bluuebunny/crossref_metadata_2025 huggingface dataset:
Activator-blocker model of transcriptional regulation by pioneer-like factors
Authors: Riesle Aileen Julia , Gao Meijiang , Rosenblatt Marcus , Hermes Jacques , Hass Helge , Gebhard Anna , Veil Marina , Grüning Björn , Timmer Jens , Onichtchouk Daria
Published: September 2023

Zygotic genome activation (ZGA) in the development of flies, fish, frogs and mammals depends on pioneer-like transcription factors (TFs). Those TFs create open chromatin regions, promote histone acetylation on enhancers, and activate transcription. Here, we use the panel of single, double and triple mutants for zebrafish genome activators Pou5f3, Sox19b and Nanog, multi-omics and mathematical modeling to investigate the combinatorial mechanisms of genome activation. We show that Pou5f3 and Nanog act differently on synergistic and antagonistic enhancer types. Pou5f3 and Nanog both bind as pioneer-like TFs on synergistic enhancers, promote histone acetylation and activate transcription. Antagonistic enhancers are activated by binding of one of these factors. The other TF binds as non-pioneer-like TF, competes with the activator and blocks all its effects, partially or completely. This activator-blocker mechanism mutually restricts widespread transcriptional activation by Pou5f3 and Nanog and prevents premature expression of late developmental regulators in the early embryo.
Assembling membraneless organelles from de novo designed proteins
Authors: Hilditch Alexander T. , Romanyuk Andrey , Cross Stephen J. , Obexer Richard , McManus Jennifer J. , Woolfson Derek N.
Published: September 2023

Recent advances in de novo protein design have delivered a diversity of discrete de novo protein structures and complexes. A new challenge for the field is to use these designs directly in cells to intervene in biological processes and augment natural systems. The bottom-up design of self-assembled objects such as microcompartments and membraneless organelles is one such challenge. Here we describe the design of genetically encoded polypeptides that form membraneless organelles in Escherichia coli. To do this, we combine de novo α-helical sequences, intrinsically disordered linkers and client proteins in single-polypeptide constructs. We tailor the properties of the helical regions to shift protein assembly from arrested assemblies to dynamic condensates. The designs are characterized in cells and in vitro using biophysical methods and soft-matter physics. Finally, we use the designed polypeptide to co-compartmentalize a functional enzyme pair in E. coli, improving product formation close to the theoretical limit.
Distinct monkeypox virus lineages co-circulating in humans before 2022
Authors: Ndodo Nnaemeka , Ashcroft Jonathan , Lewandowski Kuiama , Yinka-Ogunleye Adesola , Chukwu Chimaobi , Ahmad Adama , King David , Akinpelu Afolabi , Maluquer de Motes Carlos , Ribeca Paolo , Sumner Rebecca P. , Rambaut Andrew , Chester Michael , Maishman Tom , Bamidele Oluwafemi , Mba Nwando , Babatunde Olajumoke , Aruna Olusola , Pullan Steven T. , Gannon Benedict , Brown Colin S. , Ihekweazu Chikwe , Adetifa Ifedayo , Ulaeto David O.
Published: September 2023

The 2022 global mpox outbreak raises questions about how this zoonotic disease established effective human-to-human transmission and its potential for further adaptation. The 2022 outbreak virus is related to an ongoing outbreak in Nigeria originally reported in 2017, but the evolutionary path linking the two remains unclear due to a lack of genomic data between 2018, when virus exportations from Nigeria were first recorded, and 2022, when the global mpox outbreak began. Here, 18 viral genomes obtained from patients across southern Nigeria in 2019–2020 reveal multiple lineages of monkeypox virus (MPXV) co-circulated in humans for several years before 2022, with progressive accumulation of mutations consistent with APOBEC3 activity over time. We identify Nigerian A.2 lineage isolates, confirming the lineage that has been multiply exported to North America independently of the 2022 outbreak originated in Nigeria, and that it has persisted by human-to-human transmission in Nigeria for more than 2 years before its latest exportation. Finally, we identify a lineage-defining APOBEC3-style mutation in all A.2 isolates that disrupts gene A46R, encoding a viral innate immune modulator. Collectively, our data demonstrate MPXV capacity for sustained diversification within humans, including mutations that may be consistent with established mechanisms of poxvirus adaptation.
Conformational coupling of redox-driven Na+-translocation in Vibrio cholerae NADH:quinone oxidoreductase
Authors: Hau Jann-Louis , Kaltwasser Susann , Muras Valentin , Casutt Marco S. , Vohl Georg , Claußen Björn , Steffen Wojtek , Leitner Alexander , Bill Eckhard , Cutsail George E. , DeBeer Serena , Vonck Janet , Steuber Julia , Fritz Günter
Published: September 2023

In the respiratory chain, NADH oxidation is coupled to ion translocation across the membrane to build up an electrochemical gradient. In the human pathogen Vibrio cholerae, the sodium-pumping NADH:quinone oxidoreductase (Na+-NQR) generates a sodium gradient by a so far unknown mechanism. Here we show that ion pumping in Na+-NQR is driven by large conformational changes coupling electron transfer to ion translocation. We have determined a series of cryo-EM and X-ray structures of the Na+-NQR that represent snapshots of the catalytic cycle. The six subunits NqrA, B, C, D, E, and F of Na+-NQR harbor a unique set of cofactors that shuttle the electrons from NADH twice across the membrane to quinone. The redox state of a unique intramembranous [2Fe-2S] cluster orchestrates the movements of subunit NqrC, which acts as an electron transfer switch. We propose that this switching movement controls the release of Na+ from a binding site localized in subunit NqrB.
Microencapsulation by spray-drying and freeze-drying of extract of phenolic compounds obtained from ciriguela peel
Authors: da Silva Júnior Marcony Edson , Araújo Maria Vitória Rolim Lemos , Martins Ana Cristina Silveira , dos Santos Lima Marcos , da Silva Flávio Luiz Honorato , Converti Attilio , Maciel Maria Inês Sucupira
Published: September 2023

