bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient recurrent neural network methods for anomalously diffusing single particle short and noisy trajectories
Authors: Garibo-i-Orts Òscar , Baeza-Bosca Alba , Garcia-March Miguel A. , Conejero J. Alberto 
Published: November 2021

AbstractAnomalous diffusion occurs at very different scales in nature, from atomic systems to motions in cell organelles, biological tissues or ecology, and also in artificial materials, such as cement. Being able to accurately measure the anomalous exponent associated to a given particle trajectory, thus determining whether the particle subdiffuses, superdiffuses or performs normal diffusion, is of key importance to understand the diffusion process. Also it is often important to trustingly identify the model behind the trajectory, as it this gives a large amount of information on the system dynamics. Both aspects are particularly difficult when the input data are short and noisy trajectories. It is even more difficult if one cannot guarantee that the trajectories output in experiments are homogeneous, hindering the statistical methods based on ensembles of trajectories. We present a data-driven method able to infer the anomalous exponent and to identify the type of anomalous diffusion process behind single, noisy and short trajectories, with good accuracy. This model was used in our participation in the anomalous diffusion (AnDi) challenge. A combination of convolutional and recurrent neural networks was used to achieve state-of-the-art results when compared to methods participating in the AnDi challenge, ranking top 4 in both classification and diffusion exponent regression.
Preparation and electrochromic properties of flexible transparent WO3/AgNW-decorated nanofiber composite film
Authors: Noh Jae-Hyun , Radhakrishnan Sivaprakasam , Lee Ki Tae , Ko Tae Hoon , Kim Byoung-Suhk 
Published: November 2021

Abstract
It is well-known that tungsten oxide (WO3) is extensively used for electrochromic (EC) devices due to its special properties, such as high coloration/bleaching response time, good coloration efficiency, etc. The preparation of flexible EC devices is highly desirable for various applications. However, the fabrication of flexible EC devices with improved performance is still a major task due to their limited experimental protocols. In this study, we have prepared highly flexible transparent films consisting of WO3 and silver nanowires coated on nanofiber-reinforced composite films (WO3/AgNW-NCF). A novel flexible transparent WO3/AgNW-NCF is used for EC applications. The as-fabricated EC device based on WO3/AgNW-NCF demonstrated good coloration efficiency (161.3 cm2 C−1), excellent stability (81.5%) and rapid response time for coloration (2.9 s) and bleaching (3.2 s). The fabricated transparent flexible EC device may potentially be useful for designing an outstanding EC device for smart window applications.
Ultra-broadband perfect solar energy absorber based on tungsten ring arrays
Authors: Cheng Yu , Xiong Min , Chen Ming , Deng Shijie , Liu Houquan , Teng Chuanxin , Yang Hongyan , Deng Hongchang , Yuan Libo 
Published: November 2021

Abstract
Metamaterials play a crucial role in the research of broadband absorbers. In order to achieve broadband and efficient absorption of solar energy, a novel solar energy absorber based on tungsten ring array is proposed in this paper. The results of numerical analysis show that the absorption efficiency of the absorber is over 90% at 300∼2000 nm, the average absorption efficiency is 96.2%, and the absorption peak is 99.9%. Broadband absorption can be attributed to the excitation of plasmon and Fabry–Perot resonance effect on the surface of metal-insulator-metal. In addition, thanks to the high symmetry of the structure, it is relatively independent of incident angle and polarization angle. In the future, the absorbent will have a promising application prospect in the fields of solar energy utilization, photothermal conversion and infrared detection.
Listening to Extinction: Early Conservation Radio Sounds and the Silences of Species
Authors: Hui Alexandra 
Published: November 2021

