bluuebunny/crossref_metadata_2025 huggingface dataset:
Interannual Variability of Autumn Precipitation Over the Greater Mekong Subregion
Authors: Tian Mengping , Yang Ruowen , Cao Jie
Published: September 2022

This study investigates the interannual variability in autumn precipitation over the Greater Mekong Subregion (GMS) during the period 1981–2019 and its possible causes. Statistical analysis indicates that GMS autumn precipitation showed a seesaw pattern between the central–southern and northeastern GMS over interannual timescales. The tropical sea surface temperature anomalies (SSTAs), reflected in the tropical northeastern Pacific SST index (TNEPI), significantly modulate anomalous GMS autumn precipitation. When the TNEPI is higher than normal, the SSTAs pattern prevails during autumn, with warmer SSTAs in the tropical eastern Pacific and western Indian Ocean, and colder SSTAs in the tropical western Pacific and southeastern Indian Ocean. This SSTAs pattern excites an anomalous anticyclone in the lower troposphere over the central–southern GMS and an anomalous cyclone over the northeastern GMS by the Gill–Matsuno mechanism. Subsequently, the anomalous anticyclone with anomalous descending motion results in below‐normal autumn precipitation over the central–southern GMS via a weakening of the convergence of water vapor from the tropical western Pacific and the Bay of Bengal. The anomalous cyclone on the northern flank of anomalous anticyclone, benefiting from water vapor supply from the Bay of Bengal, leads to above‐normal autumn precipitation over the northeastern GMS. The TNEPI, incorporating signals from the eastern‐Pacific (EP) type of ENSO, Indian Ocean dipole (IOD), and SSTAs associated with the Trans‐Niño index (TNI‐like), shows a stronger relationship with GMS autumn precipitation than individual indexes that describing the EP‐type ENSO, IOD or TNI‐like pattern. Therefore, the TNEPI can be considered an efficient predictor of GMS autumn precipitation.
Pyleoclim: Paleoclimate Timeseries Analysis and Visualization With Python
Authors: Khider Deborah , Emile‐Geay Julien , Zhu Feng , James Alexander , Landers Jordan , Ratnakar Varun , Gil Yolanda
Published: September 2022

We present a Python package geared toward the intuitive analysis and visualization of paleoclimate timeseries, Pyleoclim. The code is open‐source, object‐oriented, and built upon the standard scientific Python stack, allowing users to take advantage of a large collection of existing and emerging techniques. We describe the code's philosophy, structure, and base functionalities and apply it to three paleoclimate problems: (a) orbital‐scale climate variability in a deep‐sea core, illustrating spectral, wavelet, and coherency analysis in the presence of age uncertainties; (b) correlating a high‐resolution speleothem to a climate field, illustrating correlation analysis in the presence of various statistical pitfalls (including age uncertainties); (c) model‐data confrontations in the frequency domain, illustrating the characterization of scaling behavior. We show how the package may be used for transparent and reproducible analysis of paleoclimate and paleoceanographic datasets, supporting Findable, Accessible, Interoperable, and Reusable software and an open science ethos. The package is supported by an extensive documentation and a growing library of tutorials shared publicly as videos and cloud‐executable Jupyter notebooks, to encourage adoption by new users.
SERS monitoring of photoinduced-enhanced oxidative stress amplifier on Au@carbon dots for tumor catalytic therapy
Authors: Li Linjia , Yang Jin , Wei Jiahui , Jiang Chunhuan , Liu Zhuo , Yang Bai , Zhao Bing , Song Wei
Published: September 2022

Currently, artificial enzymes-based photodynamic therapy (PDT) is attractive due to its efficient capacity to change the immunosuppressive tumor microenvironment (TME). It is of great significance to study the therapeutic mechanism of novel artificial enzymes in TME through a monitoring strategy and improve the therapeutic effect. In this study, Au@carbon dots (Au@CDs) nanohybrids with a core-shell structure are synthesized, which not only exhibit tunable enzyme-mimicking activity under near-infrared (NIR) light, but also excellent surface-enhanced Raman scattering (SERS) properties. Therefore, Au@CDs show a good capability for monitoring NIR-photoinduced peroxidase-like catalytic processes via a SERS strategy in tumor. Moreover, the Au@CDs deplete glutathione with the cascade catalyzed reactions, thus elevating intratumor oxidative stress amplifying the reactive oxygen species damage based on the NIR-photoinduced enhanced peroxidase and glutathione oxidase-like activities, showing excellent and fast PDT therapeutic effect promoted by photothermal property in 3 min, finally leading to apoptosis in cancer cells. Through SERS monitoring, it is further found that after removing the NIR light source for 33 min, the reactive oxygen species (ROS) activity of the TME is counteracted and eliminated due to the presence of glutathione. This work presents a guidance to rationally design of artificial enzyme for ROS-involved therapeutic strategies and a new spectroscopic tool to evaluate the tumor catalytic therapy.
A transcriptional metastatic signature predicts survival in clear cell renal cell carcinoma
Authors: Alchahin Adele M. , Mei Shenglin , Tsea Ioanna , Hirz Taghreed , Kfoury Youmna , Dahl Douglas , Wu Chin-Lee , Subtelny Alexander O. , Wu Shulin , Scadden David T. , Shin John H. , Saylor Philip J. , Sykes David B. , Kharchenko Peter V. , Baryawno Ninib
Published: September 2022

Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer in adults. When ccRCC is localized to the kidney, surgical resection or ablation of the tumor is often curative. However, in the metastatic setting, ccRCC remains a highly lethal disease. Here we use fresh patient samples that include treatment-naive primary tumor tissue, matched adjacent normal kidney tissue, as well as tumor samples collected from patients with bone metastases. Single-cell transcriptomic analysis of tumor cells from the primary tumors reveals a distinct transcriptional signature that is predictive of metastatic potential and patient survival. Analysis of supporting stromal cells within the tumor environment demonstrates vascular remodeling within the endothelial cells. An in silico cell-to-cell interaction analysis highlights the CXCL9/CXCL10-CXCR3 axis and the CD70-CD27 axis as potential therapeutic targets. Our findings provide biological insights into the interplay between tumor cells and the ccRCC microenvironment.
Effectiveness of COVID-19 vaccines against Omicron and Delta hospitalisation, a test negative case-control study
Authors: Stowe Julia , Andrews Nick , Kirsebom Freja , Ramsay Mary , Bernal Jamie Lopez
Published: September 2022

The Omicron variant has been associated with reduced vaccine effectiveness (VE) against mild disease with rapid waning. Meanwhile Omicron has also been associated with milder disease. Protection against severe disease has been substantially higher than protection against infection with previous variants. We used a test-negative case-control design to estimate VE against hospitalisation with the Omicron and Delta variants using PCR testing linked to hospital records. We investigated the impact of increasing the specificity and severity of hospitalisation definitions on VE. Among 18–64-year-olds using cases admitted via emergency care, VE after a 3rd dose peaked at 82.4% and dropped to 53.6% by 15+ weeks after the 3rd dose; using all admissions for > = 2 days stay with a respiratory code in the primary diagnostic field VE ranged from 90.9% to 67.4%; further restricting to those on oxygen/ventilated/intensive care VE ranged from 97.1% to 75.9%. Among 65+ year olds the equivalent VE estimates were 92.4% to 76.9%; 91.3% to 85.3% and 95.8% to 86.8%. Here we show that with milder Omicron disease contamination of hospitalisations with incidental cases is likely to reduce VE estimates. VE estimates increase, and waning is reduced, when specific hospitalisation definitions are used.
Inverse designed plasmonic metasurface with parts per billion optical hydrogen detection
Authors: Nugroho Ferry Anggoro Ardy , Bai Ping , Darmadi Iwan , Castellanos Gabriel W. , Fritzsche Joachim , Langhammer Christoph , Gómez Rivas Jaime , Baldi Andrea
Published: September 2022

Plasmonic sensors rely on optical resonances in metal nanoparticles and are typically limited by their broad spectral features. This constraint is particularly taxing for optical hydrogen sensors, in which hydrogen is absorbed inside optically-lossy Pd nanostructures and for which state-of-the-art detection limits are only at the low parts-per-million (ppm)range. Here, we overcome this limitation by inversely designing a plasmonic metasurface based on a periodic array of Pd nanoparticles. Guided by a particle swarm optimization algorithm, we numerically identify and experimentally demonstrate a sensor with an optimal balance between a narrow spectral linewidth and a large field enhancement inside the nanoparticles, enabling a measured hydrogen detection limit of 250 parts-per-billion (ppb). Our work significantly improves current plasmonic hydrogen sensor capabilities and, in a broader context, highlights the power of inverse design of plasmonic metasurfaces for ultrasensitive optical (gas) detection.
Continuously processing waste lignin into high-value carbon nanotube fibers
Authors: Liu Fuyao , Wang Qianqian , Zhai Gongxun , Xiang Hengxue , Zhou Jialiang , Jia Chao , Zhu Liping , Wu Qilin , Zhu Meifang
Published: September 2022

High value utilization of renewable biomass materials is of great significance to the sustainable development of human beings. For example, because biomass contains large amounts of carbon, they are ideal candidates for the preparation of carbon nanotube fibers. However, continuous preparation of such fibers using biomass as carbon source remains a huge challenge due to the complex chemical structure of the precursors. Here, we realize continuous preparation of high-performance carbon nanotube fibers from lignin by solvent dispersion, high-temperature pyrolysis, catalytic synthesis, and assembly. The fibers exhibit a tensile strength of 1.33 GPa and an electrical conductivity of 1.19 × 105 S m−1, superior to that of most biomass-derived carbon materials to date. More importantly, we achieve continuous production rate of 120 m h−1. Our preparation method is extendable to other biomass materials and will greatly promote the high value application of biomass in a wide range of fields.
Teaching resources for the European Open Platform for Prescribing Education (EurOP2E)—a nominal group technique study
Authors: Bakkum Michiel J. , Loobeek Bryan J. , Richir Milan C. , Papaioannidou Paraskevi , Likic Robert , Sanz Emilio J. , Christiaens Thierry , Costa João N. , Dima Lorena , de Ponti Fabrizio , Kramers Cornelis , van Smeden Jeroen , van Agtmael Michiel A. , Tichelaar Jelle ,   EurOP²E consortium, de Ponti Fabrizio , van Smeden Jeroen , van Agtmael Michiel A.
Published: September 2022

