bluuebunny/crossref_metadata_2025 huggingface dataset:
Unlocking the mysterious polytypic features within vaterite CaCO3
Authors: San Xingyuan , Hu Junwei , Chen Mingyi , Niu Haiyang , Smeets Paul J. M. , Malliakas Christos D. , Deng Jie , Koo Kunmo , dos Reis Roberto , Dravid Vinayak P. , Hu Xiaobing
Published: November 2023

Calcium carbonate (CaCO3), the most abundant biogenic mineral on earth, plays a crucial role in various fields such as hydrosphere, biosphere, and climate regulation. Of the four polymorphs, calcite, aragonite, vaterite, and amorphous CaCO3, vaterite is the most enigmatic one due to an ongoing debate regarding its structure that has persisted for nearly a century. In this work, based on systematic transmission electron microscopy characterizations, crystallographic analysis and machine learning aided molecular dynamics simulations with ab initio accuracy, we reveal that vaterite can be regarded as a polytypic structure. The basic phase has a monoclinic lattice possessing pseudohexagonal symmetry. Direct imaging and atomic-scale simulations provide evidence that a single grain of vaterite can contain three orientation variants. Additionally, we find that vaterite undergoes a second-order phase transition with a critical point of ~190 K. These atomic scale insights provide a comprehensive understanding of the structure of vaterite and offer advanced perspectives on the biomineralization process of calcium carbonate.
The protein interactome of the citrus Huanglongbing pathogen Candidatus Liberibacter asiaticus
Authors: Carter Erica W. , Peraza Orlene Guerra , Wang Nian
Published: November 2023

The bacterium Candidatus Liberibacter asiaticus (CLas) causes citrus Huanglongbing disease. Our understanding of the pathogenicity and biology of this microorganism remains limited because CLas has not yet been cultivated in artificial media. Its genome is relatively small and encodes approximately 1136 proteins, of which 415 have unknown functions. Here, we use a high-throughput yeast-two-hybrid (Y2H) screen to identify interactions between CLas proteins, thus providing insights into their potential functions. We identify 4245 interactions between 542 proteins, after screening 916 bait and 936 prey proteins. The false positive rate of the Y2H assay is estimated to be 2.9%. Pull-down assays for nine protein-protein interactions (PPIs) likely involved in flagellar function support the robustness of the Y2H results. The average number of PPIs per node in the CLas interactome is 15.6, which is higher than the numbers previously reported for interactomes of free-living bacteria, suggesting that CLas genome reduction has been accompanied by increased protein multi-functionality. We propose potential functions for 171 uncharacterized proteins, based on the PPI results, guilt-by-association analyses, and comparison with data from other bacterial species. We identify 40 hub-node proteins, including quinone oxidoreductase and LysR, which are known to protect other bacteria against oxidative stress and might be important for CLas survival in the phloem. We expect our PPI database to facilitate research on CLas biology and pathogenicity mechanisms.
Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi
Authors: Lutz Stefanie , Bodenhausen Natacha , Hess Julia , Valzano-Held Alain , Waelchli Jan , Deslandes-Hérold Gabriel , Schlaeppi Klaus , van der Heijden Marcel G. A.
Published: November 2023

Alternative solutions to mineral fertilizers and pesticides that reduce the environmental impact of agriculture are urgently needed. Arbuscular mycorrhizal fungi (AMF) can enhance plant nutrient uptake and reduce plant stress; yet, large-scale field inoculation trials with AMF are missing, and so far, results remain unpredictable. We conducted on-farm experiments in 54 fields in Switzerland and quantified the effects on maize growth. Growth response to AMF inoculation was highly variable, ranging from −12% to +40%. With few soil parameters and mainly soil microbiome indicators, we could successfully predict 86% of the variation in plant growth response to inoculation. The abundance of pathogenic fungi, rather than nutrient availability, best predicted (33%) AMF inoculation success. Our results indicate that soil microbiome indicators offer a sustainable biotechnological perspective to predict inoculation success at the beginning of the growing season. This predictability increases the profitability of microbiome engineering as a tool for sustainable agricultural management.
Validation of machine vision and action sport cameras for 3D motion analysis model reconstruction
Authors: Johnson John David , Hales Michael , Emert Randy
Published: November 2023

The study investigated the feasibility of using action sport cameras for motion analysis research. Data acquired from two different marker-based motion capture systems and six different camera combinations were analyzed for motion reconstruction accuracy. Two different calibration procedures were used to determine the influence on marker position reconstruction. Static and dynamic calibration mean merit score differences between the reference and experimental camera systems were 0.4 mm and 1.3 mm, respectively. Angular displacement difference between the reference and experimental camera systems range between 0.1 and 2.0 degrees. A systematic bias (− 0.54 to 0.19 degrees) was determined between the reference and the experimental camera systems for range of motion. The mean of the multi-trial findings suggests the machine vision camera system calibrated with a dynamic procedure generated highly accurate three-dimensional reconstructed ROM data (0.5 degree) followed closely by the four action sport cameras implementing a static calibration procedure (0.5 degree). The overall findings suggest the selected machine vision and action sport camera systems produced comparable results to the reference motion analysis system. However, the combination of camera type, processing software, and calibration procedure can influence motion reconstruction accuracy.
Top-down determinants of the numerosity–time interaction
Authors: Petrizzo Irene , Pellegrino Michele , Anobile Giovanni , Doricchi Fabrizio , Arrighi Roberto
Published: November 2023

