bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prompt Gamma based Detection and Discrimination of 2 Neutron Capture Events for NCEPT Dose 3 Quantification
Authors: Chacon Andrew , Kielly Marissa , Rutherford Harley , Franklin Daniel R. , Caracciolo Anita , Buonanno Luca , D’Adda Ilenia , Rosenfeld Anatoly , Guatelli Susanna , Carminati Marco , Fiorini Carlo , Safavi-Naeini Mitra 
Published: December 2021

Abstract
Neutron Capture Enhanced Particle Therapy (NCEPT) boosts the effectiveness of particle therapy by capturing thermal neutrons produced by beam-target nuclear interactions in and around the treatment site, using tumour-specific 10B or 157Gd-based neutron capture agents. Neutron captures release high-LET secondary particles together with prompt gamma photons with energies of 478 keV (10B) or 7.94 MeV (157Gd). A key requirement for NCEPT’s translation is the development of in vivo dosimetry techniques which can measure both the direct ion dose and the dose due to neutron capture. In this work, we report signatures which can be used to discriminate between photons resulting from neutron capture and those originating from other processes. A Geant4 Monte Carlo simulation study into timing and energy thresholds for discrimination of prompt gamma photons resulting from thermal neutron capture during NCEPT was conducted. Three simulated 300×300×300 mm3 cubic PMMA targets were irradiated by 4He or 12C ion beams with a spread out Bragg peak (SOBP) depth range of 60 mm; one target is homogeneous while the others include 10×10×10 mm3 neutron capture inserts (NCIs) of pure 10B or 157Gd located at the distal edge of the SOBP. The arrival times of photons and neutrons entering a simulated 50×50×50 mm3 ideal detector were recorded. The majority of photons resulting from neutron capture were found to arrive at the detector at least 60 ns later than photons created by other processes. A range of candidate detector and thermal neutron shielding materials were simulated, and detections meeting the proposed acceptance criteria (i.e. falling within the target energy window and arriving 60 ns post beam-off) were classified as true or false positives, depending on their origin. The ratio of true / false positives (RTF) was calculated; for targets with 10B and 157Gd NCIs, the detector materials which resulted in the highest RTF were cadmium-shielded CdTe and boron-shielded LSO, respectively. The optimal irradiation period for both carbon and helium ions was 1 µs for the 10B NCI and 1 ms for the 157Gd NCI.
Real Ambient Particulate Matter-Induced Myocardial Hypertrophy and Myocardial Lipotoxicity : Roles of PDGFRβ Methylation
Authors: Zhang Ying , Dun Xinyun , Li Benying , Bao Hongxu , Li Danchuan , Xu Zijian , Ji Angdong , Jin Zhenzhen , Wang Jianxun , Zhang Rong , Chen Rui , Chen Wen , Zheng Yuxin , Cui Lianhua 
Published: December 2021

Abstract
Background: PM exposure can lead to myocardial hypertrophy, with a potential contribution via DNA methylation. Myocardial lipotoxicity is closely related to myocardial hypertrophy. But, myocardial lipotoxicity caused by PM has not been reported. PDGFRβ, a platelet-derived growth factor receptor, is also essential for normal cardiovascular development. However, It is unclear the role of PM-induced PDGFRβ methylation in myocardial hypertrophy and myocardial lipotoxicity. We investigated the effect of PDGFRβ methylation induced by PM on myocardial hypertrophy and myocardial lipotoxicity. Results: PDGFRβ methylation caused by PM decreased PDGFRβ mRNA and protein expression in C57BL/6J mouse hearts. Thus inhibiting gene expression in its downstream pathway, ultimately leading to cardiac hypertrophy. Disturbances of myocardial lipid metabolism caused by PM in AC16 cells and C57BL/6J mouse hearts were also observed. High expression of PDGFRβ in neonatal rat primary cardiomyocytes was found to activate its downstream pathway and ameliorate the effects of PM-induced cardiac hypertrophic activity. At the same time, adenovirus was used to induce high expression of PDGFRβ in C57BL/6J mice. It was found that PDGFRβ not only improved PM-induced cardiac hypertrophy, but also alleviated PM-induced myocardial lipotoxicity. Conclusions: PDGFRβ gene methylation may be one of the potential biomarkers of myocardial hypertrophy induced by PM exposure. And high expression of PDGFRβ may be a potential way to prevent myocardial hypertrophy and cardiac lipid metabolism disorder caused by PM exposure in mice.
An integrated omics analysis reveals the gene expression profiles of rapeseed, castor bean, and maize for seed oil biosynthesis
Authors: Liu Nian , Liu Jing , Fan Shihang , Liu Hongfang , Zhou Xue-Rong , Hua Wei , Zheng Ming 
Published: December 2021