Abstract
In the first decades of the twentieth century, American radio producers used both artificial and wild-recorded sounds of nature to promote principles of environmental conservation and wildlife management. These techniques were shaped by established listening practices — especially those of birders — and also fostered new ones. Specifically, conservation radio programs like those produced by the American Wildlife Institute and the Cornell Lab of Ornithology, made it possible for listeners to experience silence in a new way; as indicative of absence, potentially even extinction, both locally and globally. By examining how conservation radio in the 1930s was a mechanism through which environmental awareness and even action was fostered, this article demonstrates the dividends of working at the intersection of sensory studies and environmental history. New inflection points and temporal framing are made apparent as is the development of the critical sensory perceptual shifts necessary for the environmental movement to come. Tracing the sounds and listening to them in individuals’ understanding of nature prompts us to consider the shifting, culturally-bound, mechanisms through which we have sensed and perceived and acted upon the world.
ResNet18DNN: prediction approach of drug-induced liver injury by deep neural network with ResNet18
Authors: Chen Zhao , Jiang Yin , Zhang Xiaoyu , Zheng Rui , Qiu Ruijin , Sun Yang , Zhao Chen , Shang Hongcai 
Published: November 2021

AbstractDrug-induced liver injury (DILI) has always been the focus of clinicians and drug researchers. How to improve the performance of the DILI prediction model to accurately predict liver injury was an urgent problem for researchers in the field of medical research. In order to solve this scientific problem, this research collected a comprehensive and accurate dataset of DILI with high recognition and high quality based on clinically confirmed DILI compound datasets, including 1446 chemical compounds. Then, the residual neural network with 18-layer by using more 5-layer blocks (ResNet18) with deep neural network (ResNet18DNN) model was proposed to predict DILI, which was an improved model for DILI prediction through vectorization of compound structure image. In predicting DILI, the ResNet18DNN learned greatly and outperformed the existing state-of-the-art DILI predictors. The results of DILI prediction model based on ResNet18DNN showed that the AUC (area under the curve), accuracy, recall, precision, F1-score and specificity of the training set were 0.973, 0.992, 0.995, 0.994, 0.995 and 0.975; those of test set were, respectively, 0.958, 0.976, 0.935, 0.947, 0.926 and 0.913, which were better than the performance of previously published described DILI prediction models. This method adopted ResNet18 embedding method to vectorize molecular structure images and the evaluation indicators of Resnet18DNN were obtained after 10 000 iterations. This prediction approach will greatly improve the performance of the predictive model of DILI and provide an accurate and precise early warning method for DILI in drug development and clinical medication.
Tumor immune microenvironment lncRNAs
Authors: Park Eun-Gyeong , Pyo Sung-Jin , Cui Youxi , Yoon Sang-Ho , Nam Jin-Wu 
Published: November 2021

AbstractLong non-coding ribonucleic acids (RNAs) (lncRNAs) are key players in tumorigenesis and immune responses. The nature of their cell type-specific gene expression and other functional evidence support the idea that lncRNAs have distinct cellular functions in the tumor immune microenvironment (TIME). To date, the majority of lncRNA studies have heavily relied on bulk RNA-sequencing data in which various cell types contribute to an averaged signal, limiting the discovery of cell type-specific lncRNA functions. Single-cell RNA-sequencing (scRNA-seq) is a potential solution for tackling this limitation despite the lack of annotations for low abundance yet cell type-specific lncRNAs. Hence, updated annotations and further understanding of the cellular expression of lncRNAs will be necessary for characterizing cell type-specific functions of lncRNA genes in the TIME. In this review, we discuss lncRNAs that are specifically expressed in tumor and immune cells, summarize the regulatory functions of the lncRNAs at the cell type level and highlight how a scRNA-seq approach can help to study the cell type-specific functions of TIME lncRNAs.
Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation
Authors: Serra Angela , Fratello Michele , Federico Antonio , Ojha Ravi , Provenzani Riccardo , Tasnadi Ervin , Cattelani Luca , del Giudice Giusy , Kinaret Pia A S , Saarimäki Laura A , Pavel Alisa , Kuivanen Suvi , Cerullo Vincenzo , Vapalahti Olli , Horvath Peter , Lieto Antonio Di , Yli-Kauhaluoma Jari , Balistreri Giuseppe , Greco Dario 
Published: November 2021

