julilili42/papers huggingface dataset:
Predictive Uncertainty-based Bias Mitigation in Ranking
2023-10-21

Societal biases that are contained in retrieved documents have received increased interest. Such biases, which are often prevalent in the training data and learned by the model, can cause societal harms, by misrepresenting certain groups, and by enforcing stereotypes. Mitigating such biases demands algorithms that balance the trade-off between maximized utility for the user with fairness objectives, which incentivize unbiased rankings. Prior work on bias mitigation often assumes that ranking scores, which correspond to the utility that a document holds for a user, can be accurately determined. In reality, there is always a degree of uncertainty in the estimate of expected document utility. This uncertainty can be approximated by viewing ranking models through a Bayesian perspective, where the standard deterministic score becomes a distribution. In this work, we investigate whether uncertainty estimates can be used to decrease the amount of bias in the ranked results, while minimizing loss in measured utility. We introduce a simple method that uses the uncertainty of the ranking scores for an uncertainty-aware, post hoc approach to bias mitigation. We compare our proposed method with existing baselines for bias mitigation with respect to the utility-fairness trade-off, the controllability of methods, and computational costs. We show that an uncertainty-based approach can provide an intuitive and flexible trade-off that outperforms all baselines without additional training requirements, allowing for the post hoc use of this approach on top of arbitrary retrieval models.
Figures, Data and Code of "Dispersionless subradiant photon storage in one-dimensional emitter chains"
2023-10-21

This project contains the figures, data and code for the publication "Dispersionless subradiant photon storage in one-dimensional emitter chains". In particular it contains: - code: - 'main.py' file to start the preparation of the figures. - 'src' directory containing the full implementation. - data: - 'data' directory containing the data produced in the preparation of the figures in the manuscript. - figures: - 'figures' directory containing the raw and finished figures of the manuscript in the respective subfolders. - documentation: - 'documentation' directory containing a html documentation of the code generated by Sphinx. The file 'index.html' is the usual entry point to the documentation.
The combination of stimulus-driven and modulatory inputs in visual thalamus depend on visual responsiveness and stimulus type
2023-10-21

In the dorsolateral geniculate nucleus (dLGN) of the thalamus, retinal signals are combined with non-retinal inputs such as corticothalamic (CT) feedback and behavioural state. How these shape dLGN activity remains an open question. We recorded extracellular responses in dLGN of awake mice to a movie stimulus, while photosuppressing CT feedback, tracking locomotion and pupil size. To assess the relative impact of retinal and non-retinal inputs, we fit single neuron responses using generalized linear models. While including CT feedback and behavioural state as predictors significantly improved the model's overall performance, the improvement was especially pronounced for a sub-population of poorly visually responsive neurons. In addition, the impact of CT feedback was faster and more prevalent in the absence of a patterned visual stimulus. Finally, for CT feedback-sensitive dLGN neurons, visual stimuli could be discriminated better when CT feedback was suppressed. Together, these results show that effects of non-retinal inputs in dLGN depend on visual responsiveness and stimulus context.
Wnt/β-catenin and NFκB signaling synergize to trigger growth factor-free regeneration of adult primary human hepatocytes
2023-10-23

Background and Aims: The liver has a remarkable capacity to regenerate, which is sustained by the ability of hepatocytes to act as facultative stem cells that, while normally quiescent, re-enter the cell cycle after injury. Growth factor signaling is indispensable in rodents, whereas Wnt/β-catenin is not required for effective tissue repair. However, the molecular networks that control human liver regeneration remain unclear. Methods: Organotypic 3D spheroid cultures of primary human or murine hepatocytes were used to identify the signaling network underlying cell cycle re-entry. Furthermore, we performed chemogenomic screening of a library enriched for epigenetic regulators and modulators of immune function to determine the importance of epigenomic control for human hepatocyte regeneration. Results: Our results showed that, unlike in rodents, activation of Wnt/β-catenin signaling is the major mitogenic cue for adult primary human hepatocytes. Furthermore, we identified TGFβ inhibition and inflammatory signaling through NF-κB as essential steps for the quiescent-to-regenerative switch that allows Wnt/β-catenin-induced proliferation of human cells. In contrast, growth factors, but not Wnt/β-catenin signaling, triggered hyperplasia in murine hepatocytes. High-throughput screening in a human model confirmed the relevance of NFκB and revealed the critical roles of polycomb repressive complex 2, as well as of the bromodomain families I, II, and IV. Conclusions: This study revealed a network of NFκB, TGFβ, and Wnt/β-catenin that controls human hepatocyte regeneration in the absence of exogenous growth factors, identified novel regulators of hepatocyte proliferation, and highlighted the potential of organotypic culture systems for chemogenomic interrogation of complex physiological processes.
The Polarized Cosmic Hand: IXPE Observations of PSR B1509−58/MSH 15−52
2023-10-23