Previous studies have reported that larger visual stimuli are perceived as lasting longer than smaller ones. However, this effect disappears when participants provide a qualitative judgment, by stating whether two stimuli have the “same or different” duration, instead of providing an explicit quantitative judgment (which stimulus lasts longer). Here, we extended these observations to the interaction between the numerosity of visual stimuli, i.e. clouds of dots, and their duration. With “longer vs shorter” responses, participants judged larger numerosities as lasting longer than smaller ones, both when the responses were related to the order (Experiment 1) or color (Experiment 4) of stimuli. In contrast, no similar effect was found with “same vs different” responses (Experiment 2) and in a time motor reproduction task (Experiment 3). The numerosity–time interference in Experiment 1 and Experiment 4 was not due to task difficulty, as sensory precision was equivalent to that of Experiment 2. We conclude that in humans the functional interaction between numerosity and time is not guided, in the main, by a shared bottom-up mechanism of magnitude coding. Rather, high-level and top-down processes involved in decision-making and guided by the use of “magnitude-related” response codes play a crucial role in triggering interference among different magnitude domains.
Auditory attention measured by EEG in neurological populations: systematic review of literature and meta-analysis
Authors: Vanbilsen Nele , Kotz Sonja A. , Rosso Mattia , Leman Marc , Triccas Lisa Tedesco , Feys Peter , Moumdjian Lousin
Published: November 2023

Sensorimotor synchronization strategies have been frequently used for gait rehabilitation in different neurological populations. Despite these positive effects on gait, attentional processes required to dynamically attend to the auditory stimuli needs elaboration. Here, we investigate auditory attention in neurological populations compared to healthy controls quantified by EEG recordings. Literature was systematically searched in databases PubMed and Web of Science. Inclusion criteria were investigation of auditory attention quantified by EEG recordings in neurological populations in cross-sectional studies. In total, 35 studies were included, including participants with Parkinson’s disease (PD), stroke, Traumatic Brain Injury (TBI), Multiple Sclerosis (MS), Amyotrophic Lateral Sclerosis (ALS). A meta-analysis was performed on P3 amplitude and latency separately to look at the differences between neurological populations and healthy controls in terms of P3 amplitude and latency. Overall, neurological populations showed impairments in auditory processing in terms of magnitude and delay compared to healthy controls. Consideration of individual auditory processes and thereafter selecting and/or designing the auditory structure during sensorimotor synchronization paradigms in neurological physical rehabilitation is recommended.
Developmental transcriptomic patterns can be altered by transgenic overexpression of Uty
Authors: Rock Kylie D. , Folts Lillian M. , Zierden Hannah C. , Marx-Rattner Ruth , Leu Nicolae Adrian , Nugent Bridget M. , Bale Tracy L.
Published: November 2023

The genetic material encoded on X and Y chromosomes provides the foundation by which biological sex differences are established. Epigenetic regulators expressed on these sex chromosomes, including Kdm6a (Utx), Kdm5c, and Ddx3x have far-reaching impacts on transcriptional control of phenotypic sex differences. Although the functionality of UTY (Kdm6c, the Y-linked homologue of UTX), has been supported by more recent studies, its role in developmental sex differences is not understood. Here we test the hypothesis that UTY is an important transcriptional regulator during development that could contribute to sex-specific phenotypes and disease risks across the lifespan. We generated a random insertion Uty transgenic mouse (Uty-Tg) to overexpress Uty. By comparing transcriptomic profiles in developmental tissues, placenta and hypothalamus, we assessed potential UTY functional activity, comparing Uty-expressing female mice (XX + Uty) with wild-type male (XY) and female (XX) mice. To determine if Uty expression altered physiological or behavioral outcomes, adult mice were phenotypically examined. Uty expression masculinized female gene expression patterns in both the placenta and hypothalamus. Gene ontology (GO) and gene set enrichment analysis (GSEA) consistently identified pathways including immune and synaptic signaling as biological processes associated with UTY. Interestingly, adult females expressing Uty gained less weight and had a greater glucose tolerance compared to wild-type male and female mice when provided a high-fat diet. Utilizing a Uty-overexpressing transgenic mouse, our results provide novel evidence as to a functional transcriptional role for UTY in developing tissues, and a foundation to build on its prospective capacity to influence sex-specific developmental and health outcomes.
Quantifying spatial acuity of frequency resolved midair ultrasound vibrotactile stimuli
Authors: Cataldo Antonio , Frier William , Haggard Patrick
Published: November 2023

Spatial acuity is a fundamental property of any sensory system. In the case of the somatosensory system, the two-point discrimination (2PD) test has long been used to investigate tactile spatial resolution. However, the somatosensory system comprises three main mechanoreceptive channels: the slowly adapting channel (SA) responds to steady pressure, the rapidly adapting channel (RA) responds to low-frequency vibration, and the Pacinian channel (PC) responds to high-frequency vibration. The use of mechanical stimuli in the classical 2PD test means that previous studies on tactile acuity have primarily focussed on the pressure-sensitive channel alone, while neglecting other submodalities. Here, we used a novel ultrasound stimulation to systematically investigate the spatial resolution of the two main vibrotactile channels. Contrary to the textbook view of poor spatial resolution for PC-like stimuli, across four experiments we found that high-frequency vibration produced surprisingly good spatial acuity. This effect remained after controlling for interchannel differences in stimulus detectability and perceived intensity. Laser doppler vibrometry experiments confirmed that the acuity of the PC channel was not simply an artifact of the skin’s resonance to high-frequency mechanical stimulation. Thus, PC receptors may transmit substantial spatial information, despite their sparse distribution, deep location, and large receptive fields.
The COVID-19 pandemic affects pregnancy complications and delivery outcomes in Japan: a large-scale nationwide population-based longitudinal study
Authors: Abe Yoshiko , Uchiyama Koji , Takaoka Nobuko , Yamamoto Keiko , Haruyama Yasuo , Shibata Eiji , Naruse Katsuhiko , Kobashi Gen
Published: November 2023

