bluuebunny/crossref_metadata_2025_split huggingface dataset:
MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning
Authors: Erikawa Daiki , Yasuo Nobuaki , Sekijima Masakazu 
Published: November 2021

AbstractThe hit-to-lead process makes the physicochemical properties of the hit molecules that show the desired type of activity obtained in the screening assay more drug-like. Deep learning-based molecular generative models are expected to contribute to the hit-to-lead process. The simplified molecular input line entry system (SMILES), which is a string of alphanumeric characters representing the chemical structure of a molecule, is one of the most commonly used representations of molecules, and molecular generative models based on SMILES have achieved significant success. However, in contrast to molecular graphs, during the process of generation, SMILES are not considered as valid SMILES. Further, it is quite difficult to generate molecules starting from a certain molecule, thus making it difficult to apply SMILES to the hit-to-lead process. In this study, we have developed a SMILES-based generative model that can be generated starting from a certain molecule. This method generates partial SMILES and inserts it into the original SMILES using Monte Carlo Tree Search and a Recurrent Neural Network. We validated our method using a molecule dataset obtained from the ZINC database and successfully generated molecules that were both well optimized for the objectives of the quantitative estimate of drug-likeness (QED) and penalized octanol-water partition coefficient (PLogP) optimization. The source code is available at https://github.com/sekijima-lab/mermaid.
[18F]FMCH PET/CT biomarkers and similarity analysis to refine the definition of oligometastatic prostate cancer
Authors: Sollini Martina , Bartoli Francesco , Cavinato Lara , Ieva Francesca , Ragni Alessandra , Marciano Andrea , Zanca Roberta , Galli Luca , Paiar Fabiola , Pasqualetti Francesco , Erba Paola Anna 
Published: November 2021

Abstract
Background
The role of image-derived biomarkers in recurrent oligometastatic Prostate Cancer (PCa) is unexplored. This paper aimed to evaluate [18F]FMCH PET/CT radiomic analysis in patients with recurrent PCa after primary radical therapy. Specifically, we tested intra-patient lesions similarity in oligometastatic and plurimetastatic PCa, comparing the two most used definitions of oligometastatic disease.

Methods
PCa patients eligible for [18F]FMCH PET/CT presenting biochemical failure after first-line curative treatments were invited to participate in this prospective observational trial. PET/CT images of 92 patients were visually and quantitatively analyzed. Each patient was classified as oligometastatic or plurimetastatic according to the total number of detected lesions (up to 3 and up to 5 or > 3 and > 5, respectively). Univariate and intra-patient lesions' similarity analysis were performed.

Results
[18F]FMCH PET/CT identified 370 lesions, anatomically classified as regional lymph nodes and distant metastases. Thirty-eight and 54 patients were designed oligometastatic and plurimetastatic, respectively, using a 3-lesion threshold. The number of oligometastic scaled up to 60 patients (thus 32 plurimetastatic patients) with a 5-lesion threshold. Similarity analysis showed high lesions' heterogeneity. Grouping patients according to the number of metastases, patients with oligometastatic PCa defined with a 5-lesion threshold presented lesions heterogeneity comparable to plurimetastic patients. Lesions within patients having a limited tumor burden as defined by three lesions were characterized by less heterogeneity.

Conclusions
We found a comparable heterogeneity between patients with up to five lesions and plurimetastic patients, while patients with up to three lesions were less heterogeneous than plurimetastatic patients, featuring different cells phenotypes in the two groups. Our results supported the use of a 3-lesion threshold to define oligometastatic PCa.
Transcriptional analysis and target genes discovery of Pseudomonas aeruginosa biofilm developed ex vivo chronic wound model
Authors: Tan Xiaojuan , Cheng Xi , Hu Mei , Zhang Yifan , Jia Aiqun , Zhou Jinwei , Zhu Guoping 
Published: November 2021

