowing behaviors, many crabs in the brachyuran superfamily Ocypodoidea are considered important bioturbators that enhance sediment turnover, energy and matter flow, and nutrient cycling in sandy beaches, mangrove forests, and estuaries. There is surprisingly little comparative work assessing the relative effects of sympatric species, even though many co-occur over broad ranges. We compared uptake of sediment water, organic matter, and carbonate by two sympatric deposit-feeding crabs from Chittagong, Bangladesh, the small sand-bubbler Dotilla intermedia De Man, 1888 and the much larger ghost crab Ocypode macrocera H. Milne Edwards, 1837. Comparisons between feeding pellets and surrounding surface sediments showed that D. intermedia reduced sediment water content by 66% and organic matter content by 67%. In contrast, feeding by O. macrocera had no significant effects on these two parameters. Although sediments excavated by O. macrocera were twice as rich in organic matter compared to surface sediments, variance was high, rendering the difference not statistically significant. Inorganic carbonate distribution was affected by both crabs in different ways. Dotilla feeding pellets had significantly less carbonate than unprocessed surface sediments. In contrast, Ocypode feeding pellets had similar carbonate concentrations to surface sediments, but sediments excavated by those crabs were significantly lower in carbonates (~28%) than those at the surface. While both crab species have the potential to affect sediment properties, they do so through different mechanisms.
Prostate-Specific Membrane Antigen Expression in Meningioma: A Promising Theranostic Target
Authors: Tubre Teddi , Hacking Sean , Alexander Abigail , Brickman Arlen , Delalle Ivana , Elinzano Heinrich , Donahue John E
Published: September 2022

Meningioma is the most common intracranial neoplasm, yet there is no effective therapy for recurrent/refractory meningiomas after surgery and radiation. Prostate-specific membrane antigen (PSMA) is an enzyme upregulated on endothelial cells of multiple neoplasms and is being investigated as a theranostic target. Until now, PSMA has not been studied in meningiomas. We aimed to verify PSMA endothelial expression in meningiomas, detect tumor grade variability, and investigate the relationship of PSMA signal with tumor recurrence. We analyzed 96 archival meningiomas including 58 de novo and 38 recurrent specimens. All specimens were stained routinely and immunostained for CD31 and PSMA. Slides were scanned and analyzed producing raw data for images of PSMA, CD31, PSMA/CD31, and PSMA/vasculature. PSMA expression was seen within 98.9% of meningioma samples. In the total cohort, higher-grade tumors had increased expression of raw PSMA and PSMA/CD31, and PSMA/vasculature ratios compared to grade 1 tumors. PSMA expression and PSMA/vasculature ratios (p = 0.0015) were higher in recurrent versus de novo tumors among paired samples. ROC curves demonstrated PSMA/CD31, PSMA/vasculature, and raw CD31 as indicators of tumor recurrence. Thus, PSMA is expressed within endothelial cells of meningiomas, is increased with tumor grade and recurrence, and persists with prior irradiation.
A non-detection of red supergiant convection in Gaia
Authors: Kochanek C S
Published: September 2022

Large-scale surface convection on red supergiants (RSGs) can lead to shifts in the photocentre of the star that might be measured by Gaia and used as a new probe of the surface dynamics of these rare but important stars. Unlike brightness variations, photocentre motions would provide information on the physical scale of the convective cells. The signal would be that RSGs show an excess astrometric noise at the level of a few per cent of the stellar radius. Unfortunately, we find that the excess astrometric noise level of Gaia EDR3 is roughly an order of magnitude too large to detect the predicted motions and that RSGs have excess astrometric noise indistinguishable from other stars of similar magnitude, colour, or parallax. The typical excess astrometric noise steadily decreases with G magnitude (for G < 11 mag), so it is crucial to compare stars of similar brightness.
Mycobacterium genavense Infections in Immunocompromised Patients Without HIV: Case Series of Solid Organ Transplant Patients and Literature Review
Authors: Baldolli Aurélie , Chocron Richard , Dargère Sylvie , Michon Jocelyn , Daurel Claire , Thuillier-Lecouf Angélique , Verdon Renaud
Published: September 2022

Background

Mycobacterium genavense infection is rare and can occur in immunocompromised patients without human immunodeficiency virus (HIV).

Methods

We describe 2 cases of M genavense infection in solid organ transplant (SOT) recipients, and we performed a literature review of immunocompromised patients without HIV.

