bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional roles of multiple Ton complex genes in a Sphingobium degrader of lignin-derived aromatic compounds
Authors: Fujita Masaya , Yano Shodai , Shibata Koki , Kondo Mizuki , Hishiyama Shojiro , Kamimura Naofumi , Masai Eiji 
Published: November 2021

AbstractTonB-dependent transporters (TBDTs) mediate outer membrane transport of nutrients using the energy derived from proton motive force transmitted from the TonB–ExbB–ExbD complex localized in the inner membrane. Recently, we discovered ddvT encoding a TBDT responsible for the uptake of a 5,5-type lignin-derived dimer in Sphingobium sp. strain SYK-6. Furthermore, overexpression of ddvT in an SYK-6-derivative strain enhanced its uptake capacity, improving the rate of platform chemical production. Thus, understanding the uptake system of lignin-derived aromatics is fundamental for microbial conversion-based lignin valorization. Here we examined whether multiple tonB-, exbB-, and exbD-like genes in SYK-6 contribute to the outer membrane transport of lignin-derived aromatics. The disruption of tonB2–6 and exbB3 did not reduce the capacity of SYK-6 to convert or grow on lignin-derived aromatics. In contrast, the introduction of the tonB1–exbB1–exbD1–exbD2 operon genes into SYK-6, which could not be disrupted, promoted the conversion of β-O-4-, β-5-, β-1-, β-β-, and 5,5-type dimers and monomers, such as ferulate, vanillate, syringate, and protocatechuate. These results suggest that TonB-dependent uptake involving the tonB1 operon genes is responsible for the outer membrane transport of the above aromatics. Additionally, exbB2/tolQ and exbD3/tolR were suggested to constitute the Tol-Pal system that maintains the outer membrane integrity.
Biphasic (5–2%) oxygen concentration strategy significantly improves the usable blastocyst and cumulative live birth rates in in vitro fertilization
Authors: Brouillet Sophie , Baron Chloé , Barry Fatima , Andreeva Aneta , Haouzi Delphine , Gala Anna , Ferrières-Hoa Alice , Loup Vanessa , Anahory Tal , Ranisavljevic Noémie , Gaspari Laura , Hamamah Samir 
Published: November 2021

AbstractOxygen (O2) concentration is approximately 5% in the fallopian tube and 2% in the uterus in humans. A “back to nature” approach could increase in vitro fertilization (IVF) outcomes. This hypothesis was tested in this monocentric observational retrospective study that included 120 couples who underwent two IVF cycles between 2014 and 2019. Embryos were cultured at 5% from day 0 (D0) to D5/6 (monophasic O2 concentration strategy) in the first IVF cycle, and at 5% O2 from D0 to D3 and 2% O2 from D3 to D5/6 (biphasic O2 concentration strategy) in the second IVF cycle. The total and usable blastocyst rates (44.4% vs. 54.8%, p = 0.049 and 21.8% vs. 32.8%, p = 0.002, respectively) and the cumulative live birth rate (17.9% vs. 44.1%, p = 0.027) were significantly higher with the biphasic (5%-2%) O2 concentration strategy. Whole transcriptome analysis of blastocysts donated for research identified 707 RNAs that were differentially expressed in function of the O2 strategy (fold-change > 2, p value < 0.05). These genes are mainly involved in embryo development, DNA repair, embryonic stem cell pluripotency, and implantation potential. The biphasic (5–2%) O2 concentration strategy for preimplantation embryo culture could increase the “take home baby rate”, thus improving IVF cost-effectiveness and infertility management.
Single-cell RNA sequencing reveals differential cell cycle activity in key cell populations during nephrogenesis
Authors: Bais Abha S. , Cerqueira Débora M. , Clugston Andrew , Bodnar Andrew J. , Ho Jacqueline , Kostka Dennis 
Published: November 2021

