julilili42/papers huggingface dataset:
Combining Instrumental Monitoring and High-Resolution Topography for Estimating Sediment Yield in a Debris-Flow Catchment
2020-12-02

ABSTRACT In mountain basins, long-term instrumental monitoring coupled with high-resolution topographic surveys can provide important information on sediment yield. The Gadria catchment, located in the eastern Italian Alps, typically features several low-magnitude flood episodes and a few debris-flow events per year, from late spring to late summer. Beginning in 2011, sensors devoted to debris-flow detection (geophones, video cameras, flow stage sensors) were installed along the main channel, upstream of a retention basin. In case of debris flows, high-resolution topographical surveys of the retention basin are carried out multiple times per year. Rainfall is measured in the lower part of the catchment and at the headwaters, while passive integrated transponder tracing of bedload was performed in the main channel during spring and summer 2014. In this work, we present the reconstruction of the sediment dynamics at the catchment scale from 2011 to 2017. Results show that (i) coarse sediment yield is dominated by the few debris flows occurring per year; (ii) debris-flow volume estimations may be significantly different—up to 30 percent lower—when performed through a digital elevation model of difference analysis, compared to the time-integration of the debris-flow discharge estimates; (iii) using this latter method, the volumes are affected by significant uncertainties, particularly for small values of flow depth; and (iv) rainfall analysis permits us to characterize debris-flow initiation but also highlights difficulties in discriminating triggering from non-triggering rainstorms if based on rainfall duration and intensity only.
Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data
2020-12-02

Abstract Background Standard preprocessing of single-cell RNA-seq UMI data includes normalization by sequencing depth to remove this technical variability, and nonlinear transformation to stabilize the variance across genes with different expression levels. Instead, two recent papers propose to use statistical count models for these tasks: Hafemeister &amp; Satija [1] recommend using Pearson residuals from negative binomial regression, while Townes et al. [2] recommend fitting a generalized PCA model. Here, we investigate the connection between these approaches theoretically and empirically, and compare their effects on downstream processing. Results We show that the model of Hafemeister and Satija produces noisy parameter estimates because it is overspecified, which is why the original paper employs post-hoc smoothing. When specified more parsimoniously, it has a simple analytic solution equivalent to the rank-one Poisson GLM-PCA of Townes et al. Further, our analysis indicates that per-gene overdispersion estimates in Hafemeister and Satija are biased, and that the data are in fact consistent with the overdispersion parameter being independent of gene expression. We then use negative control data without biological variability to estimate the technical overdispersion of UMI counts, and find that across several different experimental protocols, the data are close to Poisson and suggest very moderate overdispersion. Finally, we perform a benchmark to compare the performance of Pearson residuals, variance-stabilizing transformations, and GLM-PCA on scRNA-seq datasets with known ground truth. Conclusions We demonstrate that analytic Pearson residuals strongly outperform other methods for identifying biologically variable genes, and capture more of the biologically meaningful variation when used for dimensionality reduction.
Effects of conflict trial proportion: A comparison of the Eriksen and Simon tasks
2020-12-02

Abstract Two experiments examined global and local behavioral adaptation effects within and across the Eriksen task, where conflict is based on stimulus letter identities, and the Simon task, where conflict is based on stimulus and response locations. Trials of the two tasks were randomly intermixed, and the list-wide proportion of congruent trials was varied in both tasks (Experiment 1) or in just one task (Experiment 2). The global adaptation effect of list-wide congruency proportion (LWPC effect) was at least as large in the Simon task as in the Eriksen task. Likewise, the local adaptation effect of previous-trial congruency (Gratton effect) was at least as large in the Simon task as in the Eriksen task. In contrast to prior studies investigating transfer across Stroop and Simon tasks, there was no dissociation between global and local adaptation effects regarding their transfer across the different conflict tasks. In fact, both local and global adaptation effects appeared largely task-specific, because there was no or only little transfer of either Gratton effects or LWPC effects from the Eriksen to the Simon task or vice versa. On the whole, the results suggest that behavioral adaptation observed in the present design does not carry over from one of these tasks to the other, suggesting no involvement of a higher-order, task-general mechanism of cognitive control.
High resolution three‐dimensional imaging and measurement of lung, heart, liver, and diaphragmatic development in the fetal rat based on micro‐computed tomography (micro‐CT)
2020-12-02