The impact of the coronavirus disease 2019 (COVID-19) pandemic on pregnancy outcomes in Japan at the national level is unclear. This study aimed to assess the impact of the pandemic on pregnancy complications and delivery outcomes in Japan using nationwide population-based longitudinal data. Secondary data from the Japan Society of Obstetrics and Gynecology from 2016 to 2020 were analyzed. Obstetric information, pregnancy complications, and delivery information of pregnant women over 22 weeks of gestation were compared before and during the pandemic. The trends of hypertensive disorder of pregnancy, fetal growth restriction, and APGAR < 7 increased, whereas those of preterm birth and low birth weight decreased during the COVID-19 pandemic. Pregnancy complications and delivery outcomes have worsened during the COVID-19 pandemic in Japan. Social changes caused by unprecedented situations may have massively influenced pregnancy in several ways. Our findings suggest that even in mild lockdowns like those in Japan, the introduction of social fear during the pandemic might negatively impact pregnancy outcomes.
Low-dose brain radiation: lowering hyperphosphorylated-tau without increasing DNA damage or oncogenic activation
Authors: Iacono Diego , Murphy Erin K. , Stimpson Cheryl D. , Perl Daniel P. , Day Regina M.
Published: November 2023

Brain radiation has been medically used to alter the metabolism of cancerous cells and induce their elimination. Rarely, though, brain radiation has been used to interfere with the pathomechanisms of non-cancerous brain disorders, especially neurodegenerative disorders. Data from low-dose radiation (LDR) on swine brains demonstrated reduced levels of phosphorylated-tau (CP13) and amyloid precursor protein (APP) in radiated (RAD) versus sham (SH) animals. Phosphorylated-tau and APP are involved in Alzheimer’s disease (AD) pathogenesis. We determined if the expression levels of hyperphosphorylated-tau, 3R-tau, 4R-tau, synaptic, intraneuronal damage, and DNA damage/oncogenic activation markers were altered in RAD versus SH swine brains. Quantitative analyses demonstrated reduced levels of AT8 and 3R-tau in hippocampus (H) and striatum (Str), increased levels of synaptophysin and PSD-95 in frontal cortex (FCtx), and reduced levels of NF-L in cerebellum (CRB) of RAD versus SH swine. DNA damage and oncogene activation markers levels did not differ between RAD and SH animals, except for histone-H3 (increased in FCtx and CRB, decreased in Str), and p53 (reduced in FCtx, Str, H and CRB). These findings confirm the region-based effects of sLDR on proteins normally expressed in larger mammalian brains and support the potential applicability of LDR to beneficially interfere against neurodegenerative mechanisms.
Mitochondrial DNA copy number is associated with Crohn’s disease: a comprehensive Mendelian randomization analysis
Authors: Cai Xianlei , Li Xueying , Liang Chao , Zhang Miaozun , Xu Yuan , Dong Zhebin , Weng Yihui , Yu Weiming
Published: November 2023

Mitochondrial DNA plays a critical role in the pathophysiological process of inflammation. However, the relationship between mitochondrial DNA copy number (mtDNA-CN) and inflammatory bowel diseases (IBD) remains poorly understood. We conducted a comprehensive Mendelian randomization (MR) using three instrumental variables (IVs) to explore the causal associations between mtDNA-CN and IBD, including Crohn's disease (CD), ulcerative colitis (UC). MR-Egger regression, weighted median, inverse-variance weighted (IVW), and weighted mode methods were used to evaluate the potential causal associations. The robustness of the IVW estimates was determined using the leave-one-out sensitivity test. A meta-analysis was conducted to pool the results from the three sets of IVs. Upon analysis, the findings of the current study revealed that genetically predicted mtDNA-CN was not associated with IBD (CD + UC) and UC. The results of MR analyses between mtDNA-CN and CD risk were inconsistent by using three sets of IVs. After a meta-analysis, we found that genetically predicted mtDNA-CN was associated with CD risk (odds ratio = 2.09; 95% confidence interval: 1.37–3.18). This finding was also confirmed by multivariable MR analyses and remained robust when tested with the leave-one-out sensitivity test. In conclusion, genetically predicted mtDNA-CN was found to be associated with CD risk. Therefore, mtDNA levels in the blood could potentially be used as a marker for CD risk assessment. Further studies are needed to elucidate the underlying mechanisms and validate the results of this study.
Thiol-ene click reaction as an effective tool for the synthesis of PEG-functionalized alkoxysilanes-precursors of anti-fog coatings
Authors: Kaczmarek Marta , Przybylska Agnieszka , Szymańska Anna , Dutkiewicz Agnieszka , Maciejewski Hieronim
Published: November 2023