AbstractBacterial biofilms formation is one of the major reasons for treatment failure in chronic wound infections. Therefore, diagnostic biomarkers remain the best option for prevention and treatment of chronic wound infections by biofilms. Herein, Pseudomonas aeruginosa PAO1 was used to mimic biofilm development in porcine skin explants wells as ex vivo wound model. The microscopic imaging showed that PAO1 in porcine skin explants wells formed micro-colonies at 24 h, developed mushroom-like structure at 48 h, and at 72 h mushroom-like structure disappeared, remaining a thin bacterial lawn. RNA-seq data analysis revealed that the expression levels of genes involved in the type II hxc secretion system were significantly higher in biofilms than in planktonic cells, especially the expression of lapA encoding alkaline phosphatase. However, the expression levels of genes associated with denitrification pathway were markedly decreased in biofilms, especially the transcription of nirS encoding nitrite reductase to produce nitric oxide (NO). Therefore, their expressions and products were further detected using RT-qPCR and biochemical assays, respectively. The results found that the expression of lapA and alkaline phosphatase activity were induced, but the expression of nirS and intracellular NO were reduced at the whole biofilms cycle. The study indicates that LapA and NO would play an important role for P. aeruginosa biofilm formation in chronic wound infections. LapA would serve as potential target to monitor chronic wound infections by P. aeruginosa biofilms. Inducing NO would be used to treat chronic wound infections due to P. aeruginosa biofilms.
Effects of a traditional Chinese medicine formula containing the Coix seed and Lotus seed on the intestinal morphology and microbiota of local piglets
Authors: Li Zhaolong , Lin Zhongning , Lu Zheng , Ying Zhaoyang 
Published: November 2021

AbstractA traditional Chinese medicine formula based on the Coix seed and Lotus seed has been used as a general treatment of malnutrition, excessive fatigue, dysfunction of the spleen and stomach, and disorders of water transport in humans in China. However, there is limited information on its effects on the gut microbiota of piglets in vivo. In this study, the mix of Coix seed and Lotus were added the diet of forty weaned piglets (local piglets), and then evaluated it’s affected on the gut microbiota of piglets and on the relations within the gut bacterial community. The results indicated that this traditional Chinese medicine formula (LM) and the extract of the traditional Chinese medicine formula (LMT) downregulated pH of succus gastricus and raised pH of the ileum, and LMT obviously decreased the feed conversion ratio. Further study showed LMT and LM also significantly increased the thick and long of gastrointestinal villi. And then, 16S ribosomal DNA sequencing revealed that groups LMT and LM have higher relative abundance of the genus Lactobacillus in the colon, succus gastricus, and jejunum, which are beneficial bacteria sold as dietary supplements to aid digestion or to augment health. Meanwhile, the relative abundance levels of Prevotellaceae, Alloprevotella, and Prevotella in the colon and Clostridium in succus gastricus and jejunum were lower. These experiments highlight the usefulness of the traditional Chinese medicine formula based on the Coix seed and Lotus seed for decreasing pH in succus gastricus, for improving the structure of intestinal villi and gut microflora, and then for achieving improvements in pig production performance.
A multivariate model for successful publication of intensive care medicine randomized controlled trials in the highest impact factor journals: the SCOTI score
Authors: Pensier Joris , De Jong Audrey , Chanques Gerald , Futier Emmanuel , Azoulay Elie , Molinari Nicolas , Jaber Samir 
Published: November 2021

Abstract
Background
Critical care randomized controlled trials (RCTs) are often published in high-impact journals, whether general journals [the New England Journal of Medicine (NEJM), The Lancet, the Journal of the American Medical Association (JAMA)] or critical care journals [Intensive Care Medicine (ICM), the American Journal of Respiratory and Critical Care Medicine (AJRCCM), Critical Care Medicine (CCM)]. As rejection occurs in up to 97% of cases, it might be appropriate to assess pre-submission probability of being published. The objective of this study was to develop and internally validate a simplified score predicting whether an ongoing trial stands a chance of being published in high-impact general journals.