Microcapsules of ciriguela peel extracts obtained by ultrasound-assisted extraction were prepared by spray drying, whose results were compared with those of freeze-drying as a control. The effects of spray-drying air temperature, feed flow rate and ratio of encapsulating agents (maltodextrin and arabic gum) were studied. Encapsulation efficiency, moisture content, total phenolic compounds (TPC), water activity, hygroscopicity, solubility, colorimetric parameters, phenolic profile by HPLC/DAD, simulated gastrointestinal digestion and morphology of spray-dried and freeze-dried microcapsules were evaluated, as well as their stability of TPC during 90 days storage at 7 and 25 °C. Spray-dried extract showed higher encapsulation efficiency (98.83%) and TPC (476.82 mg GAE g−1) than freeze-dried extract. The most abundant compounds in the liquid extract of ciriguela peel flour were rutin, epicatechin gallate, chlorogenic acid and quercetin. Rutin and myricetin were the major flavonoids in the spray-dried extract, while quercetin and kaempferol were in the freeze-dried one. The simulated gastrointestinal digestion test of microencapsulated extracts revealed the highest TPC contents after the gastric phase and the lowest one after the intestinal one. Rutin was the most abundant compound after the digestion of both spray-dried (68.74 µg g−1) and freeze-dried (93.98 µg g−1) extracts. Spray-dried microcapsules were of spherical shape, freeze-dried products of irregular structures. Spray-dried microcapsules had higher phenolic compounds contents after 90 days of storage at 7 °C compared to those stored at 25 °C, while the lyophilized ones showed no significant difference between the two storage temperatures. The ciriguela agro-industrial residue can be considered an interesting alternative source of phenolic compounds that could be used, in the form of bioactive compounds-rich powders, as an ingredient in pharmaceutical, cosmetic and food industries.
Long-term monitoring of COVID-19 prevalence in raw and treated wastewater in Salvador, the largest capital of the Brazilian Northeast
Authors: de Araújo Rolo Carolina , Machado Bruna Aparecida Souza , dos Santos Matheus Carmo , dos Santos Rosângela Fernandes , Fonseca Maísa Santos , Hodel Katharine Valéria Saraiva , Silva Jéssica Rebouças , Nunes Danielle Devequi Gomes , dos Santos Almeida Edna , de Andrade Jailson Bittencourt
Published: September 2023

Wastewater-based epidemiology (WBE) becomes an interesting epidemiological approach to monitoring the prevalence of SARS-CoV-2 broadly and non-invasively. Herein, we employ for the first time WBE, associated or not with the PEG 8000 precipitation method, for the detection of SARS-CoV-2 in samples of raw or treated wastewater from 22 municipal wastewater treatment stations (WWTPs) located in Salvador, the fourth most populous city in Brazil. Our results demonstrate the success of the application of WBE for detecting SARS-CoV-2 in both types of evaluated samples, regardless of the usage of PEG 8000 concentration procedure. Further, an increase in SARS-CoV-2 positivity rate was observed in samples collected in months that presented the highest number of confirmed COVID-19 cases (May/2021, June/2021 and January/2022). While PEG 8000 concentration step was found to significantly increase the positivity rate in treated wastewater samples (p < 0.005), a strong positive correlation (r: 0.84; p < 0.002) between non-concentrated raw wastewater samples with the number of new cases of COVID-19 (April/2021–February/2022) was observed. In general, the present results reinforce the efficiency of WBE approach to monitoring the presence of SARS-CoV-2 in either low- or high-capacity WWTPs. The successful usage of WBE even in raw wastewater samples makes it an interesting low-cost tool for epidemiological surveillance.
Influence of plastic aggregate geometry on strength properties of cement-stabilized macadam
Authors: Chi Mingxiang , Shen Zhenzong , Chen Shibin , Yao Yunshi , Shen Jianjun , Li Chao , Yan Qingyao
Published: September 2023

In order to improve the toughness and flexibility of cement-stabilized macadam and inhibit crack formation and propagation, the influence of plastic aggregate geometry on the strength properties of cement-stabilized macadam is studied. The surface roughness of plastic aggregate was designed into Ra 12.5 and Ra 25. When the content of plastic coarse aggregate was gradually increased from 4 to 8%, 12%, 16%, 20%, and 24%, the compressive strength, splitting strength, and the tensile-compression ratio of the cement-stabilized macadam made of aggregate with rough surface texture were found higher than those of aggregate with smooth surface texture. The rough cylindrical, spherical, spindle, and dumbbell-shaped plastic coarse aggregates were designed and prepared for testing. The test results showed the maximum compressive strength, splitting strength, and tensile-compression ratio of cement-stabilized macadam with the dumbbell-shaped plastic coarse aggregate. The tensile-compression ratio increased by 15.2% compared to natural aggregate cement-stabilized macadam. The results show that under the same conditions, the plastic aggregate with different geometry can improve the compressive and splitting strengths of cement-stabilized macadam and significantly improve the toughness and flexibility, with dumbbell-shaped plastic coarse aggregate having the greatest improvement, especially compared with natural aggregate cement-stabilized crushed stone. This research provides insights for improving pavement engineering quality and new ideas for utilizing waste plastics.
Influence of silicon nano-particles on Avena sativa L. to alleviate the biotic stress of Rhizoctonia solani
Authors: Ahmad Faiza , Jabeen Khajista , Iqbal Sumera , Umar Aisha , Ameen Fuad , Gancarz Marek , Eldin Darwish Doaa Bahaa
Published: September 2023