The European Open Platform for Prescribing Education (EurOP2E) seeks to improve and harmonize European clinical pharmacology and therapeutics (CPT) education by facilitating international collaboration and sharing problem-based, online, open educational resources. The COVID-19 pandemic forced teachers to switch to virtual modalities, highlighting the need for high-quality online teaching materials. The goal of this study was to establish the online problem-based teaching resources needed to sustain prescribing education during the pandemic and thereafter. A nominal group technique study was conducted with prescribing teachers from 15 European countries. Results were analyzed through thematic analysis. In four meetings, 20 teachers from 15 countries proposed and ranked 35 teaching materials. According to the participants, the most necessary problem-based-online teaching materials related to three overarching themes. Related to learning outcomes for CPT, participants proposed creating prescription scenarios, including materials focusing on background knowledge and resources on personalized medicine and topical/ethical issues such as the prescription’s impact on planetary health. Second, related to teaching, they proposed online case discussions, gamification and decision support systems. Finally, in relation to faculty development, they recommend teacher courses, a repository of reusable exam questions and harmonized formularies. Future work will aim to collaboratively produce such materials.
A synchronized multimodal neuroimaging dataset for studying brain language processing
Authors: Wang Shaonan , Zhang Xiaohan , Zhang Jiajun , Zong Chengqing
Published: September 2022

We present a synchronized multimodal neuroimaging dataset for studying brain language processing (SMN4Lang) that contains functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG) data on the same 12 healthy volunteers while the volunteers listened to 6 hours of naturalistic stories, as well as high-resolution structural (T1, T2), diffusion MRI and resting-state fMRI data for each participant. We also provide rich linguistic annotations for the stimuli, including word frequencies, syntactic tree structures, time-aligned characters and words, and various types of word and character embeddings. Quality assessment indicators verify that this is a high-quality neuroimaging dataset. Such synchronized data is separately collected by the same group of participants first listening to story materials in fMRI and then in MEG which are well suited to studying the dynamic processing of language comprehension, such as the time and location of different linguistic features encoded in the brain. In addition, this dataset, comprising a large vocabulary from stories with various topics, can serve as a brain benchmark to evaluate and improve computational language models.
D-dimer, a predictor of bad outcome in gastric cancer patients undergoing radical resection
Authors: Zhang Xin , Wang Xuan , Li Wenxing , Sun Tuanhe , Dang Chengxue , Diao Dongmei
Published: September 2022

As a marker of hypercoagulability, plasma D-dimer is associated with progression of many cancers but remains controversial in gastric cancer (GC). We aim to investigate the predictive value of D-dimer for postoperative outcomes after radical gastrectomy of GC patients. We enrolled 903 consecutive patients with GC who underwent radical gastrectomy and the clinicopathological characteristics were compared. Risk factors for overall survival (OS) and disease-free survival (DFS) were determined using multivariate cox regression analysis. We also compared the survival difference based on Kaplan–Meier method after a one-to-one propensity score matching (PSM). Patients with elevated D-dimer had older age (p < 0.001), advanced TNM stage (p < 0.001), larger tumor size (p = 0.005), lower 5-year OS rate (32.8% vs 62.6%, p < 0.001) and DFS (29% vs 59.6%, p < 0.001). In multivariate analysis, elevated D-dimer was independently associated with shorter OS [hazard ratio (HR): 1.633, 95% confidence interval (CI) 1.178–2.264, p = 0.003] and DFS (HR: 1.58, 95% CI 1.151–2.169, P = 0.005). After PSM, the 5-year OS rate of patients with elevated D-dimer was still significantly lower than matched group (32.8% vs 40.6%, p = 0.005), so was DFS (29% vs 36.6%, p = 0.008). Preoperative elevated D-dimer is an independent risk factor for GC patients undergoing curative gastrectomy.
Physical interpretation of nonlocal quantum correlation through local description of subsystems
Authors: Pramanik Tanumoy , Chen Xiaojiong , Xiang Yu , Li Xudong , Mao Jun , Bao Jueming , Deng Yaohao , Dai Tianxiang , Tang Bo , Yang Yan , Li Zhihua , Gong Qihuang , He Qiongyi , Wang Jianwei
Published: September 2022

Characterization and categorization of quantum correlations are both fundamentally and practically important in quantum information science. Although quantum correlations such as non-separability, steerability, and non-locality can be characterized by different theoretical models in different scenarios with either known (trusted) or unknown (untrusted) knowledge of the associated systems, such characterization sometimes lacks unambiguous to experimentalist. In this work, we propose the physical interpretation of nonlocal quantum correlation between two systems. In the absence of complete local description of one of the subsystems quantified by the local uncertainty relation, the correlation between subsystems becomes nonlocal. Remarkably, different nonlocal quantum correlations can be discriminated from a single uncertainty relation derived under local hidden state (LHS)–LHS model only. We experimentally characterize the two-qubit Werner state in different scenarios.
miR-30c plays diagnostic and prognostic roles and mediates epithelial–mesenchymal transition (EMT) and proliferation of gliomas by affecting Notch1
Authors: Li Mengkao , Liu Wenzhi , Li Jian , Zhang Hong , Xu Jin
Published: September 2022

miR-30c functions as a tumor suppressor gene in the majority of tumors, including gliomas. In our study, we discovered that the expression levels of miR-30c in glioma tissues and plasma prior to surgery were lower than those in normal brain tissue following brain injury decompression and in plasma in healthy volunteers. The low expression of miR-30c was closely aligned with the WHO grade, tumor size, PFS, and OS. Additionally, the miR-30c expression level in tumor tissue was positively correlated with the levels in preoperative plasma. In cell biology experiments, miR-30c inhibited EMT and proliferation, migration, and invasion of glioma cells. Analysis of databases of miRNA target genes, real-time quantitative PCR, western blotting, and dual luciferase reporter assays demonstrated that Notch1 is the direct target gene of miR-30c. An inhibitor and shRNA-Notch1 were cotransfected into glioma cells, and it was found that shRNA-Notch1 reduced the enhancement of inhibitors of EMT and proliferation, migration, and invasion of glioma cells. Therefore, we believe that when utilized as a tumor suppressor gene, miR-30c can inhibit EMT and the proliferation, migration, and invasion of glioma cells by directly acting on Notch1 at the posttranscriptional level and that it is a potential diagnostic and prognostic marker.
Phylogeography and colonization pattern of subendemic round-leaved oxeye daisy from the Dinarides to the Carpathians
Authors: Konowalik Kamil
Published: September 2022