Methods
A cohort of critical care RCTs published between 1999 and 2018 in the three highest impact medical journals (NEJM, The Lancet, JAMA) or the three highest impact critical care journals (ICM, AJRCCM, CCM) was split into two samples (derivation cohort, validation cohort) to develop and internally validate the simplified score. Primary outcome was journal of publication assessed as high-impact general journal (NEJM, The Lancet, JAMA) or critical care journal (ICM, AJRCCM, CCM).

Results
A total of 968 critical care RCTs were included in the predictive cohort and split into a derivation cohort (n = 510) and a validation cohort (n = 458). In the derivation cohort, the sample size (P value < 0.001), the number of centers involved (P value = 0.01), mortality as primary outcome (P value = 0.002) or a composite item including mortality as primary outcome (P value = 0.004), and topic [ventilation (P value < 0.001) or miscellaneous (P value < 0.001)] were independent factors predictive of publication in high-impact general journals, compared to high-impact critical care journals. The SCOTI score (Sample size, Centers, Outcome, Topic, and International score) was developed with an area under the ROC curve of 0.84 (95% Confidence Interval, 0.80–0.88) in validation by split sample.

Conclusions
The SCOTI score, developed and validated by split sample, accurately predicts the chances of a critical care RCT being published in high-impact general journals, compared to high-impact critical care journals.
Latency-aware secure transmission in MEC-assisted HSR communication systems
Authors: Xu Hao , Li Ke , Cheng Jianfeng , Jiang Bo , Yu Huai 
Published: November 2021

AbstractMobile edge computing can provide short-range cloud computing capability for the mobile users, which is considered to be a promising technology in 5G communication. The mobile users offload some computing tasks to the edge server through the wireless backhaul link, which can reduce the energy consumption and the time latency. Meanwhile, due to the open characteristics of the wireless channel, the offloading tasks through the backhaul link may face the risk of eavesdropping. Therefore, the secure transmission based on physical layer security for the offloading tasks to the edge server is considered. The optimization problem of minimizing the energy consumption for the vehicular stations (VSs) in mobile edge computing-assisted high-speed railway communication system is studied in this paper. The energy consumption of the mobile users is generated by executing the local computing task and by transmitting the partial offloading task to the edge server. In this paper, a novel joint iterative optimization algorithm is proposed. By jointly optimizing the task scheduling, the task offloading and the transmission power, the energy consumption of all VSs is minimized under the constraint of the time latency. Numerical simulation results verify the effectiveness of the proposed algorithm.
A new scheme to enhance the performance of permutation index–differential chaos shift keying communications system
Authors: Al Bassam Nizar , Al-Jerew Oday 
Published: November 2021

AbstractIn this paper, a new scheme based on permutation index–differential chaos shift keying is proposed, modeled, and evaluated in AWGN channel environment. Data is sent by frames, and each frame is headed by a single reference signal and followed by some information-bearing signals. Modulation is performed through permutations of a reference signal according to the mapped data. At the receiver, each incoming information-bearing signal undergoes all inverse permutation possibilities to perform a correlation with the delayed and stored version of the received reference signal. To decode the information bits, the detector selects the highest correlator outputs. The proposed scheme named single reference–permutation index–differential chaos shift keying is an enhanced version of PI-DCSK, and uses a single reference signal for multiple information-bearing ones. Hence, the energy requirement is saved by almost a half. The bit error performance is studied using the baseband system model and analytically tested using Gaussian approximation method. Results show the BER performance outperforms other standard and recently developed differentially coherent chaos systems, including Permutation Index–DCSK by an average of 2.25 dB. Moreover, the analytical form which is developed to predict the bit error rate (BER) is validated by simulation. Results demonstrate the performance in AWGN is closely matching with the simulation results, particularly at high SNR.
Parametric codebook design for efficient signal transmission using uniform circular arrays
Authors: Shin Junsik , Suh Junyeub , Park Sangchun , Sung Wonjin 
Published: November 2021