Avena sativa L. a cereal crop that is badly affected by several abiotic and biotic stresses. In the current study, silicon nanoparticles are used to mitigate the harmful effects of root rot disease caused by Rhizoctonia solani Kuhn on the growth of A. sativa. In vitro (Petri plates) and in vivo (pots experiment) were performed to measure the various physiological and biochemical parameters i.e. osmotic potential, chlorophyll, proline content, growth parameters, sugar, fresh and dry weight, and disease index. Results revealed that physiological and biochemical parameters were reduced under fungal stress with silicon nanoparticles treatment as compared to the control group. Si nanoparticles helped to alleviate the negative effects caused by fungus i.e. germination percentage upto 80%, germination rate 4 n/d, radical and plumule length was 4.02 and 5.46, dry weight 0.08 g, and relative water content was (50.3%) increased. Fungus + Si treatment showed the maximum protein content, i.e. 1.2 µg/g as compared to Fungus (0.3 µg/g) treated group. The DI was maximum (78.82%) when the fungus directly attacked the target plant and DI reduced (44.2%) when the fungus was treated with Si nanoparticles. Thus, silicon nanoparticles were potentially effective against the stress of R. solani and also used to analyze the plant resistance against fungal diseases. These particles can use as silicon fertilizers, but further studies on their efficacy under field conditions and improvement in their synthesis are still needed.
Long-term changes in physical fitness components determining the motor performance of young people studying physiotherapy in 2001–2020
Authors: Lewandowski Andrzej , Siedlaczek Marcin , Piekorz Zuzanna
Published: September 2023

The aim of the study is to assess changes in basic somatic features and motor components of physical fitness of physiotherapy students in the years 2001–2020. Hypotheses were made about the lack of a secular trend in body height and weight, the deterioration of motor efficiency and the lack of conditioning of the examined changes by social factors. Every year, students of physiotherapy at Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń (Poland) were examined in terms of height, weight, chest circumference, balance, speed, power, agility and endurance. The results were obtained from 1161 female students and 464 male students. There was weight gain in the group of women (R2 = 0.41, p = 0.00314), deterioration of speed (for women R2 = 0.579, p = 0.001; for men R2 = 0.301, p = 0.0185) and deterioration of power (for women R2 = 0.51, p = 0.001, p = 0.001; for men R2 = 0.0432, p = 0.00303). The stability of the remaining features was also found, as well as the lack of their conditioning by social factors. Predictors of maintaining motor fitness were identified, i.e. male gender, fitness exam qualifying for studies and chest circumference. The creation of conditions and requirements encouraging greater care for the appropriate level of motor fitness of people undertaking physiotherapy studies seems justified. This observation may apply to other academia providing training for the profession of physiotherapist.
Wideband dispersion-free THz waveguide platform
Authors: Rohrbach David , Kang Bong Joo , Zyaee Elnaz , Feurer Thomas
Published: September 2023

We present a versatile THz waveguide platform for frequencies between 0.1 THz and 1.5 THz, designed to exhibit vacuum-like dispersion and electric as well as magnetic field enhancement. While linear THz spectroscopy benefits from the extended interaction length in combination with moderate losses, nonlinear THz spectroscopy profits from the field enhancement and zero dispersion, with the associated reshaping-free propagation of broadband single- to few-cycle THz pulses. Moreover, the vacuum-like dispersion allows for velocity matching in mixed THz and visible to infrared pump-probe experiments. The platform is based on the motif of a metallic double ridged waveguide. We experimentally characterize essential waveguide properties, for instance, propagation and bending losses, but also demonstrate a junction and an interferometer, essentially because those elements are prerequisites for THz waveform synthesis, and hence, for coherently controlled linear and nonlinear THz interactions.
Genetic risk assessment based on association and prediction studies
Authors: Astrologo Nicole Cathlene N. , Gaudillo Joverlyn D. , Albia Jason R. , Roxas-Villanueva Ranzivelle Marianne L.
Published: September 2023