The article presents a very simple method of glass modification to obtain the anti-fog effect. Silanes containing two types of functional groups, namely a hydrophilic and polar polyether group and an alkoxysilyl group (to bond with the surface of the modified material) were synthesized in thiol-ene reactions. The hydrothiolation reactions of polyethers containing a C=C terminal bond with mercaptoalkoxysilane proceeded efficiently, yielding quantitatively appropriate products under mild reaction conditions. This method enabled the synthesis of a series of alkoxysilanes functionalized with polyethers, differing in structure. The group of obtained derivatives was characterized by 1H, 13C, 29Si NMR, and FT-IR analyses, and then used to prepare coatings on glass using the sol–gel method. The coated glass surfaces exhibited transparency, superhydrophilic or hydrophilic properties, anti-fog and anti-frost performance.
Impact of malt concentration in solid substrate on mycelial growth and network connectivity in Ganoderma species
Authors: Nussbaum Natalie , von Wyl Tabea , Gandia Antoni , Romanens Edwina , Rühs Patrick Alberto , Fischer Peter
Published: November 2023

With its distinctive material properties, fungal mycelium has emerged as an innovative material with a diverse array of applications across various industries. This study focuses on how the growth strategies of wood fungi adapt to nutrient availability. The effect of malt extract concentration in the growth medium on radial growth kinetics, morphology, mycelium network connectivity, and mechanical characteristics of mycelium from two Ganoderma species were investigated. While an evident pattern of radial growth rate enhancement with malt concentrations was not apparent, there was a discernible trend towards denser mycelium network characteristics as revealed by spectrophotometry. Increased malt extract contents corresponded to elevated optical density measurements and were visually confirmed by denser mycelium networks in photographic images. Investigating the mechanical characteristics of mycelium cultivated on varying solid substrate concentrations, the Young’s modulus exhibited a substantial difference between mycelium grown on 5 wt% malt substrate and samples cultivated on 2 wt% and 0.4 wt% malt substrates. The obtained results represent a new understanding of how malt availability influences mycelial growth of two Ganoderma species, a crucial insight for potentially refining mycelium cultivation across diverse applications, including meat alternatives, smart building materials, and alternative leather.
Local niches explain coexistence in environmentally-distinct contact zones between Western Mediterranean vipers
Authors: Freitas Inês , Tarroso Pedro , Zuazo Óscar , Zaldívar Ricardo , Álvarez Javier , Meijide-Fuentes Manuel , Meijide Federico , Martínez-Freiría Fernando
Published: November 2023

Species’ ecological niches are frequently analysed to gain insights into how anthropogenic changes affect biodiversity. Coping with these changes often involves shifts in niche expression, which can disrupt local biotic interactions. Secondary contact zones, where competition and ecological segregation commonly occur, are ideal for studying the ecological factors influencing species’ niches. In this study, we investigated the effect of climate and landscape factors on the ecological niches of two viper species,Vipera aspisandVipera latastei, across three contact zones in northern Iberia, characterized by varying levels of landscape alteration. Using niche overlap tests, ecological niche models and spatial analyses we observed local variation in the expression of the species’ niches across the three contact zones, resulting from the different abiotic and biotic conditions of each area. Rather than spatial niche segregation, we observed high niche overlap, suggesting niche convergence. A pattern of asymmetrical niche variation was identified in all contact zones, driven by species' climatic tolerances and the environmental conditions of each area.V. aspisgenerally exhibited a wider niche, except in the southernmost zone where the pure Mediterranean climate favoredV. latastei. Human-induced landscape changes intensified niche asymmetry, by favoring the most generalistV. aspisover the specialistV. latastei, increasing habitat overlap, and likely competition. This study presents a comprehensive analysis of niche expression at range margins, anticipating a heightened impact of landscape changes inV. latastei. The methodological framework implemented here, and our findings, hold significant relevance for biodiversity management and conservation in human-impacted areas.
KRAS4A and KRAS4B in liquid biopsy of metastatic lung adenocarcinoma patients treated with Pembrolizumab or chemotherapy plus Pembrolizumab
Authors: Chiari Rita , Palladino Silvia , Emili Rita , De Lisa Mariagrazia , Sarti Donatella , Catalano Vincenzo , Magnani Mauro , Graziano Francesco , Ruzzo Annamaria
Published: November 2023

KRAS is involved in the stability and expression of PD-L1. We investigated the expression of circulating mRNA (cmRNA) of KRAS4A and KRAS4B and the possible impact on progression-free survival (PFS) of patients with metastatic lung adenocarcinoma treated with immunotherapy. Patients without driver mutations undergoing Pembrolizumab (P) or P plus chemotherapy (PC) were prospectively accrued for liquid biopsy analysis of KRAS4A, KRAS4B, and PD-L1 cmRNA. Both KRAS isoforms were also studied for association with PD-L1 cmRNA. Of 56 patients, 28 received P and 28 PC. Patients with high levels of both KRAS isoforms showed significantly better PFS. The median PFS for KRAS4A was 29 months (95% CI 22–29 months) and KRAS4B 24 months (95% CI 13–29 months), respectively. The median PFS of patients with low levels of both isoforms was 12 months (95% CI 6–15 months for KRAS4A and 95% CI 5–20 months for KRAS4B). High KRAS4A retained a significant positive association with PFS in the multivariate model. An exploratory analysis in treatment subgroups found a positive association between high KRAS4A and KRAS4B with PFS in patients treated with P. PD-L1 cmRNA was significantly higher in patients with high KRAS isoforms levels and this effect was pronounced for high KRAS4A carriers. KRAS4A deserves further investigation as a potential marker for defining patients who may benefit the most from immune checkpoint inhibitors therapy and improving personalized cancer immunotherapeutic strategies.
Heterogeneous Oriented Structure model of thermoelectric transport in conducting polymers
Authors: Limelette Patrice , Leclerc Nicolas , Brinkmann Martin
Published: November 2023