Abstract Understanding of normal fetal organ development is crucial for the evaluation of the pathogenesis of congenital anomalies. Various techniques have been used to generate imaging of fetal rat organogenesis, such as histological dissection with 3‐dimensional reconstruction and scanning electron microscopy. However, these techniques did not imply quantitative measurements of developing organs (volumes, surface areas of organs). Furthermore, a partial or total destruction of the embryos prior to analysis was inevitable. Recently, micro‐computed tomography (micro‐CT) has been established as a novel tool to investigate embryonic development in non‐dissected embryos of rodents. In this study, we used the micro‐CT technique to generate 4D datasets of rat embryos aged between embryonic day 15–22 and newborns. Lungs, hearts, diaphragms, and livers were digitally segmented in order to measure organ volumes and analyze organ development as well as generate high‐resolution 3D images. These data provide objective values compiling a 4D atlas of pulmonary, cardiac, diaphragmatic, and hepatic development in the fetal rat.
Geographical variation of the merging between dental and retroflex sibilants in Taiwan Mandarin
2020-12-02

This study investigates the geographical distribution of pronunciation variation of voiceless dental and retroflex sibilants in Taiwan Mandarin. Previous studies indicated that the merging of the two sibilants is geographically dependent (Line, 1983; Chuang, 2009). However, the geographical effects in these studies are not easy to interpret due to the limited number of speakers and regions. For the current study, we recruited 331 native speakers of Taiwan Mandarin from 120 regions in Taiwan. In a picture-naming task, 30 dental/retroflex-initial words were elicited from each speaker. The data were analysed with Generalized Additive Mixed models (Wood, 2004). The analysis revealed a robust effect of geographical location, with merging being less common in metropolitan cities as compared to the surrounding areas.
Negligible effects of birth order on selection into scientific and artistic careers, creativity, and status attainment
2020-12-02

We tested birth order effects on selection into different careers (scientific, artistic, and creative) and status attainment (educational attainment, occupational prestige, and income) using a large sample ( n = 3763), a longitudinal design, and relevant controls. Additionally, we tested mediation of birth order effects on career outcomes via personality traits, intelligence, and educational attainment. We found negligible birth order effects ranging from 0.02 to 0.12 on a correlational metric, where firstborns (vs. laterborns) selected into more creative careers and attained higher prestige and education. Conditional on the theoretically based mediation models tested, results showed that intelligence and educational attainment (but not personality traits) accounted for a statistically significant portion of the variance in the links between birth order and career outcomes. No direct effects of birth order on career outcomes remained when accounting for indirect effects through educational attainment. These findings bring modest support to the confluence model, no support to the niche-finding model, and suggest that one possible route via which birth order might impact career outcomes (if at all) could be via educational attainment.
On the processing of nonwords in word naming and auditory lexical decision
2020-12-02

Nonwords are often used to clarify how lexical processing takes place in the absence of semantics. This study shows that nonwords are not semantically vacuous. We used Linear Discriminative Learning (Baayen et al., 2019) to estimate the meanings of nonwords in the MALD database (Tucker et al., 2018) from the speech signal. We show that measures gauging nonword semantics significantly improve model fit for both acoustic durations and RTs. Although nonwords do not evoke meanings that afford conscious reflexion, they do make contact with the semantic space, and the angles and distances of nonwords with respect to actual words co-determine articulation and lexicality decisions.
Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)
2020-12-02

Abstract Although regulatory small RNAs have been reported in photosynthetic cyanobacteria, the lack of clear RNA chaperones involved in their regulation poses a conundrum. Here, we analyzed the full complement of cellular RNAs and proteins using gradient profiling by sequencing (Grad-seq) in Synechocystis 6803. Complexes with overlapping subunits such as the CpcG1-type versus the CpcL-type phycobilisomes or the PsaK1 versus PsaK2 photosystem I pre(complexes) could be distinguished, supporting the high quality of this approach. Clustering of the in-gradient distribution profiles followed by several additional criteria yielded a short list of potential RNA chaperones that include an YlxR homolog and a cyanobacterial homolog of the KhpA/B complex. The data suggest previously undetected complexes between accessory proteins and CRISPR-Cas systems, such as a Csx1-Csm6 ribonucleolytic defense complex. Moreover, the exclusive association of either RpoZ or 6S RNA with the core RNA polymerase complex and the existence of a reservoir of inactive sigma–antisigma complexes is suggested. The Synechocystis Grad-seq resource is available online at https://sunshine.biologie.uni-freiburg.de/GradSeqExplorer/ providing a comprehensive resource for the functional assignment of RNA–protein complexes and multisubunit protein complexes in a photosynthetic organism.
“Mind the Gap”: An 85-Year-Old Man with Severe Tricuspid Valve Regurgitation Who Underwent Percutaneous Edge-to-Edge Valve Leaflet Plication Using the New and Advanced MitraClip XTR System
2020-12-02