The genetic basis of phenotypic emergence provides valuable information for assessing individual risk. While association studies have been pivotal in identifying genetic risk factors within a population, complementing it with insights derived from predictions studies that assess individual-level risk offers a more comprehensive approach to understanding phenotypic expression. In this study, we established personalized risk assessment models using single-nucleotide polymorphism (SNP) data from 200 Korean patients, of which 100 experienced hepatitis B surface antigen (HBsAg) seroclearance and 100 patients demonstrated high levels of HBsAg. The risk assessment models determined the predictive power of the following: (1) genome-wide association study (GWAS)-identified candidate biomarkers considered significant in a reference study and (2) machine learning (ML)-identified candidate biomarkers with the highest feature importance scores obtained by using random forest (RF). While utilizing all features yielded 64% model accuracy, using relevant biomarkers achieved higher model accuracies: 82% for 52 GWAS-identified candidate biomarkers, 71% for three GWAS-identified biomarkers, and 80% for 150 ML-identified candidate biomarkers. Findings highlight that the joint contributions of relevant biomarkers significantly influence phenotypic emergence. On the other hand, combining ML-identified candidate biomarkers into the pool of GWAS-identified candidate biomarkers resulted in the improved predictive accuracy of 90%, demonstrating the capability of ML as an auxiliary analysis to GWAS. Furthermore, some of the ML-identified candidate biomarkers were found to be linked with hepatocellular carcinoma (HCC), reinforcing previous claims that HCC can still occur despite the absence of HBsAg.
Development of a nomogram model for the early prediction of sepsis-associated acute kidney injury in critically ill patients
Authors: Peng Milin , Deng Fuxing , Qi Desheng
Published: September 2023

Sepsis-associated acute kidney injury is a common complication of sepsis, but it is difficult to predict sepsis-associated acute kidney injury. In this retrospective observational study, adult septic patients were recruited from the MIMIC-III database as the training cohort (n = 4764) and from Xiangya Hospital (n = 1568) and Zhang’s database as validation cohorts. We identified eleven predictors with seven independent risk predictors of sepsis-associated acute kidney injury [fluid input_day1 ≥ 3390 ml (HR hazard ratio 1.42), fluid input_day2 ≥ 2734 ml (HR 1.64), platelet_min_day5 ≤ 224.2 × 109/l (HR 0.86), length of ICU stay ≥ 2.5 days (HR 1.24), length of hospital stay ≥ 5.8 days (HR 1.18), Bun_max_day1 ≥ 20 mmol/l (HR 1.20), and mechanical ventilation time ≥ 96 h (HR 1.11)] by multivariate Cox regression analysis, and the eleven predictors were entered into the nomogram. The nomogram model showed a discriminative ability for estimating sepsis-associated acute kidney injury. These results indicated that clinical parameters such as excess input fluid on the first and second days after admission and longer mechanical ventilation time could increase the risk of developing sepsis-associated acute kidney injury. With our study, we built a real-time prediction model for potentially forecasting acute kidney injury in septic patients that can help clinicians make decisions as early as possible to avoid sepsis-associated acute kidney injury.
Profiling tear film enzymes reveals major metabolic pathways involved in the homeostasis of the ocular surface
Authors: Akkurt Arslan Murat , Brignole-Baudouin Françoise , Chardonnet Solenne , Pionneau Cédric , Blond Frédéric , Baudouin Christophe , Kessal Karima
Published: September 2023

The ocular surface (OS) enzymes are of great interest due to their potential for novel ocular drug development. We aimed first to profile and classify the enzymes of the OS to describe major biological processes and pathways that are involved in the maintenance of homeostasis. Second, we aimed to compare the enzymatic profiles between the two most common tear collection methods, capillary tubes (CT) and Schirmer strips (ScS). A comprehensive tear proteomic dataset was generated by pooling all enzymes identified from nine tear proteomic analyses of healthy subjects using mass spectrometry. In these studies, tear fluid was collected using CT (n = 4), ScS (n = 4) or both collection methods (n = 1). Classification and functional analysis of the enzymes was performed using a combination of bioinformatic tools. The dataset generated identified 1010 enzymes. The most representative classes were hydrolases (EC 3) and transferases (EC 2). Phosphotransferases, esterases and peptidases were the most represented subclasses. A large portion of the identified enzymes was common to both collection methods (n = 499). More enzymes were specifically detected in the ScS-extracted proteome. The major pathways in which the identified enzymes participate are related to the immune system and protein, carbohydrate and lipid metabolism. Metabolic processes for nucleosides, cellular amides, sugars and sulfur compounds constituted the most enriched biological processes. Knowledge of these molecules highly susceptible to pharmacological manipulation might help to predict the metabolism of ophthalmic medications and develop novel prodrug strategies as well as new drug delivery systems. Combining such extensive knowledge of the OS enzymes with new analytical approaches and techniques might create new prospects for understanding, predicting and manipulating the metabolism of ocular pharmaceuticals. Our study reports new, essential data on OS enzymes while also comparing the enzyme profiles obtained via the two most popular methods of tear collection, capillary tubes and Schirmer strips.
In-depth proteome analysis of brain tissue from Ewsr1 knockout mouse by multiplexed isobaric tandem mass tag labeling
Authors: Jung Jin Woo , Kim Hyeyoon , Park Joonho , Woo Jongmin , Jeon Eunji , Lee Geeeun , Park Minseo , Kim Sarang , Seo Hoseok , Cheon Seongmin , Dan Kisoon , Lee Junghee , Ryu Hoon , Han Dohyun
Published: September 2023

