Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent developments in spatial analysis : spatial statistics, behavioural modelling, and computational intelligence

M.M. Fischer, A. Getis: Advances in Spatial Science. - Spatial Data Analysis: E. Casetti: Mixed Estimation and the Expansion Method: An Application to the Spatial Science Modelling of the AIDS Epidemic. - L. Anselm, S. Bao: Exploratory Spatial Data Analysis Linking SpaceStat and ArcView. - A.S. Fotheringham, M. Charlton, C. Brunsdon: Measuring Spatial Variations in Relationships with Geographically Weighted Regression. - S. Wise, R. Haining, J. Ma: Regionalisation Tools for the Exploratory Spatial Analysis of Health Data. - J.D. Logan, A.D. Cliff: A Structural Time Series Approach to Forecasting the Space-Time Incidence of Infectious Diseases: Post-War Measles Elimination Programmes in the Unites States and Iceland. - R. Thomas, F. Smyth: Estimating the Impact of Preventative Action on the Space-Time Incidence of HIV/AIDS. - Behavioural Modelling: J. Odland: Longitudinal Approaches to Analyzing Migration Behaviour in the Context of Personal Histories. - M. -P. Kwan, R.G. Golledge: Computational Process Modelling of Disaggregate Travel Behaviour. - J-C. Thill, J.L. Horowitz: Modelling Non-Work Destination Choices with Choice Sets Defined by Travel-Time Constraints. - R.G. V. Baker: Space-Time Consumer Modelling, Store Wars and Retail Trading Hour Policy in Australia. - T.A. Arentze, A.W. J. Borgers, H.J.P. Timmermans: A Multi-Objective Model for Developing Retail Location Strategies in a DSS Environment. - J.O. Huff, A.S. Huff: Recent Developments in the Modelling of Strategy Reformulation. - G.F. Mulligan: Some Implications of Behaviour in Agricultural Markets. - CI-based Spatial Analysis: G.G. Wilkinson: Neurocomputing for Earth Observation - Recent Developments and Future Challenges. - S. Gopal, M.M. Fischer: Fuzzy ARTMAP - A Neural Classifier for Multispectral Image Classification. - Y. Leung: Feedforward Neural Network Models s and Spatial Data Classfication and Rule Learning. - S. Opensahw: Building Fuzzy Spatial Inetraction Models. - M.M. Fischer, A. Getis: Epilogue.
Non–fuzzy sets for intuitionistic fuzzy sets

Abstract We examine an important paper of Gerstenkorn and Mańko that was published in Fuzzy Sets and Systems. Their paper is the pioneer for correlation coefficient similarity measure. We point out several questionable results and then provide our improvement that will useful to develop theoretical structure for similarity measures under intuitionistic fuzzy sets environment.
Malaria trends in districts that were targeted and not-targeted for seasonal malaria chemoprevention in children under five years of age in Guinea, 2014 - 2021

Background. Seasonal malaria chemoprevention (SMC) is one of the main interventions recommended by WHO to prevent and reduce childhood malaria. Since 2015, Guinea has implemented SMC targeting children aged 3 - 59 months (CU5) in districts with high and seasonal malaria transmission. Objective. We assessed the programmatic impact of SMC in Guinea s context of scaled-up malaria intervention programming by comparing malaria-related outcomes in 14 districts that had (n = 8) or had not (n = 6) been targeted for SMC. Methods. Using routine health management information system data, we calculated the district-level monthly test positivity rate (TPR) and monthly uncomplicated and severe malaria incidence for the whole population and disaggregated age groups (<5yrs and >= 5yrs of age). Changes in malaria indicators through time were analyzed by calculating the district-level compound annual growth rate (CAGR) from 2014 to 2021; we used statistical analyses to describe the time trend of the number of tested clinical cases, TPR, uncomplicated malaria incidence, and severe malaria incidence. Results. The CAGR of TPR of all age groups was statistically lower in SMC (median = -7.8%, range [IQR] = -9.7%, -5.5%) compared to non-SMC (median = -3.0%, IQR = -3.0%, -1.2%) districts. Similarly, the CAGR in uncomplicated malaria incidence was significantly lower in SMC (median = 1.8%, IQR = -0.9%, 3.5%) compared to non-SMC (median = 11.5%, IQR = 8.8%, 14.0%) districts. For both TPR and uncomplicated malaria incidence the observed difference was also significant age disaggregated. The CAGR of severe malaria incidence showed that all age groups experienced a decline in severe malaria in both SMC and non-SMC districts. However, this decline was significantly higher in SMC (median = -22.3%, IQR= -27.6%, -18.2%) than in non-SMC (median = -5.1%, IQR= -7.7; -3.6) districts for the entire population, as well as both CU5 and people over 5 years of age. Conclusion. Our results provide evidence to support that --even in an operational programming context--adding SMC to the comprehensive package of malaria interventions yields a positive epidemiological impact and results in greater reduction in TPR, as well as the incidence of uncomplicated and severe malaria in CU5.
Collaborative and privacy-preserving workflows on a clinical data warehouse: an example developing natural language processing pipelines to detect medical conditions