Patient: Male, 85-year-old Final Diagnosis: Severe tricuspid regurgitation Symptoms: Cardiac decompenstion • dyspnea Medication: — Clinical Procedure: Edge-to-edge valve repair using MitraCLip System XTR Specialty: Cardiology OBJECTIVE: Unusual clinical course BACKGROUND: Severe tricuspid valve regurgitation (TR) is associated with high cardiovascular mortality. Safe and feasible interventional approaches to treat severe TR are of clinical relevance. The MitraClip is a device that has been approved by the US Food and Drug Administration (FDA) for the repair of mitral valve lesions. Percutaneous femoral venous access with fluoroscopic and echocardiographic guidance is used to deliver a cobalt-chromium clip to secure the mitral valve leaflets. We report on an 85-year-old man with tricuspid valve regurgitation who underwent percutaneous edge-to-edge tricuspid valve leaflet plication with the new, advanced MitraClip XTR System. CASE REPORT: An 85-year-old man with severe TR due to annulus dilation of the right ventricle and short septal leaflet presented repeatedly at our hospital with severe right heart failure symptoms. Transesophageal echocardiography revealed severe TR with a large coaptation gap size of 10.6 mm. Percutaneous edge-to-edge valve repair with the new-generation MitraClip System XTR with wider clip arms could overcome the large coaptation gap. We achieved a strong reduction of TR after deploying 2 MitraClips XTR. The patient recovered quickly and has not been admitted to hospital due to heart failure symptoms since the intervention for more than 6 months. CONCLUSIONS: Previous studies have shown the safety and effectiveness of the MitraClip device and supported FDA approval for tricuspid valve repair. This report of a patient with complex tricuspid regurgitation demonstrated the feasible use of the new MitraClip XTR System, which improved edge-to-edge tricuspid valve repair due to its increased span and improved grip.
Toward catchment hydro‐biogeochemical theories
2020-12-03

Abstract Headwater catchments are the fundamental units that connect the land to the ocean. Hydrological flow and biogeochemical processes are intricately coupled, yet their respective sciences have progressed without much integration. Reaction kinetic theories that prescribe rate dependence on environmental variables (e.g., temperature and water content) have advanced substantially, mostly in well‐mixed reactors, columns, and warming experiments without considering the characteristics of hydrological flow at the catchment scale. These theories have shown significant divergence from observations in natural systems. On the other hand, hydrological theories, including transit time theory, have progressed substantially yet have not been incorporated into understanding reactions at the catchment scale. Here we advocate for the development of integrated hydro‐biogeochemical theories across gradients of climate, vegetation, and geology conditions. The lack of such theories presents barriers for understanding mechanisms and forecasting the future of the Critical Zone under human‐ and climate‐induced perturbations. Although integration has started and co‐located measurements are well under way, tremendous challenges remain. In particular, even in this era of “big data,” we are still limited by data and will need to (1) intensify measurements beyond river channels and characterize the vertical connectivity and broadly the shallow and deep subsurface; (2) expand to older water dating beyond the time scales reflected in stable water isotopes; (3) combine the use of reactive solutes, nonreactive tracers, and isotopes; and (4) augment measurements in environments that are undergoing rapid changes. To develop integrated theories, it is essential to (1) engage models at all stages to develop model‐informed data collection strategies and to maximize data usage; (2) adopt a “simple but not simplistic,” or fit‐for‐purpose approach to include essential processes in process‐based models; (3) blend the use of process‐based and data‐driven models in the framework of “theory‐guided data science.” Within the framework of hypothesis testing, model‐data fusion can advance integrated theories that mechanistically link catchments' internal structures and external drivers to their functioning. It can not only advance the field of hydro‐biogeochemistry, but also enable hind‐ and fore‐casting and serve the society at large. Broadly, future education will need to cultivate thinkers at the intersections of traditional disciplines with hollistic approaches for understanding interacting processes in complex earth systems. This article is categorized under: Engineering Water &gt; Methods
Defining colchicine resistance/intolerance in patients with familial Mediterranean fever: a modified-Delphi consensus approach
2020-12-03

Abstract Objectives Colchicine is the main treatment for FMF. Although a number of individuals with FMF are intolerant/resistant to colchicine, there is no standard definition of colchicine resistance/intolerance. We developed a set of evidence-based core statements defining colchicine resistance/intolerance in patients with FMF that may serve as a guide for clinicians and health authorities. Methods A set of statements was identified using a modified-Delphi consensus-based approach. The process involved development of an initial colchicine resistance/intolerance-related questionnaire derived from a systematic literature review. The questionnaire, which was completed by an international panel of 11 adult and paediatric rheumatologists with expertise in FMF, was analysed anonymously. The results informed draft consensus statements that were discussed by a round-table expert panel, using a nominal group technique to agree on the selection and wording of the final statements. Results Consensus among the panel was achieved on eight core statements defining colchicine resistance/intolerance in patients with FMF. A definition of resistance was agreed upon that included recurrent clinical attacks (average one or more attacks per month over a 3-month period) or persistent laboratory inflammation in between attacks. Other core statements recognize the importance of assessing treatment adherence, and the impact of active disease and intolerance to colchicine on quality of life. Conclusion Based on expert opinion, a set of evidence-based core statements defining colchicine resistance/intolerance in patients with FMF were identified to help guide clinicians and health authorities in the management of patients with FMF.
SmartPeak Automates Targeted and Quantitative Metabolomics Data Processing
2020-12-03