Abstract We describe IXPE polarization observations of the pulsar wind nebula (PWN) MSH 15−5 2 , the “Cosmic Hand.” We find X-ray polarization across the PWN, with B -field vectors generally aligned with filamentary X-ray structures. High-significance polarization is seen in arcs surrounding the pulsar and toward the end of the “jet,” with polarization degree PD &gt; 70%, thus approaching the maximum allowed synchrotron value. In contrast, the base of the jet has lower polarization, indicating a complex magnetic field at significant angle to the jet axis. We also detect significant polarization from PSR B1509−58 itself. Although only the central pulse phase bin of the pulse has high individual significance, flanking bins provide lower-significance detections and, in conjunction with the X-ray image and radio polarization, can be used to constrain rotating vector model solutions for the pulsar geometry.
Domain adapted brain network fusion captures variance related to pubertal brain development and mental health
2023-10-23

Abstract Puberty demarks a period of profound brain dynamics that orchestrates changes to a multitude of neuroimaging-derived phenotypes. This complexity poses a dimensionality problem when attempting to chart an individual’s brain development over time. Here, we illustrate that shifts in subject similarity of brain imaging data relate to pubertal maturation in the longitudinal ABCD study. Given that puberty depicts a critical window for emerging mental health issues, we additionally show that our model is capable of capturing variance in the adolescent brain related to psychopathology in a population-based and a clinical cohort. These results suggest that low-dimensional reference spaces based on subject similarities render useful to chart variance in brain development in youths.
Big five personality and recreation specialization are related to satisfaction with life in birders
2023-10-23

Personality traits and recreation specialization are related to an individual's satisfaction with life. In addition, previous research has identified relationships between personality traits and recreational specialization. However, little is known about the interrelationship of the two variables in relation to life satisfaction. In this study, we addressed these relationships in birdwatchers. 555 birders (<i>M</i><sub>age</sub> = 49.11 years, <i>SD</i><sub>age</sub> = 17.14; 380 males, 170 females, 2 diverse, 3 without answer) from German-speaking countries filled out an online survey. The participants rated the BFI-10, a global assessment of life satisfaction, and three dimensions of recreation specialization (skill/knowledge, behavior, commitment). Satisfaction with life was positively correlated with extraversion, agreeableness, and conscientiousness, and negatively with neuroticism. Concerning recreation specialization, positive relationships between satisfaction with life and skill/knowledge as well as behavior were found; especially the dimension of skill/knowledge was positively related to conscientiousness and negatively to neuroticism. Openness was negatively related to the three dimensions of recreation specialization. The mediation analyses showed that skill/knowledge is directly and indirectly related to satisfaction with life. Birding as active outdoor activity has positive relationship with life satisfaction, and this seems to be mainly based on the cognitive component, with a high knowledge related to a higher life satisfaction.
An ancient cis‐element targeted by Ralstonia solanacearum TALE‐like effectors facilitates the development of a promoter trap that could confer broad‐spectrum wilt resistance
2023-10-23

