julilili42/papers huggingface dataset:
Learning Processes in Interactive CALL Systems: Linking Automatic Feedback, System Logs, and Learning Outcomes
2022-01-10

Interactive digital tools increasingly used for language learning can provide detailed system logs (e.g., number of attempts, responses submitted), and thereby a window into the user’s learning processes. To date, SLA researchers have made little use of such data to understand the relationships between learning conditions, processes, and outcomes. To fill this gap, we analyzed and interpreted detailed logs from an ICALL system used in a randomized controlled field study where 205 German learners of English in secondary school received either general or specific corrective feedback on grammar exercises. In addition to explicit pre-/post-test results, we derived 19 learning process variables from the system log. Exploratory factor analysis revealed three latent factors underlying these process variables: effort,accuracy focus, and time on task. Accuracy focus and finish time (a process variable that did not load well on any factors) significantly predicted pre-/post-test gain scores with a medium effect size. We then clustered learners based on their process patterns and found that the specific feedback group tended to demonstrate particular learning processes and that these patterns moderate the advantage of specific feedback. We discuss the implications of analyzing system logs for SLA, CALL, and education researchers and call for more collaboration.
Common variants in breast cancer risk loci predispose to distinct tumor subtypes.
2022-01-10

BACKGROUND: Genome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER) status, but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear. METHODS: Among 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes. RESULTS: Eighty-five of 173 variants were associated with at least one tumor feature (false discovery rate
Data from: Inheritance of DNA methylation differences in the mangrove Rhizophora mangle
2022-01-10

This record contains supplementary information for the article "Inheritance of DNA methylation differences in the mangrove Rhizophora mangle" published in Evolution&amp;Development. It contains the barcodes (barcodes.txt), the reference contigs (contigs.fasta.gz), the annotation of the reference contigs (mergedAnnot.csv.gz), the SNPs (snps.vcf.gz), the methylation data (methylation.txt.gz), and the experimental design (design.txt). All data are unfiltered. Short reads are available on SRA (PRJNA746695). Note that demultiplexing of the pooled reads (SRX11452376) will fail because the barcodes are already removed and the header information is lost during SRA submission. Instead, use the pre-demultiplexed reads that are as well linked to PRJNA746695. <br> <strong>Table S13 (TableS13_DSSwithGeneAnnotation.offspringFams.csv.gz): </strong> Differential cytosine methylation between families using the mother data set. The first three columns fragment number ("chr"), the position within the fragment ("pos"), and the sequence context ("context"). Columns with the pattern FDR_&lt;X&gt;_vs_&lt;Y&gt; contain false discovery rates of a test comparing population X with population Y. Average DNA methylation levels for each population are given in the columns "AC", "FD", "HI", "UTB", "WB", and "WI". The remaining columns contain the annotation of the fragment, for example whether it matches to a gene and if yes, the gene name ID and description are provided.
Conflicted Energy Transition—Conception of a Theoretical Framework for Its Investigation
2022-01-11

Energy transition plays a central role in efforts to reduce anthropogenic global warming. However, energy transition involves physical manifestations, for example in the form of wind turbines, photovoltaic plants, and power lines, which trigger resistance, especially among those who live in the vicinity of the (planned) plants. The reasons for this resistance are complex, as they relate to residents’ emotional ties and/or stereotypical common-sense expectations of landscape. The complexity of landscape conflicts in general, and energy transition-related conflicts in particular, makes it difficult to capture the intricacy of the subject matter by means of a single theoretical perspective. To address this difficulty, a neopragmatic approach of identifying and combining appropriate theoretical perspectives is utilized to develop an analytic framework for understanding these conflicts. To this end, we draw on Dahrendorf’s conflict theory and the framing approach. Both have high complementary explanatory potential and empirical applicability, with the framing approach broadening the theoretical prism to include micro-individuals and groups to Dahrendorf’s meso-social perspective.
Evaluation of decision-making in the treatment of acetabular fractures
2022-01-11