Understanding transport phenomena in conducting polymers (CP) is a main issue in order to optimize their performance and despite intense investigations, the influence of their microstructure remains controversial. By analyzing the thermoelectric measurements performed on highly oriented and non-oriented CP films, we show that an Heterogeneous Oriented Structure (HOSt) model considering both ordered and disordered domains is able to account for the thermoelectric transport in CP. This model unveils the key role of the crystallinity, the anisotropy and the alignment degree of these domains. It points out the importance of the thermal conductivity in the interpretation of the thermopower $$\alpha $$
α
and explains the frequently observed electrical conductivity $$\sigma $$
σ
cut-off in the $$\alpha -\sigma $$

α
-
σ

curves due to the disordered domains. By varying the alignment degree depending on the orientation and the anisotropy according to the face-on or the edge-on polymers conformation, the HOSt model successfully describes the overall measured thermoelectric properties by demonstrating its applicability to a wide variety of both oriented and non-oriented CP.
Weakened weekdays: lockdown disrupts the weekly cycle of risk tolerance
Authors: Fedrigo Virginia , Guenther Benno , Jenkins Rob , Galizzi Matteo M. , Sanders Jet G.
Published: November 2023

Risk tolerance decreases from Monday to Thursday and increases on Friday. Antecedents of this weekly risk cycle are difficult to investigate experimentally as manipulating the seven-day cycle is impractical. Here we used temporal disorientation during the UK COVID-19 lockdown to conduct a natural experiment. In two studies, we measured responses to risk in participants with either a strong or weak sense of weekday, after either a short or long period of disruption to their weekly routine by lockdown. In Study 1 (N = 864), the weekly risk cycle was consistent in risk attitude measures specifically to participants who reported a strong sense of weekday. In Study 2 (N = 829), the weekly risk cycle was abolished, even for participants who retained a strong sense of weekday. We propose that two factors sustain the weekly risk cycle. If the sense of weekday is lacking, then weekday will have little effect because the current day is not salient. If weekday associations decay, then weekday will have little effect because the current day is not meaningful. The weekly risk cycle is strong and consistent when (i) sense of weekday is robust and (ii) weekday associations are maintained.
Analysis of diurnal to seasonal variations and trends in air pollution potential in an urban area
Authors: Soleimanpour Mahshad , Alizadeh Omid , Sabetghadam Samaneh
Published: November 2023

Air pollution is the world’s largest environmental health threat to humans and has wide-ranging adverse effects on the environment. The term ventilation coefficient (VC), which is a function of the average wind speed through the planetary boundary layer (PBL) and the PBL height (PBLH), can be used to estimate air pollution potential. We analyzed PBLH, wind speed through PBL, and VC over Tehran using ERA5, and PM2.5 surface concentration using MERRA-2 during 1991–2020. Both PBLH and VC undergo substantial diurnal variations, with higher values during the day and much lower values at night. As a result, PM2.5 concentration in Tehran is the maximum in the early morning, while it is relatively lower in the afternoon. The average wind speed through PBL shows the same diurnal variation in all seasons, except in winter when winds in PBL are stronger at night than during the day. Both PBLH and VC over Tehran show substantial seasonal variations, with much higher values in summer followed in decreasing order by spring, autumn, and winter, highlighting an extremely high air pollution potential in winter. Hence, due to high pollutant emissions, the occurrence of severe air pollution is expected to be a common feature in Tehran in winter. PBLH has significantly increased over Tehran both during the day and at night for the period 1991–2020, primarily in response to the surface warming in recent decades, while wind speed through PBL has significantly declined only at night. The overall impact of such changes is an increase in VC over Tehran both during the day and at night, although the increasing trend of VC is statistically significant only at night. Our results highlight the urgent need for the implementation of effective sustainable policies to reduce air pollution and its adverse effects in winter when air pollution potential is high in Tehran.
The impact of phage treatment on bacterial community structure is minor compared to antibiotics
Authors: Gundersen Madeleine S. , Fiedler Alexander W. , Bakke Ingrid , Vadstein Olav
Published: November 2023

