bluuebunny/crossref_metadata_2025_split huggingface dataset:
3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal
Authors: Chen Pin , Wang Yu , Yan Hui , Gao Sen , Xu Zexin , Li Yangzhong , Mo Qing , Huang Junkang , Tao Jun , Pan GeChuanqi , Li Jiahui , Du Yunfei 
Published: January 2020

Abstract
Background
The increasing number of organic and inorganic structures promotes the development of the “Big Data” in chemistry and material science, and raises the need for cross-platform and web-based methods to search, view and edit structures. Many web-based three-dimensional (3D) structure tools have been developed for displaying existing models, building new models, and preparing initial input files for external calculations. But few of these tools can deal with crystal structures.

Results
We developed a user-friendly and versatile program based on standard web techniques, such as Hyper Text Markup Language 5 (HTML5), Cascade Style Sheet (CSS) and JavaScript. Both non-periodic organic molecule and crystal structure can be visualized, built and edited interactively. The atom, bond, angle and dihedral in a molecule can be viewed and modified using sample mouse operations. A wide range of cheminformatics algorithms for crystal structure are provided, including cleaving surfaces, establishing vacuum layers, and building supercells. Four displayed styles, namely “Primitive cell”, “Original”, “In-cell” and “Packing” can be used to visualize a unit cell. Additionally, the initial input files for Vienna Ab-initio Simulation Package (VASP) and Gaussian can be obtained by interacting with dialog boxes in 3DStructGen.

Conclusions
3DStructGen is a highly platform-independent program. It can provide web service independently or can be integrated into other web platforms. Other than local desktop software, it does not require any additional effort to install the system but a web browser supporting HTML5. 3DStructGen may play a valuable role in online chemistry education and pre-processing of quantum calculations. The program has been released under MIT open-source license and is available on: https://matgen.nscc-gz.cn/Tools.html.
Low-dose 18F-FDG TOF-PET/MR for accurate quantification of brown adipose tissue in healthy volunteers
Authors: ter Voert Edwin E. G. W. , Svirydenka Hanna , Müller Julian , Becker Anton S. , Balaz Miroslav , Efthymiou Vissarion , Maushart Claudia Irene , Gashi Gani , Wolfrum Christian , Betz Matthias J. , Burger Irene A. 
Published: January 2020

Abstract
Background
Positron emission tomography (PET) is increasingly applied for in vivo brown adipose tissue (BAT) research in healthy volunteers. To limit the radiation exposure, the injected 18F-FDG tracer dose should be as low as possible. With simultaneous PET/MR imaging, the radiation exposure due to computed tomography (CT) can be avoided, but more importantly, the PET acquisition time can often be increased to match the more extensive magnetic resonance (MR) imaging protocol. The potential gain in detected coincidence counts, due to the longer acquisition time, can then be applied to decrease the injected tracer dose. The aim of this study was to investigate the minimal 18F-FDG dose for a 10-min time-of-flight (TOF) PET/MR acquisition that would still allow accurate quantification of supraclavicular BAT volume and activity.

Methods
Twenty datasets from 13 volunteers were retrospectively included from a prospective clinical study. PET emission datasets were modified to simulate step-wise reductions of the original 75 MBq injected dose. The resulting PET images were visually and quantitatively assessed and compared to a 4-min reference scan. For the visual assessment, the image quality and artifacts were scored using a 5-point and a 3-point Likert scale. For the quantitative analysis, image noise and artifacts, BAT metabolic activity, BAT metabolic volume (BMV), and total BAT glycolysis (TBG) were investigated.

Results
The visual assessment showed still good image quality for the 35%, 30%, and 25% activity reconstructions with no artifacts. Quantitatively, the background noise was similar to the reference for the 35% and 30% activity reconstructions and the artifacts started to increase significantly in the 25% and lower activity reconstructions. There was no significant difference in supraclavicular BAT metabolic activity, BMV, and TBG between the reference and the 35% to 20% activity reconstructions.

