Miracle-dz/UniFAR-FTUs huggingface dataset:
Data-Centric Collaborative Innovation to Address Social Problems: The Experience and Lessons of “Data for Social Good” Projects

A collaborative approach involving public, private sector and citizen volunteers has been used to generate new ideas and design new solutions for government management and service. This study explores how collaborative innovation works in the field of data analysis by examining five data-centric collaborative projects initiated by a private company in Taiwan. These projects address important social issues such as domestic violence and poverty. Interviews of government and non-government actors revealed that these collaborative projects are suitable for experiments with new ideas and systems. The transformative learning process that occurred in the collaboration project illustrates the advantage of enlisting the support of people from different fields. The outcomes of collaboration brought new insights to predict the risk of domestic violence or other threats to children and adolescents, or the success rate of participants in job training programs. The diffusion of the collaborative model was also observed. However, there are several barriers to collaborative innovation and issues of equity, challenges to privacy and accountability, and the application of collaborative outcomes. This study brings us closer to understanding how collaborative innovation operates and can inform public managers on how to promote data-centric collaborative innovation in the future.
Benefits and Challenges of Digitalization: An Expert Study on Norwegian Public Organizations

The implementation of and research on digital transformation in the context of public organizations have increased substantially in the past few years. A wide range of drivers, benefits, and challenges associated with digitalization have been suggested in the literature. However, these suggestions appear fragmented and disconnected, and do not offer a clear overview of the main drivers, challenges, and benefits. Moreover, research in this regard in the Norwegian and Scandinavian contexts is lacking. Therefore, there is a need to clarify the drivers, benefits, and challenges of digital transformation. To address this need, seven Norwegian public organizations were investigated by gathering data through thirteen interviews. The findings pointed to an extensive number of drivers, benefits, and challenges, some of which stood out from the rest. Handling turbulent environment seemed to be the most mentioned driver, reducing costs were the most mentioned benefit and laws and regulations were the most mentioned challenge. This paper presents an overview of these aspects, explains them in detail, and suggests avenues for further research.
Mathematical Modeling into the Teaching Method of Higher Mathematics Courses in Application-Oriented Universities under the Epidemic Situation

The application of mathematics has become an important task of mathematics education. Mathematical modeling is a bridge between mathematics and the real world, a mathematical abstraction of real problems, and a higher level of comprehensive literacy. It can effectively improve students’ comprehensive practical ability and their ability to acquire knowledge independently, and at the same time, it is conducive to students’ achievement of other core mathematical literacy goals. Therefore, it is very necessary to apply the thought of mathematical modeling in mathematics classes of colleges and universities. It is found that the specific method and case implementation of applying mathematical modeling idea to classroom teaching is not thorough enough. The purpose of this paper is to study the method of integrating mathematical modeling into higher mathematics teaching in applied universities under the epidemic situation. In this article, through classroom practice and take the questionnaire research method, from the Angle of subjective and objective respectively from students’ mathematical modeling ideas on the improvement of their teaching and learning situation, etc to investigate, using mathematical modeling thought teaching can change students’ attitude and understanding of mathematics, and the ability to change students mathematics study, help students to set up the correct view of mathematics and mathematics learning concept. The proportion that “modeling ideas can stimulate learning interest” is above 40%.
Analysis of PAHs in Particulate Matter of a Diesel Engine by Gas Chromatography-Mass Spectrometry

It is difficult to analyze polycyclic aromatic hydrocarbons(PAHs) in particulate matter(PM) from diesel engine due to two reasons.One is the difficulty to completely extract PAHs due to carbon surrounding them,another is a large part of soluble organic fraction(SOF) in diesel PM emissions.In this paper,solvent and ultrasonic extraction methods were used to distill the SOF from PM emissions in state stage 3 and 4 diesel engines.By optimization of gas chromatography mass spectrometry equipment in-line sampling methods,ion source and chromatography temperature,a method which could analyse 16 kinds polycyclic aromatic hydrocarbons in diesel particulate matter was set up through utilization of full-scan mode for qualitative analysis and selected ion scan mode for quantitative analysis.The result showed that SOF fraction of PM emission in stage 4 diesel engine is lower than that of stage 3 engine under ESC test.The volume concentration of 16 PAHs in stage 4 engine is 10%-30% of stage 3 diesel engine.Under ETC test,the percent of PAHs is 14%-22%. There is little difference for PAHs emission between different emission control strategies for diesel engines under comparable emission level at the same operating condition.Total PAHs emission concentrations of stage 3 and 4 diesel engines under ETC test are 2 or 3 times to that of ESC test.
Decomposition of available potential energy for networks of connected volumes