AbstractThe pharmacological arsenal against the COVID-19 pandemic is largely based on generic anti-inflammatory strategies or poorly scalable solutions. Moreover, as the ongoing vaccination campaign is rolling slower than wished, affordable and effective therapeutics are needed. To this end, there is increasing attention toward computational methods for drug repositioning and de novo drug design.Here, multiple data-driven computational approaches are systematically integrated to perform a virtual screening and prioritize candidate drugs for the treatment of COVID-19. From the list of prioritized drugs, a subset of representative candidates to test in human cells is selected. Two compounds, 7-hydroxystaurosporine and bafetinib, show synergistic antiviral effects in vitro and strongly inhibit viral-induced syncytia formation. Moreover, since existing drug repositioning methods provide limited usable information for de novo drug design, the relevant chemical substructures of the identified drugs are extracted to provide a chemical vocabulary that may help to design new effective drugs.
Building family connectedness—A new practice tool for social workers
Authors: Woodman Elise , Ross and Jessica 
Published: November 2021

Abstract
Family connectedness is important for youth mental health and well-being. Social workers can help families build and maintain connections during adolescence. Evidence-based practice tools which approach youth well-being through a whole-of-family lens help legitimise social work’s person-in-environment approach to mental health. In this study, fifteen Australian social workers piloted a new practice tool to support family connectedness. The tool outlines key elements of family connectedness from the perspectives of young people and provides detailed examples to help understand and strengthen family connections. The social workers trialled the Family Connectedness Practice Tool for two months. Before the trial, participants were surveyed on which skills, theories and practice approaches they used to support family connectedness. After the trial, participants were surveyed on how they used the tool and how useful it was in their practice. The findings highlight the range of knowledge informing practice with children, youth and families. The tool was considered very useful by participants and helped with family connectedness education, assessment and intervention. The findings raise questions about how much young people’s perspectives are valued in practice and the challenges social workers face when using a whole-of-family approach.
Learning from children and youth: A qualitative study about the changes that young people identify through a positive parenting programme
Authors: Urrea-Monclús Aida , Ponce Alifonso Carmen , Balsells Bailón M Àngels 
Published: November 2021

Abstract
This article presents the results of an investigation regarding the perceptions of people participating in a programme on parental competencies for family reunification about the changes achieved through the same. This included the perceptions of children, adolescents, and their parents. A qualitative research was carried out based on thirteen focus groups comprising n = 59 children and adolescents out of the total 135 programme participants. Contributions of the young persons allowed the identification of changes in (1) parental competency related to foster care measures, visits and contact during foster care; (2) parental competency related to family adjustment and parental role during the return home and (3) personal awareness about foster care and family members’ reunification process. Additionally, two other concepts emerged, which are considered cross-sectional to the process of foster care and family reunification: (4) the child-rights approach and (5) resources supporting parental education. The findings indicated the importance of resilience phases, communication skills and emotional competencies and attitude and awareness regarding the process of fostering and reuniting families.
NPTX1 mutations trigger endoplasmic reticulum stress and cause autosomal dominant cerebellar ataxia
Authors: Coutelier Marie , Jacoupy Maxime , Janer Alexandre , Renaud Flore , Auger Nicolas , Saripella Ganapathi-Varma , Ancien François , Pucci Fabrizio , Rooman Marianne , Gilis Dimitri , Larivière Roxanne , Sgarioto Nicolas , Valter Rémi , Guillot-Noel Léna , Le Ber Isabelle , Sayah Sabrina , Charles Perrine , Nümann Astrid , Pauly Martje G , Helmchen Christoph , Deininger Natalie , Haack Tobias B , Brais Bernard , Brice Alexis , Trégouët David-Alexandre , El Hachimi Khalid H , Shoubridge Eric A , Durr Alexandra , Stevanin Giovanni 
Published: November 2021