EWS RNA binding protein 1 (EWSR1) is a multifunctional protein whose epigenetic signatures contribute to the pathogenesis of various human diseases, such as neurodegenerative disorders, skin development, and tumorigenic processes. However, the specific cellular functions and physiological characteristics of EWSR1 remain unclear. In this study, we used quantitative mass spectrometry-based proteomics with tandem mass tag labeling to investigate the global proteome changes in brain tissue in Ewsr1 knockout and wild-type mice. From 9115 identified proteins, we selected 118 differentially expressed proteins, which is common to three quantitative data processing strategies including only protein level normalizations and spectrum-protein level normalization. Bioinformatics analysis of these common differentially expressed proteins revealed that proteins up-regulated in Ewsr1 knockout mouse are mostly related to the positive regulation of bone remodeling and inflammatory response. The down-regulated proteins were associated with the regulation of neurotransmitter levels or amino acid metabolic processes. Collectively, these findings provide insight into the physiological function and pathogenesis of EWSR1 on protein level. Better understanding of EWSR1 and its protein interactions will advance the field of clinical research into neuronal disorders. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD026994.
Enhancing the performance of a mutant pyrrolysyl-tRNA synthetase to create a highly versatile eukaryotic cell-free protein synthesis tool
Authors: Schloßhauer Jeffrey L. , Zemella Anne , Dondapati Srujan K. , Thoring Lena , Meyer Manpreet , Kubick Stefan
Published: September 2023

Modification of proteins with a broad range of chemical functionalities enables the investigation of protein structure and activity by manipulating polypeptides at single amino acid resolution. Indeed, various functional groups including bulky non-canonical amino acids like strained cyclooctenes could be introduced by the unique features of the binding pocket of the double mutant pyrrolysyl-tRNA synthetase (Y306A, Y384F), but the instable nature of the enzyme limits its application in vivo. Here, we constructed a cell-free protein production system, which increased the overall enzyme stability by combining different reaction compartments. Moreover, a co-expression approach in a one-pot reaction allowed straightforward site-specific fluorescent labeling of the functional complex membrane protein cystic fibrosis transmembrane conductance regulator. Our work provides a versatile platform for introducing various non-canonical amino acids into difficult-to-express proteins for structural and fluorescence based investigation of proteins activity.
Tele-monitoring system for intensive care ventilators in isolation rooms
Authors: Kim Su Hyeon , Seo Hyo-Chang , Choi Sanghoon , Joo Segyeong
Published: September 2023

The COVID-19 pandemic and discovery of new mutant strains have a devastating impact worldwide. Patients with severe COVID-19 require various equipment, such as ventilators, infusion pumps, and patient monitors, and a dedicated medical team to operate and monitor the equipment in isolated intensive care units (ICUs). Medical staff must wear personal protective equipment to reduce the risk of infection. This study proposes a tele-monitoring system for isolation ICUs to assist in the monitoring of COVID-19 patients. The tele-monitoring system consists of three parts: medical-device panel image processing, transmission, and tele-monitoring. This system can monitor the ventilator screen with obstacles, receive and store data, and provide real-time monitoring and data analysis. The proposed tele-monitoring system is compared with previous studies, and the image combination algorithm for reconstruction is evaluated using structural similarity index (SSIM) and peak signal-to-noise ratio (PSNR). The system achieves an SSIM score of 0.948 in the left side and a PSNR of 23.414 dB in the right side with no obstacles. It also reduces blind spots, with an SSIM score of 0.901 and a PSNR score of 18.13 dB. The proposed tele-monitoring system is compatible with both wired and wireless communication, making it accessible in various situations. It uses camera and performs live data monitoring, and the two monitoring systems complement each other. The system also includes a comprehensive database and an analysis tool, allowing medical staff to collect and analyze data on ventilator use, providing them a quick, at-a-glance view of the patient's condition. With the implementation of this system, patient outcomes may be improved and the burden on medical professionals may be reduced during the COVID-19 pandemic-like situations.
Effects of oxygen availability on mycobenthic communities of marine coastal sediments
Authors: Yang Yanyan , Rivera Pérez Carmen Alicia , Richter-Heitmann Tim , Nimzyk Rolf , Friedrich Michael W. , Reich Marlis
Published: September 2023

In coastal marine sediments, oxygen availability varies greatly, and anoxic conditions can develop quickly over low spatial resolution. Although benthic fungi are important players in the marine carbon cycle, little is known about their adaptation to fluctuating availability of oxygen as terminal electron acceptor. Here, we study which part of a mycobenthic community from oxic coastal sediments can thrive under temporarily anoxic conditions. We test whether phylogeny or certain fungal traits promote plasticity in respect to changes in oxygen availability. Therefore, we incubated mycobenthos under oxic and anoxic conditions, performed ITS2 Illumina tag-sequencing and an additional meta-analysis on a literature survey. Half of all OTUs showed a plasticity towards changing oxygen availability and exhibited different strategies towards anoxic conditions, with rapid response within hours or a delayed one after several days. The strategy of dimorphism and facultative yeasts were significantly linked to OTU occurrence in anoxic conditions, while phylogeny and other traits had less effect. Our results suggest that different fungal niches are formed over the duration of prolonged anoxic conditions. The taxon-specific proliferation seems to be regulated by the fine-tuning of various traits and factors. It is essential to take these results into account when conducting conceptual work on the functionality of the marine benthos.
Effects of C-reactive protein trajectories of critically ill patients with sepsis on in-hospital mortality rate
Authors: Jiang Xuandong , Zhang Chenlu , Pan Yuting , Cheng Xuping , Zhang Weimin
Published: September 2023