The Carpathians are an important biodiversity hotspot and a link between mountain ranges on the European continent. This study investigated the phylogeography of one the Carpathian subendemics,Leucanthemum rotundifolium, which is distributed throughout the range and in one isolated population outside it. Range-wide sampling was used to examine phylogeographic patterns by sequencing uniparentally inherited chloroplast markers that exemplify seed dispersal. Reconstruct Ancestral State in Phylogenies (RASP) software, Bayesian binary Markov Chain Monte Carlo (BBM) analysis, and ecological niche modeling based on concatenated results of five algorithms were used to infer migration routes and examine links with other species through phylogeny. The round-leaved oxeye daisy is an example of organisms that reached the Carpathians through a southern “Dacian” migration route, most probably through long-distance dispersal. Dating placed the events in the Pleistocene and supported migrations during cooler periods and stasis/isolation followed by separation in the interglacials. Haplotype diversification indicated that afterL. rotundifoliumreached the area around the Fagaras Mountains, several migration events occurred leading to colonization of the Southern Carpathians followed by migration to the Apuseni Mountains, the Eastern Carpathians, and finally the Western Carpathians. The results are consistent with previous phylogeographic studies in this region and indicate several novel patterns.
Experimental infection of aquatic bird bornavirus in Muscovy ducks
Authors: Iverson Melanie , Leacy Alexander , Pham Phuc H. , Che Sunoh , Brouwer Emily , Nagy Eva , Lillie Brandon N. , Susta Leonardo
Published: September 2022

Aquatic bird bornavirus (ABBV-1), an avian bornavirus, has been reported in wild waterfowl from North America and Europe that presented with neurological signs and inflammation of the central and peripheral nervous systems. The potential of ABBV-1to infect and cause lesions in commercial waterfowl species is unknown. The aim of this study was to determine the ability of ABBV-1 to infect and cause disease in day-old Muscovy ducks (n = 174), selected as a representative domestic waterfowl. Ducklings became infected with ABBV-1 through both intracranial and intramuscular, but not oral, infection routes. Upon intramuscular infection, the virus spread centripetally to the central nervous system (brain and spinal cord), while intracranial infection led to virus spread to the spinal cord, kidneys, proventriculus, and gonads (centrifugal spread). Infected birds developed both encephalitis and myelitis by 4 weeks post infection (wpi), which progressively subsided by 8 and 12 wpi. Despite development of microscopic lesions, clinical signs were not observed. Only five birds had choanal and/or cloacal swabs positive for ABBV-1, suggesting a low potential of Muscovy ducks to shed the virus. This is the first study to document the pathogenesis of ABBV-1 in poultry species, and confirms the ability of ABBV-1 to infect commercial waterfowl.
Benefits of sustained physical activity from middle age to early old age on quality of life in early old age
Authors: Lee Mikyung , Lee Hyeonkyeong , Song Kijun , Lee Young-Me
Published: September 2022

This study aimed to examine changes in physical activity (PA) over time (2009–2017) in the same participants and to determine an association between changes in PA and health-related quality of life (HRQoL) in early older adults (n = 994) using data from the Korea Health Panel Survey. HRQoL was measured using the EuroQol system, and the amount of PA was grouped into four activity levels: remained inactive, became inactive, became active, and remained active. The association of changes in PA over 8 years with HRQoL was examined using logistic regression analysis while controlling for socioeconomic and behavioral factors. Total PA decreased from 1859.72 ± 1760.01 MET-minutes in 2009 to 1264.80 ± 1251.14 MET-minutes in 2017 (P < 0.001). In 2017, 142 (14.3%) remained inactive, whereas 419 (42.2%) remained active. Participants who remained inactive in early old age were more likely to be in the lowest 10% HRQoL of the sample (odds ratio = 1.95, 95% confidence interval = 1.09–3.48). These findings indicate that health education and promotion must be prioritized for middle-aged adults, who are relatively inactive, so that they increase their current PA and improve their HRQoL to maximize the benefits of PA in old age.
Morphological and anatomical characterization of yellow diploid potato flower for effective breeding program
Authors: de los Angeles Bohórquez-Quintero María , Galvis-Tarazona Daicy Yaneth , Arias-Moreno Diana Marcela , Ojeda-Peréz Zaida Zarely , Ochatt Sergio , Rodríguez-Molano Luis Ernesto
Published: September 2022