Summary Ralstonia solanacearum , a species complex of bacterial plant pathogens that causes bacterial wilt, comprises four phylotypes that evolved when a founder population was split during the continental drift ~180 million years ago. Each phylotype contains strains with RipTAL proteins structurally related to transcription activator‐like (TAL) effectors from the bacterial pathogen Xanthomonas . RipTALs have evolved in geographically separated phylotypes and therefore differ in sequence and potentially functionality. Earlier work has shown that phylotype I RipTAL Brg11 targets a 17‐nucleotide effector binding element ( EBE ) and transcriptionally activates the downstream arginine decarboxylase ( ADC ) gene. The predicted DNA binding preferences of Brg11 and RipTALs from other phylotypes are similar, suggesting that most, if not all, RipTALs target the Brg11‐EBE motif and activate downstream ADC genes. Here we show that not only phylotype I RipTAL Brg11 but also RipTALs from other phylotypes activate host genes when preceded by the Brg11‐EBE motif. Furthermore, we show that Brg11 and RipTALs from other phylotypes induce the same quantitative changes of ADC‐dependent plant metabolites, suggesting that most, if not all, RipTALs induce functionally equivalent changes in host cells. Finally, we report transgenic tobacco lines in which the RipTAL‐binding motif Brg11‐EBE mediates RipTAL‐dependent transcription of the executor‐type resistance ( R ) gene Bs4C from pepper, thereby conferring resistance to RipTAL‐delivering R. solanacearum strains. Our results suggest that cell death‐inducing executor‐type R genes, preceded by the RipTAL‐binding motif Brg11‐EBE , could be used to genetically engineer broad‐spectrum bacterial wilt resistance in crop plants without any apparent fitness penalty.
Targeted memory reactivation is not more effective during slow wave sleep than sleep stage 2
2023-10-23

Abstract Sleep facilitates memory consolidation, which is assumed to rely on the reactivation of newly encoded memories orchestrated by the temporal interplay of slow oscillations (SO), fast spindles and ripples. SO as well as the number of spindles coupled to SO are more frequent during slow wave sleep (SWS) compared to lighter sleep stage 2 (S2). But, it is unclear whether memory reactivation is more effective during SWS than during S2. To test this question, we applied Targeted Memory Reactivation (TMR) by presenting learning-associated sound cues during SWS vs. S2 in a counterbalanced within-subject design. Contrary to our hypothesis, memory performance was not significantly better when cues were presented during SWS. Event-related potential (ERP) amplitudes were significantly higher for cues presented during SWS than S2, and the density of SO and SO-spindle complexes was generally higher during SWS than during S2. Whereas SO density increased during and after the TMR period, SO-spindle complexes decreased. None of the parameters were associated with memory performance. These findings suggest that the efficacy of TMR does not depend on whether it is administered during SWS or S2, despite differential processing of memory cues in these sleep stages.
T1 and FLAIR signal intensities are related to tau pathology in dominantly inherited Alzheimer disease
2023-10-23

Abstract Carriers of mutations responsible for dominantly inherited Alzheimer disease provide a unique opportunity to study potential imaging biomarkers. Biomarkers based on routinely acquired clinical MR images, could supplement the extant invasive or logistically challenging) biomarker studies. We used 1104 longitudinal MR, 324 amyloid beta, and 87 tau positron emission tomography imaging sessions from 525 participants enrolled in the Dominantly Inherited Alzheimer Network Observational Study to extract novel imaging metrics representing the mean ( μ ) and standard deviation ( σ ) of standardized image intensities of T1‐weighted and Fluid attenuated inversion recovery (FLAIR) MR scans. There was an exponential decrease in FLAIR‐μ in mutation carriers and an increase in FLAIR and T1 signal heterogeneity (T1‐ σ and FLAIR‐ σ ) as participants approached the symptom onset in both supramarginal, the right postcentral and right superior temporal gyri as well as both caudate nuclei, putamina, thalami, and amygdalae. After controlling for the effect of regional atrophy, FLAIR‐ μ decreased and T1‐ σ and FLAIR‐ σ increased with increasing amyloid beta and tau deposition in numerous cortical regions. In symptomatic mutation carriers and independent of the effect of regional atrophy, tau pathology demonstrated a stronger relationship with image intensity metrics, compared with amyloid pathology. We propose novel MR imaging intensity‐based metrics using standard clinical T1 and FLAIR images which strongly associates with the progression of pathology in dominantly inherited Alzheimer disease. We suggest that tau pathology may be a key driver of the observed changes in this cohort of patients.
Comprehensive reanalysis for CNVs in ES data from unsolved rare disease cases results in new diagnoses
2023-10-23