Results

Fifty-two cases are reported. Predisposing factors were receipt of SOT (40.4%) and autoimmune disease (36.5%). Infection was disseminated in 86.5% of cases. Organs involved were lymph nodes (72.3%), gastrointestinal tract (56.5%), lung (35.5%), and bone marrow (28.8%). Most patients were treated with at least 3 antimycobacterial agents (98%), with a clinical cure achieved in 54.9%. In multivariate analysis, lack for cure was associated with age of the time infection (odds ratio [OR], 15.81 [95% confidence interval {CI}, 2.92–152.93]; P = .011) and positive bone marrow culture (OR, 1.05 [95% CI, 1.01–1.12]; P = .042).

Conclusions

Mycobacterium genavense infection is a rare and generally disseminated disease with a poor prognosis. Optimal treatment regimen and its duration remain to be defined.
Performance of Nanopore and Illumina Metagenomic Sequencing for Pathogen Detection and Transcriptome Analysis in Infantile Central Nervous System Infections
Authors: Horiba Kazuhiro , Torii Yuka , Aizawa Yuta , Yamaguchi Makoto , Haruta Kazunori , Okumura Toshihiko , Suzuki Takako , Kawano Yoshihiko , Kawada Jun-ichi , Hara Shinya , Saitoh Akihiko , Giske Christian G , Ogi Tomoo , Ito Yoshinori
Published: September 2022

Background

Infantile central nervous system infections (CNSIs) can be life-threatening and cause severe sequelae. However, the causative microorganism remains unknown in >40% of patients with aseptic infections. This study aimed to analyze the metagenome for detection of pathogens and the transcriptome for host immune responses during infection in a single cerebrospinal fluid (CSF) sample using 2 different next-generation sequencing (NGS) platforms, Nanopore and Illumina.

Methods

Twenty-eight CNSIs patients (<12 months) were enrolled, and 49 clinical samples (28 CSF and 21 blood) were collected. The DNA extracted from all 49 samples was sequenced using the Illumina sequencer for the detection of pathogens. Extracted RNA was obtained in sufficient quantities from 23 CSF samples and subjected to sequencing on both Nanopore and Illumina platforms. Human-derived reads subtracted during pathogen detection were used for host transcriptomic analysis from both Nanopore and Illumina sequencing.

Results

RNA metagenomic sequencing using both sequencing platforms revealed putative viral pathogens in 10 cases. DNA sequencing using the Illumina sequencer detected 2 pathogens. The results of Nanopore and Illumina RNA sequencing were consistent; however, the mapping coverage and depth to the detected pathogen genome of Nanopore RNA sequencing were greater than those of Illumina. Host transcriptomic analysis of Nanopore sequencing revealed highly expressed genes related to the antiviral roles of innate immunity from pathogen-identified cases.

Conclusions

The use of Nanopore RNA sequencing for metagenomic diagnostics of CSF samples should help to elucidate both pathogens and host immune responses of CNSI and could shed light on the pathogenesis of these infections.
Tourism and Visual Culture
Authors: Young Patrick
Published: September 2022

The relationship between tourism and visual culture has been an intimate, interdependent and ever-evolving one from the middle of the eighteenth century to the present. Over this period, tourist visual culture played a vital role in organizing, and conventionalizing, specifically modern (and now-global) ways of seeing, and of representing the seen. This is evident, for example, in the development and elaboration of discourses of the picturesque, which invested specific landscapes and sites with visual, emotional, and experiential qualities and criteria of value. Tourist visual culture was also essential to the production of colonial knowledge and difference, contributing both to the making of empire and also its unmaking. A now-global tourist industry remains instrumental in the production and dissemination of destination imagery and place myths, though actual and potential tourists themselves play a greater role as “coproducers” of the tourist image.
Alpine Tourism
Authors: Mathieu Jon
Published: September 2022

Climbing, skiing, and hiking are widely popular touristic activities with roots in the early days of tourism history. This chapter traces the complex global development of “Alpine” or “mountain” tourism from the early modern period to the present day. The first section offers a short glance at mountain cults in Asia during the seventeenth and eighteenth centuries. The second focuses on Europe during its expansion in the long nineteenth century, and follows the evolution of the Alpine tourism model. The last section deals with the global development of mountain-related sports in the twentieth century, when the Alpine model was used and refashioned in many ways.
Tourism Alone and in Groups
Authors: Barton Susan
Published: September 2022

