Miracle-dz/UniFAR-FTUs huggingface dataset:
A qualitative exploration of experiences of diagnosis amongst people living with type 2 diabetes

Background: Previous research has found that experiences of being diagnosed with Type 2 Diabetes (T2D) shape how people regard their condition, which can later have an impact on self management. This research examines experiences of diagnosis reported by people living with T2D. Methods: Using semi-structured interviews (N = 25), focus groups (3 x N = 12 participants) and open-ended questionnaires (N = 6), people living with T2D were recruited from a community-based T2D participation group. Data were analysed thematically using a framework analysis. Results: Patients’ accounts of diagnosis yielded 3 main themes: (1) Routes to diagnosis; (2) Symptom status during diagnosis experience; and (3) Responses to T2D diagnosis. It was found that participants’ routes to diagnosis and their experiences of symptoms prior to, and during, the diagnosis process presented varying barriers and facilitators to receiving, understanding and/or acting on, the ramifications of their condition. This, in turn, shaped how participants’ responded to their diagnosis. Conclusion: The paper concludes that positive experiences of diagnosis may be possible if barriers to receiving a T2D diagnosis are removed through health promotion measures. Equally, healthcare professionals should seek to resolve the uncertainties that people experience around the time of diagnosis. It is recommended that the latter could be achieved by tailoring patient information and support according to 1) routes to diagnosis, and 2) the stage of the condition has reached at the time of diagnosis.
Home range and activity of two sympatric fox species in the Bolivian Dry Chaco

Two fox species inhabit the Kaa Iya del Gran Chaco National Park in Bolivia: the crab eating fox Cerdocyon thous and the pampas fox Pseudalopex gymnocercus. We present the results of a study of the spatial ecology of these two species in Kaa Iya. In a series of bi-monthly systematic camera trap surveys, we set between 21 and 32 camera traps at different research camps over a four-year period (2001-2005). We recorded 215 photos of crab-eating foxes and 206 photos of pampas foxes. We captured three pampas foxes and four crab-eating foxes and fitted them with radio telemetry collars. Activity patterns of foxes (obtained from camera trap photos) were similar for both species: the activity peak was between 18:00 and 23:00h, with less activity between 10:00 and 17:00h. Home ranges of crab-eating foxes were between 155 and 293ha and for pampas foxes between 73 and 183ha. Female home ranges for both species were smaller than for males and only in one individual we observed a seasonal home range shift. Introduction The Gran Chaco is the third most extensive ecosystem in South America, covering more than one million km2. Canids are widely represented by two species, crab-eating fox and pampas fox, with the bush dog Speothos venaticus recently reported for the first time in the Kaa-Iya del Gran Chaco National Park, and the maned wolf Chrysocyon brachyurus in Copo National Park (Argentina). Even though both fox species inhabit a wide variety of Chaco habitats frequently in sympatry, the pampas fox is found more frequently in drier areas from southern Bolivia to central Argentina, while the crab-eating fox is more generalist, distributed in diverse environments below 2,000m (except Amazonia), and is scarce and even absent in the drier areas of Chaco (Eisenberg and Redford 1999, Emmons and Feer 1999). This paper compares home ranges and activity patterns of these two species in the Kaa-Iya National Park. Maffei et al. Sympatric foxes in Bolivia
Simulating Sequences of Earthquakes and Aseismic Slip