Objective To develop and validate advanced natural language processing pipelines that detect 18 conditions in clinical notes written in French, among which 16 comorbidities of the Charlson index, while exploring a collaborative and privacy-preserving workflow. Materials and methods The detection pipelines relied both on rule-based and machine learning algorithms for named entity recognition and entity qualification, respectively. We used a large language model pre-trained on millions of clinical notes along with clinical notes annotated in the context of three cohort studies related to oncology, cardiology and rheumatology, respectively. The overall workflow was conceived to foster collaboration between studies while complying to the privacy constraints of the data warehouse. We estimated the added values of both the advanced technologies and the collaborative setting. Results The 18 pipelines reached macro-averaged F1-score, positive predictive value, sensitivity and specificity of 95.7 (95%CI 94.5 - 96.3), 95.4 (95%CI 94.0 - 96.3), 96.0 (95%CI 94.0 - 96.7) and 99.2 (95%CI 99.0 - 99.4), respectively. F1-scores were superior to those observed using either alternative technologies or non-collaborative settings. The models were shared through a secured registry. Conclusions We demonstrated that a community of investigators working on a common clinical data warehouse could efficiently and securely collaborate to develop, validate and use sensitive artificial intelligence models. In particular, we provided efficient and robust natural language processing pipelines that detect conditions mentioned in clinical notes.
Recent advances in upstream process development for production of recombinant adeno‐associated virus

Recombinant adeno‐associated virus (rAAV) is rapidly emerging as the preferred delivery vehicle for gene therapies, with promising advantages in safety and efficacy. Key challenges in systemic in‐vivo rAAV gene therapy applications are the gap in production capabilities versus potential market demand and complex production process. This review summarizes current available information on rAAV upstream manufacturing processes and proposed optimizations for production. The advancements in rAAV production media were reviewed with proposals to speed up the cell culture process development. Furthermore, major methods for genetic element delivery to host cells were summarized with their advantages, limitations, and future directions for optimization. In addition, culture vessel selection criteria were listed based on production cell system, scale, and development stage. Process control at the production step was also outlined with an in‐depth understanding of production kinetics and quality control.
A pan-cancer analysis of pituitary tumor-transforming 3, pseudogene.

