bluuebunny/crossref_metadata_2025_split huggingface dataset:
FAM3D is essential for colon homeostasis and host defense against inflammation associated carcinogenesis
Authors: Liang Weiwei , Peng Xinjian , Li Qingqing , Wang Pingzhang , Lv Ping , Song Quansheng , She Shaoping , Huang Shiyang , Chen Keqiang , Gong Wanghua , Yuan Wuxing , Thovarai Vishal , Yoshimura Teizo , O’huigin Colm , Trinchieri Giorgio , Huang Jiaqiang , Lin Shuye , Yao Xiaohong , Bian Xiuwu , Kong Wei , Xi Jianzhong , Wang Ji Ming , Wang Ying 
Published: November 2020

AbstractThe physiological homeostasis of gut mucosal barrier is maintained by both genetic and environmental factors and its impairment leads to pathogenesis such as inflammatory bowel disease. A cytokine like molecule, FAM3D (mouse Fam3D), is highly expressed in mouse gastrointestinal tract. Here, we demonstrate that deficiency in Fam3D is associated with impaired integrity of colonic mucosa, increased epithelial hyper-proliferation, reduced anti-microbial peptide production and increased sensitivity to chemically induced colitis associated with high incidence of cancer. Pretreatment of Fam3D−/− mice with antibiotics significantly reduces the severity of chemically induced colitis and wild type (WT) mice co-housed with Fam3D−/− mice phenocopy Fam3D-deficiency showing increased sensitivity to colitis and skewed composition of fecal microbiota. An initial equilibrium of microbiota in cohoused WT and Fam3D−/− mice is followed by an increasing divergence of the bacterial composition after separation. These results demonstrate the essential role of Fam3D in colon homeostasis, protection against inflammation associated cancer and normal microbiota composition.
Optical probes of molecules as nano-mechanical switches
Authors: Kos Dean , Di Martino Giuliana , Boehmke Alexandra , de Nijs Bart , Berta Dénes , Földes Tamás , Sangtarash Sara , Rosta Edina , Sadeghi Hatef , Baumberg Jeremy J. 
Published: November 2020

AbstractMolecular electronics promises a new generation of ultralow-energy information technologies, based around functional molecular junctions. Here, we report optical probing that exploits a gold nanoparticle in a plasmonic nanocavity geometry used as one terminal of a well-defined molecular junction, deposited as a self-assembled molecular monolayer on flat gold. A conductive transparent cantilever electrically contacts individual nanoparticles while maintaining optical access to the molecular junction. Optical readout of molecular structure in the junction reveals ultralow-energy switching of ∼50 zJ, from a nano-electromechanical torsion spring at the single molecule level. Real-time Raman measurements show these electronic device characteristics are directly affected by this molecular torsion, which can be explained using a simple circuit model based on junction capacitances, confirmed by density functional theory calculations. This nanomechanical degree of freedom is normally invisible and ignored in electrical transport measurements but is vital to the design and exploitation of molecules as quantum-coherent electronic nanodevices.
Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes
Authors: Niu Yiming , Suzuki Hiroshi , Hosford Christopher J. , Walz Thomas , Chappie Joshua S. 
Published: November 2020

AbstractMcrBC complexes are motor-driven nucleases functioning in bacterial self-defense by cleaving foreign DNA. The GTP-specific AAA + protein McrB powers translocation along DNA and its hydrolysis activity is stimulated by its partner nuclease McrC. Here, we report cryo-EM structures of Thermococcus gammatolerans McrB and McrBC, and E. coli McrBC. The McrB hexamers, containing the necessary catalytic machinery for basal GTP hydrolysis, are intrinsically asymmetric. This asymmetry directs McrC binding so that it engages a single active site, where it then uses an arginine/lysine-mediated hydrogen-bonding network to reposition the asparagine in the McrB signature motif for optimal catalytic function. While the two McrBC complexes use different DNA-binding domains, these contribute to the same general GTP-recognition mechanism employed by all G proteins. Asymmetry also induces distinct inter-subunit interactions around the ring, suggesting a coordinated and directional GTP-hydrolysis cycle. Our data provide insights into the conserved molecular mechanisms governing McrB family AAA + motors.
Understanding sex differences in long-term outcomes after a first episode of psychosis
Authors: Ayesa-Arriola Rosa , de la Foz Víctor Ortíz-García , Setién-Suero Esther , Ramírez-Bonilla María Luz , Suárez-Pinilla Paula , Son Jacqueline Mayoral-van , Vázquez-Bourgon Javier , Juncal-Ruiz María , Gómez-Revuelta Marcos , Tordesillas-Gutiérrez Diana , Crespo-Facorro Benedicto 
Published: November 2020