Conclusions
This study indicates that when the PET acquisition time is matched to the 10-min MRI protocol, the injected 18F-FDG tracer dose can be reduced to approximately 19 MBq (25%) while maintaining image quality and accurate supraclavicular BAT quantification. This could decrease the effective dose from 1.4 mSv to 0.36 mSv.
Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota
Authors: Chijiiwa Rieka , Hosokawa Masahito , Kogawa Masato , Nishikawa Yohei , Ide Keigo , Sakanashi Chikako , Takahashi Kai , Takeyama Haruko 
Published: January 2020

Abstract

Background
The gut microbiota can have dramatic effects on host metabolism; however, current genomic strategies for uncultured bacteria have several limitations that hinder their ability to identify responders to metabolic changes in the microbiota. In this study, we describe a novel single-cell genomic sequencing technique that can identify metabolic responders at the species level without the need for reference genomes, and apply this method to identify bacterial responders to an inulin-based diet in the mouse gut microbiota.

Results
Inulin-feeding changed the mouse fecal microbiome composition to increase Bacteroides spp., resulting in the production of abundant succinate in the mouse intestine. Using our massively parallel single-cell genome sequencing technique, named SAG-gel platform, we obtained 346 single-amplified genomes (SAGs) from mouse gut microbes before and after dietary inulin supplementation. After quality control, the SAGs were classified as 267 bacteria, spanning 2 phyla, 4 classes, 7 orders, and 14 families, and 31 different strains of SAGs were graded as high- and medium-quality draft genomes. From these, we have successfully obtained the genomes of the dominant inulin-responders, Bacteroides spp., and identified their polysaccharide utilization loci and their specific metabolic pathways for succinate production.

Conclusions
Our single-cell genomics approach generated a massive amount of SAGs, enabling a functional analysis of uncultured bacteria in the intestinal microbiome. This enabled us to estimate metabolic lineages involved in the bacterial fermentation of dietary fiber and metabolic outcomes such as short-chain fatty acid production in the intestinal environment based on the fibers ingested. The technique allows the in-depth isolation and characterization of uncultured bacteria with specific functions in the microbiota and could be exploited to improve human and animal health.
Lessons from the welding booth: theories in practice in vocational education
Authors: Asplund Stig-Börje , Kilbrink Nina 
Published: January 2020

AbstractThis article reports results from a Learning study in which two university based researchers collaborate with a vocational teacher at an upper secondary vocational school. During three iterative cycles, two different theories (Conversational Analysis and Variation Theory) have gradually been incorporated when teaching how to TIG-weld. Through concrete empirical examples from video recorded lessons the article explores how these theoretical perspectives (termed CAVTA) can be used together and integrated in practice when analysing the teaching and learning processes that take shape when teacher and students interact in relation to the object of learningto TIG-weld,and how these theories can be used as didactical tools. The analyses highlights concrete changes in the teacher’s teaching, and it is argued that the approach used in the study can lead to a development where we can find forms for teaching specific subject content within vocational education.
Comparison of microwave drying and oven-drying techniques for moisture determination of three paddy (Oryza sativa L.) varieties
Authors: Nirmaan A. M. C. , Rohitha Prasantha B. D. , Peiris B. L. 
Published: January 2020

Abstract
Background
The standard method for grain moisture measurement is the conventional air oven-drying technique. This method requires a longer period of time to determine the moisture content (m.c.). Although electric moisture meters are popular in rice industries, it has to be calibrated frequently with the oven-drying method. Therefore, an alternative but fast and reliable method is required, especially, for the grain marketing industries.

Results
Three different sizes of paddy (Oryza sativa L.) samples (Bg 300-intermediate bold, Bg 358-short round and At 405-long slender) were used for this study. Five different moisture levels (12–20% wet basis) were prepared by adding known amounts of water. Relationship between the microwave oven and hot air oven moisture values were evaluated using Pearson, Spearman and Kendall correlation coefficient methods. The linear regression relationship was also established between hot air oven and microwave oven moisture determination methods. According to the data, except for 870 W of absorbed MW power setting level, the other two MW power setting (265 W and 550 W) showed a significant statistical correlation (r > 0.55, P < 0.01) between the air oven and MW oven m.c. values of the three paddy samples. However, MW settings of 550 W for 7 min of absorbed power indicated a significantly higher regression coefficient of determination (r2 = 0.94, P < 0.01) with air oven m.c. values.