The diploid yellow potato (Solanum tuberosum L. Phureja Group) is an important plant genetic resource. In this study, we report for the first time the characterization of anther development and pollen formation in the cultivar Criolla Colombia. The description of morphological and histological characters of buds and flowers at different developmental stages permitted to identify ten main stages, from the differentiation of the male cells of the sporangium, meiosis, microspores formation and maturation, to the release of mature pollen. In addition, the results provide a graphic guide of the development of the anther, through the sequential and orderly formation of the epidermis, the endothecium, the middle layer and the nutritive layer or tapetum. This microanatomical information will be useful for work focused on androgenesis and identification of gene regulation in floral biology and gamete formation. Therefore, this study determined that to efficiently obtain haploids, flower buds between 5 and 8.9 mm long (stage 6 to 8) should be used, in which tetrads and microspores are in the early uninucleate and binucleate stage.
Novel electro-oxidation unit for electro-disinfection of E. coli and some waterborne pathogens during wastewater treatment: batch and continuous experiments
Authors: Hellal Mohamed S. , Hemdan Bahaa A. , Youssef Marwa , El-Taweel Gamila E. , Abou Taleb Enas M.
Published: September 2022

The prime objective of the current investigation is to evaluate a promising alternative method for disinfection wastewater using a novel electro-oxidation unit. The study focused on determining the best-operating conditions from a techno-economic point of view to be applied to continuous flow simulating actual disinfection modules. The treatment unit consisted of a Plexiglas container with a 3 L volume containing nine cylindrical shape electrodes (6 graphite as anode and 3 stainless steel as a cathode) connected to a variable DC power supply. Determination of the best operating parameters was investigated in batch mode on synthetic wastewater by studying the effect of contact time, current density (CD), total dissolved solids concentration (TDS), and bacterial density. Moreover, the continuous mode experiment was considered on real wastewater from an agricultural drain and the secondary wastewater treatment plant effluent before chlorination. The batch mode results revealed that the best applicable operational conditions that achieved the complete removal of E. coli were at a contact time of less than 5 min, TDS of 2000 mg/L, and CD of 4 mA/cm2. Application of these conditions on the continuous mode experiment indicated the complete removal of all bacterial indicators after 5 min in the drainage wastewater and after 3 min in the secondary treated wastewater. Physico-chemical characterization also suggested that no chlorine by-products displaying the hydroxide ion formed due to water electrolysis is the main reason for prohibiting the growth of pathogenic microbes. The electrical consumption was calculated in the continuous mode and found to be 0.5 kWh/m3 with an operational cost of about 0.06 $/m3, including the cost of adding chemicals to increase the TDS. The results proved that this novel electro-oxidation unit is a robust and affordable disinfection method for complete bacterial removal from wastewater and is more environmentally benign than other conventional disinfection methods.
siRNA-mediated gene knockdown via electroporation in hydrozoan jellyfish embryos
Authors: Masuda-Ozawa Tokiha , Fujita Sosuke , Nakamura Ryotaro , Watanabe Hiroshi , Kuranaga Erina , Nakajima Yu-ichiro
Published: September 2022

As the sister group to bilaterians, cnidarians stand in a unique phylogenetic position that provides insight into evolutionary aspects of animal development, physiology, and behavior. While cnidarians are classified into two types, sessile polyps and free-swimming medusae, most studies at the cellular and molecular levels have been conducted on representative polyp-type cnidarians and have focused on establishing techniques of genetic manipulation. Recently, gene knockdown by delivery of short hairpin RNAs into eggs via electroporation has been introduced in two polyp-type cnidarians, Nematostella vectensis and Hydractinia symbiolongicarpus, enabling systematic loss-of-function experiments. By contrast, current methods of genetic manipulation for most medusa-type cnidarians, or jellyfish, are quite limited, except for Clytia hemisphaerica, and reliable techniques are required to interrogate function of specific genes in different jellyfish species. Here, we present a method to knock down target genes by delivering small interfering RNA (siRNA) into fertilized eggs via electroporation, using the hydrozoan jellyfish, Clytia hemisphaerica and Cladonema paciificum. We show that siRNAs targeting endogenous GFP1 and Wnt3 in Clytia efficiently knock down gene expression and result in known planula phenotypes: loss of green fluorescence and defects in axial patterning, respectively. We also successfully knock down endogenous Wnt3 in Cladonema by siRNA electroporation, which circumvents the technical difficulty of microinjecting small eggs. Wnt3 knockdown in Cladonema causes gene expression changes in axial markers, suggesting a conserved Wnt/β-catenin-mediated pathway that controls axial polarity during embryogenesis. Our gene-targeting siRNA electroporation method is applicable to other animals, including and beyond jellyfish species, and will facilitate the investigation and understanding of myriad aspects of animal development.
On Curie temperature of B20-MnSi films
Authors: Li Zichao , Yuan Ye , Begeza Viktor , Rebohle Lars , Helm Manfred , Nielsch Kornelius , Prucnal Slawomir , Zhou Shengqiang
Published: September 2022

B20-type MnSi is the prototype magnetic skyrmion material. Thin films of MnSi show a higher Curie temperature than their bulk counterpart. However, it is not yet clear what mechanism leads to the increase of the Curie temperature. In this work, we grow MnSi films on Si(100) and Si(111) substrates with a broad variation in their structures. By controlling the Mn thickness and annealing parameters, the pure MnSi phase of polycrystalline and textured nature as well as the mixed phase of MnSi and MnSi1.7 are obtained. Surprisingly, all these MnSi films show an increased Curie temperature of up to around 43 K. The Curie temperature is likely independent of the structural parameters within our accessibility including the film thickness above a threshold, strain, cell volume and the mixture with MnSi1.7. However, a pronounced phonon softening is observed for all samples, which can tentatively be attributed to slight Mn excess from stoichiometry, leading to the increased Curie temperature.
Th1/Th2 polarization of peripheral immune response in atherothrombotic and cardioembolic stroke: a prospective study
Authors: Bellavia Simone , Scala Irene , Rizzo Pier Andrea , Brunetti Valerio , Broccolini Aldobrando , Della Marca Giacomo , Calabresi Paolo , Frisullo Giovanni
Published: September 2022