Phage treatment is suggested as an alternative to antibiotics; however, there is limited knowledge of how phage treatment impacts resident bacterial community structure. When phages induce bacterial lysis, resources become available to the resident community. Therefore, the density of the target bacterium is essential to consider when investigating the effect of phage treatment. This has never been studied. Thus, we invaded microcosms containing a lake-derived community with Flavobacterium columnare strain Fc7 at no, low or high densities, and treated them with either the bacteriophage FCL-2, the antibiotic Penicillin or kept them untreated (3 × 3 factorial design). The communities were sampled over the course of one week, and bacterial community composition and density were examined by 16S rDNA amplicon sequencing and flow cytometry. We show that phage treatment had minor impacts on the resident community when the host F. columnare Fc7 of the phage was present, as it caused no significant differences in bacterial density α- and β-diversity, successional patterns, and community assembly. However, a significant change was observed in community composition when the phage host was absent, mainly driven by a substantial increase in Aquirufa. In contrast, antibiotics induced significant changes in all community characteristics investigated. The most crucial finding was a bloom of γ-proteobacteria and a shift from selection to ecological drift dominating community assembly. This study investigated whether the amount of a bacterial host impacted the effect of phage treatment on community structure. We conclude that phage treatment did not significantly affect the diversity or composition of the bacterial communities when the phage host was present, but introduced changes when the host was absent. In contrast, antibiotic treatment was highly disturbing to community structure. Moreover, higher amounts of the bacterial host of the phage increased the contribution of stochastic community assembly and resulted in a feast-famine like response in bacterial density in all treatment groups. This finding emphasises that the invader density used in bacterial invasion studies impacts the experimental reproducibility. Overall, this study supports that phage treatment is substantially less disturbing to bacterial communities than antibiotic treatments.
Study on the relation of the solar coronal rotation with magnetic field structures
Authors: Xiang N. B. , Zhao X. H. , Deng L. H. , Li F. Y. , Zheng S.
Published: November 2023

Daily solar spectral irradiances (SSIs) at the spectral intervals 1–40, 116–264 and 950–1600 nm and four categories of solar small-scale magnetic elements ($$MF_{no}$$

M

F

no

, $$MF_{anti}$$

M

F

anti

, $$MF_{tran}$$

M

F

tran

and $$MF_{in}$$

M

F

in

) are used to study the temporal variation of coronal rotation and investigate the relation of the coronal rotation with magnetic field structures through continuous wavelet transform and Pearson correlation analysis. The results reveal the contributions of different magnetic structures to the temporal variation of the rotation for the coronal atmosphere during different phases of the solar cycle. During the solar maximum, the temporal variation of rotation for the coronal plasma atmosphere is mainly dominated by the small-scale magnetic elements of $$MF_{anti}$$

M

F

anti

; whereas during the epochs of the relatively weak solar activity, it is controlled by the joint effect of the small-scale magnetic elements of both $$MF_{anti}$$

M

F

anti

and $$MF_{in}$$

M

F

in

. The weaker the solar activity, the stronger the effect of $$MF_{in}$$

M

F

in

would be. Furthermore, this study presents an explanation for the inconsistent results for the coronal rotation issue among the previous studies, and also reveals the reason why the coronal atmosphere rotates faster than the lower photosphere.
Smart city construction and new-type urbanization quality improvement
Authors: Zhou RongJun , Chen Siqi , Zhang Bingbing
Published: November 2023

First, utilising text quantitative analysis techniques, this paper analyses the smart city pilot policy in depth and clarifies its theoretical mechanism that influence the quality of new-type urbanisation. The revised entropy technique is then used to calculate the new-type urbanisation quality of 276 Chinese cities with a prefecture level or higher from 2007 to 2018. The above action mechanism is evaluated using the Difference-in-Difference model, employing the smart city pilot policy as a quasi-natural experiment (DID). The results indicate that the implementation of the smart city pilot policy can significantly enhance the quality of new-type urbanisation, and this conclusion is robust under a variety of conditions, including parallel trend testing, tendency score matching, exclusion of other policy interference and placebo testing. The analysis of heterogeneity indicates that the smart city pilot strategy has a greater impact on the qualitative improvement of new-type urbanisation in historic industrial bases, resource-based cities, and large-scale cities. The mechanism test confirmed that the construction of smart cities has improved the quality of new-type urbanisation primarily through the optimization and upgrading of industrial structure brought about by smart industrial policy and scientific and technological innovation fostered by smart government and smart people's livelihood policies.
Elucidating salient site-specific functional connectivity features and site-invariant biomarkers in schizophrenia via deep neural networks
Authors: Chan Yi Hao , Yew Wei Chee , Chew Qian Hui , Sim Kang , Rajapakse Jagath C.
Published: November 2023

Schizophrenia is a highly heterogeneous disorder and salient functional connectivity (FC) features have been observed to vary across study sites, warranting the need for methods that can differentiate between site-invariant FC biomarkers and site-specific salient FC features. We propose a technique named Semi-supervised learning with data HaRmonisation via Encoder-Decoder-classifier (SHRED) to examine these features from resting state functional magnetic resonance imaging scans gathered from four sites. Our approach involves an encoder-decoder-classifier architecture that simultaneously performs data harmonisation and semi-supervised learning (SSL) to deal with site differences and labelling inconsistencies across sites respectively. The minimisation of reconstruction loss from SSL was shown to improve model performance even within small datasets whilst data harmonisation often led to lower model generalisability, which was unaffected using the SHRED technique. We show that our proposed model produces site-invariant biomarkers, most notably the connection between transverse temporal gyrus and paracentral lobule. Site-specific salient FC features were also elucidated, especially implicating the paracentral lobule for our local dataset. Our examination of these salient FC features demonstrates how site-specific features and site-invariant biomarkers can be differentiated, which can deepen our understanding of the neurobiology of schizophrenia.
A Notch signaling-related lncRNA signature for predicting prognosis and therapeutic response in clear cell renal cell carcinoma
Authors: Zhang Lulu , Li Yulei , Cai Bin , Chen Jiajun , Zhao Keyuan , Li Mengyao , Lang Juan , Wang Kaifang , Pan Shouhua , Zhu Ke
Published: November 2023