Abstract A decomposition of available potential energy is derived for Boussinesq fluid flow in networks of connected control volumes. The two constituent parts of the decomposition are positive definite and therefore meaningful representations of available energy. The first (inner) part accounts for available potential energy that is intrinsic to each control volume, while the second (outer) part accounts for the context provided by the larger parent volume to which each smaller control volume belongs. While the intended application casts the control volumes as connected rooms in a building, the formulation can be applied to any domain that is partitioned by either physical boundaries or abstract zones and can be invoked recursively to clarify the hierarchical dependence of available potential energy on scale and context. By deriving budgets for the decomposition, two ways in which available potential energy can be redistributed between its inner and outer parts are identified. The first accounts for an apparent generation of available potential energy due to diapycnal mixing within a control volume that is constrained by removable boundaries. The second involves the reversible conversion between inner and outer parts that occurs when mass or heat is transported between control volumes and accounts for the concomitant change in context. Analytical expressions are derived for the hierarchy of contributions to available potential energy in an example involving three connected spaces, before budgets for the decomposition from a direct numerical simulation are analysed. Finally, the dependence of mixing efficiency on remote regions that was identified by Davies Wykes et al. (J. Fluid Mech., vol. 781, 2015, pp. 261–275) is revisited to demonstrate the precise way in which the proposed decomposition quantifies context.
‘It looks like a breadbox’: a pilot study investigating implementation of the Pepi-Pod® program with Aboriginal families in metropolitan South Australia

Abstract Aims: To collaboratively explore the cultural acceptance of the Pepi-Pod® program as an alternate safe sleep space and to explore the process of implementing the Pepi-Pod® program in a mainstream health service for Aboriginal families living in urban South Australia. Background: Aboriginal and Torres Strait Islander infants continue to die from sudden infant death syndrome (SIDS) and sudden unexpected death in infancy (SUDI) at rates three to four times greater than other infants born in Australia despite Council of Australian Governments commitment to halve the gap in the Indigenous infant mortality rate by 2018. The Pepi-Pod® program is evidenced in New Zealand and Queensland to provide a culturally appropriate safe sleep alternative that contributes to the reduction of SIDS and SUDI. We have no evidence of acceptability or feasibility when offered through mainstream services in metropolitan South Australia. Methods: With a focus on decolonizing the research process through a two-way process for mutual learning between Aboriginal and non-Aboriginal team members and community, a novel qualitative design was employed including photo elicited yarning sessions (n = 7), focus groups (n = 2), and field notes (n = 15). Results: Four themes emerged: ‘you don’t have to worry’; ‘a way of sharing knowledge’; ‘it looks like a bread box? ’ and ‘need for consistent safe sleep messages’. The findings suggest that participants believe the Pepi-Pod® program may enrich Aboriginal families’ lives evoking feelings of comfort and safety; however, the design could be improved to make them more culturally appropriate. There was confusion around safe sleep processes and education with a call for streamlining safe sleep messaging.
Phytochemical investigation and in vitro antioxidant activity of an indigenous medicinal plant Alpinia nigra B.L.Burtt

Objective:To investigate antioxidant potential of methanol extract of Alpinia nigra leaves. Methods:The study was done by using various in vitro methods such as 1,1-diphenyl—2picrylhydrazy](DPPH),2,2—azino-bis(3-ethylbenzthiazoline-6-sulphonic acid)(ABTS),nitricoxide and hydrogen peroxide radical scavenging assays.Phylochemical constituents,total phenolic content and total flavonoid content of the extract at different concentrations(10-500 μg/ mL)were determined. Results:Alpinia nigra leaves showed high free radical scavenging activity as evidenced by the low EC_(50) values in DPPH(64.51 μg/mL),in ABTS(28.32 μg/mL),in nitric oxide(80.02 μg/mL) and in H_2O_2(77.45 μg/mL) scavenging assays.Furthermore the TPC and TFC of the extract were found to be 69.25 mg gallic acid equivalent per grain of extract and 78.84 mg quercetin equivalent per gram of extract respectively. Conclusions:The results of present comprehensive analysis demonstrated that Alpinia nigra leaves possess high phenolic,llavonoid contents and potential antioxidant activity,and could be used as a viable source of natural antioxidants and might be exploited for functional foods and neutracentical applications.
Bidirectional cooperation between Ubtf1 and SL1 determines RNA Polymerase I promoter recognition in cell and is negatively affected in the UBTF-E210K neuroregression syndrome