AbstractWhile sex differences in schizophrenia have long been reported and discussed, long-term sex differences in outcomes among first episode of psychosis (FEP) patients in terms of the efficacy of Early Intervention Services (EIS) has been an under-explored area. A total of 209 FEP patients (95 females and 114 males) were reassessed after a time window ranging from 8 to 16 years after their first contact with an EIS program (PAFIP) that we will call the 10-year PAFIP cohort. Multiple clinical, cognitive, functioning, premorbid, and sociodemographic variables were explored at 1-year, 3-year and 10-year follow-ups. At first contact, females were older at illness onset, had higher premorbid adjustment and IQ, and were more frequently employed, living independently, and accompanied by a partner and/or children. Existence of a schizophrenia diagnosis, and cannabis and alcohol consumption were more probable among men. During the first 3 years, women showed a significantly better response to minimal antipsychotic dosages and higher rates of recovery than men (50% vs. 30.8%). Ten years later, more females continued living independently and had partners, while schizophrenia diagnoses and cannabis consumption continued to be more frequent among men. Females also presented a lower severity of negative symptoms; however, functionality and recovery differences did not show significant differences (46.7% vs. 34.4%). Between the 3- and 10-year follow-up sessions, an increase in dosage of antipsychotics was observed. These results suggest that the better outcomes seen among women during the first 3 years (while they were treated in an EIS) were in the presence of more favourable premorbid and baseline characteristics. After an average period of 10 years, with the only difference being in negative symptoms course, outcomes for women approximated those of men, drawing particular attention to the increase in dosage of antipsychotic medication once FEP patients were discharged from the EIS program towards community-based services. These findings help to pose the question of whether it is advisable to target sexes and lengthen EIS interventions.
Induction of TOC and TIC genes during photomorphogenesis is mediated primarily by cryptochrome 1 in Arabidopsis
Authors: Fukazawa Hitoshi , Tada Akari , Richardson Lynn G. L. , Kakizaki Tomohiro , Uehara Susumu , Ito-Inaba Yasuko , Inaba Takehito 
Published: November 2020

AbstractThe majority of genes encoding photosynthesis-associated proteins in the nucleus are induced by light during photomorphogenesis, allowing plants to establish photoautotrophic growth. Therefore, optimizing the protein import apparatus of plastids, designated as the translocon at the outer and inner envelope membranes of chloroplast (TOC–TIC) complex, upon light exposure is a prerequisite to the import of abundant nuclear-encoded photosynthesis-associated proteins. However, the mechanism that coordinates the optimization of the TOC–TIC complex with the expression of nuclear-encoded photosynthesis-associated genes remains to be characterized in detail. To address this question, we investigated the mechanism by which plastid protein import is regulated by light during photomorphogenesis in Arabidopsis. We found that the albino plastid protein import2 (ppi2) mutant lacking Toc159 protein import receptors have active photoreceptors, even though the mutant fails to induce the expression of photosynthesis-associated nuclear genes upon light illumination. In contrast, many TOC and TIC genes are rapidly induced by blue light in both WT and the ppi2 mutant. We uncovered that this regulation is mediated primarily by cryptochrome 1 (CRY1). Furthermore, deficiency of CRY1 resulted in the decrease of some TOC proteins in vivo. Our results suggest that CRY1 plays key roles in optimizing the content of the TOC–TIC apparatus to accommodate the import of abundant photosynthesis-associated proteins during photomorphogenesis.
Comparing the permeability of human and porcine small intestinal mucus for particle transport studies
Authors: Krupa Lukasz , Bajka Balazs , Staroń Robert , Dupont Didier , Singh Harjinder , Gutkowski Krzysztof , Macierzanka Adam 
Published: November 2020