Abstract We report the diagnostic results of a comprehensive copy number variant (CNV) reanalysis of 9,171 exome sequencing (ES) datasets from 5,757 families, including 6,143 individuals affected by a rare disease (RD). The data analysed was extremely heterogeneous, having been generated using 28 different exome enrichment kits, and sequenced on multiple short-read sequencing platforms, by 42 different research groups across Europe partnering in the Solve-RD project. Each of these research groups had previously undertaken their own analysis of the ES data but had failed to identify disease-causing variants. We applied three CNV calling algorithms to maximise sensitivity: ClinCNV, Conifer, and ExomeDepth. Rare CNVs overlapping genes of interest in custom lists provided by one of four partner European Reference Networks (ERN) were identified and taken forward for interpretation by clinical experts in RD. To facilitate interpretation, Integrative Genomics Viewer (IGV) screenshots incorporating a variety of custom-made tracks were generated for all prioritised CNVs. These analyses have resulted in a molecular diagnosis being provided for 51 families in this sample, with ClinCNV performing the best of the three algorithms in identifying disease-causing CNVs. We also identified pathogenic CNVs that are partially explanatory of the proband’s phenotype in a further 34 individuals. This work illustrates the value of reanalysing ES cold cases for CNVs even where analyses had been undertaken previously. Crucially, identification of these previously undetected CNVs has resulted in the conclusion of the diagnostic odyssey for these RD families, some of which had endured decades.
Fully endoscopic posterior fossa decompression for Chiari malformation type I: illustrative case
2023-10-23

BACKGROUND Surgery for symptomatic Arnold-Chiari malformation type I involves posterior fossa decompression. There are various approaches, including endoscope-assisted ones. New possibilities and fields of application of fully endoscopic techniques are currently being developed since new and advanced endoscopic equipment and instrumentation are available. OBSERVATIONS The authors describe the case of a fully endoscopic microsurgical procedure in a 30-year-old female patient with progressive vertigo who was diagnosed with Chiari malformation type I. Neuronavigation and neuromonitoring were used during the surgery. LESSONS Fully endoscopic surgery can be successfully performed in patients with Chiari malformation I. Intraoperative neuromonitoring and neuronavigation increase safety during this procedure.
Accelerated 2D Cartesian MRI with an 8‐channel local B0 coil array combined with parallel imaging
2023-10-23

Abstract Purpose In MRI, the magnetization of nuclear spins is spatially encoded with linear gradients and radiofrequency receivers sensitivity profiles to produce images, which inherently leads to a long scan time. Cartesian MRI, as widely adopted for clinical scans, can be accelerated with parallel imaging and rapid magnetic field modulation during signal readout. Here, by using an 8‐channel local coil array, the modulation scheme optimized for sampling efficiency is investigated to speed up 2D Cartesian scans. Theory and Methods An 8‐channel local coil array is made to carry sinusoidal currents during signal readout to accelerate 2D Cartesian scans. An MRI sampling theory based on reproducing kernel Hilbert space is exploited to visualize the efficiency of nonlinear encoding in arbitrary sampling duration. A field calibration method using current monitors for local coils and the ESPIRiT algorithm is proposed to facilitate image reconstruction. Image acceleration with various modulation field shapes, aliasing control, and distinct modulation frequencies are scrutinized to find an optimized modulation scheme. A safety evaluation is conducted. In vivo 2D Cartesian scans are accelerated by the local coils. Results For 2D Cartesian MRI, the optimal modulation field by this local array converges to a nearly linear gradient field. With the field calibration technique, it accelerates the in vivo scans (i.e., proved safe) by threefold and eightfold free of visible artifacts, without and with SENSE, respectively. Conclusion The nonlinear encoding analysis tool, the field calibration method, the safety evaluation procedures, and the in vivo reconstructed scans make significant steps to push MRI speed further with the local coil array.
Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum
2023-10-23

