julilili42/papers huggingface dataset:
Leveraging Unlabeled Electroencephalographic Data to Predict Neurologic Recovery after Cardiac Arrest
2023-11-26

In response to the 2023 George B. Moody PhysioNet Challenge, we propose an automated, unsupervised pre-training approach to boost the performance of models that predict neurologic outcomes after cardiac arrest. Our team, (BrownBAI), developed a model architecture consisting of three parts: a pre-processor to convert raw electroencephalograms (EEGs) into two-dimensional spectrograms, a three-layer convolutional neural network (CNN) encoder for unsupervised pre-training, and a time series transformer (TST) model. We trained the CNN encoder on unlabeled five-minute EEG samples from the Temple University EEG Corpus (TUEG), which included more than 20x the patients available in the PhysioNet competition training dataset. We then incorporated the pre-trained encoder into the TST as a base layer and trained the composite model as a classifier on EEGs from the 2023 PhysioNet Challenge dataset. Our team was not able to submit an official competition entry and was therefore not scored on the test set. However, in a side-by-side comparison on the competition training dataset, our model performed better with a pretrained (competition score 0.351), rather than randomly initialized (competition score 0.211) CNN encoder layer. These results show the potential benefits of leveraging unlabeled data to boost task-specific performance of predictive EEG models.
Open Innovation in Schools: A New Imperative for Organising Innovation in Education?
2023-11-27

Abstract Schools are considered knowledge-creating organisations that find it difficult to develop and implement innovations on their own. Knowledge mobilisation is seen as the key to overcoming this problem. In particular, the use of external sources of knowledge is regarded as an important lever for change. However, there is a lack of concepts and empirical studies in educational research on the extent to which external knowledge is used for innovation in schools. Based on a sample of N = 411 schools, this article explores whether the concept of open innovation can be used in the context of education. Originating from the field of innovation research, open innovation regimes are seen as imperative if organisations are to create and benefit from technology. Multinomial logistic regression analyses show that mobilising external knowledge significantly increases the likelihood of implementing innovations in schools. A machine-learning approach reveals that it is necessary to tailor open innovation regimes to the specific conditions of any given school. In particular, with regard to the use of new technologies and innovations in the field of digitalisation, open innovation can be a lever for change.
The Implicative Conditional
2023-11-27

Abstract This paper investigates the implicative conditional, a connective intended to describe the logical behavior of an empirically defined class of natural language conditionals, also named implicative conditionals , which excludes concessive and some other conditionals. The implicative conditional strengthens the strict conditional with the possibility of the antecedent and of the contradictory of the consequent. <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>p</mml:mi><mml:mo>⇒</mml:mo><mml:mi>q</mml:mi></mml:mrow></mml:math> is thus defined as <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>¬</mml:mo><mml:mo>◊</mml:mo><mml:mrow><mml:mo>(</mml:mo><mml:mi>p</mml:mi><mml:mo>∧</mml:mo><mml:mo>¬</mml:mo><mml:mi>q</mml:mi><mml:mo>)</mml:mo><mml:mo>∧</mml:mo></mml:mrow><mml:mo>◊</mml:mo><mml:mrow><mml:mi>p</mml:mi><mml:mo>∧</mml:mo></mml:mrow><mml:mo>◊</mml:mo><mml:mrow><mml:mo>¬</mml:mo><mml:mi>q</mml:mi></mml:mrow></mml:mrow></mml:math> . We explore the logical properties of this conditional in a reflexive normal Kripke semantics, provide an axiomatic system and prove it to be sound and complete for our semantics. The implicative conditional validates transitivity and contraposition, which we take to be integral parts of reasoning and communication. But it only validates restricted versions of strengthening the antecedent, right weakening, simplification, and rational monotonicity. Apparent counterexamples to some of these properties are explained as due to contextual factors. Finally, the implicative conditional avoids the paradoxes of material and strict implication, and validates some connexive principles such as Aristotle’s theses and weak Boethius’ thesis, as well as some highly entrenched principles of conditionals, such as conjunction of consequents, disjunction of antecedents, modus ponens, cautious monotonicity and cut.
Evaluation of coaxial dipole antennas as transceiver elements of human head array for ultra‐high field MRI at 9.4T
2023-11-27