Abstract
With more than 40 causative genes identified so far, autosomal dominant cerebellar ataxias exhibit a remarkable genetic heterogeneity. Yet, half the patients are lacking a molecular diagnosis.
In a large family with nine sampled affected members, we performed exome sequencing combined with whole-genome linkage analysis. We identified a missense variant in NPTX1, NM_002522.3:c.1165G&gt;A: p.G389R, segregating with the phenotype. Further investigations with whole-exome sequencing and an amplicon-based panel identified four additional unrelated families segregating the same variant, for whom a common founder effect could be excluded. A second missense variant, NM_002522.3:c.980A&gt;G: p.E327G, was identified in a fifth familial case. The NPTX1-associated phenotype consists of a late-onset, slowly progressive, cerebellar ataxia, with downbeat nystagmus, cognitive impairment reminiscent of cerebellar cognitive affective syndrome, myoclonic tremor and mild cerebellar vermian atrophy on brain imaging.
NPTX1 encodes the neuronal pentraxin 1, a secreted protein with various cellular and synaptic functions. Both variants affect conserved amino acid residues and are extremely rare or absent from public databases. In COS7 cells, overexpression of both neuronal pentraxin 1 variants altered endoplasmic reticulum morphology and induced ATF6-mediated endoplasmic reticulum stress, associated with cytotoxicity. In addition, the p.E327G variant abolished neuronal pentraxin 1 secretion, as well as its capacity to form a high molecular weight complex with the wild-type protein. Co-immunoprecipitation experiments coupled with mass spectrometry analysis demonstrated abnormal interactions of this variant with the cytoskeleton. In agreement with these observations, in silico modelling of the neuronal pentraxin 1 complex evidenced a destabilizing effect for the p.E327G substitution, located at the interface between monomers. On the contrary, the p.G389 residue, located at the protein surface, had no predictable effect on the complex stability.
Our results establish NPTX1 as a new causative gene in autosomal dominant cerebellar ataxias. We suggest that variants in NPTX1 can lead to cerebellar ataxia due to endoplasmic reticulum stress, mediated by ATF6, and associated to a destabilization of NP1 polymers in a dominant-negative manner for one of the variants.
Diabetic retinopathy as a potential marker of Parkinson’s disease: a register-based cohort study
Authors: Larsen Maria E C , Thykjaer Anne S , Pedersen Frederik N , Möller Sören , Laugesen Caroline S , Andersen Nis , Andresen Jens , Hajari Javad , Heegaard Steffen , Højlund Kurt , Kawasaki Ryo , Schielke Katja C , Rubin Katrine H , Blaabjerg Morten , Stokholm Lonny , Grauslund Jakob 
Published: November 2021

Abstract
Neurodegeneration is an early event in the pathogenesis of diabetic retinopathy, and an association between diabetic retinopathy and Parkinson’s disease has been proposed. In this nationwide register-based cohort study, we investigated the prevalence and incidence of Parkinson’s disease among patients screened for diabetic retinopathy in a Danish population-based cohort. Cases (n = 173 568) above 50 years of age with diabetes included in the Danish Registry of Diabetic Retinopathy between 2013 and 2018 were matched 1:5 by gender and birth year with a control population without diabetes (n = 843 781). At index date, the prevalence of Parkinson’s disease was compared between cases and controls. To assess the longitudinal relationship between diabetic retinopathy and Parkinson’s disease, a multivariable Cox proportional hazard model was estimated. The prevalence of Parkinson’s disease was 0.28% and 0.44% among cases and controls, respectively. While diabetic retinopathy was not associated with present (adjusted odds ratio 0.93, 95% confidence interval 0.72–1.21) or incident Parkinson’s disease (adjusted hazard ratio 0.77, 95% confidence interval 0.56–1.05), cases with diabetes were in general less likely to have or to develop Parkinson’s disease compared to controls without diabetes (adjusted odds ratio 0.79, 95% confidence interval 0.71–0.87 and adjusted hazard ratio 0.88, 95% confidence interval 0.78–1.00). In a national cohort of more than 1 million persons, patients with diabetes were 21% and 12% were less likely to have prevalent and develop incident Parkinson’s disease, respectively, compared to an age- and gender-matched control population without diabetes. We found no indication for diabetic retinopathy as an independent risk factor for incident Parkinson’s disease.
Human variation in error-based and reinforcement motor learning is associated with entorhinal volume
Authors: de Brouwer Anouk J , Areshenkoff Corson N , Rashid Mohammad R , Flanagan J Randall , Poppenk Jordan , Gallivan Jason P 
Published: November 2021