Introduction: Genome-scale metabolic models (GEMs) are organism-specific knowledge bases which can be used to unravel pathogenicity or improve production of specific metabolites in biotechnology applications. However, the validity of predictions for bacterial proliferation in in vitro settings is hardly investigated. Methods: The present work combines in silico and in vitro approaches to create and curate strain-specific genome-scale metabolic models of Corynebacterium striatum . Results: We introduce five newly created strain-specific genome-scale metabolic models (GEMs) of high quality, satisfying all contemporary standards and requirements. All these models have been benchmarked using the community standard test suite Metabolic Model Testing (MEMOTE) and were validated by laboratory experiments. For the curation of those models, the software infrastructure refineGEMs was developed to work on these models in parallel and to comply with the quality standards for GEMs. The model predictions were confirmed by experimental data and a new comparison metric based on the doubling time was developed to quantify bacterial growth. Discussion: Future modeling projects can rely on the proposed software, which is independent of specific environmental conditions. The validation approach based on the growth rate calculation is now accessible and closely aligned with biological questions. The curated models are freely available via BioModels and a GitHub repository and can be used. The open-source software refineGEMs is available from https://github.com/draeger-lab/refinegems .
Dataset for the article "Blindly separated spontaneous network-level oscillations predict corticospinal excitability"
2023-10-23

&amp;lt;p&amp;gt;This repository contains a dataset supporting results in the manuscript: Ermolova, M., Metsomaa, J., Belardinelli, P., Zrenner, C., &amp;amp; Ziemann, U. (2024). Blindly separated spontaneous network-level oscillations predict corticospinal excitability. &amp;lt;em&amp;gt;Journal of Neural Engineering&amp;lt;/em&amp;gt;, &amp;lt;em&amp;gt;21&amp;lt;/em&amp;gt;(3), 036041.&amp;lt;/p&amp;gt;\\n&amp;lt;p&amp;gt;REFTEP dataset: TMS-EEG experiment on awake healthy human subjects. Single-pulse TMS was applied in resting state over primary motor cortex, with simultaneous EEG recording from the scalp and EMG recording from hand muscles. &amp;nbsp;&amp;lt;/p&amp;gt;\\n&amp;lt;p&amp;gt;The dataset is intended for use by the code published at: https://github.com/mariaermolova/CSPAnalysis. The dataset is structured as follows: each .mat file corresponds to a single subject and contains a matlab structure with the following substructs.&amp;nbsp;&amp;lt;/p&amp;gt;\\n&amp;lt;p&amp;gt;1. EEG data from 1.5 sec. before each TMS pulse (&amp;lt;em&amp;gt;&amp;lt;strong&amp;gt;eeg&amp;lt;/strong&amp;gt;&amp;lt;/em&amp;gt;). The data was preprocessed: bad trials and channels removed, signals detrended, ICA components corresponding to oculographic artefacts removed.&amp;nbsp;&amp;lt;/p&amp;gt;\\n&amp;lt;p&amp;gt;2. EEG channel locations on the scalp (&amp;lt;em&amp;gt;&amp;lt;strong&amp;gt;chanlocs&amp;lt;/strong&amp;gt;&amp;lt;/em&amp;gt;) and indices of channels removed during preprocessing (&amp;lt;em&amp;gt;&amp;lt;strong&amp;gt;removedChannels&amp;lt;/strong&amp;gt;&amp;lt;/em&amp;gt;).&amp;nbsp;&amp;lt;/p&amp;gt;\\n&amp;lt;p&amp;gt;3. Peak-to-peak amplitudes of Motor Evoked Potentials for each trial (&amp;lt;em&amp;gt;&amp;lt;strong&amp;gt;mepSize&amp;lt;/strong&amp;gt;&amp;lt;/em&amp;gt;) and excitability labels for each trial based on the amplitude of the corresponding MEP (&amp;lt;em&amp;gt;&amp;lt;strong&amp;gt;labels&amp;lt;/strong&amp;gt;&amp;lt;/em&amp;gt;). Labels correspond to high (1) vs low (0) MEP amplitude.&amp;lt;/p&amp;gt;