Transcription of the ∼200 mouse and human ribosomal RNA genes (rDNA) by RNA Polymerase I (RPI/PolR1) accounts for 80% of total cellular RNA, around 35% of all nuclear RNA synthesis, and determines the cytoplasmic ribosome complement. It is therefore a major factor controlling cell growth and its misfunction has been implicated in hypertrophic and developmental disorders. Activation of each rDNA repeat requires nucleosome replacement by the architectural multi-HMGbox factor UBTF to create a 15kbp nucleosome free region (NFR). Formation of this NFR is also essential for recruitment of the TBP-TAFI factor SL1 and for preinitiation complex (PIC) formation at the gene and enhancer-associated promoters of the rDNA. However, these promoters show little sequence commonality and neither UBTF nor SL1 display significant DNA sequence binding specificity, making what drives PIC formation a mystery. Here we show that cooperation between SL1 and the longer UBTF1 splice variant generates the specificity required for rDNA promoter recognition in cell. We find that conditional deletion of the Taf1b subunit of SL1 causes a striking depletion UBTF at both rDNA promoters but not elsewhere across the rDNA. We also find that while both UBTF1 and −2 variants bind throughout the rDNA NFR, only UBTF1 is present with SL1 at the promoters. The data strongly suggest an induced-fit model of RPI promoter recognition in which UBTF1 plays an architectural role. Interestingly, a recurrent UBTF-E210K mutation and the cause of a pediatric neurodegeneration syndrome provides indirect support for this model. E210K knock-in cells show enhanced levels of the UBTF1 splice variant and a concomitant increase in active rDNA copies. In contrast, they also display reduced rDNA transcription and promoter recruitment of SL1. We suggest the underlying cause of the UBTF-E210K syndrome is therefore a reduction in cooperative UBTF1-SL1 promoter recruitment that may be partially compensated by enhanced rDNA activation.
drda: An R package for dose-response data analysis

Analysis of dose-response data is an important step in many scientific disciplines, including but not limited to pharmacology, toxicology, and epidemiology. The R package drda is designed to facilitate the analysis of dose-response data by implementing efficient and accurate functions with a familiar interface. With drda, it is possible to fit models by the method of least squares, perform goodness of fit tests, and conduct model selection. Compared to other similar packages, drda provides, in general, more accurate estimates in the least-squares sense. This result is achieved by a smart choice of the starting point in the optimization algorithm and by implementing the Newton method with a trust region with analytical gradients and Hessian matrices. In this article, drda is presented through the description of its methodological components and examples of its user-friendly functions. Performance is finally evaluated using a real, large-scale drug sensitivity screening dataset.
Depletion of TAX1BP1 Amplifies Innate Immune Responses during Respiratory Syncytial Virus Infection

Respiratory syncytial virus (RSV), which is the leading cause of lower respiratory tract illness in infants, remains a medical problem in the absence of a vaccine or efficient treatment. This virus is also recognized as a main pathogen in the elderly and immunocompromised people, and the occurrence of coinfections (with other respiratory viruses and bacteria) amplifies the risks of developing respiratory distress. ABSTRACT Respiratory syncytial virus (RSV) is the main cause of acute respiratory infections in young children and also has a major impact on the elderly and immunocompromised people. In the absence of a vaccine or efficient treatment, a better understanding of RSV interactions with the host antiviral response during infection is needed. Previous studies revealed that cytoplasmic inclusion bodies (IBs), where viral replication and transcription occur, could play a major role in the control of innate immunity during infection by recruiting cellular proteins involved in the host antiviral response. We recently showed that the morphogenesis of IBs relies on a liquid-liquid-phase separation mechanism depending on the interaction between viral nucleoprotein (N) and phosphoprotein (P). These scaffold proteins are expected to play a central role in the recruitment of cellular proteins to IBs. Here, we performed a yeast two-hybrid screen using RSV N protein as bait and identified the cellular protein TAX1BP1 as a potential partner of this viral protein. This interaction was validated by pulldown and immunoprecipitation assays. We showed that TAX1BP1 suppression has only a limited impact on RSV infection in cell cultures. However, RSV replication is decreased in TAX1BP1-deficient (TAX1BP1 knockout [TAX1BP1KO]) mice, whereas the production of inflammatory and antiviral cytokines is enhanced. In vitro infection of wild-type or TAX1BP1KO alveolar macrophages confirmed that the innate immune response to RSV infection is enhanced in the absence of TAX1BP1. Altogether, our results suggest that RSV could hijack TAX1BP1 to restrain the host immune response during infection. IMPORTANCE Respiratory syncytial virus (RSV), which is the leading cause of lower respiratory tract illness in infants, remains a medical problem in the absence of a vaccine or efficient treatment. This virus is also recognized as a main pathogen in the elderly and immunocompromised people, and the occurrence of coinfections (with other respiratory viruses and bacteria) amplifies the risks of developing respiratory distress. In this context, a better understanding of the pathogenesis associated with viral respiratory infections, which depends on both viral replication and the host immune response, is needed. The present study reveals that the cellular protein TAX1BP1, which interacts with the RSV nucleoprotein N, participates in the control of the innate immune response during RSV infection, suggesting that the N-TAX1BP1 interaction represents a new target for the development of antivirals.
Limits and potential of combined folding and docking