Sepsis, a life-threatening condition caused by an inflammatory response to systemic infection, results in a significant social burden and healthcare costs. This study aimed to investigate the relationship between the C-reactive protein (CRP) trajectories of patients with sepsis in the intensive care unit (ICU) and the in-hospital mortality rate. We reviewed 1464 patients with sepsis treated in the ICU of Dongyang People’s Hospital from 2010 to 2020 and used latent growth mixture modeling to divide the patients into four classes according to CRP trajectory (intermediate, gradually increasing, persistently high, and persistently low CRP levels). We found that patients with intermediate and persistently high CRP levels had the lowest (18.1%) and highest (32.6%) in-hospital mortality rates, respectively. Multiple logistic regression analysis showed that patients with persistently high (odds ratio [OR] = 2.19, 95% confidence interval [CI] = 1.55–3.11) and persistently low (OR = 1.41, 95% CI = 1.03–1.94) CRP levels had a higher risk of in-hospital mortality than patients with intermediate CRP levels. In conclusion, in-hospital mortality rates among patients with sepsis differ according to the CRP trajectory, with patients with intermediate CRP levels having the lowest mortality rate. Further research on the underlying mechanisms is warranted.
Environmental DNA detects biodiversity and ecological features of phytoplankton communities in Mediterranean transitional waters
Authors: Specchia Valeria , Zangaro Francesco , Tzafesta Eftychia , Saccomanno Benedetta , Vadrucci Maria Rosaria , Pinna Maurizio
Published: September 2023

Climate changes and anthropogenic pressures are causing a biodiversity decline in terms of species number and genetic diversity, reducing the adaptability and evolvability of natural communities. Transitional water ecosystems are more sensitive to habitat reduction and degradation and, thus, are more exposed to biodiversity declines requiring biodiversity monitoring programs for their conservation. Environmental DNA (eDNA) metabarcoding represents a high-throughput tool for biodiversity assessment that is facilitating data collection for biodiversity monitoring. In this study, we applied, for the first time, eDNA metabarcoding in a Mediterranean coastal lagoon to assess the ecological features of eukaryotic phytoplankton communities. We sampled water in seven different lagoon sites and amplified the extracted DNA with primers targeting the variable region 4 (V4) of the 18S rRNA gene marker. The results demonstrated the validity of eDNA studies to provide insights into lagoon phytoplankton composition, establish the structure and spatial variation of phytoplankton communities, and evaluate its correlation to abiotic factors. Finally, the genetic distances analysis suggests that the different spatial distribution of OTUs, at least for the Tetraselmis genus, reflects the genetic background.
Interaction between genetic susceptibility to obesity and food intake on BMI in Finnish school-aged children
Authors: Viljakainen Heli , Sorlí Jose V. , Dahlström Emma , Agrawal Nitin , Portolés Olga , Corella Dolores
Published: September 2023

Diet modulates the genetic risk of obesity, but the modulation has been rarely studied using genetic risk scores (GRSs) in children. Our objectives were to identify single nucleotide polymorphisms (SNPs) that drive the interaction of specific foods with obesity and combine these into GRSs. Genetic and food frequency data from Finnish Health in Teens study was utilized. In total, 1142 11-year-old subjects were genotyped on the Metabochip array. BMI-GRS with 30 well-known SNPs was computed and the interaction of individual SNPs with food items and their summary dietary scores were examined in relation to age- and sex-specific BMI z-score (BMIz). The whole BMI-GRS interacted with several foods on BMIz. We identified 7–11 SNPs responsible for each interaction and these were combined into food-specific GRS. The most predominant interaction was witnessed for pizza (p < 0.001): the effect on BMIz was b − 0.130 (95% CI − 0.23; − 0.031) in those with low-risk, and 0.153 (95% CI 0.072; 0.234) in high-risk. Corresponding, but weaker interactions were verified for sweets and chocolate, sugary juice drink, and hamburger and hotdog. In total 5 SNPs close to genes NEGR1, SEC16B, TMEM18, GNPDA2, and FTO were shared between these interactions. Our results suggested that children genetically prone to obesity showed a stronger association of unhealthy foods with BMIz than those with lower genetic susceptibility. Shared SNPs of the interactions suggest common differences in metabolic gene-diet interactions, which warrants further investigation.
RAB10 promotes breast cancer proliferation migration and invasion predicting a poor prognosis for breast cancer
Authors: Zhuo Jian , Han Jianjun , Zhao Yanchun , Hao Ruiying , shen Chong , Li He , Dai Luxian , Sheng Ankang , Yao Hanyu , Yang Xiaohong , Liu Weiguang
Published: September 2023

RAB10, a member of the small GTPase family, has complex biological functions, but its role in breast cancer (BC) remains unclear. The aim of this study was to investigate the relationship between RAB10's role in BC, its biological functions, and BC prognosis. An online database was used to analyze the correlation between differential expression of RAB10 in BC and prognosis. The results of immunohistochemical assays in clinical cohorts were combined with the database analysis. The chi-square test and COX regression were employed to analyze the correlation between RAB10 and pathological features of BC. MTT, Transwell, and wound healing assays were conducted to detect BC cell proliferation, invasion, and metastatic ability. Bioinformatics techniques were employed to explore the correlation between RAB10 and BC tumor immune cell infiltration, and to speculate the biological function of RAB10 in BC and related signaling pathways. Our findings suggest that RAB10 expression is elevated in BC and is associated with HER2 status, indicating a poor prognosis for BC patients. RAB10 can promote the proliferation, migration, and invasion ability of BC cells in vitro. RAB10 is also associated with BC immune cell infiltration and interacts with multiple signaling pathways. RAB10 is a potential biomarker or molecular target for BC.
All-inorganic perovskite photovoltaics for power conversion efficiency of 31%
Authors: Karna Lipsa Rani , Upadhyay Rohitash , Ghosh Avijit
Published: September 2023