Treatment of acetabular fractures is challenging and risky, especially when surgery is performed. Yet, stability and congruity of the hip joint need to be achieved to ensure early mobilization, painlessness, and good function. Therefore, coming up with an accurate decision, whether surgical treatment is indicated or not, is the key to successful therapy. Data from the German pelvic Trauma Registry ( n = 4213) was evaluated retrospectively, especially regarding predictors for surgery. Furthermore, a logistic regression model with surgical treatment as the dependent variable was established. In total, 25.8% of all registered patients suffered from an acetabular fracture and 61.9% of them underwent surgery. The fracture classification is important for the indication of surgical therapy. Anterior wall fractures were treated surgically in 10.2%, and posterior column plus posterior wall fractures were operated on in 90.2%. Also, larger fracture gaps were treated surgically more often than fractures with smaller gaps (&gt;3 mm 84.4%, &lt;1 mm 20%). In total, 51.4% of women and 66.0% of men underwent surgery. Apart from the injury severity score (ISS), factors that characterize the overall picture of the injury were of no importance for the indication of a surgical therapy (isolated pelvic fracture: 62.0%, polytrauma: 58.8%). The most frequent reason for non-operative treatment was ‘minimal displacement’ in 42.2%. Besides fracture classification and fracture characteristics, no factors characterizing the overall injury, except for the ISS, and unexpectedly gender, are important for making a treatment decision. Further studies are needed to determine the relevance of these factors, and whether they should be used for the decision-making process, in particular surgeons with less experience in pelvic surgery, can orient themselves to.
Genome-Wide Association Study Identifies Two Common Loci Associated with Pigment Dispersion Syndrome/Pigmentary Glaucoma and Implicates Myopia in its Development
2022-01-11

Common SNPs relating to the GSAP and GRM5/TYR genes are associated risk factors for the development of PDS and PG. Although myopia is a known risk factor, this study uses genetic data to demonstrate that myopia is, in part, a cause of PDS and PG.
Efficient coding of natural scenes improves neural system identification
2022-01-11

Neural system identification aims at learning the response function of neurons to arbitrary stimuli using experimentally recorded data, but typically does not leverage normative principles such as efficient coding of natural environments. Visual systems, however, have evolved to efficiently process input from the natural environment. Here, we present a normative network regularization for system identification models by incorporating, as a regularizer, the efficient coding hypothesis, which states that neural response properties of sensory representations are strongly shaped by the need to preserve most of the stimulus information with limited resources. Using this approach, we explored if a system identification model can be improved by sharing its convolutional filters with those of an autoencoder which aims to efficiently encode natural stimuli. To this end, we built a hybrid model to predict the responses of retinal neurons to noise stimuli. This approach did not only yield a higher performance than the “stand-alone” system identification model, it also produced more biologically-plausible filters. We found these results to be consistent for retinal responses to different stimuli and across model architectures. Moreover, our normatively regularized model performed particularly well in predicting responses of direction-of-motion sensitive retinal neurons. In summary, our results support the hypothesis that efficiently encoding environmental inputs can improve system identification models of early visual processing.
Privacy-Preserving Federated Neural Network Learning for Disease-Associated Cell Classification
2022-01-11

ABSTRACT Training accurate and robust machine learning models requires a large amount of data that is usually scattered across data-silos. Sharing or centralizing the data of different healthcare institutions is, however, unfeasible or prohibitively difficult due to privacy regulations. In this work, we address this problem by using a novel privacy-preserving federated learning-based approach, PriCell , for complex machine learning models such as convolutional neural networks. PriCell relies on multiparty homomorphic encryption and enables the collaborative training of encrypted neural networks with multiple healthcare institutions. We preserve the confidentiality of each institutions’ input data, of any intermediate values, and of the trained model parameters. We efficiently replicate the training of a published state-of-the-art convolutional neural network architecture in a decentralized and privacy-preserving manner. Our solution achieves an accuracy comparable to the one obtained with the centralized solution, with an improvement of at least one-order-of-magnitude in execution time with respect to prior secure solutions. Our work guarantees patient privacy and ensures data utility for efficient multi-center studies involving complex healthcare data.
TAT–RHIM: a more complex issue than expected
2022-01-11

Murine cytomegalovirus protein M45 contains a RIP homotypic interaction motif (RHIM) that is sufficient to confer protection of infected cells against necroptotic cell death. Mechanistically, the N-terminal region of M45 drives rapid self-assembly into homo-oligomeric amyloid fibrils, and interacts with the endogenous RHIM domains of receptor-interacting serine/threonine protein kinases (RIPK) 1, RIPK3, Z-DNA-binding protein 1, and Toll/interleukin-1 receptor domain-containing adaptor-inducing interferon-β. Remarkably, all four aforementioned mammalian proteins harbouring such a RHIM domain are key components of inflammatory signalling and regulated cell death (RCD) processes. Immunogenic cell death by regulated necrosis causes extensive tissue damage in a wide range of diseases, including ischaemia reperfusion injury, myocardial infarction, sepsis, stroke, and solid organ transplantation. To harness the cell death suppression properties of M45 protein in a therapeutically usable manner, we developed a synthetic peptide encompassing only the RHIM domain of M45. To trigger delivery of RHIM into target cells, we fused the transactivator protein transduction domain of human immunodeficiency virus 1 to the N-terminus of the peptide. The fused peptide could efficiently penetrate eukaryotic cells, but unexpectedly it eradicated or destroyed all tested cancer cell lines and primary cells irrespective of species without further stimulus through a necrosis-like cell death. Typical inhibitors of different forms of RCD cannot impede this process, which appears to involve a direct disruption of biomembranes. Nevertheless, our finding has potential clinical relevance; reliable induction of a necrotic form of cell death distinct from all known forms of RCD may offer a novel therapeutic approach to combat resistant tumour cells.
On Maintenance and Metabolisms in Soil Microbial Communities
2022-01-11