AbstractThe gastrointestinal mucus layer represents the last barrier between ingested food or orally administered pharmaceuticals and the mucosal epithelium. This complex gel structure plays an important role in the process of small intestinal absorption. It provides protection against hazardous particles such as bacteria but allows the passage of nutrients and drug molecules towards the intestinal epithelium. In scientific research, mucus from animal sources is usually used to simulate difficult-to-obtain human small intestinal mucus for investigating the intramucus transport of drug delivery systems or food nanoparticles. However, there is a lack of evidence the human mucus can be reliably substituted by animal counterparts for human-relevant transport models. In this report, a procedure for collecting human mucus has been described. More importantly, the permeability characteristics of human and porcine small intestinal mucus secretions to sub-micron sized particles have been compared under simulated intestinal conditions. Negatively charged, 500 nm latex beads were used in multiple-particle tracking experiments to examine the heterogeneity and penetrability of mucus from different sources. Diffusion of the probe particles in adult human ileal mucus and adult pig jejunal and ileal mucus revealed no significant differences in microstructural organisation or microviscosity between the three mucus types (P > 0.05). In contrast to this interspecies similarity, the intraspecies comparison of particle diffusivity in the mucus obtained from adult pigs vs. 2-week old piglets showed better penetrability of the piglet mucus. The mean Stokes–Einstein viscosity of the piglet jejunal mucus was approx. two times lower than the viscosity of the pig jejunal mucus (P < 0.05). All mucus structures were also visualised by scanning electron microscopy. This work validates the use of porcine small intestinal mucus collected from fully-grown pigs for studying colloidal transport of sub-micron sized particles in mucus under conditions mimicking the adult human small intestinal environment.
Lesions in the right Rolandic operculum are associated with self-rating affective and apathetic depressive symptoms for post-stroke patients
Authors: Sutoko Stephanie , Atsumori Hirokazu , Obata Akiko , Funane Tsukasa , Kandori Akihiko , Shimonaga Koji , Hama Seiji , Yamawaki Shigeto , Tsuji Toshio 
Published: November 2020

AbstractStroke survivors majorly suffered from post-stroke depression (PSD). The PSD diagnosis is commonly performed based on the clinical cut-off for psychometric inventories. However, we hypothesized that PSD involves spectrum symptoms (e.g., apathy, depression, anxiety, and stress domains) and severity levels. Therefore, instead of using the clinical cut-off, we suggested a data-driven analysis to interpret patient spectrum conditions. The patients’ psychological conditions were categorized in an unsupervised manner using the k-means clustering method, and the relationships between psychological conditions and quantitative lesion degrees were evaluated. This study involved one hundred sixty-five patient data; all patients were able to understand and perform self-rating psychological conditions (i.e., no aphasia). Four severity levels—low, low-to-moderate, moderate-to-high, and high—were observed for each combination of two psychological domains. Patients with worse conditions showed the significantly greater lesion degree at the right Rolandic operculum (part of Brodmann area 43). The dissimilarities between stress and other domains were also suggested. Patients with high stress were specifically associated with lesions in the left thalamus. Impaired emotion processing and stress-affected functions have been frequently related to those lesion regions. Those lesions were also robust and localized, suggesting the possibility of an objective for predicting psychological conditions from brain lesions.
Quantitative optimization of drainage strategy of coalbed methane well based on the dynamic behavior of coal reservoir permeability
Authors: Yan Xinlu , Zhang Songhang , Tang Shuheng , Li Zhongcheng , Zhang Qian , Wang Jingyu , Deng Zhiyu 
Published: November 2020

AbstractThe development of coalbed methane (CBM) is not only affected by geological factors, but also by engineering factors, such as artificial fracturing and drainage strategies. In order to optimize drainage strategies for wells in unique geological conditions, the characteristics of different stages of CBM production are accurately described based on the dynamic behavior of the pressure drop funnel and coal reservoir permeability. Effective depressurization is achieved by extending the pressure propagation radius and gas desorption radius to the well-controlled boundary, in the single-phase water flow stage and the gas–water flow stage, respectively, with inter-well pressure interference accomplished in the single-phase gas flow stage. A mathematic model was developed to quantitatively optimize drainage strategies for each stage, with the maximum bottom hole flow pressure (BHFP) drop rate and the maximum daily gas production calculated to guide the optimization of CBM production. Finally, six wells from the Shizhuangnan Block in the southern Qinshui Basin of China were used as a case study to verify the practical applicability of the model. Calculation results clearly indicate the differences in production characteristics as a result of different drainage strategies. Overall, if the applied drainage strategies do not achieve optimal drainage results, the coal reservoir could be irreversibly damaged, which is not conducive to expansion of the pressure drop funnel. Therefore, this optimization model provides valuable guidance for rational CBM drainage strategy development and efficient CBM production.
Robust alternative to the righting reflex to assess arousal in rodents
Authors: Gao Sijia , Calderon Diany Paola 
Published: November 2020