10 Numerical simulations of Sequences of Earthquakes and Aseismic Slip (SEAS) have 11 made great progress over the past decades to address important questions in earthquake 12 physics and fault mechanics. However, significant challenges in SEAS modeling remain 13 in resolving multiscale interactions between aseismic fault slip, earthquake nucleation, 14 and dynamic rupture; and understanding physical factors controlling observables such 15 as seismicity and ground deformation. The increasing capability and complexity of 16 SEAS modeling calls for extensive efforts to verify codes and advance these simulations 17 with rigor, reproducibility, and broadened impact. In 2018, we initiated a community 18 code-verification exercise for SEAS simulations, supported by the Southern California 19 Earthquake Center (SCEC). Here we report the findings from our first two benchmark 20 problems (BP1 and BP2), designed to test the capabilities of different computational 21 methods in correctly solving a mathematically well-defined, basic problem in crustal 22 faulting. These benchmarks are for a 2D antiplane problem, with a 1D planar vertical 23 strike-slip fault obeying rate-and-state friction, embedded in a 2D homogeneous, linear 24 elastic half-space. Sequences of quasi-dynamic earthquakes with periodic occurrences 25 (BP1) or bimodal sizes (BP2) and their interactions with aseismic slip are simulated. 26 The comparison of >70 simulation results from 11 groups using different numerical 27 methods, uploaded to our online platform, show excellent agreements in long-term and 28 coseismic evolution of fault properties. In BP1, we found that the truncated domain 29 boundaries influence interseismic fault stressing, earthquake recurrence, and coseismic 30 rupture process, and that agreement between models is only achieved with sufficiently 31 large domain sizes. In BP2, we found that complexity of long-term fault behavior 32 depends on how well important physical length scales related to spontaneous nucleation 33 and rupture propagation are resolved. Poor numerical resolution can result in the 34 generation of artificial complexity, impacting simulation results that are of potential 35 interest for characterizing seismic hazard, such as earthquake size distributions, moment 36 release, and earthquake recurrence times. These results inform the development of more 37 advanced SEAS models, contributing to our further understanding of earthquake system 38
Modelling Real Private Consumption Expenditure in South Africa to Test the Absolute Income Hypothesis

This paper explores, the hotly debated topic among economists and policymakers, whether fiscal and monetary policies impact on households by examining the relevance of the absolute income hypothesis in explaining private consumption expenditure and its relationship with household disposable income in South Africa. Worldwide, private consumption expenditure remains a big puzzle for leading consumption function theories. Friedmanâ€™s permanent income hypothesis posits that private consumption expenditure is not affected by how much consumers earn on a daily basis, but by what they expect to earn during their lifetime. Friedmanâ€™s permanent income hypothesis is at odds with Keynesâ€™s absolute income hypothesis, that private consumption expenditure is affected by fiscal stimulus policies, which are effective for increasing economic activity and employment. Subscribing to the former underrates the potential power of fiscal stimulus policies and other monetary or trade policies that boost short-term income. The overarching objective of this paper is to ascertain whether patterns of private consumption expenditure in South Africa are determined by Friedman or Keynesâ€™s theory. The paper specified econometric equations with quarterly seasonally adjusted data from the South African Reserve Bank for the sample period 1984 to 2015 and estimated them with cointegration techniques consisting of the Engle-Granger two-step approach. The importance of the paper and its scientific novelty are that it is more realistic since it specified models that take into account the reaction time of the dependent variable when the independent variable changes by imposing lags on the variables. The empirical results indicate that in South Africa, when household disposable income changes over time, private consumption expenditure depends more on a householdâ€™s previous disposable income than its current disposable income. The main empirical finding is that the absolute income hypothesis is not appropriate in explaining private consumption expenditure in this country. Even when the interest rate was included in a modified absolute income hypothesis, the overall estimates were not robust. Hence, estimates of the short- and long-run regression models were not consistent with the absolute income hypothesis. This is in line with arguments put forward in some extant studies using this model, that the fiscal stimulus policies might not generate the desired increased economic activity and employment. If households use money from the fiscal stimulus policies to bail themselves out of existing debts rather than consume additional goods and services which, would be the catalyzer to increase Gross Domestic Product (GDP).
Poly(ADP-Ribose) Polymerase-3 Regulates Regeneration in Planarians