Tourism’s development as a mass activity depended on the breaking down of the barriers of time, cost, and fear of the unknown. In preindustrial times, extensive leisure travel was the preserve of those without the time constraints of work, and who had the wealth to meet the expense of staying away from home for long periods, typified by the Grand Tour. These barriers to travel began to be broken down by technological changes. Beginning with railways, then flight, combined with the bundling together of accommodation, entertainment, and travel for sale as a package became increasingly attractive, not least for its cost savings. Traveling in a group was economical and provided support for nervous travelers. As prices fell and incomes rose in the twentieth century, tourism became available beyond a privileged elite. From the 1990s, the internet combined with budget airlines and online booking platforms, facilitated a boom in solo travel for confident tourists.
Homosociality, Sexual Misconduct and Gendered Violence in England’s Pre-Modern Legal Profession
Authors: McVitty Amanda
Published: September 2022

Fifteenth- and sixteenth-century evidence shows that common lawyers and law students regularly engaged in sexual misconduct and violence against women. Social histories of the early legal profession give little attention to such incidents, treating them as aberrations or as the ‘natural’ excess of privileged youth. By contrast, this article uses gender analysis to argue that sexual misconduct and gendered violence were structural features of all-male legal culture, contributing to homosocial bonding and to lawyers’ performance of masculinity. Records from the Inns of Court, London civic administration and royal government reveal law students asserting manhood through shared involvement in sexual misconduct and violence. However, it is significant for the history of the profession that young men were not the only offenders. While senior practitioners condemned misconduct and violence in rules and disciplinary regulations, in practice they shielded fellow lawyers from consequences and participated themselves. As perpetrators went on to become barristers, serjeants-at-law, judges and public office-holders, a tradition of toleration and intergenerational complicity was sustained across time. These findings generate new insights into how the training and socialization of lawyers contributed to the gendered violence inherent in the patriarchal judicial system of pre-modern England.
Formation and Preservation of Brucite and Awaruite in Serpentinized and Tectonized Mantle in Central British Columbia: Implications for Carbon Mineralization and Nickel Mining
Authors: Steinthorsdottir Katrin , Dipple Gregory M , Cutts Jamie A , Turvey Connor C , Milidragovic Dejan , Peacock Simon M
Published: September 2022

The serpentinized and tectonized mantle in the Decar area in central British Columbia, including rocks that host the Baptiste Ni Deposit, consists of several ultramafic protolith lithologies that were variably altered to serpentinite, ophicarbonate, soapstone and listvenite. Alteration minerals include brucite (Mg[OH]2), which can be used to sequester atmospheric CO2 and awaruite (Ni3Fe), which is an economically attractive nickel alloy. This study examines the formation and preservation of brucite (up to 13 wt%) and awaruite (up to 0.12 wt%) in the Decar area and demonstrates that both minerals are formed during serpentinization and destroyed during carbonate alteration of mantle rocks. We distinguish five alteration stages that occurred primarily in a continental environment: (1) low-temperature lizardite serpentinization from meteoric fluids at <300°C, (2) high-temperature antigorite (±metamorphic olivine) serpentinization from metamorphic fluids at >300°C, (3) carbonate alteration, (4) chrysotile veining (±antigorite) serpentinization, and (5) later carbonate alteration from crustal fluids. Brucite formed primarily during late lizardite serpentinization and is most abundant in rocks that originally had high olivine–pyroxene ratios. Awaruite formed during both late lizardite serpentinization and during antigorite serpentinization and is most abundant in serpentinized olivine-rich harzburgite. The stability and abundance of brucite and awaruite are controlled by both the host rock composition and degree of serpentinization. The coexistence of brucite and awaruite reflects formation in serpentinized olivine-rich peridotite and creates an opportunity for carbon-neutral nickel mining.
The coiled-coil protein gene WPRb confers recessive resistance to Cucumber green mottle mosaic virus
Authors: Cai Lingmin , Liu Jie , Wang Shuchang , Gong Zihui , Yang Siyu , Xu Fengyuan , Hu Zhongyuan , Zhang Mingfang , Yang Jinghua
Published: September 2022

Cucumber green mottle mosaic virus (CGMMV) is one of the major global quarantine viruses and causes severe symptoms in Cucurbit crops, particularly with regard to fruit decay. However, the genetic mechanisms that control plant resistance to CGMMV have yet to be elucidated. Here, we found that WPRb, a weak chloroplast movement under blue light 1 and plastid movement impaired 2-related protein family gene, is recessively associated with CGMMV resistance in watermelon (Citrullus lanatus). We developed a reproducible marker based on a single non-synonymous substitution (G1282A) in WPRb, which can be used for marker-assisted selection for CGMMV resistance in watermelon. Editing of WPRb conferred greater tolerance to CGMMV. We found WPRb targets to the plasmodesmata (PD) and biochemically interacts with the CGMMV movement protein, facilitating viral intercellular movement by affecting the permeability of PD. Our findings enable us to genetically control CGMMV resistance in planta by using precise genome editing techniques targeted to WPRb.