BACKGROUND Although evidence regarding pituitary tumor-transforming 3, pseudogene (PTTG3P) involvement in human cancers has been acquired via human and animal model-based molecular studies, there is a lack of pan-cancer analysis of this gene in human tumors. METHODS Tumor-causing effects of PTTG3P in 24 human tumors were explored using The Cancer Genome Atlas (TCGA) datasets from different bioinformatics databases and applying in silico tools such as The University of ALabama at Birmingham CANcer (UALCAN), Human Protein Atlas (HPA), Kaplan Meier (KM) plotter, cBioPortal, Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), Cytoscape, Database for Annotation, Visualization, and Integrated Discovery (DAVID), Tumor IMmune Estimation Resource (TIMER), and Comparative Toxicogenomics Database (CTD). Then, via in vitro experiments, including RNA sequencing (RNA-seq) and targeted bisulfite sequencing (bisulfite-seq), expression and promoter methylation levels of PTTG3P were verified in cell lines. RESULTS The PTTG3P expression was overexpressed across 23 malignancies and its overexpression was further found significantly effecting the overall survival (OS) durations of the esophageal carcinoma (ESCA) and head and neck cancer (HNSC) patients. This important information helps us to understand that PTTG3P plays a significant role in the development and progression of ESCA and HNSC. As for PTTG3P functional mechanisms, this gene along with its other binding partners was significantly concentrated in "Oocyte meiosis", "Cell cycle", "Ubiquitin mediated proteolysis", and "Progesterone-mediated oocyte maturation". Moreover, ESCA and HNSC tissues having the higher expression of PTTG3P were found to have lower promoter methylation levels of PTTG3P and higher CD8+ T immune cells level. Additionally, PTTG3P expression-regulatory drugs were also explored in the current manuscript for designing appropriate treatment strategies for ESCA and HNSC with respect to PTTG3P expression. CONCLUSION Our pan-cancer based findings provided a comprehensive account of the oncogenic role and utilization of PTTG3P as a novel molecular biomarker of ESCA and HNSC.
Social media opposition to the 2022/2023 UK nurse strikes.

Previous research has established that the success of strikes, and social movements more broadly, depends on their ability to garner support from the public. However, there is scant published research investigating the response of the public to strike action by healthcare workers. In this study, we address this gap through a study of public responses to UK nursing strikes in 2022-2023, using a data set drawn from Twitter of more than 2300 publicly available tweets. We focus on negative tweets, investigating which societal discourses social media users draw on to oppose strike action by nurses. Using a combination of corpus-based approaches and discourse analysis, we identified five categories of opposition: (i) discourse discrediting nurses; (ii) discourse discrediting strikes by nurses; (iii) discourse on the National Health System; (iv) discourse about the fairness of strikers' demands and (v) discourse about potential harmful impact. Our findings show how social media users operationalise wider societal discourses about the nursing profession (e.g., associations with care, gender, vocation and sacrifice) as well as recent crises such as the Covid-19 pandemic to justify their opposition. The results also provide valuable insights into misconceptions about nursing, strike action and patient harm, which can inform strategies for public communication.
De l'imagerie chimique à la micro-cartographie Pression-Température-Déformation : évolution minéralogique et transport de matière dans des systèmes en déséquilibre thermomécanique. Applications aux métapélites et aux matériaux de stockage de déchets radioactifs

Les roches metamorphiques ou les materiaux industriels voient leur composition mineralogique evoluer lorsqu'ils sont soumis a des desequilibres thermomecaniques, c'est-a-dire a une evolution spatiale ou temporelle de la pression et de la temperature, ou des desequilibres chimiques comme des variations des conditions redox, du pH. Par exemple, a basse temperature, les roches sous l'influence des processus metamorphiques ne se reequilibrent que partiellement, sauvegardant ainsi des equilibres thermodynamiques de maniere locale et augmentant leurs heterogeneites chimiques spatiales. La comprehension de tels systemes en evolution P-T et le dechiffrage des modalites de leur evolution mineralogique impliquent de reconnaitre et de caracteriser la taille de ces « paleo equilibres » locaux, et donc d'avoir une information chimique spatiale au moins en 2 dimensions. Afin d'obtenir cette information, des images microsondes de fluorescence X ont ete utilisees. Pour accroitre leur potentiel et les employer a des fins thermobarometriques, des scripts informatiques ont alors ete developpes sous Matlab. Ils permettent de quantifier ces images semi-quantitatives mais egalement de les coupler avec la technique thermodynamique des multi-equilibres afin de produire des cartes de P-T de formation des mineraux. Comme le montrent les premieres applications realisees sur deux metapelites provenant de la ceinture schiste bleu de Sambagawa au Japon et de la zone eclogitique preservee de la chaine Caledonienne au Spitzberg, les cartes chimiques quantitatives sont tres riches d'enseignement sur l'histoire metamorphique d'une roche. De ces cartes chimiques ont ete derivees des cartes de P-T-temps-redox-deformation d'echantillons, permettant de caracteriser les conditions P-T de formation des mineraux et donc le chemin P-T de l'echantillon, l'etat d'oxydation du fer dans la phase chlorite, de souligner la relation entre deformation et cristallisation, de proposer une chronologie relative de cristallisation des mineraux et des deformations. La carte de la teneur en Fe3+ dans les chlorites calculee par la thermodynamique a egalement ete validee grâce a une cartographie µ-XANES au seuil K du fer mesuree a l'ESRF (ID24) avec une methode innovante. La derniere application concerne une etude experimentale de materiaux argileux, principaux constituants d'un modele analogique d'un type de site de stockage de dechets nucleaires. Les images chimiques ont permis de caracteriser en 2 dimensions l'evolution mineralogique des argiles vers des poles riches en fer. Elles ont egalement ete utilisees comme donnees de base pour la realisation d'un modele numerique 2D par elements finis visant a estimer le coefficient de diffusion du fer dans les argiles a basse temperature, donnee importante pour modeliser la destabilisation au cours du temps d'un site de stockage de dechets radioactifs.
Genome-wide identification of transcriptional enhancers during human placental development and association with function, differentiation, and disease