Abstract
Error-based and reward-based processes are critical for motor learning and are thought to be mediated via distinct neural pathways. However, recent behavioral work in humans suggests that both learning processes can be bolstered by the use of cognitive strategies, which may mediate individual differences in motor learning ability. It has been speculated that medial temporal lobe regions, which have been shown to support motor sequence learning, also support the use of cognitive strategies in error-based and reinforcement motor learning. However, direct evidence in support of this idea remains sparse. Here we first show that better overall learning during error-based visuomotor adaptation is associated with better overall learning during the reward-based shaping of reaching movements. Given the cognitive contribution to learning in both of these tasks, these results support the notion that strategic processes, associated with better performance, drive intersubject variation in both error-based and reinforcement motor learning. Furthermore, we show that entorhinal cortex volume is larger in better learning individuals—characterized across both motor learning tasks—compared with their poorer learning counterparts. These results suggest that individual differences in learning performance during error and reinforcement learning are related to neuroanatomical differences in entorhinal cortex.
Bacterial Endosymbionts of Bactericera maculipennis and Three Mitochondrial Haplotypes of B. cockerelli (Hemiptera: Psylloidea: Triozidae)
Authors: Cooper W Rodney , Horton David R , Swisher-Grimm Kylie , Krey Karol , Wildung Mark R 
Published: November 2021

Abstract
Insects harbor bacterial endosymbionts that provide their hosts with nutritional benefit or with protection against natural enemies, plant defenses, insecticides, or abiotic stresses. We used directed sequencing of 16S rDNA to identify and compare endosymbionts of Bactericera maculipennis (Crawford) and the western, central, and northwestern haplotypes of B. cockerelli (Šulc) (Hemiptera: Psylloidea: Triozidae). Both species are native to North America, are known to harbor the plant pathogen ‘Candidatus Liberibacter solanacearum’ and develop on shared host plants within the Convolvulaceae. The Old-World species Heterotrioza chenopodii (Reuter) (Psylloidea: Triozidae), now found in North America, was included as an outgroup. 16S sequencing confirmed that both Bactericera species harbor ‘Candidatus Liberibacter solanacearum’ and revealed that both species harbor unique strains of Wolbachia and Sodalis. However, the presence of Wolbachia and Sodalis varied among haplotypes of B. cockerelli. The central and western haplotypes harbored the same strains of Wolbachia, which was confirmed by Sanger sequencing of the wsp and ftsZ genes. Wolbachia was also detected in very low abundance from the northwestern haplotype by high-throughput sequencing of 16S but was not detected from this haplotype by PCR screening. The northwestern and central haplotypes also harbored Sodalis, which was not detected in the western haplotype. Heterotrioza chenopodii harbored an entirely different community of potential endosymbionts compared with the Bactericera spp. that included Rickettsia and an unidentified bacterium in the Enterobacteriaceae. Results of this study provide a foundation for further research on the interactions between psyllids and their bacterial endosymbionts.
Welcomeness for people with substance use disorders to general practice: a qualitative study
Authors: Abbott Penelope , Watt Kelly , Magin Parker , Davison Joyce , Hu Wendy C Y 
Published: November 2021

AbstractBackgroundGood primary care for people with substance use disorders (SUDs) is crucial given the high prevalence of SUDs and overdose deaths.ObjectiveTo explore general practice care for people with a history of SUDs from the perspectives of women involved with the criminal justice system.MethodsQualitative interview study with pre- and postrelease interviews, undertaken in Australian prisons and community settings. We utilized thematic analysis informed by constructivist grounded theory.ResultsWe undertook 65 interviews with 39 women. Access to and experience of general practitioner (GP) care was affected by perceived welcomeness, decisions around disclosure, and consultation experiences related to medication prescription. Participants reported that they were not as welcome as other patients, welcome could be conditional on not disclosing SUDs or only requesting unrelated healthcare, and GPs did not always differentiate between past and current drug use. Participants perceived difficulty finding general practices where the potential benefit of disclosing SUDs outweighed the risks of stigmatized reactions and lack of GP skills and interest. Participants did not always recognize that care beyond physical health could occur in general practice. The pejorative implications of labelling patients as “doctor shoppers” were challenged by participants, as they considered it could be necessary to attend multiple GPs to find a welcoming practice.ConclusionsPeople with histories of SUDs do not uniformly experience welcomeness in general practice, perpetuating poor engagement in healthcare and poor outcomes related to SUDs. Programmes targeting prescription drug misuse through general practice should also promote welcomeness for people with SUDs.