Abstract Biochemistry is an essential yet often undervalued aspect of soil ecology, especially in soil C cycling. We assume based on tradition, intuition or hope that the complexity of biochemistry is confined to the microscopic world, and can be ignored when dealing with whole soil systems. This opinion paper draws attention to patterns caused by basic biochemical processes that permeate the world of ecosystem processes. From these patterns, we can estimate activities of the biochemical reactions of the central C metabolic network and gain insights into the ecophysiology of microbial biosynthesis and growth and maintenance energy requirements; important components of Carbon Use Efficiency (CUE).The biochemical pathways used to metabolize glucose vary from soil to soil, with mostly glycolysis in some soils, and pentose phosphate or Entner-Doudoroff pathways in others. However, notwithstanding this metabolic diversity, glucose use efficiency is high and thus substrate use for maintenance energy and overflow respiration is low in these three soils. These results contradict current dogma based on four decades of research in soil ecology. We identify three main shortcomings in our current understanding of substrate use efficiency: 1) in numeric and conceptual models, we lack appreciation of the strategies that microbes employ to quickly reduce energy needs in response to starvation; 2) production of exudates and microbial turnover affect whole-soil CUE more than variation in maintenance energy demand; and 3) whether tracer experiments can be used to measure the long-term substrate use efficiency of soil microbial communities depends critically on the ability of non-growing cells to take up tracer substrates, how biosynthesis responds to these substrates, as well as on how cellular activities scale to the community level.To move the field of soil ecology forward, future research must consider the details of microbial ecophysiology and develop new tools that enable direct measurement of microbial functioning in intact soils. We submit that 13C metabolic flux analysis is one of those new tools.
Spironolactone is associated with reduced mitotane levels in adrenocortical carcinoma patients
2022-01-11

Adrenocortical carcinoma (ACC) is a rare endocrine malignancy with a poor prognosis. Mitotane, a derivative of the pesticide dichlorodiphenyltrichloroethane, has been used successfully as first line chemotherapy since the 1960s, if maintained within a narrow therapeutic window. Spironolactone (SPL) is frequently used to treat glucocorticoid excess-associated adverse effects such as severe hypokalemia. Although data of a previous case report indicate a link, valid data regarding SPL use and mitotane plasma concentrations in a human cohort are lacking.This retrospective analysis includes data from 54 mitotane-receiving ACC patients (14 co-administered with SPL) treated between January 2005 and April 2020 (20 male, mean age 54.1 ± 2.2 years). All available mitotane concentrations, treatment doses, tumor stage and evidence of hormone activity were collected. Primary outcomes included mitotane levels and concentration/dose ratios as well as time-in-range (TR) in patients with and without additional SPL treatment. The SPL group was characterized by higher glucocorticoid secretion. Other features such as tumor stage, size and anthropometrics were similar between groups. Interestingly, the SPL group had significantly lower mitotane levels despite higher doses. Mitotane TR was significantly reduced in the SPL group, as was time-in-range to progression. These data provide first evidence in a human cohort for potential SPL-mitotane interactions (beyond mentioned case report), which affect dose response and may modulate treatment outcomes. This should caution clinicians to carefully adjust mitotane doses during SPL treatment in ACC patients or choose alternative therapeutic options.
Optimism and pessimism in optimised replay
2022-01-12

The replay of task-relevant trajectories is known to contribute to memory consolidation and improved task performance. A wide variety of experimental data show that the content of replayed sequences is highly specific and can be modulated by reward as well as other prominent task variables. However, the rules governing the choice of sequences to be replayed still remain poorly understood. One recent theoretical suggestion is that the prioritization of replay experiences in decision-making problems is based on their effect on the choice of action. We show that this implies that subjects should replay sub-optimal actions that they dysfunctionally choose rather than optimal ones, when, by being forgetful, they experience large amounts of uncertainty in their internal models of the world. We use this to account for recent experimental data demonstrating exactly pessimal replay, fitting model parameters to the individual subjects’ choices.
Shared leave, happier parent couples? Parental leave and relationship satisfaction in Germany
2022-01-12