Conclusion
From the study, it can be concluded that the domestic microwave oven can be successfully used to determine the moisture content of different paddy varieties as an alternative method to the conventional air oven-drying method.
PSMA PET for primary lymph node staging of intermediate and high-risk prostate cancer: an expedited systematic review
Authors: Petersen Lars J. , Zacho Helle D. 
Published: January 2020

Abstract
Background
PSMA PET is a promising method for primary lymph node staging in prostate cancer. However, recent systematic reviews have identified only a limited number of studies with histopathology as a reference test.

Methods
A systematic search was performed in PubMed and the Cochrane Library. An expedited systematic review was performed where we identified diagnostic studies in prostate cancer where a preoperative PSMA PET for primary lymph node staging was compared to histopathology. The trials must have diagnostic data on a patient level.

Results
Eighteen eligible clinical trials included 969 patients. The median patient number per study was 32 (range 10 to 208). Five trials were prospective, and nine trials had a consecutive enrolment of patients. Sixteen studies used Ga-68-PSMA-11; there was one study with Cu-64-PSMA and one study with F-18-DCDFPyL. Twelve studies used PET/CT, four trials used PET/MR. Most trials included patients with intermediate and high-risk. Diagnostic accuracy varied notably among the studies; sensitivity ranged from 23 to 100%, specificity 67–100%, positive predictive value 20–100%, and negative predictive value 41–100%. Weighted sensitivity was 59%, weighted specificity was 93%. Four studies compared PSMA PET with anatomical imaging (CT or MRI); in all cases, sensitivity and specificity were superior with PSMA PET. Three studies compared PSMA PET with multi-parametric or diffusion-weighted MRI with mixed results.

Conclusions
PSMA PET showed promising diagnostic accuracy for primary lymph node staging with pathology as reference. Recommendation for PSMA PET for high-risk patients in clinical guidelines should be supported by confirmatory, prospective trials with patient-relevant outcomes.
Dosimetry after peptide receptor radionuclide therapy: impact of reduced number of post-treatment studies on absorbed dose calculation and on patient management
Authors: Chicheportiche Alexandre , Ben-Haim Simona , Grozinsky-Glasberg Simona , Oleinikov Kira , Meirovitz Amichay , Gross David J. , Godefroy Jeremy 
Published: January 2020

Abstract
Background
After each cycle of [177Lu]-DOTA-TATE peptide receptor radionuclide therapy (PRRT) dosimetry is performed to enable precise calculation of the radiation-absorbed dose to tumors and normal organs. Absorbed doses are routinely calculated from three quantitative single-photon emission computed tomography (SPECT) studies corrected by computed tomography (CT) acquired at t1 = 24 h, t2 = 96 h, and t3 = 168 h after the first cycle of treatment. After following cycles, a single SPECT/CT study is performed. The aim of the present study is to assess the feasibility of a “two time point” quantitative SPECT/CT protocol after the first PRRT cycle and its impact on patient management.
Quantitative SPECT/CT data of 25 consecutive patients with metastatic neuroendocrine tumors after PRRT were retrospectively analyzed. Radiation-absorbed doses calculated using the standard protocol with three SPECT/CT studies acquired at (t1, t2, t3) were compared to those obtained from three different “two time point” protocols with SPECT/CT studies performed at (t1, t2), (t1, t3), or (t2, t3).

Results
The best agreement for the cumulative doses absorbed by the kidneys, bone marrow, liver, spleen, and tumors with the conventional protocol was obtained with the (t1, t3) protocol with mean relative differences of − 1.0% ± 2.4%, 0.4% ± 3.1%, − 0.9% ± 4.0%, − 0.8% ± 1.1%, and − 0.5% ± 2.0%, respectively, and correlation coefficients of r = 0.99 for all.
In all patients, there was no difference in the management decision of whether or not to stop PRRT because of unsafe absorbed dose to risk organs using either the standard protocol or the (t1, t3) protocol.