AbstractIn order to improve the quality of the received signal and system spectral efficiency, accurate beamforming using a given antenna array is essential for multiple-input multiple-output (MIMO) systems. To obtain desired MIMO transmission performance, construction of codebooks which are composed of matching beamforming vectors to the array structure is important. To effectively cover different types of mobile traffic, the base station for 5G new radio employs antenna arrays in various sizes and shapes. Nevertheless, the codebooks adopted by the 3GPP standard so far are based on the uniform linear array and the uniform planar array, necessitating design techniques for a wider class of antenna arrays. In this paper, we propose codebook construction methods for the uniform circular array with parameters to flexibly set the initial phase and step size based on the channel characteristics of the user equipment (UE). When tested over the 3GPP spatial channel model, the proposed codebooks show a substantial amount of gain over the conventional codebooks in all UE locations within the cell.
Existence and asymptotic behavior of Radon measure-valued solutions for a class of nonlinear parabolic equations
Authors: Nkombo Quincy Stévène , Li Fengquan , Tathy Christian 
Published: November 2021

AbstractIn this paper we address the weak Radon measure-valued solutions associated with the Young measure for a class of nonlinear parabolic equations with initial data as a bounded Radon measure. This problem is described as follows: $$ \textstyle\begin{cases} u_{t}=\alpha u_{xx}+\beta [\varphi (u) ]_{xx}+f(u) &\text{in} \ Q:=\Omega \times (0,T), \\ u=0 &\text{on} \ \partial \Omega \times (0,T), \\ u(x,0)=u_{0}(x) &\text{in} \ \Omega , \end{cases} $$

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The effect of landscape structure on the evolution of two alternative dispersal strategies
Authors: Sieger C. S. , Hovestadt T. 
Published: November 2021

Abstract
Background
Dispersal is an important event for most organisms at least once in their life cycle. The evolution of dispersal can be influenced by local adaptation, landscape structure, and perceived temporal and spatial variation. The interaction between local adaptation, landscape heterogeneity, temporal variability and rules of dispersal may be more complex than previously assumed. Therefore, we sought to understand the influence of emigration rules and landscape structure on emerging dispersal rates and traits. Here, we implemented an individual-based model (IBM) of trait evolution in scenarios characterized by different landscape structures and different degrees of spatial heterogeneity and global temporal variation. Individuals could evolve two traits coding for their environmental niche (position of niche optimum and niche width), and two traits determining nearest-neighbor dispersal: an individual emigrates with a probability defined by the first trait (random emigration), but emigrates with certainty if the fertility expected in the patch of residence falls below a threshold specified by the second trait (habitat-dependent emigration).

Results
We note an interaction effect between dispersal strategy and spatial variance—lower emigration under habitat-dependent than under random emigration if spatial heterogeneity is low, but eventually a reversal of this ranking if heterogeneity becomes large. Landscapes with sharp transition of habitat attributes result in a high degree of spatial sorting, while fractal landscapes do not. Emigration rates are overall lowest, when spatial variation is highest.

Conclusions
We conclude that emergent emigration rates are influenced more by landscape structure and spatio-temporal heterogeneity than by the emigration strategy. With the ongoing land use change more research into this topic could help highlight the difficulties species might face under the change from landscapes characterized by gradual transition zones to landscapes dominated by abrupt ecotones, the latter typical for agricultural and urban settings.
Digging into the behaviour of an active hunting predator: arctic fox prey caching events revealed by accelerometry
Authors: Clermont Jeanne , Woodward-Gagné Sasha , Berteaux Dominique 
Published: November 2021

Abstract
Background
Biologging now allows detailed recording of animal movement, thus informing behavioural ecology in ways unthinkable just a few years ago. In particular, combining GPS and accelerometry allows spatially explicit tracking of various behaviours, including predation events in large terrestrial mammalian predators. Specifically, identification of location clusters resulting from prey handling allows efficient location of killing events. For small predators with short prey handling times, however, identifying predation events through technology remains unresolved. We propose that a promising avenue emerges when specific foraging behaviours generate diagnostic acceleration patterns. One such example is the caching behaviour of the arctic fox (Vulpes lagopus), an active hunting predator strongly relying on food storage when living in proximity to bird colonies.