AbstractThe kidney is a complex organ composed of more than 30 terminally differentiated cell types that all are required to perform its numerous homeostatic functions. Defects in kidney development are a significant cause of chronic kidney disease in children, which can lead to kidney failure that can only be treated by transplant or dialysis. A better understanding of molecular mechanisms that drive kidney development is important for designing strategies to enhance renal repair and regeneration. In this study, we profiled gene expression in the developing mouse kidney at embryonic day 14.5 at single-cell resolution. Consistent with previous studies, clusters with distinct transcriptional signatures clearly identify major compartments and cell types of the developing kidney. Cell cycle activity distinguishes between the “primed” and “self-renewing” sub-populations of nephron progenitors, with increased expression of the cell cycle-related genes Birc5, Cdca3, Smc2 and Smc4 in “primed” nephron progenitors. In addition, augmented expression of cell cycle related genes Birc5, Cks2, Ccnb1, Ccnd1 and Tuba1a/b was detected in immature distal tubules, suggesting cell cycle regulation may be required for early events of nephron patterning and tubular fusion between the distal nephron and collecting duct epithelia.
TGF-β-mediated epithelial–mesenchymal transition and tumor-promoting effects in CMT64 cells are reflected in the transcriptomic signature of human lung adenocarcinoma
Authors: Miyashita Naoya , Enokido Takayoshi , Horie Masafumi , Fukuda Kensuke , Urushiyama Hirokazu , Strell Carina , Brunnström Hans , Micke Patrick , Saito Akira , Nagase Takahide 
Published: November 2021

AbstractEpithelial–mesenchymal transition (EMT) is a cellular process during which epithelial cells acquire mesenchymal phenotypes. Cancer cells undergo EMT to acquire malignant features and TGF-β is a key regulator of EMT. Here, we demonstrate for the first time that TGF-β could elicit EMT in a mouse lung adenocarcinoma cell line. TGF-β signaling activation led to cell morphological changes corresponding to EMT and enhanced the expression of mesenchymal markers and EMT-associated transcription factors in CMT64 lung cancer cells. RNA-sequencing analyses revealed that TGF-β increases expression of Tead transcription factors and an array of Tead2 target genes. TGF-β stimulation also resulted in alternative splicing of several genes including Cd44, tight junction protein 1 (Tjp1), and Cortactin (Cttn). In parallel with EMT, TGF-β enhanced cell growth of CMT64 cells and promoted tumor formation in a syngeneic transplantation model. Of clinical importance, the expression of TGF-β-induced genes identified in CMT64 cells correlated with EMT gene signatures in human lung adenocarcinoma tissue samples. Furthermore, TGF-β-induced gene enrichment was related to poor prognosis, underscoring the tumor-promoting role of TGF-β signaling in lung adenocarcinoma. Our cellular and syngeneic transplantation model would provide a simple and useful experimental tool to study the significance of TGF-β signaling and EMT.
Effects of species and geo-information on the 137Cs concentrations in edible wild mushrooms and plants collected by residents after the Fukushima nuclear accident
Authors: Komatsu Masabumi , Hashimoto Shoji , Matsuura Toshiya 
Published: November 2021

AbstractAfter the accident at the Fukushima Daiichi Nuclear Power Plant (FDNPP), much of the wild and edible mushrooms and plants in the surrounding areas were contaminated with radiocesium (137Cs). To elucidate their concentration characteristics, we analyzed 137Cs radioactivity data in edible forest products brought in for food inspection by the residents of Kawauchi Village, 12–30 km away from the FDNPP, from 2012 to 2019. A Bayesian model to estimate 137Cs concentration was constructed. Parameters of the normalized concentration of species (NCsp) for mushrooms were similar to those of the same species obtained in a previous study. Although NCsp values were highly varied among species, mycorrhizal mushrooms tended to have high NCsp values, followed by saprotrophic mushrooms, and wild edible plants values were low. Also, half of mycorrhizal mushroom species (8 of 16) showed an increasing trend in concentration with time; however, saprotrophic mushrooms and wild plants generally demonstrated a decreasing trend (22 of 24). The model considering the sub-village location information decreased the error of individual samples by 40% compared to the model not considering any location information, indicating that the detailed geo-information improved estimation accuracy. Our results indicate that the radioactivity data from samples collected by local residents can be used to accurately assess internal exposure to radiation due to self-consumption of contaminated wild mushrooms and plants.
Novel role of zonulin in the pathophysiology of gastro-duodenal transit: a clinical and translational study
Authors: Martinez Enid E. , Lan Jinggang , Konno Takumi , Miranda-Ribera Alba , Fiorentino Maria , Mehta Nilesh M. , Fasano Alessio 
Published: November 2021