Protein ADP-ribosylation is a reversible post-translational modification (PTM) process that plays fundamental roles in cell signaling. The covalent attachment of ADP ribose polymers is executed by PAR polymerases (PARP) and it is essential for chromatin organization, DNA repair, cell cycle, transcription, and replication, among other critical cellular events. The process of PARylation or polyADP-ribosylation is dynamic and takes place across many tissues undergoing renewal and repair, but the molecular mechanisms regulating this PTM remain mostly unknown. Here, we introduce the use of the planarian Schmidtea mediterranea as a tractable model to study PARylation in the complexity of the adult body that is under constant renewal and is capable of regenerating damaged tissues. We identified the evolutionary conservation of PARP signaling that is expressed in planarian stem cells and differentiated tissues. We also demonstrate that Smed-PARP-3 homolog is required for proper regeneration of tissues in the anterior region of the animal. Furthermore, our results demonstrate, Smed-PARP-3(RNAi) disrupts the timely location of injury-induced cell death near the anterior facing wounds and also affects the regeneration of the central nervous system. Our work reveals novel roles for PARylation in large-scale regeneration and provides a simplified platform to investigate PARP signaling in the complexity of the adult body.
Development and Evaluation of a Deep Learning System for Screening Retinal Hemorrhage Based on Ultra-Widefield Fundus Images

Purpose To develop and evaluate a deep learning (DL) system for retinal hemorrhage (RH) screening using ultra-widefield fundus (UWF) images. Methods A total of 16,827 UWF images from 11,339 individuals were used to develop the DL system. Three experienced retina specialists were recruited to grade UWF images independently. Three independent data sets from 3 different institutions were used to validate the effectiveness of the DL system. The data set from Zhongshan Ophthalmic Center (ZOC) was selected to compare the classification performance of the DL system and general ophthalmologists. A heatmap was generated to identify the most important area used by the DL model to classify RH and to discern whether the RH involved the anatomical macula. Results In the three independent data sets, the DL model for detecting RH achieved areas under the curve of 0.997, 0.998, and 0.999, with sensitivities of 97.6%, 96.7%, and 98.9% and specificities of 98.0%, 98.7%, and 99.4%. In the ZOC data set, the sensitivity of the DL model was better than that of the general ophthalmologists, although the general ophthalmologists had slightly higher specificities. The heatmaps highlighted RH regions in all true-positive images, and the RH within the anatomical macula was determined based on heatmaps. Conclusions Our DL system showed reliable performance for detecting RH and could be used to screen for RH-related diseases. Translational Relevance As a screening tool, this automated system may aid early diagnosis and management of RH-related retinal and systemic diseases by allowing timely referral.
Transcriptome analysis reveals the GRAS family in Salvia miltiorrhiza hairy roots in response to gibberellin

Background: Salvia miltiorrhiza is one of the most important traditional Chinese medicinal plants with high medicinal value. Gibberellins are growth-promoting phytohormones that regulate numerous growth and developmental processes. However, their role in regulating secondary metabolism has not been investigated. Results: In this study, we found that GA can promote hairy roots growth and increase the content of tanshinones and phenolic acids. Transcriptome sequencing revealed that secondary metabolism pathway genes were enriched in the GA-responded. After further analysis of the changes of GA signaling pathway genes, it was found that the GRAS transcription factors family had a significant response to GA. We identified 35 SmGRAS genes in S. miltiorrhiza. SmGRAS genes can be divided into ten subfamilies in which members of the same subfamily showed similar conserved motifs and gene structures, suggesting the possible conserved functions.Conclusions: Most SmGRAS genes are significantly responsive to GA, indicating that they may play an important role in the GA signaling pathway and participate in GA regulation of root growth and secondary metabolism in S. miltiorrhiza.
Complex Rupture of an Immature Fault Zone: A Simultaneous Kinematic Model of the 2019 Ridgecrest, CA Earthquakes

The 4 July 2019 Mw6.4 and subsequent 6 July 2019 Mw7.1 Ridgecrest sequence earthquakes (CA, USA) ruptured orthogonal fault planes in a low slip rate (1 mm/year) dextral fault zone in the area linking the Eastern California Shear Zone and Walker Lane. This region accommodates nearly one fourth of plate boundary motion and has been proposed to be an incipient transform fault system that could eventually become the main tectonic boundary, replacing the San Andreas Fault. We investigate the rupture process of these events using a novel simultaneous kinematic slip method with joint inversion of high‐rate GNSS, strong motion, GNSS static offset, and Interferometric Synthetic Aperture Radar data. We model the Coulomb stress change to evaluate how the Mw6.4 earthquake may have affected the subsequent Mw7.1 event. Our findings suggest complex interactions between several fault structures, including dynamic and static triggering, and provide important context for regional seismic source characterization and hazard models.
Estimating abundance and growth rates in a wild mountain gorilla population