The lead-free perovskite halides emerge as the great alternative for highly efficient and environment friendly photovoltaics due to the inherent optoelectronic properties. In this paper, the numerical study of all-inorganic regular n–i–p structured perovskite photovoltaics using solar cells capacitance simulator (SCAPS-1D) has been performed. The optimised device structure using rGO provided best performance compared to the other hole transport layers (HTLs) like CuI, CuSCN, Cu2O, NiO, WSe2, MoO3 with CsSnI3 as an active material and TiO2 as electron transport layer (ETL). Furthermore, WS2 as an ETL compared to TiO2, Li-TiO2, ZnO, Al-ZnO, etc. provided the best performance with rGO as HTL and CsSnI3 as active material. Therefore, the optimized solar cell structure (FTO/WS2/CsSnI3/rGO/Pt) showed best photovoltaic performance with power conversion efficiency (PCE) of 31%, fill factor (FF) of 88.48%, open circuit voltage (VOC) of 1.15 V, and short circuit current density (JSC) of 30.47 mA/cm2, respectively. Consequently, the effect of variation of temperature, thickness, defect density, doping density of active layer and variation of illumination intensity on the photovoltaic performance of the optimised device are also analysed. Furthermore, this study is also focused on the analysis of photovoltaic parameters for the optimized structure using concept of ideality factor associated with the illumination intensity. Therefore, this analysis suggests a route for further development of all-inorganic, lead-free perovskite photovoltaics experimentally with improved photovoltaic performance.
Magnetization reversals in core–shell sphere clusters: finite-element micromagnetic simulation and machine learning analysis
Authors: Park Hyeon-Kyu , Kim Sang-Koog
Published: September 2023

Recently developed permanent magnets, featuring specially engineered microstructures of inhomogeneous magnetic phases, are being considered as cost-effective alternatives to homogeneous single-main-phase hard magnets composed of Nd2Fe14B, without compromising performance. In this study, we conducted a comprehensive examination of a core–shell sphere cluster model of Ce-substituted inhomogeneous Nd2-δCeδFe14B phases versus homogeneous magnetic phases, utilizing finite-element micromagnetic simulation and machine learning methods. This involved a meticulous, sphere-by-sphere analysis of individual demagnetization curves calculated from the cluster model. The grain-by-grain analyses unveiled that these individual demagnetization curves can elucidate the overall magnetization reversal in terms of the nucleation and coercive fields for each sphere. Furthermore, it was observed that Nd-rich spheres exhibited much broader ranges of nucleation and coercive field distributions, while Nd-lean spheres showed relatively narrower ranges. To identify the key parameter responsible for the notable differences in the nucleation fields, we constructed a machine learning regression model. The model utilized numerous hyperparameter sets, optimized through the very fast simulated annealing algorithm, to ensure reliable training. Using the kernel SHapley Additive eXplanation (SHAP) technique, we inferred that stray fields among the 11 parameters were closely related to coercivity. We further substantiated the machine learning models’ inference by establishing an analytical model based on the eigenvalue problem in classical micromagnetic theory. Our grain-by-grain interpretation can guide the optimal design of granular hard magnets from Nd2Fe14B and other abundant rare earth transition elements, focusing on extraordinary performance through the careful adjustment of microstructures and elemental compositions.
Genetic atlas of hygro-and thermosensory cells in the vinegar fly Drosophila melanogaster
Authors: Corthals Kristina , Andersson Vilma , Churcher Allison , Reimegård Johan , Enjin Anders
Published: September 2023

The ability of animals to perceive and respond to sensory information is essential for their survival in diverse environments. While much progress has been made in understanding various sensory modalities, the sense of hygrosensation, which involves the detection and response to humidity, remains poorly understood. In this study, we focused on the hygrosensory, and closely related thermosensory, systems in the vinegar fly Drosophila melanogaster to unravel the molecular profile of the cells of these senses. Using a transcriptomic analysis of over 37,000 nuclei, we identified twelve distinct clusters of cells corresponding to temperature-sensing arista neurons, humidity-sensing sacculus neurons, and support cells relating to these neurons. By examining the expression of known and novel marker genes, we validated the identity of these clusters and characterized their gene expression profiles. We found that each cell type could be characterized by a unique expression profile of ion channels, GPCR signaling molecules, synaptic vesicle cycle proteins, and cell adhesion molecules. Our findings provide valuable insights into the molecular basis of hygro- and thermosensation. Understanding the mechanisms underlying hygro- and thermosensation may shed light on the broader understanding of sensory systems and their adaptation to different environmental conditions in animals.
Phase estimation of definite photon number states by using quantum circuits
Authors: Najafi Peyman , Naeimi Ghasem , Saeidian Shahpoor
Published: September 2023

We propose a method to map the conventional optical interferometry setup into quantum circuits. The unknown phase shift inside a Mach–Zehnder interferometer in the presence of photon loss is estimated by simulating the quantum circuits. For this aim, we use the Bayesian approach in which the likelihood functions are needed, and they are obtained by simulating the appropriate quantum circuits. The precision of four different definite photon-number states of light, which all possess six photons, is compared. The measurement scheme that we have considered is counting the number of photons detected after the final beam splitter of the interferometer, and photon loss is modeled by using fictitious beam splitters in the arms of the interferometer. Our results indicate that three of the four definite photon-number states considered can have better precision than the standard interferometry limit whenever the photon loss rate is in a specific range. In addition, the Fisher information for the four definite photon-number states in the setup is also estimated to check the optimality of the chosen measurement scheme.
Predicting lung adenocarcinoma prognosis, immune escape, and pharmacomic profile from arginine and proline-related genes
Authors: Wang Ziqiang , Zhang Jing , Shi Shuhua , Ma Hongyu , Wang Dongqin , Zuo Chao , Zhang Qiang , Lian Chaoqun
Published: September 2023