Abstract
Background

Seed storage lipids are valuable for human diet and for the sustainable development of mankind. In recent decades, many lipid metabolism genes and pathways have been identified, but the molecular mechanisms that underlie species differences in seed oil biosynthesis are not fully understood.
Results

To investigate the molecular mechanisms of seed oil accumulation in different species, we performed comparative genome and transcriptome analyses of rapeseed and castor bean, which have high seed oil contents, and maize, which has a low seed oil content. The results uncovered the molecular mechanism of the low and high seed oil content in maize and castor bean, respectively. Transcriptome analyses showed that more than 61% of the lipid- and carbohydrate-related genes were regulated in rapeseed and castor bean, but only 20.1% of the lipid-related genes and 22.5% of the carbohydrate-related genes were regulated in maize. Compared to rapeseed and castor bean, fewer lipid biosynthesis genes but more lipid metabolism genes were regulated in the maize embryo. More importantly, most maize genes encoding lipid-related transcription factors, triacylglycerol (TAG) biosynthetic enzymes, pentose phosphate pathway (PPP) and Calvin Cycle proteins were not regulated during seed oil synthesis, despite the presence of many homologs in the maize genome. These results revealed the molecular underpinnings of the low seed oil content in maize. In castor bean, we observed differential regulation of vital oil biosynthetic enzymes and extremely high expression levels of oil biosynthetic genes, which were consistent with the rapid accumulation of oil in castor bean developing seeds.
Conclusions

Compared to oil seed (rapeseed and castor bean), less oil biosynthetic genes were regulated during the seed development in non-oil seed (maize). These results shed light on molecular mechanisms of lipid biosynthesis in rapeseed, castor bean, and maize. They can provide information on key target genes that may be useful for future experimental manipulation of oil production in oilseed crops.
Organic Matter Decomposition in River Ecosystems: the Role of Microbial Interactions Regulated by Environmental Factors
Authors: Liu Yibo , Zhang Baiyu , Zhang Yixin , Shen Yanping , Cheng Cheng , Yuan Weilin , Guo Ping 
Published: December 2021

Abstract
Microbes are the critical contributors to the organic matter decomposition (OMD) in river ecosystems. However, the role of microbial interactions on the OMD in river ecosystems and the regulation of environmental factors to the microbial interactions were not considered previously thus tacked in this study. Cotton strip (CS) as a substitute for organic matter was introduced to Luanhe River Basin in China. The results indicated that CS selectively enriched bacterial and fungal groups related to cellulose decomposition, leading to the cotton strip decomposition (CSD). In these groups, bacterial phyla Proteobacteria, fungal phyla Rozellomycota and Ascomycota were the dominant groups associated with the CSD. Bacteria and fungi on CS cooperatively formed a co-occurrence network to achieve the CSD. In the network, the key modules 2 and 4, mainly composed of phyla Proteobacteria and Ascomycota, directly promoted the CSD. Keystone taxa maintained the stability of microbial network structure and function, and regulated microbial groups associated with CSD in the key modules, rather than directly decomposing the CS. Notably, this study profoundly revealed that water temperature and total nitrogen (TN) regulated the keystone taxa and key modules in microbial interactions and then promoted the OMD. The two key modules 2 and 4 were significantly correlated with water temperature and TN in water, and two keystone taxa (bacterial genera Emticicia and Flavihumibacter) were significantly associated with TN. The research findings help us to understand the microbial mechanism of the OMD in rivers, which provides valuable insights into improving effective management strategies for river ecosystems.
Genetic Dissection of the Breakdown of Durable Resistance in Indica Rice Variety PTB33 to Brown Planthoppers Nilaparvata Lugens (Stål)
Authors: Tabata Shusaku , Yamagata Yoshiyuki , Fujita Daisuke , Sanada-Morimura Sachiyo , Matsumura Masaya , Yasui Hideshi 
Published: December 2021