Monitoring population size and growth over time is vital for the conservation of endangered species. Mountain gorillas Gorilla beringei beringei remain in two small populations that span the borders of the Democratic Republic of Congo, Rwanda and Uganda. Each population contains two subpopulations that receive differing levels of protection: the monitored groups are visited daily by park staff and researchers and can be counted by sight, whereas the number and growth rate of unmonitored gorillas must be estimated indirectly. Here, we re‐analyze published data from a survey in 2010 combined with new results from a survey conducted during two sampling occasions in 2015 and 2016 to estimate mountain gorilla abundance and growth in the Virunga Massif between 2010 and 2016. Using genetic analysis of non‐invasively collected samples and two capture–mark–recapture estimates, we estimated that the 186 detected genotypes represented 221 (95% credible interval: 204–243) to 251 (205–340) unmonitored gorillas in 2016. Together with the 418 monitored gorillas, the overall population of the Virunga Massif thus reached 639 (622–661) to 669 (623–758) individuals. We estimated the growth of the entire Virunga Massif population at about 3% per year, but determined that the growth of the monitored gorillas (4.4%) mainly drove that increase. In contrast, the trend of the unmonitored subpopulation could not be determined with confidence because both models provided 95% CI that encompassed zero: 0.5% per year (−0.7% to +1.7%) and 1.1% (−2.7% to +4.4%). While the overall growth rate represents a rare success story for primate conservation, our results highlight the need for greater protection of unmonitored gorillas.
Simulating protein–ligand binding with neural network potentials

Drug molecules adopt a range of conformations both in solution and in their protein-bound state. The strain and reduced flexibility of bound drugs can partially counter the intermolecular interactions that drive protein–ligand binding. To make accurate computational predictions of drug binding affinities, computational chemists have attempted to develop efficient empirical models of these interactions, although these methods are not always reliable. Machine learning has allowed the development of highly-accurate neural-network potentials (NNPs), which are capable of predicting the stability of molecular conformations with accuracy comparable to state-of-the-art quantum chemical calculations but at a billionth of the computational cost. Here, we demonstrate that these methods can be used to represent the intramolecular forces of protein-bound drugs within molecular dynamics simulations. These simulations are shown to be capable of predicting the protein–ligand binding pose and conformational component of the absolute Gibbs energy of binding for a set of drug molecules. Notably, the conformational energy for anti-cancer drug erlotinib binding to its target was found to be considerably overestimated by a molecular mechanical model, while the NNP predicts a more moderate value. Although the ANI-1ccX NNP was not trained to describe ionic molecules, reasonable binding poses are predicted for charged ligands, but this method is not suitable for modeling charged ligands in solution.
Fabrication of vertically aligned ferromagnetic ZnO nanopillar arrays on sapphire substrates by polymer-assisted deposition

Vertically aligned ferromagnetic ZnO nanopillar arrays have been fabricated on single-crystal sapphire substrates through polymer-assisted deposition. X-ray diffraction and transmission electron microscopy analysis show that the arrays are ZnO hexagonal crystal structure along the c-axial direction. The existence of room temperature ferromagnetism of the arrays was confirmed by the superconducting quantum interference device measurements. The enhancement of ferromagnetism in ZnO nanopillar arrays is found to be correlated with the increase in Zn1− vacancies and the decrease in oxygen interstitials, which was shown by photoluminescence measurements of the samples. Our results provide a viable way to fabricate ferromagnetic vertical arrays of ZnO nanopillars.Vertically aligned ferromagnetic ZnO nanopillar arrays have been fabricated on single-crystal sapphire substrates through polymer-assisted deposition. X-ray diffraction and transmission electron microscopy analysis show that the arrays are ZnO hexagonal crystal structure along the c-axial direction. The existence of room temperature ferromagnetism of the arrays was confirmed by the superconducting quantum interference device measurements. The enhancement of ferromagnetism in ZnO nanopillar arrays is found to be correlated with the increase in Zn1− vacancies and the decrease in oxygen interstitials, which was shown by photoluminescence measurements of the samples. Our results provide a viable way to fabricate ferromagnetic vertical arrays of ZnO nanopillars.
In silico prediction of neuropeptides from the neural ganglia of Pacific abalone Haliotis discus hannai (Mollusca: Gastropoda)