In the last decade, de novo protein structure prediction accuracy for individual proteins has improved significantly by utilising deep learning (DL) methods for harvesting the co-evolution information from large multiple sequence alignments (MSA). In CASP14, the best groups predicted the structure of most proteins with impressive accuracy. The same approach can, in principle, also be used to extract information about evolutionary-based contacts across protein-protein interfaces. However, most of the earlier studies have not used the latest DL methods for inter-chain contact distance prediction. This paper introduces a fold-and-dock method, PconsDock, based on predicted residue-residue distances with trRosetta. PconsDock can simultaneously predict the tertiary and quaternary structure of a protein pair, even when the structures of the monomers are not known. The straightforward application of this method to a standard dataset for protein-protein docking yielded limited success. However, using alternative methods for MSA generating allowed us to dock accurately significantly more proteins. We also introduced a novel scoring function, PconsDock, that accurately separates 98% of correctly and incorrectly folded and docked proteins. The average performance of the method is comparable to the use of traditional, template-based or ab initio shape-complementarity-only docking methods. However, no a priori structural information for the individual proteins is needed. Moreover, the results of conventional and fold-and-dock approaches are complementary, and thus a combined docking pipeline could increase overall docking success significantly. PconsDocck contributed to the best model for one of the CASP14 oligomeric targets, H1065.
A Xeno-free Media for the In Vitro Expansion of Human Spermatogonial Stem Cells

In vitro expansion of spermatogonial stem cells (SSCs) has been established using animal-derived fetal bovine serum (FBS) and bovine serum albumin (BSA). However, the use of animal components during cell culture introduces the risk of contaminating cells with pathogens, and leads to animal epitope expression, rendering them unsuitable for medical use. Therefore, this study set out to develop a xeno-free, fully defined media for the expansion of human SSCs. We show that the molecules Prostaglandin D2 (PGD-2) and Insulin-Like Growth Factor 1 (IGF-1) can replace FBS and BSA in cell culture media without loss of viability or expansion capability, and that Rho-Associated, Coiled-Coil Containing Protein Kinase (ROCK) inhibitor Y-27632 supplementation improves viability after cryopreservation. Long-term SSC cultures expanded in xeno-free, defined culture conditions shared identical protein expression profiles for well-known SSC markers, while gene expression analyses revealed a significant improvement in quiescent SSC and pan-germ markers. This xeno-free, defined formulation allows for standardized SSC culture free of animal pathogens.
Reducing Susceptibility Distortion Related Image Blurring in Diffusion MRI EPI Data

Diffusion magnetic resonance imaging (MRI) is an increasingly popular technique in basic and clinical neuroscience. One promising application is to combine diffusion MRI with myelin maps from complementary MRI techniques such as multi-parameter mapping (MPM) to produce g-ratio maps that represent the relative myelination of axons and predict their conduction velocity. Statistical Parametric Mapping (SPM) can process both diffusion data and MPMs, making SPM the only widely accessible software that contains all the processing steps required to perform group analyses of g-ratio data in a common space. However, limitations have been identified in its method for reducing susceptibility-related distortion in diffusion data. More generally, susceptibility-related image distortion is often corrected by combining oppositely phase-encoded images (blip-up and blip-down) using the arithmetic mean (AM), however, this can lead to blurred images. In this study we sought to (1) improve the susceptibility-related distortion correction for diffusion MRI data in SPM; (2) deploy an alternative approach to the AM to reduce image blurring in diffusion MRI data when combining blip-up and blip-down EPI data after susceptibility-related distortion correction; and (3) assess the benefits of these changes for g-ratio mapping. We found that the new processing pipeline, called consecutive HySCO, improved distortion correction when compared to the standard approach in the ACID toolbox for SPM. Moreover, using a weighted average (WA) method to combine the distortion corrected data from each phase-encoding polarity achieved greater overlap of diffusion and more anatomically faithful structural white matter probability maps derived from minimally distorted multi-parameter maps as compared to the AM. Third, we showed that the consecutive HySCO WA performed better than the AM method when combined with multi-parameter maps to perform g-ratio mapping. These improvements mean that researchers can conveniently access a wide range of diffusion-related analysis methods within one framework because they are now available within the open-source ACID toolbox as part of SPM, which can be easily combined with other SPM toolboxes, such as the hMRI toolbox, to facilitate computation of myelin biomarkers that are necessary for g-ratio mapping.