Abstract
BackgroundTo avoid and delay the resistance breakdown of varieties against pathogens and insect pests, broad-spectrum and durable resistance by multiple genes pyramiding are expected to be one of the practical approaches. The indica rice variety PTB33 (Oryza sativa L.) shows high and durable resistance to the brown planthopper (BPH, Nilaparvata lugens Stål). However, this variety gradually lost its resistance against the recent virulence development of BPH. However, breakdown processes are not fully elucidated by individual genetic loci. ResultsEffective QTLs were explored across the whole genomic region against four BPH populations collected in Japan in 1988, 1989, 1999, and 2013 using high-density single-nucleotide polymorphism (SNP) markers obtained by genotyping-by-sequencing. Among seven genomic regions of PTB33 likely conferring BPH resistance, four QTLs, qFSA4a, qFSA6, qFSA11, and qFSA12 on chromosomes 4, 6, 11, and 12, respectively, were validated as BPH resistance QTLs. The PTB33 alleles at the four QTLs positively contributed to BPH resistance. Infestation of monogenic segregating lines showed that the PTB33 alleles at qFSA11, qFSA12, and qFSA4a lost resistance effects at least in 1989, 1999, and 2013, respectively. ConclusionThis study showed breakdown of durable resistance in PTB33 was explained by step-by-step losses of genetic effects at each resistance locus and probably multiple acquisitions of virulence genes in BPH in a gene-by-gene specific manner.
Welding Parameters Optimization in Plunging and Dwelling Phase of FSW Medium Thickness 2219 Aluminum Alloy
Authors: Lu Xiaohong , Qiao Jinhui , Qian Junyu , Sun Shixuan , Liang Steven Y. 
Published: December 2021

Abstract
The influence of welding parameters on temperature distribution in plunging and dwelling phase of friction stir welding (FSW) medium thickness 2219 aluminum alloy is blank. Improper selection of welding parameters will result in uneven temperature distribution along the thickness of the weldment, which will lead to welding defects and ultimately affect the mechanical properties of the weldment. To realize the prediction of temperature distribution and achieve the optimization of welding parameters, a simulation model of FSW 18mm thick 2219 aluminum alloy is built based on DEFORM. The validity of the simulation model is verified by temperature measurement experiments. With the minimum temperature difference in the core area of the weldment as target value, and weldable temperature range of 2219 aluminum alloy as constraint conditions, orthogonal experiments are conducted considering the rotational speed, the press amount, the tool tilt angle, the plunging traverse speed and the dwelling time. The results of variance analysis show that the rotational speed and the dwelling time are significant factors affecting temperature field during plunging and dwelling phase. Through single factor simulation, the welding parameters in plunging and dwelling phase are optimized. This study provides a reference for realizing high-quality welding of a heavy rocket fuel tank.
Parental Decision Regret after Consenting to or Refusing Hypospadias Repair: an Australian Survey
Authors: Vavilov Sergey , Roberts Elysa , Smith Grahame HH , Starkey Malcolm , Pockney Peter , Deshpande Aniruddh V. 
Published: December 2021