Methods
We equipped 16 Arctic foxes from Bylot Island (Nunavut, Canada) with GPS and accelerometers, yielding 23 fox-summers of movement data. Accelerometers recorded tri-axial acceleration at 50 Hz while we obtained a sample of simultaneous video recordings of fox behaviour. Multiple supervised machine learning algorithms were tested to classify accelerometry data into 4 behaviours: motionless, running, walking and digging, the latter being associated with food caching. Finally, we assessed the spatio-temporal concordance of fox digging and greater snow goose (Anser caerulescens antlanticus) nesting, to test the ecological relevance of our behavioural classification in a well-known study system dominated by top-down trophic interactions.

Results
The random forest model yielded the best behavioural classification, with accuracies for each behaviour over 96%. Overall, arctic foxes spent 49% of the time motionless, 34% running, 9% walking, and 8% digging. The probability of digging increased with goose nest density and this result held during both goose egg incubation and brooding periods.

Conclusions
Accelerometry combined with GPS allowed us to track across space and time a critical foraging behaviour from a small active hunting predator, informing on spatio-temporal distribution of predation risk in an Arctic vertebrate community. Our study opens new possibilities for assessing the foraging behaviour of terrestrial predators, a key step to disentangle the subtle mechanisms structuring many predator–prey interactions and trophic networks.
Whole-body diffusion-weighted MRI of normal lymph nodes: prospective apparent diffusion coefficient histogram and nodal distribution analysis in a healthy cohort
Authors: Donners Ricardo , Yiin Raphael Shih Zhu , Blackledge Matthew , Koh Dow-Mu 
Published: November 2021

Abstract
Background
Whole body DWI (WB-DWI) enables the identification of lymph nodes for disease evaluation. However, quantitative data of benign lymph nodes across the body are lacking to allow meaningful comparison of diseased states. We evaluated apparent diffusion coefficient (ADC) histogram parameters of all visible lymph nodes in healthy volunteers on WB-DWI and compared differences in nodal ADC values between anatomical regions.

Methods
WB-DWI was performed on a 1.5 T MR system in 20 healthy volunteers (7 female, 13 male, mean age 35 years). The b900 images were evaluated by two radiologists and all visible nodes from the neck to groin areas were segmented and individual nodal median ADC recorded. All segmented nodes in a patient were summated to generate the total nodal volume. Descriptors of the global ADC histogram, derived from individual node median ADCs, including mean, median, skewness and kurtosis were obtained for the global volume and each nodal region per patient. ADC values between nodal regions were compared using one-way ANOVA with Bonferroni post hoc tests and a p-value ≤0.05 was deemed statistically significant.

Results
One thousand sixty-seven lymph nodes were analyzed. The global mean and median ADC of all lymph nodes were 1.12 ± 0.27 (10− 3 mm2/s) and 1.09 (10− 3 mm2/s). The average median ADC skewness was 0.25 ± 0.02 and average median ADC kurtosis was 0.34 ± 0.04. The ADC values of intrathoracic, portal and retroperitoneal nodes were significantly higher (1.53 × 10− 3, 1.75 × 10− 3 and 1.58 × 10− 3 mm2/s respectively) than in other regions. Intrathoracic, portal and mesenteric nodes were relatively uncommon, accounting for only 3% of the total nodes segmented.

Conclusions
The global mean and median ADC of all lymph nodes were 1.12 ± 0.27 (10− 3 mm2/s) and 1.09 (10− 3 mm2/s). Intrathoracic, portal and retroperitoneal nodes display significantly higher ADCs. Normal intrathoracic, portal and mesenteric nodes are infrequently visualized on WB-DWI of healthy individuals.

Trial registration
Royal Marsden Hospital committee for clinical research registration number 09/H0801/86, 19.10.2009.