Increasing evidence has confirmed the vital role of Notch signaling in the tumorigenesis of clear cell renal cell carcinoma (ccRCC). The underlying function of long non-coding RNA (lncRNA) related to Notch signaling in ccRCC remains unclear. In present study, the prognostic value and therapeutic strategy of Notch signaling-related lncRNA are comprehensively explored in ccRCC. In total, we acquired 1422 NSRlncRNAs, of which 41 lncRNAs were identified the key NSRlncRNAs associated with the occurrence of ccRCC. The prognostic signature containing five NSRlncRNAs (AC092611.2, NNT-AS1, AGAP2-AS1, AC147651.3, and AC007406.3) was established and validated, and the ccRCC patients were clustered into the high- and low-risk groups. The overall survival of patients in the low-risk group were much more favorable than those in the high-risk group. Multivariate Cox regression analysis indicated that the risk score was an independent prognostic biomarker. Based on the risk score and clinical variables, a nomogram for predicting prognosis of ccRCC patients was constructed, and the calibration curves and DCA curves showed the superior predictive ability of nomogram. The risk score was correlated with immune cell infiltration, targeted therapy or chemotherapy sensitivity, and multiple oncogenic pathways. Additionally, consensus clustering analysis stratified the ccRCC patients into four clusters with obvious different outcomes, immune microenvironments, and expression of immune checkpoints. The constructed NSRlncRNA-based signature might serve as a potential biomarker for predicting prognosis and response to immunotherapy or targeted therapy in patients with ccRCC.
Modelling local and general quantum mechanical properties with attention-based pooling
Authors: Buterez David , Janet Jon Paul , Kiddle Steven J. , Oglic Dino , Liò Pietro
Published: November 2023

Atom-centred neural networks represent the state-of-the-art for approximating the quantum chemical properties of molecules, such as internal energies. While the design of machine learning architectures that respect chemical principles has continued to advance, the final atom pooling operation that is necessary to convert from atomic to molecular representations in most models remains relatively undeveloped. The most common choices, sum and average pooling, compute molecular representations that are naturally a good fit for many physical properties, while satisfying properties such as permutation invariance which are desirable from a geometric deep learning perspective. However, there are growing concerns that such simplistic functions might have limited representational power, while also being suboptimal for physical properties that are highly localised or intensive. Based on recent advances in graph representation learning, we investigate the use of a learnable pooling function that leverages an attention mechanism to model interactions between atom representations. The proposed pooling operation is a drop-in replacement requiring no changes to any of the other architectural components. Using SchNet and DimeNet++ as starting models, we demonstrate consistent uplifts in performance compared to sum and mean pooling and a recent physics-aware pooling operation designed specifically for orbital energies, on several datasets, properties, and levels of theory, with up to 85% improvements depending on the specific task.
Nearly half of the world is suitable for diversified farming for sustainable intensification
Authors: Kamau Hannah , Roman Shahrear , Biber-Freudenberger Lisa
Published: November 2023

Sustainable intensification, defined as increasing production per unit without harming the environment, has potential to transform agricultural systems. While questions persist about which practices and conditions lead to sustainable intensification, diversification has gained prominence as a proposed solution. Here we apply niche modelling using maximum entropy modelling approach to predict the global spatial distribution of profitable diversified farming systems under different socio-economic conditions. We found about 47% of the world is suitable for profitable diversified systems with a larger area in the global North. When we combined our findings with knowledge about biophysical potential for cropland expansion and intensification, we found that different areas could benefit from diversification to achieve sustainable intensification through cropland expansion (e.g., Europe), intensification (e.g., sub-tropics and tropics), or both (e.g., West Africa). With these results, we provide insights in which way diversification can support sustainable intensification and contribute to the debate on land sharing vs sparing.
Engineering a defect-rich Prussian blue analog composite for enhanced Cs+ removal performance
Authors: Wei Zhenwei , Zhao Weilian , Hu Jiayin , Deng Tianlong , Zhang Nan
Published: November 2023

A defect-rich Zn–PBA/NPC composite was engineered for the first time, and it demonstrated excellent Cs+ removal performance, with an ultrafast Cs+ adsorption rate and high adsorption capacity.
Continuous selective conversion of methane to methanol over a Cu-KFI zeolite catalyst using a water–O2 mixture as the oxygen source
Authors: Zhang Hailong , Guo Jiaxiu , Cao Yi
Published: November 2023

The article highlights the potential of Cu-KFI zeolites as catalysts in the continuous conversion of methane to methanol using water and O2 as the oxidants.
Molybdenum sulphide clusters as redox-active supports for low-valent uranium
Authors: Patra Kamaless , Brennessel William W. , Matson Ellen M.
Published: November 2023

The preparation of an actinide substituted cubane cluster, (Cp*3Mo3S4)Cp*UI2, and its reduced derivatives are reported.
Exploring the structural stability and electrochemical performance of B doped T-graphene nanotubes from first-principles calculations
Authors: Zhang Ruyan , Hou Yuhua , Guo Xialei , Li Xinyu , Li Wei , Tao Xiaoma , Huang Youlin
Published: November 2023