Abstract
Background: Parental decision regret in hypospadias surgery is a recognised source of long-lasting psycho-social morbidity. Its reported prevalence is high but until now, it has not been studied in Australasian context or among parents who declined the repair for their son. The aim of this study is to report on decision regret in an Australian cohort of parents, including parents who accepted or who declined repair for their son and explore underlying factors for decision-making, satisfaction, and regret. Methods: An online anonymous survey was administered to three groups: 1) parents who consented for hypospadias repair, 2) parents who declined repair and 3) a control group who requested circumcision for their child. Operations occurred between 2010 and 2020. The survey included a validated decision regret assessment tool and additional questions to explore the possible basis of the opinions. Results: One hundred and eighteen parents (eligible 381, response rate 31%) participated. Decision regret was present in group 1 (n=89) – 55% (moderate-to-severe 15%), in group 2 (n= 14) – 71% (moderate-to-severe 57%), and in the control group (n=15) – 15% (moderate-to-severe 8%) of parents. There was a significant difference in the median decision regret score between all three groups. Parents who chose hypospadias repair were mostly concerned about function. They named the direction of the urine from the tip of the penis as the most satisfying outcome, and the appearance of the foreskin and the need for several operations as the least satisfying outcomes of the repair. Conclusions: The prevalence of decision regret among Australian parents who consented for their son’s hypospadias repair was lower compared with the mean decision regret reported in the literature to date (55% vs 65%). Decision regret and its severity were highest among parents who declined hypospadias repair. New strategies are needed to reduce decision regret in parents whether or not they elect for surgery.
Fractal scaling of C. elegans behavior is shaped by insulin signaling
Authors: Arata Yukinobu , Shiga Itsuki , Ikeda Yusaku , Kimura Hiroshi , Jurica Peter , Kiyono Ken , Sako Yasushi 
Published: December 2021

Abstract
Fractal scaling governs the complex behavior of various animal species and, in humans, can be altered by neurodegenerative diseases and aging1. However, the mechanism underlying fractal scaling remains unknown. Here, we videorecorded C. elegans that had been cultured in a microfluidic device for 3 days and analyzed temporal patterns of C. elegans actions by fractal analyses. The residence-time distribution of C. elegans shared a common feature with those of human and mice2–4. Specifically, the residence-time power-law distribution of the active state changed to an exponential-like decline at a longer time scale, whereas this change did not occur in the inactive state. The exponential-like decline disappeared in starved C. elegans but was restored by culturing animals with glucose. The exponential-like decline similarly disappeared in insulin-signaling daf-2 and daf-16 mutants. Therefore, we conclude that insulin signaling regulates fractal scaling of C. elegans behavior. Our findings indicate that neurosensory modulation of C. elegans behavior by insulin signaling is achieved by regulation of fractal scaling. In humans, diabetes mellitus is associated with depression, bipolar disorder, and anxiety disorder5, which affect daily behavioral activities. We hypothesize that comorbid behavioral defects in patients with diabetes may be attributed to altered fractal scaling of human behavior.
Tonsil-Derived Mesenchymal Stem Cells Inhibit the Proliferation of Hematological Cancer Cells through Downregulation of IL-6 Gene Expression under Hyperthermia
Authors: Yüce Melek , Albayrak Esra 
Published: December 2021

Abstract
Stem cells are extensively being studied as promising biological therapeutic candidates in cancer treatment. In various cancer types, some studies show proliferative effects while others show inhibitory effects of MSCs on tumors. Some studies have reported that MSCs isolated from different sources display different anti-cancer properties. Tonsils are one of the secondary lymphoid organs that form an important part of the immune system and located at the mucosal interface. The relation between secondary lymphoid organs and cancer progression lead us to investigate the effect of tonsil-derived MSCs (T-MSC) on cancer treatment. Therefore, we aimed to determine the anti-tumoral effects of tonsil-derived MSCs cultured at febrile temperature on hematological cancer cell lines. We found that co-culture of K562 cells and MOLT-4 with T-MSCs significantly decreased the viable cell number post 7 days of the culture under the febrile and normal culture conditions. Besides, the T-MSC co-culture not only induced the apoptosis on K562 and MOLT-4 cells but also, induced the cell cycle arrest at G2-M phase on MOLT-4 cells. The apoptotic effect of T-MSC co-culture under febrile stimulation was confirmed by upregulation of Bax, c-myc genes for K562 cells and upregulation of Bax, p53 and c-myc genes for MOLT-4 cells in transcriptional level. Our study has contributed to highlight the effect of the cellular interaction between the T-MSCs and human hematological cancer cells during in vitro co-culture under hyperthermia for tumor progression. In the light of these results, we indicated that tonsil-derived MSCs have promising therapeutic potential for cancer therapy.
Asset-Based, Sustainable Local Economic Development: Using Community Participation to Improve Quality of Life Across Rural, Small-Town, and Urban Communities
Authors: Kammer-Kerwick Matt , Takasaki Kara , Kellison J. Bruce , Sternberg Jeff 
Published: December 2021