Conclusion
These preliminary results demonstrate that dosimetry calculations using two quantitative SPECT/CT studies acquired at 24 and 168 h after the first PRRT cycle are feasible and are in good agreement with the standard imaging protocol with no change in patient management decisions, while enabling improved patient comfort and reduced scanner and staff time.
Review on carbon storage estimation of forest ecosystem and applications in China
Authors: Sun Wanlong , Liu Xuehua 
Published: January 2020

Abstract
Background
The accuracy in estimating forest ecosystem carbon storage has drawn extensive attention of researchers in the field of global climate change. However, incomparable data sources and various estimation methods have led to significant differences in the estimation of forest carbon storage at large scales.

Methods
In this study, we reviewed fundamental types of forest carbon storage estimation methods and their applications in China.

Results
Results showed that the major forest carbon storage estimation methods were classified into 3 major categories and 15 subcategories focusing on vegetation carbon storage estimation, soil carbon storage estimation, and litter carbon storage estimation, respectively. The application in China showed that there have been 3 development stages of research in China since the 1990s. Studies of forest carbon storage estimation in province scales were conducted more frequently in the northeastern, eastern and southwestern provinces such as Zhejiang, Heilongjiang and Sichuan with high forest coverage or large forest area. Inventory-based methods, soil type method, and biomass model were the main forest estimation methods used in China, focusing on vegetation, soil and litter carbon storage estimation respectively. Total forest carbon storage of China was approximate 28.90 Pg C, and the average vegetation carbon density (42.04 ± 5.39 Mg·ha− 1) was much lower than that of the whole world (71.60 Mg·ha− 1). Vegetation carbon density from average biomass method was the highest (57.07 Mg·ha− 1) through comparing nine types of vegetation carbon storage estimation methods applied during 1989 to 1993.

Conclusions
Many studies on forest carbon storages have been carried out in China at patch scales or regional scales. These efforts enabled the research of forest carbon storage to reach a relatively advanced stage. Meanwhile, the accumulation of massive research data provides the basis for subsequent research work. Some challenges are also existing. This review could provide a reference for more accurate estimation of forest carbon storage in the future.
Educating the new Chinese middle-class youth: the role of quality education on ideas of class and status
Authors: Ponzini Arianna 
Published: January 2020

AbstractThis article attempts to answer the questions: “Why is quality education so important for the new Chinese middle class and what implications does quality education have on ideas of status and social standing?” My efforts to answer these questions are guided by two key concepts: social distinction and capital convertibility, which have been presented and analyzed in the work of Bourdieu. The present article advances a new framework for analyzing the different effects of schooling and youth education on ideas of class and social status for the new Chinese middle class. I do this by exploring different dimensions of cultural capital and their effects on social standing and class membership. My core argument is that youth quality education, which implies the accumulation of cultural capital, and therefore of suzhi, is the strongest driving force affecting middle-class families’ life strategies, as well as their ideas of status. Furthermore, cultural capital is the primary resource that can generate other forms of capital, essential for middle-class reproduction. Ultimately, due to the fact that in China the access to quality education is strongly connected to housing strategies, housing and neighborhood have been selected as the salient lens for analysis.
What biologists want from their chloride reporters – a conversation between chemists and biologists
Authors: Zajac Matthew , Chakraborty Kasturi , Saha Sonali , Mahadevan Vivek , Infield Daniel T. , Accardi Alessio , Qiu Zhaozhu , Krishnan Yamuna 
Published: January 2020

ABSTRACT
Impaired chloride transport affects diverse processes ranging from neuron excitability to water secretion, which underlie epilepsy and cystic fibrosis, respectively. The ability to image chloride fluxes with fluorescent probes has been essential for the investigation of the roles of chloride channels and transporters in health and disease. Therefore, developing effective fluorescent chloride reporters is critical to characterizing chloride transporters and discovering new ones. However, each chloride channel or transporter has a unique functional context that demands a suite of chloride probes with appropriate sensing characteristics. This Review seeks to juxtapose the biology of chloride transport with the chemistries underlying chloride sensors by exploring the various biological roles of chloride and highlighting the insights delivered by studies using chloride reporters. We then delineate the evolution of small-molecule sensors and genetically encoded chloride reporters. Finally, we analyze discussions with chloride biologists to identify the advantages and limitations of sensors in each biological context, as well as to recognize the key design challenges that must be overcome for developing the next generation of chloride sensors.
Bioluminescence induction in the ophiuroid Amphiura filiformis (Echinodermata)
Authors: Mallefet Jerome , Duchatelet Laurent , Coubris Constance 
Published: January 2020