AbstractThe righting reflex (RR) is frequently used to assess level of arousal and applied to animal models of a range of neurological disorders. RR produces a binary result that, when positive, is used to infer restoration of consciousness, often without further behavioral corroboration. We find that RR is an unreliable metric for arousal/recovery of consciousness. Instead, cortical activity and motor behavior that accompany RR are a non-binary, superior criterion that accurately calibrates and establishes level of arousal in rodents.
Plant health status effects on arbuscular mycorrhizal fungi associated with Lavandula angustifolia and Lavandula intermedia infected by Phytoplasma in France
Authors: Binet Marie- Noëlle , Marchal Camille , Lipuma Justine , Geremia Roberto A. , Bagarri Olivier , Candaele Bert , Fraty Delphine , David Benjamin , Perigon Sophie , Barbreau Viviane , Mouhamadou Bello 
Published: November 2020

AbstractWe investigated root communities of arbuscular mycorrhizal fungi (AMF) in relation to lavender (Lavandula angustifolia) and lavandin (Lavandula intermedia) health status from organic and conventional fields affected by Phytoplasma infection. The intensity of root mycorrhizal colonization was significantly different between diseased and healthy plants and was higher in the latter regardless of agricultural practice. This difference was more pronounced in lavender. The root AMF diversity was influenced by the plant health status solely in lavender and only under the conventional practice resulting in an increase in the AMF abundance and richness. The plant health status did not influence the distribution of root AMF communities in lavandin unlike its strong impact in lavender in both agricultural practices. Finally, among the most abundant molecular operational taxonomic units (MOTUs), four different MOTUs for each plant species were significantly abundant in the roots of healthy lavender and lavandin in either agricultural practice. Our study demonstrated that the plant health status influences root colonization and can influence the diversity and distribution of root AMF communities. Its effects vary according to plant species, can be modified by agricultural practices and allow plants to establish symbiosis with specific AMF species.
Serum pentraxin 3 as a biomarker of hepatocellular carcinoma in chronic hepatitis B virus infection
Authors: Deng Huan , Fan Xiude , Wang Xiaoyun , Zeng Lu , Zhang Kun , Zhang Xiaoge , Li Na , Han Qunying , Lv Yi , Liu Zhengwen 
Published: November 2020

AbstractBiomarkers for early diagnosis of hepatocellular carcinoma (HCC) are needed in chronic hepatitis B virus (HBV) infection, a leading cause of HCC. We evaluated whether measurement of serum pentraxin 3 (PTX3) could improve diagnosis of HCC in chronic HBV infection. Data from patients with HBV-related chronic hepatitis (n = 159), cirrhosis (n = 99) and HCC (n = 107), and healthy controls (n = 151) were analyzed. Serum PTX3 concentration was measured by immunoassay. Area under the receiver operating characteristic curve (AUC) was applied to assess diagnostic accuracy. PTX3 levels were significantly higher in HBV patients than in healthy controls (P < 0.001) and in HCC than in chronic hepatitis (P < 0.001) or cirrhosis patients (P < 0.001). PTX3 was an independent risk factor of HCC [odds ratio (OR) 1.617,P < 0.001] and could distinguish HCC in chronic HBV infection [cutoff 9.231 ng/mL, AUC 0.929 with 95% confidence interval (CI) of 0.898–0.953], including α-fetoprotein (AFP) negative [cutoff 8.985 ng/mL, AUC (95%CI) 0.947 (0.908–0.973)] and early-stage HCC [cutoff 9.359 ng/mL, AUC (95%CI) 0.920 (0.885–0.947)]. Combination of PTX3 with AFP improved the discrimination of early HCC from chronic HBV infection [AUC (95%CI) 0.948 (0.918–0.970)]. In short, PTX3 measurement could identify HCC, including AFP-negative and early-stage HCC, in chronic HBV infection.
Identification and quantification of target metabolites combined with transcriptome of two rheum species focused on anthraquinone and flavonoids biosynthesis
Authors: Liu Jing , Leng Liang , Liu Yan , Gao Han , Yang Wei , Chen Sha , Liu An 
Published: November 2020