This study investigates how parental leave policies and uptake may impact heterosexual couples’ relationship satisfaction. It focuses on Germany as an example of a country with a history of familialist policies and long maternal leaves that has recently undergone a significant policy shift. We extend the literature by examining the effects of maternal and paternal leave duration on both partners’ relationship satisfaction while distinguishing between the length of solo, joint and overall leave. The study applies two different methods on data from the Panel Analysis of Intimate Relationships and Family Dynamics (pairfam). First, the study applies fixed-effects regression models ( n = 1046 couples) to investigate the impact of parental leave duration on the change in mothers’ and fathers’ satisfaction over the child’s early years. Second, drawing on exogenous variation as a result of the parental leave reform of 2007, which shortened paid leave for mothers and incentivised fathers’ leave take-up, difference-in-difference analyses ( n = 1403 couples) analyse reform effects on relationship satisfaction of parents with 3-year-old children. The fixed-effects models indicated a consistent negative impact of maternal – especially solo – leave duration on both mothers’ and fathers’ relationship satisfaction. No significant effects of paternal leave length were found. The difference-in-difference approach revealed a positive reform effect on mothers’ relationship satisfaction. In combination, these results suggest that the reduction in maternal leave as part of the reform has had a greater impact on couples’ relationship quality than the relatively short duration of leave taken by most fathers after the introduction of the individual leave entitlement.
Cross-linking of the Endolysosomal System Reveals Flotillin Structures and Putative Cargo
2022-01-12

SUMMARY Lysosomes are well-established as the main cellular organelles for the degradation of macromolecules and emerging as regulatory centers of metabolism. They are of crucial importance for cellular homeostasis, which is exemplified by a plethora of disorders related to alterations in lysosomal function. In this context, protein complexes play a decisive role, regulating not only metabolic lysosomal processes, but also lysosome biogenesis, transport, and interaction with other organelles. Using cross-linking mass spectrometry, we analyzed lysosomes and early endosomes. Based on the identification of 5,376 cross-links, we investigated protein-protein interactions and structures of lysosome- and endosome-related proteins. In particular, we present evidence for a tetrameric assembly of the lysosomal hydrolase PPT1 and heterodimeric/- multimeric structures of FLOT1/FLOT2 at lysosomes and early endosomes. For FLOT1-/FLOT2- positive early endosomes, we identified &gt;300 proteins presenting putative cargo, and confirm the latrophilin family of adhesion G protein-coupled receptors as substrates for flotillin-dependent endocytosis.
Multidimensional cerebellar computations for flexible kinematic control of movements
2022-01-12

Abstract Both the environment and our body keep changing dynamically. Hence, ensuring movement precision requires adaptation to multiple demands occurring simultaneously. Here we show that the cerebellum performs the necessary multi-dimensional computations for the flexible control of different movement parameters depending on the prevailing context. This conclusion is based on the identification of a manifold-like activity in both mossy fibers (MF, network input) and Purkinje cells (PC, output), recorded from monkeys performing a saccade task. Unlike MFs, the properties of PC manifolds developed selective representations of individual movement parameters. Error feedback-driven climbing fiber input modulated the PC manifolds to predict specific, error type-dependent changes in subsequent actions. Furthermore, a feed-forward network model that simulated MF-to-PC transformations revealed that amplification and restructuring of the lesser variability in the MF activity is a pivotal circuit mechanism. Therefore, flexible control of movement by the cerebellum crucially depends on its capacity for multi-dimensional computations.
Root tissue segmentation dataset
2022-01-12

The PHDFM dataset is composed of fluorescence microscopy images of root tissue samples from <em>A. thaliana</em>, using the ratiometric fluorescent indicator 8‐hydroxypyrene‐1,3,6‐trisulfonic acid trisodium salt (HPTS). This semantic segmentation training dataset consists of 2D microscopy images (the brightfield channel for excitation at 405 nm), each containing a segmentation mask as an additional image channel (manually annotated by plant biologists). The segmentation masks classify pixels into the following 5 labels with the corresponding IDs: background (0), root tissue (1), early elongation zone (2), late elongation zone (3), and meristematic zone (4).
DRP1 interacts directly with BAX to induce its activation and apoptosis
2022-01-13

The apoptotic executioner protein BAX and the dynamin-like protein DRP1 co-localize at mitochondria during apoptosis to mediate mitochondrial permeabilization and fragmentation. However, the molecular basis and functional consequences of this interplay remain unknown. Here, we show that BAX and DRP1 physically interact, and that this interaction is enhanced during apoptosis. Complex formation between BAX and DRP1 occurs exclusively in the membrane environment and requires the BAX N-terminal region, but also involves several other BAX surfaces. Furthermore, the association between BAX and DRP1 enhances the membrane activity of both proteins. Forced dimerization of BAX and DRP1 triggers their activation and translocation to mitochondria, where they induce mitochondrial remodeling and permeabilization to cause apoptosis even in the absence of apoptotic triggers. Based on this, we propose that DRP1 can promote apoptosis by acting as noncanonical direct activator of BAX through physical contacts with its N-terminal region.