AbstractWe examined the relationship between zonulin and gastric motility in critical care patients and a translational mouse model of systemic inflammation. Gastric motility and haptoglobin (HP) 2 isoform quantification, proxy for zonulin, were examined in patients. Inflammation was triggered by lipopolysaccharide (LPS) injection inC57Bl/6zonulin transgenic mouse (Ztm) and wildtype (WT) mice as controls, and gastro-duodenal transit was examined by fluorescein-isothiocyanate, 6 and 12 h after LPS-injection. Serum cytokines and zonulin protein levels, and zonulin gastric-duodenal mRNA expression were examined. Eight of 20 patients [14 years, IQR (12.25, 18)] developed gastric dysmotility and were HP2 isoform-producing. HP2 correlated with gastric dysmotility (r = − 0.51, CI − 0.81 to 0.003, p = 0.048). LPS injection induced a time-dependent increase in IL-6 and KC-Gro levels in all mice (p < 0.0001). Gastric dysmotility was reduced similarly in Ztm and WT mice in a time-dependent manner. Ztm had 16% faster duodenal motility than WT mice 6H post-LPS, p = 0.01. Zonulin mRNA expression by delta cycle threshold (dCT) was higher in the stomach (9.7, SD 1.4) than the duodenum (13.9, SD 1.4) 6H post-LPS, p = 0.04. Serum zonulin protein levels were higher in LPS-injected mice compared to vehicle-injected animals in a time-dependent manner. Zonulin correlated with gastric dysmotility in patients. A mouse model had time-dependent gastro-duodenal dysmotility after LPS-injection that paralleled zonulin mRNA expression and protein levels.
The brain’s structural differences between postherpetic neuralgia and lower back pain
Authors: Qiu Jianxing , Du Mengjiao , Yang Junzhe , Lin Zengmao , Qin Naishan , Sun Xiaowei , Li Linling , Zou Rushi , Wei Juan , Wu Bing , Liu Jing , Zhang Zhiguo 
Published: November 2021

AbstractThe purpose is to explore the brain’s structural difference in local morphology and between-region networks between two types of peripheral neuropathic pain (PNP): postherpetic neuralgia (PHN) and lower back pain (LBP). A total of 54 participants including 38 LBP and 16 PHN patients were enrolled. The average pain scores were 7.6 and 7.5 for LBP and PHN. High-resolution structural T1 weighted images were obtained. Both grey matter volume (GMV) and morphological connectivity (MC) were extracted. An independent two-sample t-test with false discovery rate (FDR) correction was used to identify the brain regions where LBP and PHN patients showed significant GMV difference. Next, we explored the differences of MC network between LBP and PHN patients and detected the group differences in network properties by using the two-sample t-test and FDR correction. Compared with PHN, LBP patients had significantly larger GMV in temporal gyrus, insula and fusiform gyrus (p < 0.05). The LBP cohort had significantly stronger MC in the connection between right precuneus and left opercular part of inferior frontal gyrus (p < 0.05). LBP patients had significantly stronger degree in left anterior cingulate gyrus and left rectus gyrus (p < 0.05) while had significantly weaker degree than PHN patients in left orbital part of middle frontal gyrus, left supplementary motor area and left superior parietal lobule (p < 0.05). LBP and PHN patients had significant differences in the brain’s GMV, MC, and network properties, which implies that different PNPs have different neural mechanisms concerning pain modulation.
Identifying subtypes of depression in clinician-annotated text: a retrospective cohort study
Authors: Kung Benson , Chiang Maurice , Perera Gayan , Pritchard Megan , Stewart Robert 
Published: November 2021

AbstractCurrent criteria for depression are imprecise and do not accurately characterize its distinct clinical presentations. As a result, its diagnosis lacks clinical utility in both treatment and research settings. Data-driven efforts to refine criteria have typically focused on a limited set of symptoms that do not reflect the disorder’s heterogeneity. By contrast, clinicians often write about patients in depth, creating descriptions that may better characterize depression. However, clinical text is not commonly used to this end. Here we show that clinically relevant depressive subtypes can be derived from unstructured electronic health records. Five subtypes were identified amongst 18,314 patients with depression treated at a large mental healthcare provider by using unsupervised machine learning: severe-typical, psychotic, mild-typical, agitated, and anergic-apathetic. Subtypes were used to place patients in groups for validation; groups were found to be associated with future outcomes and characteristics that were consistent with the subtypes. These associations suggest that these categorizations are actionable due to their validity with respect to disease prognosis. Moreover, they were derived with automated techniques that might theoretically be widely implemented, allowing for future analyses in more varied populations and settings. Additional research, especially with respect to treatment response, may prove useful in further evaluation.
Microplastics increase susceptibility of amphibian larvae to the chytrid fungus Batrachochytrium dendrobatidis
Authors: Bosch Jaime , Thumsová Barbora , López-Rojo Naiara , Pérez Javier , Alonso Alberto , Fisher Matthew C. , Boyero Luz 
Published: November 2021