Technological advances in high-resolution mass spectrometry (MS) vastly increased the number of samples that can be processed in a life science experiment, as well as volume and complexity of the generated data. To address the bottleneck of high-throughput data processing, we present SmartPeak (https://github.com/AutoFlowResearch/SmartPeak), an application that encapsulates advanced algorithms to enable fast, accurate, and automated processing of capillary electrophoresis-, gas chromatography-, and liquid chromatography (LC)-MS(/MS) data and high-pressure LC data for targeted and semitargeted metabolomics, lipidomics, and fluxomics experiments. The application allows for an approximate 100-fold reduction in the data processing time compared to manual processing while enhancing quality and reproducibility of the results.
Structural order enhances charge carrier transport in self-assembled Au-nanoclusters
2020-12-03

Abstract The collective properties of self-assembled nanoparticles with long-range order bear immense potential for customized electronic materials by design. However, to mitigate the shortcoming of the finite-size distribution of nanoparticles and thus, the inherent energetic disorder within assemblies, atomically precise nanoclusters are the most promising building blocks. We report an easy and broadly applicable method for the controlled self-assembly of atomically precise Au 32 ( n Bu 3 P) 12 Cl 8 nanoclusters into micro-crystals. This enables the determination of emergent optoelectronic properties which resulted from long-range order in such assemblies. Compared to the same nanoclusters in glassy, polycrystalline ensembles, we find a 100-fold increase in the electric conductivity and charge carrier mobility as well as additional optical transitions. We show that these effects are due to a vanishing energetic disorder and a drastically reduced activation energy to charge transport in the highly ordered assemblies. This first correlation of structure and electronic properties by comparing glassy and crystalline self-assembled superstructures of atomically precise gold nanoclusters paves the way towards functional materials with novel collective optoelectronic properties.
CNS Invasion in Meningioma—How the Intraoperative Assessment Can Improve the Prognostic Evaluation of Tumor Recurrence
2020-12-03

The detection of the infiltrative growth of meningiomas into CNS tissue has been integrated into the WHO classification as a stand-alone marker for atypical meningioma. However, its prognostic impact has been questioned. Infiltrative growth can also be detected intraoperatively. The prognostic impact of the intraoperative detection of the central nervous system tissue invasion of meningiomas was analyzed and compared to the histopathological assessment. The clinical data of 1517 cases with follow-up data regarding radiographic recurrence was collected. Histopathology and operative reports were reviewed and invasive growth was seen during resection in 23.7% (n = 345) while histopathology detected it in 4.8% (n = 73). The histopathological and intraoperative assessments were compatible in 63%. The prognostic impact of histopathological and intraoperative assessment was significant in the univariate but not in the multivariate analysis. Both methods of assessment combined reached statistical significance in the multivariate analysis (p = 0.0409). A score including all independent prognostic factors divided the cohort into three prognostic subgroups with a risk of recurrence of 33.8, 64.7 and 88.5%, respectively. The intraoperative detection of the infiltrative growth of primary meningiomas into the central nervous system tissue can complement the histopathological assessment of CNS invasion. The combined assessment is an independent prognostic factor regarding tumor recurrence and allows a risk-adapted tumor stratification.
Neural changes in early visual processing after 6 months of mindfulness training in older adults
2020-12-03

Abstract Mindfulness has been shown to improve attentional performance, which is known to decline in aging. Long-latency electroencephalographic (EEG) event-related potential (ERP) changes have been reported immediately after mindfulness training, however the enduring stability of these effects is unknown. Furthermore, the ability of mindfulness to impact earlier stages of information processing is unclear. We examined neural activation using high density EEG in older adults engaged in mindfulness training to examine the long-term stability of training effects. After 6 months of training, mindfulness practitioners displayed enhanced neural activation during sensory encoding and perceptual processing of a visual cue. Enhanced perceptual processing of a visual cue was associated with increased neural activation during post-perceptual processing of a subsequent target. Similar changes were not observed in a control group engaged in computer-based attention training over the same period. Neural changes following mindfulness training were accompanied by behavioural improvements in attentional performance. Our results are suggestive of increased efficiency of the neural pathways subserving bottom-up visual processing together with an enhanced ability to mobilise top-down attentional processes during perceptual and post-perceptual processing following mindfulness training. These results indicate that mindfulness may enhance neural processes known to deteriorate in normal aging and age-related neurodegenerative diseases.