Compelling evidence suggest a key role of immune system in the development and progression of ischemic stroke. Although the balance between proinflammatory CD4 + T helper (Th)-1 lymphocytes, expressing T-bet transcription factor, and anti-inflammatory Th2 cells expressing GATA3 seems to influence the outcome in experimental stroke, the role of peripheral immune response in acute stroke patients is poorly understood. We aimed to evaluate the peripheral Th1/Th2 balance in acute atherothrombotic (ATHS) and cardioembolic stroke (CES) patients and in age- and sex-matched healthy subjects. Using flow cytometry, we analyzed the percentage of CD4 + T-bet + T cells and CD4 + GATA3 + T cells from peripheral blood of ATHS and CES patients (2,4 and 7 days after stroke onset). Patients and controls were screened for infectious conditions, autoimmune, inflammatory, or cancerous diseases. On day 2 circulating CD4 + T-bet + T cells were significantly higher in stroke patients compared to controls, and in ATHS compared to CES and controls. On day 7, we observed a significant increase of CD4 + T-bet + T cells in both ATHS and CES patients compared to baseline. No difference was observed in circulating CD4 + GATA3 + T cells among ATHS, CES patients, and controls. These data suggest that circulating CD4 + T-bet + T cells could be useful marker indicating atherothrombotic genesis of stroke and provide new insight into the peripheral adaptive immune response in acute stroke.
Study of cattle microbiota in different regions of Kazakhstan using 16S metabarcoding analysis
Authors: Daugaliyeva Aida , Daugaliyeva Saule , Ashanin Alexander , Kanatbayev Serik , Beltramo Chiara , Peletto Simone
Published: September 2022

Methane (CH4) is an important greenhouse gas (GHG). Enteric methane emissions from farmed ruminant livestock account for approximately 15% of global GHG emissions, with approximately 44% of livestock emissions in the form of methane. The purpose of the research is to study the influence of feeding types and regional characteristics of Kazakhstan on the microbiota of feces and the number of methane-forming archaea of beef and meat-and-dairy cattle productivity. For this purpose, fecal samples were taken rectally from 37 cattle heads from four regions of Kazakhstan (Western, Southern, Northern and Southeast). The taxonomic composition of the community in all samples was determined by 16S metabarcoding; additionally alpha and beta diversities were calculated. The dominant phyla were: Firmicutes (57.30%), Bacteroidetes (17.00%), Verrucomicrobia (6.88%), Euryarchaeota (6.49%), Actinobacteria (4.77%) and Patescibacteria (3.38%). Significant differences with regard to methanogens bacteria were found: Euryarchaeota were less present in animals from Western Kazakhstan (2.40%), while Methanobacteriales and Methanobrevibacter were prevalent in Southeast, and less abundant in Western region. Western Kazakhstan differs from the other regions likely because animals are mainly grazed in the pasture. Thus, grazing animals has an impact on their microbiota thus leading to a decrease in methane emissions.
Crystal structures of FNIP/FGxxFN motif-containing leucine-rich repeat proteins
Authors: Huyton Trevor , Jaiswal Mamta , Taxer Waltraud , Fischer Matthias , Görlich Dirk
Published: September 2022

The Cafeteria roenbergensis virus (Crov), Dictyostelium, and other species encode a large family of leucine-rich repeat (LRR) proteins with FGxxFN motifs. We determined the structures of two of them and observed several unique structural features that set them aside from previously characterized LRR family members. Crov588 comprises 25 regular repeats with a LxxLxFGxxFNQxIxENVLPxx consensus, forming a unique closed circular repeat structure. Novel features include a repositioning of a conserved asparagine at the middle of the repeat, a double phenylalanine spine that generates an alternate core packing arrangement, and a histidine/tyrosine ladder on the concave surface. Crov539 is smaller, comprising 12 repeats of a similar LxxLxFGxxFNQPIExVxW/LPxx consensus and forming an unusual cap-swapped dimer structure. The phenylalanine spine of Crov539 is supplemented with a tryptophan spine, while a hydrophobic isoleucine-rich patch is found on the central concave surface. We present a detailed analysis of the structures of Crov588 and Crov539 and compare them to related repeat proteins and other LRR classes.
Panels of mRNAs and miRNAs for decoding molecular mechanisms of Renal Cell Carcinoma (RCC) subtypes utilizing Artificial Intelligence approaches
Authors: Hosseiniyan Khatibi Seyed Mahdi , Ardalan Mohammadreza , Teshnehlab Mohammad , Vahed Sepideh Zununi , Pirmoradi Saeed
Published: September 2022