AbstractMicroplastics (MPs), a new class of pollutants that pose a threat to aquatic biodiversity, are of increasing global concern. In tandem, the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) causing the disease chytridiomycosis is emerging worldwide as a major stressor to amphibians. We here assess whether synergies exist between this infectious disease and MP pollution by mimicking natural contact of a highly susceptible species (midwife toads, Alytes obstetricans) with a Bd-infected reservoir species (fire salamanders, Salamandra salamandra) in the presence and absence of MPs. We found that MP ingestion increases the burden of infection by Bd in a dose-dependent manner. However, MPs accumulated to a greater extent in amphibians that were not exposed to Bd, likely due to Bd-damaged tadpole mouthparts interfering with MP ingestion. Our experimental approach showed compelling interactions between two emergent processes, chytridiomycosis and MP pollution, necessitating further research into potential synergies between these biotic and abiotic threats to amphibians.
Magnetic composite of γ-Fe2O3 hollow sphere and palladium doped nitrogen-rich mesoporous carbon as a recoverable catalyst for C–C coupling reactions
Authors: Malmir Masoume , Heravi Majid M. , Amiri Zahra , Kafshdarzadeh Kosar 
Published: November 2021

AbstractIn this article, palladated-magnetic nitrogen doped porous carbon was prepared from nano magneticγ-Fe2O3hollow sphere (h-Fe2O3) with high specific surface area and pore volume. To the purpose, initially h-Fe2O3was prepared and covered with glucose via hydrothermal treatment with subsequent polymerization of organic shell. The polymerization of melamine-resorcinol–formaldehyde (MRF) was achieved in the presence of Cl-functionalized glucose coated h-Fe2O3(h-Fe2O3@glu-MRF). Next, the prepared magnetic core–shell hollow sphere was palladated followed by carbonization to yield Pd@h-Fe2O3@C introducing more pores in its structure. The resulted compound, Pd@h-Fe2O3@C, was fully characterized, showing that carbonization process expressively increased the specific surface area. The resulted Pd@h-Fe2O3@C was successfully used for promoting C–C coupling reactions under mild reaction conditions as a heterogeneous catalyst and its activity was compared with some prepared control catalysts. This novel catalyst was magnetically separated simply by a magnet bar and recycled and reused at least in five consecutive runs, without considerable loss of its activity. It is note mentioning that, high recyclability with low Pd leaching are another gains of this protocol.
Optical and magnetic characterization of one-dimensional Cu(ii)-based perovskite: a high UV–Vis–NIR absorber
Authors: Jabeur Wiem , Msalmi Rawia , Korb Marcus , Holub Mariia , Mosconi Edoardo , Čižmár Erik , Tozri Anowar , Althubiti Numa A. , Naïli Houcine 
Published: November 2021

A 1-D Cu(ii)-based perovskite (C5H8N3)[CuCl3], with gap energy “Eg” of 2.21 eV, has been successfully investigated as a good UV–Vis–NIR absorber. The magnetic analysis suggests that this material can be described by the model of S = 1/2 AFM dimers.
COVID-19: The Patients' Perceived Impact on Dental Care
Authors: Amato Alessandra , Iandolo Alfredo , Scelza Giuseppe , Spirito Francesca , Martina Stefano 
Published: November 2021

Abstract
Objectives The present study aims to investigate the effect of the COVID-19 pandemic on people's mental and physical balance, oral hygiene habits, type of diet, perceived safety of returning to the dentist, and aesthetics with the use of masks.
Materials and Methods An online questionnaire was submitted to the Italian population between December 2020 and January 2021. It was sent via online platforms and included 21 questions.
Statistical Analysis Differences in rates were calculated by using the Chi-square test. The level of significance was set at p <0.05.
Results A total of 1,008 individuals completed the questionnaire. About 72% of participants were not concerned about returning to the dentist. Approximately 45% of the individuals intensified their oral hygiene and preventive rules. About 38% of participants increased their carbohydrate intake, while 28% increased their fat consumption. Furthermore, 75% of the participants felt that the mask did not diminish the beauty of their smile.
Conclusions Most participants felt comfortable returning to the dentist but only for more urgent treatment. However, most people reported that they had not stepped up their home oral hygiene measures. The biggest changes in the population's eating habits involved increased carbohydrate and fat consumption. Finally, most participants responded that mask use did not compromise their aesthetics.
Endoscopy in Pregnancy: A Systematic Review
Authors: Pal Partha , Reddy D. Nageshwar , Tandan Manu 
Published: November 2021