Abstract The placenta is a dynamic organ that must perform a remarkable variety of functions during its relatively short existence in order to support a developing fetus. These functions include nutrient delivery, gas exchange, waste removal, hormone production, and immune barrier protection. Proper placenta development and function are critical for healthy pregnancy outcomes, but the underlying genomic regulatory events that control this process remain largely unknown. We hypothesized that mapping sites of transcriptional enhancer activity and associated changes in gene expression across gestation in human placenta tissue would identify genomic loci and predicted transcription factor activity related to critical placenta functions. We used a suite of genomic assays [i.e., RNA-sequencing (RNA-seq), Precision run-on-sequencing (PRO-seq), and Chromatin immunoprecipitation-sequencing (ChIP-seq)] and computational pipelines to identify a set of >20 000 enhancers that are active at various time points in gestation. Changes in the activity of these enhancers correlate with changes in gene expression. In addition, some of these enhancers encode risk for adverse pregnancy outcomes. We further show that integrating enhancer activity, transcription factor motif analysis, and transcription factor expression can identify distinct sets of transcription factors predicted to be more active either in early pregnancy or at term. Knockdown of selected identified transcription factors in a trophoblast stem cell culture model altered the expression of key placental marker genes. These observations provide a framework for future mechanistic studies of individual enhancer–transcription factor–target gene interactions and have the potential to inform genetic risk prediction for adverse pregnancy outcomes. Summary Sentence Mapping sites of transcriptional enhancer activity and associated gene expression in human placenta across gestation identifies genomic loci and predicted transcription factor activity related to critical placenta functions. Graphical Abstract
Working memory performance in glioma patients is associated with functional connectivity between the right dorsolateral prefrontal cortex and default mode network

In healthy subjects, activity in the default mode network (DMN) and the frontoparietal network (FPN) has consistently been associated with working memory (WM). In particular, the dorsolateral prefrontal cortex (DLPFC) is important for WM. The functional–anatomical basis of WM impairment in glioma patients is, however, still poorly understood. We investigated whether WM performance of glioma patients is reflected in resting‐state functional connectivity (FC) between the DMN and FPN, additionally focusing on the DLPFC. Resting‐state functional MRI data were acquired from 45 glioma patients prior to surgery. WM performance was derived from a pre‐operative N‐back task. Scans were parcellated into ROIs using both the Gordon and Yeo atlas. FC was calculated as the average Pearson correlation between functional time series. The FC between right DLPFC and DMN was inversely related to WM performance for both the Gordon and Yeo atlas (p = .010). No association was found for FC between left DLPFC and DMN, nor between the whole FPN and DMN. The results are robust and not dependent on atlas choice or tumor location, as they hold for both the Gordon and Yeo atlases, and independently of location variables. Our findings show that WM performance of glioma patients can be quantified in terms of interactions between regions and large‐scale networks that can be measured with resting‐state fMRI. These group‐based results are a necessary step toward development of biomarkers for clinical management of glioma patients, and provide additional evidence that global disruption of the DMN relates to cognitive impairment in glioma patients.
Clasificaciones climáticas aplicadas a Galicia: revisión desde una perspectiva biogeográfica