Renal Cell Carcinoma (RCC) encompasses three histological subtypes, including clear cell RCC (KIRC), papillary RCC (KIRP), and chromophobe RCC (KICH) each of which has different clinical courses, genetic/epigenetic drivers, and therapeutic responses. This study aimed to identify the significant mRNAs and microRNA panels involved in the pathogenesis of RCC subtypes. The mRNA and microRNA transcripts profile were obtained from The Cancer Genome Atlas (TCGA), which were included 611 ccRCC patients, 321 pRCC patients, and 89 chRCC patients for mRNA data and 616 patients in the ccRCC subtype, 326 patients in the pRCC subtype, and 91 patients in the chRCC for miRNA data, respectively. To identify mRNAs and miRNAs, feature selection based on filter and graph algorithms was applied. Then, a deep model was used to classify the subtypes of the RCC. Finally, an association rule mining algorithm was used to disclose features with significant roles to trigger molecular mechanisms to cause RCC subtypes. Panels of 77 mRNAs and 73 miRNAs could discriminate the KIRC, KIRP, and KICH subtypes from each other with 92% (F1-score ≥ 0.9, AUC ≥ 0.89) and 95% accuracy (F1-score ≥ 0.93, AUC ≥ 0.95), respectively. The Association Rule Mining analysis could identify miR-28 (repeat count = 2642) and CSN7A (repeat count = 5794) along with the miR-125a (repeat count = 2591) and NMD3 (repeat count = 2306) with the highest repeat counts, in the KIRC and KIRP rules, respectively. This study found new panels of mRNAs and miRNAs to distinguish among RCC subtypes, which were able to provide new insights into the underlying responsible mechanisms for the initiation and progression of KIRC and KIRP. The proposed mRNA and miRNA panels have a high potential to be as biomarkers of RCC subtypes and should be examined in future clinical studies.
Spatio-temporal dynamics of phytoplankton community in a well-mixed temperate estuary (Sado Estuary, Portugal)
Authors: Santos M. , Amorim A. , Brotas V. , Cruz J. P. C. , Palma C. , Borges C. , Favareto L. R. , Veloso V. , Dâmaso-Rodrigues M. L. , Chainho P. , Félix P. M. , Brito A. C.
Published: September 2022

Estuaries are highly productive ecosystems, which are strongly affected by several anthropogenic pressures. Phytoplankton is a key element for assessing the ecological quality status in these transitional waters. Moreover, understanding physico-chemical and biological drivers is crucial to disentangle their effect on the structure of phytoplankton community. The present work aims to study the effect of the main physico-chemical drivers on the phytoplankton community structure and dynamics in a temperate well-mixed estuary (Sado Estuary). Four sampling stations were analyzed monthly in three regions of the estuary, from 2018 to 2019. Surface water samples were collected to analyze the phytoplankton community and several concomitant physico-chemical parameters. Temperature, turbidity, salinity, and nutrients availability were the drivers that best explained the spatio-temporal patterns observed in the phytoplankton community. The upper estuary was characterized by higher phytoplankton cell abundances and biomass. Three phytoplankton groups stood out in the characterization of the estuarine assemblages: diatoms, cryptophytes, and dinoflagellates. Diatoms were the dominant group most of the year, being dominated by small cell species (single and chain-forming) upstream, and by larger chain-forming species downstream. Cryptophytes had a high contribution to the community in the inner regions of the estuary, while dinoflagellates contributed more for the community composition downstream, where high abundances of harmful algal species were sporadically found. Previous studies on the phytoplankton community dynamics in this estuary are limited to the 1990s. Thus, the present study provides insight into changes in the dominant phytoplankton groups of the Sado Estuary in the last 25 years, namely an increase in cryptophytes over diatoms in the inner estuarine regions, and an increase in dinoflagellates near the estuary mouth.
Minimizing complications following transinguinal preperitoneal modified Kugel mesh herniorrhaphy: a double blind prospective randomized clinical trial
Authors: Chiang Heng-Chieh , Lin Jesun , Chen Jian-Ting , Hsu Yu-Chi , Chen Pao-Hwa
Published: September 2022

Transinguinal preperitoneal (TIPP) single-layer mesh herniorrhaphy has been proven effective. Mesh manufacturers make either a single-unit, two-layer mesh design or a separate optional onlay with the pre-peritoneal mesh. For peace of mind, most surgeons still incorporate the optional onlay. This study evaluated any counterproductive effects of adding the onlay to single-layer TIPP mesh herniorrhaphy and compared the long-term efficacy. This prospective, single-surgeon, single-center, randomized trial compared two groups of 50 consecutive patients at a 1 to 1 ratio. The control group received a single-layer modified Kugel mesh in the preperitoneal space, while the study group received the optional onlay mesh in the inguinal canal with preperitoneal mesh placement. A single surgeon performed the same operation to place the preperitoneal mesh in both groups, the only difference being the placement of the optional onlay mesh in the study group. A blinded researcher performed post-operative interviews using a series of questions at 1, 3, 6, and 12 months after surgery, and another unblinded researcher organized and performed statistical analysis of the peri-operative and post-operative data. The primary endpoints included foreign body sensation, pain, and any other discomfort in the inguinal region following surgery; and the secondary endpoints included recurrence and any complications related to surgery. The patient demographics were similar between the two groups. The average follow-up period was 29 months. Two patients in the 1-layer group and one patient in the 2-layer group were lost to follow-up. Postoperative pain, numbness and soreness were similar between groups. No patients experienced a foreign body sensation after 3 months in the 1-layer group, while five patients still had a foreign body sensation at 12 months in the 2-layer group. No recurrence was noted in either group during the follow-up period. Adequate dissection of the preperitoneal space is the key to a successful single-layer TIPP herniorrhaphy. With decreased materials in the inguinal canal, single-layer TIPP has a lower rate of long-term postoperative discomfort without increasing the risk of future recurrence.