AbstractBackground Fetomaternal outcomes are of primary concern for gastrointestinal (GI) endoscopy in pregnancy. We aimed to systematically review the safety and utility of endoscopic procedures in pregnancy.Methods A systematic literature search was performed using PubMed. All original research articles with sample size > 10 involving endoscopy in pregnancy were included for the review along with case report/series describing novel/rare techniques from 1948 to July 2021.Results After screening 12,197 references, 216 citations were found and finally 66 references were included. Esophagogastroduodenoscopy had favorable fetal outcome (>95%) based on two large retrospective studies and a review of case reports. Sclerotherapy and band ligation of varices were safe according to case series. A large nationwide cohort study established safety of endotherapy for nonvariceal bleed. Botulinum toxin and pneumatic dilation in achalasia are only supported by case reports. Percutaneous endoscopic gastrostomy can be useful to support nutrition based on case reports. A retrospective case–control and cohort study with systemic review justified flexible sigmoidoscopy if strongly indicated. Low birth weight was more common when sigmoidoscopy was done in inflammatory bowel disease based on a prospective study. Colonoscopy was considered safe in second trimester based on a case–control study whereas it can be performed otherwise only in presence of strong indication like malignancy. Capsule endoscopy is promising and can be useful in acute small bowel bleeding although risk of capsule retention is unknown. There are no reports of enteroscopy in pregnancy. Twelve retrospective studies and one prospective study showed high success rate of therapeutic endoscopic retrograde cholangiopancreatography (ERCP) (> 90%) in all trimesters and can be performed if strongly indicated. Pregnancy was an independent risk factor for post-ERCP pancreatitis in a large nationwide case–control study. Radiation-free ERCP with wire-guided bile observation, stent-guided or precut sphincterotomy, endoscopic ultrasound (EUS) guidance, and spyscopy have been described. Safety of EUS is limited to case series and can be used in intermediate probability of choledocholithiasis to guide ERCP and endoscopic cystogastrostomy.Conclusion This review concludes that GI endoscopy during pregnancy can be done effectively if strongly indicated with good fetomaternal outcomes. Precautions are advocated during procedures where radiation exposure is expected.
241Am/Be source optimum geometry for DSRS management-based Monte Carlo simulations
Authors: Guembou Shouop Cebastien Joel , Ndontchueng Moyo Maurice , Nguelem Mekongtso Eric Jilbert , Beyala Ateba Jean Felix , Strivay David 
Published: November 2021

The geometry form related to 241Am/Be spontaneous neutron sources has been investigated to evaluate the most optimizing geometry for disused sealed radioactive source (DSRS) disposal. Nine source geometries were assessed: point, disk, sphere 1, sphere 2, sphere 3, cylinder 1, cylinder 2, rectangle 1, and rectangle 2. The most radiological optimizing geometries were found to be the disk, followed by the point source, sphere 1, and cylinder 1, while the rectangle or parallelepiped 2 source forms were the worst cases. Neutron and photon generated fluxes were computed, and the parallelepiped 2 source geometry generated the lower value of flux inversely to the effective dose rate computed in the decision-making area, where it was found to be the highest value. The obtained results were in agreement with the as low as reasonably achievable principle for the exposure rate optimization. The obtained exposure dose rates were found to be &lt;∼2 µSv/h (maximum value on horizontal calculation) and 1.75 µSv/h (maximum value on vertical computation), which are lower than the 2.5 µSv/h acceptable limit for the public area. Whenever possible, the DSRSs should be pressed into a disk form (or a cylindrical form with a small height) before embedding them into the Am1 P60 capsule for disposal purposes. The dose profile for the 241Am/Be source obtained, the neutron flux, and the gamma generated from neutron absorption showed agreement with the expected experimental physical data. The supported data contribute to postulate that Monte Carlo methods are effective computational tools that can be used to select the most effective radioactive waste form for disposal purposes.