DFT calculations show that the intrinsic and B doped T-graphene nanotubes exhibit different properties for different tube lengths.
The regulatory function of the d-orbital structure in TM@g-t-C4N3 for bifunctional catalysis of the oxygen evolution/reduction reaction
Authors: Wang Zhenduo , Wu Meichen , Huang Yuhong , Zhang Jianmin , Wei Xiumei
Published: November 2023

A series of bifunctional OER/ORR SACs supported on g-t-C4N3 is proposed. It is found from DFT calculations that the d-orbital structure can regulate the catalytic activity of g-t-C4N3-based SACs.
Computational screening of single-atom doped In2O3 catalysts for the reverse water gas shift reaction
Authors: Wang Yuchen , Li Shenggang
Published: November 2023

Density functional theory calculations and microkinetic simulations predict the Ir/In2O3 single-atom catalyst to have the highest CO2 reactivity at relatively high reaction temperature.
Boosting the oxygen reduction reaction activity of dual-atom catalysts on N-doped graphene by regulating the N coordination environment
Authors: Li Lei , Wu Xiaoxia , Du Qiuying , Bai Narsu , Wen Yuhua
Published: November 2023

FeNiN5(OH2) and CoNiN5(OH2) exhibit excellent ORR catalytic activity, superior to Pt catalyst.
Atomic-level design of metalloenzyme-like active pockets in metal–organic frameworks for bioinspired catalysis
Authors: Xu Weiqing , Wu Yu , Gu Wenling , Du Dan , Lin Yuehe , Zhu Chengzhou
Published: November 2023

This review systematically summarizes the significant advances in MOF-based metalloenzyme mimics for bioinspired catalysis with a special emphasis on active pocket engineering at the atomic level.
Progress and future of the computational design of antimicrobial peptides (AMPs): bio-inspired functional molecules
Authors: Nedyalkova Miroslava , Paluch Andrew S. , Vecini Diana Potes , Lattuada Marco
Published: November 2023

The effectiveness of antibiotics is greatly enhanced by their ability to target invasive organisms involved in the ancient evolutionary battle between hosts and pathogens.
The effect of temperature and relative humidity on secondary organic aerosol formation from ozonolysis of Δ3-carene
Authors: Thomsen Ditte , Iversen Emil Mark , Skønager Jane Tygesen , Luo Yuanyuan , Li Linjie , Roldin Pontus , Priestley Michael , Pedersen Henrik B. , Hallquist Mattias , Ehn Mikael , Bilde Merete , Glasius Marianne
Published: November 2023

This study investigates the effects of temperature and relative humidity on the formation of secondary organic aerosol from Δ3-carene, a prevalent monoterpene in boreal forests.
Synergy between the coordination and trace ionization of co-solvents enables reversible magnesium electroplating/stripping behavior
Authors: Wang Min , Sun Wenhao , Zhang Kun , Zhang Zhonghua , Du Aobing , Dong Shanmu , Zhang Jinlei , Liu Jing , Chen Xi , Zhou Zhenfang , Li Fujun , Li Zhenjiang , Li Guicun , Cui Guanglei
Published: November 2023

The synergy between coordination and trace ionization induces active ionic species formation and simultaneously alleviates electrolyte decomposition.
Hydrophobic interaction is the dominant mechanism of zwitterionic PFAS adsorption to carbon-based sorptive materials in water and soil
Authors: Kabiri Shervin , Monaghan Carly Lee , Navarro Divina , McLaughlin Michael J.
Published: November 2023

The diversity, persistence, bioaccumulation potential and mobility of per- or polyfluoroalkyl substances (PFASs) make these contaminants particularly formidable when determining their environmental fate and behaviour.
Progress in the applications of biocompatible ionic liquids: renewable commodity production, catalytic and pharmaceutical approaches – a review
Authors: Costa Josiel Martins , Forster-Carneiro Tânia , Hallett Jason P.
Published: November 2023

This review addressed the recent advances of biocompatible ionic liquids that include the production of renewable commodities and approaches in catalysis and the pharmaceutical field. Likewise, patents and future perspectives are discussed.
Green and sustainable synthesis of TPD-based donor–acceptor-type conjugated polymer photocatalysts for hydrogen production under visible light
Authors: Chang Menghan , Zhang Xinjuan , Wang Lin , Wang Di , Zhang Qiang , Lu Yan
Published: November 2023

The conjugated polymers are synthesized via greener direct C–H/C–H cross-coupling polycondensation for application in photocatalytic hydrogen production.
Elemental analysis of liquid samples by nanoparticle-enhanced laser-induced breakdown spectroscopy: using ordered nano-arrays with a tunable nanoparticle size and inter-particle distance
Authors: Nan Chen , Xinjian Shen , Jiahui Wangchen , Jian Wu , Bin Li , Yande Liu
Published: November 2023

NELIBS analysis of liquid samples using ordered nanoparticle arrays with a precisely tunable nanoparticle size and inter-particle distance, which provide excellent homogeneity to ensure signal reproducibility and enhancement.
Pushing the limits of microfluidic droplet production efficiency: engineering microchannels with seamlessly implemented 3D inverse colloidal crystals
Authors: Mashiyama Shota , Hemmi Runa , Sato Takeru , Kato Atsuya , Taniguchi Tatsuo , Yamada Masumi
Published: November 2023

Although droplet microfluidics has been studied for the past two decades, its applications are still limited due to the low productivity of microdroplets resulting from the low integration of planar microchannel structures.