Trial registration: ISRCTN 47111213
Obesity affects pulmonary function in Japanese adult patients with asthma, but not those without asthma
Authors: Tashiro Hiroki , Takahashi Koichiro , Kurihara Yuki , Sadamatsu Hironori , Kuwahara Yuki , Tajiri Ryo , Kimura Shinya , Sueoka-Aragane Naoko
Published: September 2022

Obesity is associated with the severity of asthma, which is characterized by airway obstruction. Pulmonary function testing is one of the important examinations for evaluating airway obstruction. However, the impact of obesity on pulmonary function in patients with asthma is not fully understood. A total of 193 patients with asthma and 2159 patients without asthma who visited Saga University Hospital were investigated retrospectively. Obesity was defined as a body mass index (BMI) greater than 25 kg/m2. Pulmonary functions including forced vital capacity (FVC) and forced expiratory volume in 1 s (FEV1) were compared between patients with and without asthma, focusing especially on obesity. FVC percent predicted and FEV1 percent predicted were significantly lower in patients with asthma than in those without asthma (p = 0.03, < 0.01 respectively). In patients with asthma, FVC percent predicted and FEV1 percent predicted were significantly lower in patients with obesity than in those without obesity (all p < 0.01). In addition, BMI was negatively correlated with FEV1 (r =− 0.21, p = 0.003) and FVC (r = − 0.15, p = 0.04), along with the percent predicted. On multivariate analysis in patients with asthma, FVC (β [95% confidence interval] 0.12 [0.02–0.22], p = 0.02) and FEV1 (0.13 [0.05–0.22], p < 0.01) were still significantly different between patients with and without obesity. However, these obesity-associated differences were not observed in patients without asthma. Obesity reduces pulmonary function, including FVC and FEV1, in patients with asthma, but not in those without asthma.
Association between testosterone levels and bone mineral density in females aged 40–60 years from NHANES 2011–2016
Authors: Zhang Han , Ma Kun , Li Run-Min , Li Jia-Ni , Gao Shan-Feng , Ma Lin-Na
Published: September 2022

Growing evidence indicates that testosterone is a conspicuous marker for assessing male bone mineral density (BMD). However, research regarding testosterone levels and BMD is sparse and controversial for females. Hence, we aimed to investigate the association between testosterone levels and BMD among adult females aged 40–60 years in the United States. In this cross-sectional study, all participants were part of the National Health and Nutrition Examination Survey (2011–2016). A weighted general linear model was used to estimate the association between testosterone levels and lumbar BMD. Age, race, income level, education level, body mass index (BMI), blood urea nitrogen (BUN) level, serum uric acid (UA) level, serum calcium (Ca) level, serum phosphorus (P) level, the use of oral contraceptive pills, the use of hormone replacement therapy (HRT), smoking status, drinking status, and the use of corticosteroids were adjusted using a weighted multiple regression model. Subgroup analyses were performed using the same regression model. We included 2198 female participants in the study, and testosterone levels were positively associated with lumbar BMD after adjusting for all the covariates (β = 1.12, 95% CI 0.31, 1.93). In subgroup analyses, the associations in the fourth quartile of testosterone levels were stronger for the participants aged 40–50 years old (quartile 4, β = 42.92, 95% CI 7.53, 78.30 vs. quartile 1) and 50 to 60-year-old (quartile 4, β = 32.41, 95% CI 0.14, 64.69 vs. quartile 1). Similar results were found in other subgroups, including subgroups for race (Non-Hispanic Black, Other), income level (income ≤ 1.3, income > 3.5), education level (college or higher), BMI > 25 kg/m2, BUN levels ≤ 20 mg/dL, UA levels ≤ 6 mg/dL, Ca levels ≤ 10.1 mg/dL, P levels ≤ 5 mg/dL, drinking status, never smoker, never taking birth control pills, and HRT user. There was no interaction among the covariates in the association between lumbar BMD and testosterone levels (P for interaction > 0.05). In US adult females aged 40–60 years, the testosterone level was a positive predictor of the lumbar BMD after adjusting for covariates.
Machine learning to improve the interpretation of intercalating dye-based quantitative PCR results
Authors: Godmer A. , Bigot J. , Giai Gianetto Q. , Benzerara Y. , Veziris N. , Aubry A. , Guitard J. , Hennequin C.
Published: September 2022

This study aimed to evaluate the contribution of Machine Learning (ML) approach in the interpretation of intercalating dye-based quantitative PCR (IDqPCR) signals applied to the diagnosis of mucormycosis. The ML-based classification approach was applied to 734 results of IDqPCR categorized as positive (n = 74) or negative (n = 660) for mucormycosis after combining “visual reading” of the amplification and denaturation curves with clinical, radiological and microbiological criteria. Fourteen features were calculated to characterize the curves and injected in several pipelines including four ML-algorithms. An initial subset (n = 345) was used for the conception of classifiers. The classifier predictions were combined with majority voting to estimate performances of 48 meta-classifiers on an external dataset (n = 389). The visual reading returned 57 (7.7%), 568 (77.4%) and 109 (14.8%) positive, negative and doubtful results respectively. The Kappa coefficients of all the meta-classifiers were greater than 0.83 for the classification of IDqPCR results on the external dataset. Among these meta-classifiers, 6 exhibited Kappa coefficients at 1. The proposed ML-based approach allows a rigorous interpretation of IDqPCR curves, making the diagnosis of mucormycosis available for non-specialists in molecular diagnosis. A free online application was developed to classify IDqPCR from the raw data of the thermal cycler output (http://gepamy-sat.asso.st/).