Abstract
We analyze survey data from 5,487 residents of 85 Texas communities, including rural communities, small towns, medium-sized cities, and the five largest urban centers, to model the influence of the degree of urbanity and rurality of a community as well as residents’ social position, values, and their satisfaction with local assets. The paper’s central argument is that a wide range of factors impact how community members think about their needs and thus should be considered in any community development process. This human-centered approach to looking at how these factors impact economic and quality-of-life development project preferences will support the adaptation of community development decision-making processes to the conditions of each community. For the sake of parsimony, the present study presents results for three community development project concepts: 1) renovating some downtown buildings as mixed-use facilities with retail shops and apartments, 2) opening a community health center, and 3) and deploying gigabit high-speed fiber broadband internet in the downtown area. Our findings specifically highlight areas where participatory processes can be introduced to guide further interactions between experts and community members to 1) identify groups in the community to bring into the process who may be most impacted by the choice of one intervention over another, and 2) target areas where further community discussion and deliberation is necessary around which community dialogues (round tables, town halls, workshops, etc.) could be facilitated.
Intraparietal stimulation disrupts negative distractor effects in human multi-alternative decision-making
Authors: Kohl Carmen , Wong Michelle , Wong Jing Jun , Rushworth Matthew , Chau Bolton 
Published: December 2021

Abstract
There has been debate about whether addition of an irrelevant distractor option to an otherwise binary decision influences which of the two choices is taken. We show that disparate views on this question are reconciled if distractors exert two opposing but not mutually exclusive effects. Each effect predominates in a different part of decision space: 1) a positive distractor effect predicts high-value distractors improve decision-making; 2) a negative distractor effect, of the type associated with divisive normalisation models, entails decreased accuracy with increased distractor values. Here, we demonstrate both distractor effects coexist in human decision making but in different parts of a decision space defined by the choice values. We show disruption of the medial intraparietal area (MIP) by transcranial magnetic stimulation (TMS) increases positive distractor effects at the expense of negative distractor effects. Furthermore, individuals with larger MIP volumes are also less susceptible to the disruption induced by TMS. These findings also demonstrate a causal link between MIP and the impact of distractors on decision-making via divisive normalization.
A Conformal Predictive System for Distribution Regression with Random Features
Authors: Zhang Wei , He Zhen , WANG Di 
Published: December 2021

Abstract
Distribution regression is the regression case where the input objects are distributions. Many machine learning problems can be analysed in this framework, such as multi-instance learning and learning from noisy data. This paper attempts to build a conformal predictive system(CPS) for distribution regression, where the prediction of the system for a test input is a cumulative distribution function(CDF) of the corresponding test label. The CDF output by a CPS provides useful information about the test label, as it can estimate the probability of any event related to the label and be transformed to prediction interval and prediction point with the help of the corresponding quantiles. Furthermore, a CPS has the property of validity as the prediction CDFs and the prediction intervals are statistically compatible with the realizations. This property is desired for many risk-sensitive applications, such as weather forecast. To the best of our knowledge, this is the first work to extend the learning framework of CPS to distribution regression problems. We first embed the input distributions to a reproducing kernel Hilbert space using kernel mean embedding approximated by random Fourier features, and then build a fast CPS on the top of the embeddings. While inheriting the property of validity from the learning framework of CPS, our algorithm is simple, easy to implement and fast. The proposed approach is tested on synthetic data sets and can be used to tackle the problem of statistical postprocessing of ensemble forecasts, which demonstrates the effectiveness of our algorithm for distribution regression problems.
Topological Data Analysis Gives Two Folding Paths in HP35(nle-nle), Double Mutant of Villin Headpiece Subdomain
Authors: Ichinomiya Takashi 
Published: December 2021

Abstract
The folding dynamics of proteins is a primary area of interest in protein science. We carried out topological data analysis (TDA) of the folding process of HP35(nle-nle), double-mutant of villin headpiece subdomain. Using persistent homology and non-negative matrix factorization, we reduced the dimension of protein structure into two, and investigate the flow in the reduced space. We found this protein has two folding paths, distinguished by the pairings of inter-helix residues. Our analysis showed the excellent performance of TDA in capturing the formation of tertiary structure.