En este trabajo se revisan los principales métodos de clasificación climática que han sido aplicados al territorio gallego, haciendo especial énfasis en aquellos orientados a explicar la relación entre parámetros climáticos y la distribución de los vegetales sobre la superficie terrestre (bioclimatología). Igualmente, se presentan por primera vez expresiones cartográficas de detalle (macrobioclimas, bioclimas, termotipos y ombrotipos) resultantes de la aplicación de la “Clasificación Bioclimática Mundial” de S. Rivas-Martínez a una base de 209 estaciones meteorológicas de Galicia y territorios próximos. Según esta clasificación bioclimática, la mayor parte del territorio de Galicia se encuentra dentro del macrobioclima templado, perteneciendo una proporción elevada del mismo a su variante submediterránea, mientras que solamente el tramo final de la cuenca del Río Sil y sus principales afluentes (Bibei, Xares, Lor) pertenecen al macrobioclima mediterráneo-pluviestacional. En cuanto al grado de continentalidad, se puede considerar que la mayor parte de Galicia presenta un clima poco contrastado (bioclimas hiperoceánicos y semioceánicos), debido al efecto modulador del mar. De esta tendencia se aleja únicamente el extremo SE que se incluye en el bioclima semicontinental. Los termotipos presentes en las áreas templadas son termotemplado, mesotemplado, supratemplado, orotemplado y criorotemplado, este último restringido a las cumbres más elevadas del macizo de Trevinca-Sanabria; dentro de las áreas mediterráneas se reconoce exclusivamente el termotipo mesomediterráneo. Los ombrotipos representados comprenden desde el subhúmedo inferior al ultrahiperhúmedo, siendo dominantes los de tipo húmedo (inferior y superior). Por último, se discuten algunas cuestiones relativas a las limitaciones derivadas de la red de estaciones meteorológicas empleada así como la necesidad de su mejora para cubrir las crecientes demandas de información relativas al calentamiento global y su posible influencia en los hábitats terrestres, especialmente en las áreas de montaña.
Screening for ADHD in Adult Patients With Epilepsy: Prevalence of Symptoms and Challenges to Diagnosis

Objective: Given the complex nature of seizure disorders and their treatments, ADHD may be underdiagnosed in this population. We hypothesized that a higher percentage of patients presenting to a seizure clinic would endorse ADHD symptoms compared to rates reported in the general population and that formal screening for ADHD symptoms would identify patients with previously undiagnosed comorbid ADHD. Methods: In this study, we surveyed 312 adults in a seizure clinic using the Adult ADHD Self-Report Scale (ASRS-v1.1). Results: We found that 90 patients (28.8%) screened positive with the ASRS-v1.1, but only nine of these patients were able to complete neuropsychological testing,. Out of these patients, only one was diagnosed with possible ADHD. Conclusion: Through this process, we identified many challenges to making a new ADHD diagnosis in this population, including attention deficits due to other medical or psychiatric diagnoses, a positive urine drug screen, lack of collateral report/information about developmental history, and barriers to neuropsychological evaluation.
Gamma Drop Size Distribution Assumptions in Bulk Model Parameterizations and Radar Polarimetry and Their Impact on Polarimetric Radar Moments

A suitable formulation of the rain drop size distribution (DSD) is a prerequisite for a successful assimilation of radar polarimetric information on rain into a numerical weather prediction model. Popular DSD parameterizations in two-moment bulk microphysics schemes use relations between the so-called mean-mass diameter and the DSD shape parameter μ, in order to prevent overly strong size sorting in the models. In radar polarimetry constrained-gamma DSDs with empirical relations between the shape and scale parameter are commonly used. This study compares the different DSD formulations and highlights the differences. Synthetic polarimetric radar observations for X band (9.39 GHz) and S band (3 GHz) were calculated from the different DSDs using the T-matrix method. Depending on the constraint that is assumed for the DSDs, the polarimetric moments exhibit quite different dependencies on the mean diameter, which are particularly striking for differential reflectivity ZDR. To successfully assimilate observed polarimetric moments into atmospheric models, formulations—possibly more flexible than those investigated in this study—have to be found that sufficiently represent microphysical processes and at the same time are consistent with empirical relations derived from disdrometer and radar polarimetric measurements.