AbstractRheum emodi is a perennial herb and an important medicinal plant, with anthraquinones and flavonoids as its main bioactive compounds. However, there is little knowledge about the biosynthetic pathway of anthraquinones in rhubarbs. In this study, we qualitatively and quantitatively assessed 62 pharmacological metabolites in rhubarb using dynamic multiple reaction monitoring (dMRM) of triple-quadrupole mass spectrometry (QqQ-MS), including 21 anthraquinones, 17 flavonoids, 6 stilbenes, 12 gallate esters, 3 tannins, and 3 others. Besides, the metabolomics results showed significant differences among all the 60 metabolites, except for gallic acid and piceatannol-O-β-glucoside. The combined transcriptome data of R. palmatum L. (RPL) and R. officinale Baill. (ROB) showed that 21,691 unigenes were annotated in the metabolic pathways. Taken together, 17 differentially expressed genes (DEGs) were associated with the anthraquinone biosynthetic pathway. Additionally, a significant correlation between anthraquinone peak intensity and DEG expression level existed, validating that DEGs contribute to the anthraquinone biosynthetic pathway. RT-qPCR results showed that the cluster-14354.38156 gene may catalyze the O-methylation of emodin to produce physcion. This study provides a useful resource for further studies on secondary metabolism in rhubarb and the combination analysis of transcriptome and metabolome, which can help with the discovery of enzyme genes involved in metabolite biosynthesis.
Computer-aided diagnosis of pectus excavatum using CT images and deep learning methods
Authors: Lai Lixuan , Cai Siqi , Huang Luyu , Zhou Haiyu , Xie Longhan 
Published: November 2020

AbstractPectus excavatum (PE) is one of the most common chest wall defects. Accurate assessment of PE deformities is critical for effective surgical intervention. Index-based evaluations have become the standard for objectively estimating PE, however, these indexes cannot represent the whole information of chest CT images and may associated with significant error due to the individual differences. To overcome these limitations, this paper developed a computer-aided diagnosis (CAD) system based on the convolutional neural network (CNN) to automatically learn discriminative features and classify PE images. We also adopted block-wise fine-tuning methods based on the transfer learning strategy to reduce the potential risk of overfitting caused by limited data and experimentally explored the best fine-tuning degree. Our method achieved a high level of classification accuracy with 94.76% for PE diagnosis. Furthermore, we proposed a majority rule-based voting method to provide a comprehensively diagnostic results for each patient, which integrated the classification results of the whole thorax. The promising results support the feasibility of our proposed CNN-based CAD system for automatic PE diagnosis, which paves a way for comprehensive assessments of PE in clinics.
Blackbody-cavity ideal absorbers for solar energy harvesting
Authors: Tian Yanpei , Liu Xiaojie , Ghanekar Alok , Chen Fangqi , Caratenuto Andrew , Zheng Yi 
Published: November 2020

AbstractSpectrally selective solar absorbers (SSAs), which harvest heat from sunlight, are the key to concentrated solar thermal systems. An ideal SSA must have an absorptivity of unity in the solar irradiance wavelength region (0.3–2.5 $$\upmu $$
μ
m), and its infrared thermal emissivity must be zero to depress spontaneous blackbody irradiation (2.5–25 $$\upmu $$
μ
m). Current SSA designs which utilize photonic crystals, metamaterials, or cermets are either cost-inefficient due to the complexity of the required nanofabrication methods, or have limited applicability due to poor thermal stability at high temperatures. We conceptually present blackbody-cavity solar absorber designs with nearly ideal spectrally selective properties, capable of being manufactured at scale. The theoretical analyses show that the unity solar absorptivity of the blackbody cavity and nearly zero infrared emissivity of the SSA’s outer surface allow for a stagnation temperature of 880 $$^\circ $$

∘

C under 10 suns. The performance surpasses state-of-the-art SSAs manufactured using nanofabrication methods. This design relies only on traditional fabrication methods, such as machining, casting, and polishing. This makes it suitable for large-scale industrial applications, and the “blackbody cavity” feature enables easy integration with existing concentrated solar thermal systems using the parabolic reflector and Fresnel lens as optical concentrators.