Lung adenocarcinoma (LUAD) is a highly heterogeneous disease that ranks first in morbidity and mortality. Abnormal arginine metabolism is associated with inflammatory lung disease and may influence alterations in the tumor immune microenvironment. However, the potential role of arginine and proline metabolic patterns and immune molecular markers in LUAD is unclear. Gene expression, somatic mutations, and clinicopathological information of LUAD were downloaded from The Cancer Genome Atlas (TCGA) database. Univariate Cox regression analysis was performed to identify metabolic genes associated with overall survival (OS). Unsupervised clustering divided the sample into two subtypes with different metabolic and immunological profiles. Gene set enrichment analysis (GESA) and gene set variation analysis (GSVA) were used to analyze the underlying biological processes of the two subtypes. Drug sensitivity between subtypes was also predicted; then prognostic features were developed by multivariate Cox regression analysis. In addition, validation was obtained in the GSE68465, and GSE50081 dataset. Then, gene expression, and clinical characterization of hub genes CPS1 and SMS were performed; finally, in vitro validation experiments for knockdown of SMS were performed in LUAD cell lines. In this study, we first identified 12 arginine and proline-related genes (APRGs) significantly associated with OS and characterized the clinicopathological features and tumor microenvironmental landscape of two different subtypes. Then, we established an arginine and proline metabolism-related scoring system and identified two hub genes highly associated with prognosis, namely CPS1, and SMS. In addition, we performed CCK8, transwell, and other functional experiments on SMS to obtain consistent results. Our comprehensive analysis revealed the potential molecular features and clinical applications of APRGs in LUAD. A model based on 2 APRGs can accurately predict survival outcomes in LUAD, improve our understanding of APRGs in LUAD, and pave a new pathway to guide risk stratification and treatment strategy development for LUAD patients.
Machine learning model for predicting late recurrence of atrial fibrillation after catheter ablation
Authors: Budzianowski Jan , Kaczmarek-Majer Katarzyna , Rzeźniczak Janusz , Słomczyński Marek , Wichrowski Filip , Hiczkiewicz Dariusz , Musielak Bogdan , Grydz Łukasz , Hiczkiewicz Jarosław , Burchardt Paweł
Published: September 2023

Late recurrence of atrial fibrillation (LRAF) in the first year following catheter ablation is a common and significant clinical problem. Our study aimed to create a machine-learning model for predicting arrhythmic recurrence within the first year since catheter ablation. The study comprised 201 consecutive patients (age: 61.8 ± 8.1; women 36%) with paroxysmal, persistent, and long-standing persistent atrial fibrillation (AF) who underwent cryoballoon (61%) and radiofrequency ablation (39%). Five different supervised machine-learning models (decision tree, logistic regression, random forest, XGBoost, support vector machines) were developed for predicting AF recurrence. Further, SHapley Additive exPlanations were derived to explain the predictions using 82 parameters based on clinical, laboratory, and procedural variables collected from each patient. The models were trained and validated using a stratified fivefold cross-validation, and a feature selection was performed with permutation importance. The XGBoost model with 12 variables showed the best performance on the testing cohort, with the highest AUC of 0.75 [95% confidence interval 0.7395, 0.7653]. The machine-learned model, based on the easily available 12 clinical and laboratory variables, predicted LRAF with good performance, which may provide a valuable tool in clinical practice for better patient selection and personalized AF strategy following the procedure.
Calculation method of HJC constitutive model parameters of natural joint angle slate
Authors: Wan Antong , Tao Tiejun , Tian Xingchao , Xie Caijin , Jia Jian
Published: September 2023

In the course of underground engineering, layered slate is often encountered. Understanding the mechanical characteristics of layered slate is a prerequisite for engineering construction and disaster prevention and mitigation. As a result, at the beginning of a project, a large number of indoor tests are required, which are time-consuming and laborious. In addition, the natural joint angle of the layered slate is random, so it is extremely difficult to establish a database of the mechanical characteristics of layered slate. Hence, it is necessary to find a simple, feasible, and high-precision method to determine the Holmquist–Johnson–Cook (HJC) constitutive model parameters for naturally jointed layered slate with different dip angles. This study first determines the HJC constitutive model parameters of layered slate with five specific joint dip angles (0°, 30°, 45°, 60°, and 90°) through static tests and the split Hopkinson pressure bar (SHPB) test. Furthermore, by employing sensitivity analysis methods, the influence of key parameters of the HJC constitutive model on the dynamic peak stress of slate is determined. Among them, parameters A and B have the most significant impact on stress, exceeding 50%. Thirdly, a nonlinear fitting regression method is used to determine the HJC constitutive model parameters of naturally jointed angular slate. The relationship between the HJC model parameters and the inclination angle of slate joints is derived, and the accuracy of these parameters is verified through numerical simulation methods. The error between the numerical simulation and indoor experiments is within 10%, indicating a high level of simulation accuracy. The research findings provide a highly precise numerical simulation method for similar projects.