Abstract Neuropeptides play a central role in the regulation of reproduction, growth, development, and various other physiological processes. In our study, 26 neuropeptide precursors were identified from the pleuropedal and cerebral ganglia of Pacific abalone using transcriptome analysis. Of them, two (neuromacin and neuroglian) were potentially novel and two (myomodulin and FMRFamide) were involved in the reproductive regulation of mollusks. A BLAST search indicated that most of these neuropeptides exhibited the highest homologies with neuropeptides of other protostomian species. Myomodulin, FMRFamide, and molluscan insulin-related peptides shared 87%, 72%, and 88% sequence identities with homologous peptides of the tropical gastropod mollusk, Haliotis asinina. In silico analysis revealed that these identified neuropeptide precursors were likely to be extracellular secreted proteins. Alignment of multiple cerebrin, FFamide, and insulin-related peptide sequences illustrated that most of their biologically active residues were highly conserved with other invertebrate homologous neuropeptide residues. Three-dimensional (3D) structures of adipokinetic hormone, allatostain (A, B, and C), allatotropin, cerebrin, clionin, conopressin, elevenin, and neuromycin precursors in H. discus hannai exhibited a helix-loop-helix structure. Based on phylogenetic analysis, buccalin A1 and A2, allatostain B, and FCAP neuropeptide precursors of Pacific abalone formed a clade with other gastropod and bivalve mollusks neuropeptide precursors. This study provides a novel insight for further functional studies of abalone and other gastropod mollusks.
EDGE in Roux-en-Y gastric bypass: How does it compare to laparoscopy-assisted and balloon enteroscopy ERCP: a systematic review and meta-analysis

Abstract Background and study aims Endoscopic ultrasound-directed transgastric ERCP (EDGE) is a new endoscopic procedure to perform ERCP in Roux-en-y gastric bypass (RYGB) patients. The aim of this study was to conduct a systematic review and meta-analysis to evaluate technical success, clinical success and adverse effects of EDGE and compare it to laparoscopic ERCP (LA-ERCP) and balloon ERCP (BE-ERCP). Patients and methods We conducted a comprehensive search of several databases and conference proceedings including PubMed, EMBASE, Google-Scholar, LILACS, SCOPUS, and Web of Science databases to identify studies reporting on EDGE, LA-ERCP, and BE-ERCP. The primary outcome was to evaluate technical and clinical success of all three procedures and the secondary analysis focused on calculating the pooled rate of all adverse events (AEs), along with the commonly reported AE subtypes. Results Twenty-four studies on 1268 patients were included in our analysis with the majority of the population being males with mean age 53.72 years. Pooled rates of technical and clinical success with EDGE wer 95.5 % and 95.9 %, with LA-ERCP were 95.3 % and 92.9 % and were BE-ERCP were 71.4 % and 58.7 %, respectively. Pooled rates of all AEs with EDGE were 21.9 %, with LA-ERCP 17.4 % and with BE-ERCP 8.4 %. Stent migration was the most common AE with EDGE with 13.3 % followed by bleeding with 6.6 %. Conclusion Our meta-analysis demonstrated that the technical and clinical success of EDGE procedure is better than BE-ERCP and comparable to that of LA-ERCP in RYGB patients. EDGE also has a similar safety profile as compared to LA-ERCP but has higher AE rate as compared to BE-ERCP.