Bioluminescence is a widespread phenomenon in the marine environment. Among luminous substrates, coelenterazine is the most widespread luciferin, found in more than nine phyla. The wide phylogenetic coverage of this light-emitting molecule has led to the hypothesis of its dietary acquisition that was demonstrated in one cnidarian and one lophogastrid shrimp species so far. Within Ophiuroidea, the dominant class of luminous echinoderms, Amphiura filiformis is a model species known to use coelenterazine as substrate of a luciferin / luciferase luminous system.
The aim of this study was to perform a long-term monitoring of A. filiformis luminescent capabilities during captivity. Our results show (i) depletion of luminescent capabilities within five months when the ophiuroid is fed with a coelenterazine-free diet and (ii) a quick recovery of luminescent capabilities when the ophiuroid is fed with coelenterazine-supplemented food. The present work demonstrates for the first time a trophic acquisition of coelenterazine in A. filiformis to maintain light emission capabilities.
Design of Fluorescent Peptide Nucleic Acid Probes Carrying Cyanine Dyes for Targeting Double-Stranded RNAs for Analytical Applications
Authors: Sato Yusuke 
Published: January 2020

Abstract
With the increasing knowledge about the diverse roles of RNAs within cells, much attention has been paid to the development of RNA-binding fluorescent probes for the study of RNA functions. Especially, the probes for double-stranded RNA (dsRNA) structures are highly useful given the importance of the secondary and tertiary RNA structures on their biological functions. This account describes our recent efforts to develop synthetic fluorescent probes based on peptide nucleic acids (PNAs) carrying fluorogenic cyanine dyes for targeting the overhang structures of dsRNAs with a view toward the analysis of the intracellular delivery process of small interfering RNAs. We also describe the design of triplex-forming PNA probes carrying cyanine dye base surrogates for the sequence-selective detection of dsRNAs.
Syntheses and Characterizations of Functional Polycyclic Aromatic Hydrocarbons and Graphene Nanoribbons
Authors: Xu Xiushang , Müllen Klaus , Narita Akimitsu 
Published: January 2020

Abstract
In contrast to zero-bandgap graphene, nanostructures of graphene, such as graphene quantum dots (GQDs) and graphene nanoribbons (GNRs) have open bandgaps due to the quantum confinement effect, and are thus highly interesting for semiconductor applications, for example in nanoelectronics and optoelectronics. While conventional methods cannot provide GQDs and GNRs with chemically precise structures, large polycyclic aromatic hydrocarbon (PAH) molecules can be regarded as atomically precise GQDs. Moreover, extension of the PAH synthesis can lead to GNRs with well-defined chemical structures. In this account, we summarize our recent achievements in our synthetic exploration of PAHs and GNRs with novel structures and properties. For example, we have developed new PAHs having zigzag edges, such as dibenzo[hi,st]ovalene derivatives with strong red luminescence and stimulated emission, which are promising for light-emitting devices and bioimaging applications. We have also accomplished a synthesis of magnetic GNRs through edge functionalization with organic radicals, which can be interesting for spintronic as well as quantum computing applications. Moreover, incorporation of zigzag edges in GNR structures, through on-surface syntheses under ultrahigh (UHV) vacuum conditions, allowed for significant modulations of the electronic structures of GNRs, leading to the emergence of topological quantum phases. On the other hand, we have also explored on-surface synthesis of GNRs without UHV, namely using a setup for chemical vapor deposition (CVD). Scalable fabrication of GNR films could thus be achieved on gold on mica substrates, which could be integrated into field-effect transistor devices. These results highlight the importance of developing novel PAHs and GNRs and their potentials for various applications, including quantum technologies, energy and optoelectronic devices, and bioimaging.