Abstract Purpose The aim of this work is to evaluate a new eight‐channel transceiver (TxRx) coaxial dipole array for imaging of the human head at 9.4T developed to improve specific absorption rate ( SAR ) performance, and provide for a more compact and robust alternative to the state‐of‐the art dipole arrays. Methods First, the geometry of a single coaxial element was optimized to minimize peak SAR and sensitivity to the load variation. Next, a multi‐tissue voxel model was used to numerically simulate a TxRx array coil that consisted of eight coaxial dipoles with the optimal configuration. Finally, we compared the developed array to other human head dipole arrays. Results of numerical simulations were verified on a bench and in the scanner including in vivo measurements on a healthy volunteer. Results The developed eight‐element coaxial dipole TxRx array coil showed up to 1.1times higher SAR ‐efficiency than a similar in geometry folded‐end and fractionated dipole array while maintaining whole brain coverage and low sensitivity of the resonance frequency to variation in the head size. Conclusion As a proof of concept, we developed and constructed a prototype of a 9.4T (400 MHz) human head array consisting of eight TxRx coaxial dipoles. The developed array improved SAR ‐efficiency and provided for a more compact and robust alternative to the folded‐end dipole design. To the best of our knowledge, this is the first example of using coaxial dipoles for human head MRI at ultra‐high field.
Leapfrog Methods for Relativistic Charged-Particle Dynamics
2023-11-27

A basic leapfrog integrator and its energy-preserving and variational/symplectic variants are proposed and studied for the numerical integration of the equations of motion of relativistic charged particles in an electromagnetic field. The methods are based on a four-dimensional formulation of the equations of motion. Structure-preserving properties of the numerical methods are analyzed, in particular conservation and long-time near-conservation of energy and mass shell as well as preservation of volume in phase space. In the non-relativistic limit, the considered methods reduce to the Boris algorithm for non-relativistic charged-particle dynamics and its energy-preserving and variational/symplectic variants.
Characterization of the cystargolide biosynthetic gene cluster and functional analysis of the methyltransferase CysG
2023-11-27

Cystargolides are natural products originally isolated from Kitasatospora cystarginea NRRL B16505 as inhibitors of the proteasome. They are composed of a dipeptide backbone linked to a β-lactone warhead. Recently, we identified the cystargolide biosynthetic gene cluster, but systematic genetic analyses had not been carried out because of the lack of a heterologous expression system. Here, we report the discovery of a homologous cystargolide biosynthetic pathway in Streptomyces durhamensis NRRL-B3309 by genome mining. The gene cluster was cloned via transformation-associated recombination and heterologously expressed in Streptomyces coelicolor M512. We demonstrate that it contains all genes necessary for the production of cystargolide A and B. Single gene deletion experiments reveal that only five of the eight genes from the initially proposed gene cluster are essential for cystargolide synthesis. Additional insights into the cystargolide pathway could be obtained from in vitro assays with CysG and chemical complementation of the respective gene knockout. This could be further supported by the in vitro investigation of the CysG homolog BelI from the belactosin biosynthetic gene cluster. Thereby, we confirm that CysG and BelI catalyze a cryptic SAM-dependent transfer of a methyl group that is critical for the construction of the cystargolide and belactosin β-lactone warheads.
Convergent functional effects of antidepressants in major depressive disorder: a neuroimaging meta-analysis
2023-11-27

Abstract Background Neuroimaging studies have provided valuable insights into the macroscale impacts of antidepressants on brain functions in patients with major depressive disorder. However, the findings of individual studies are inconsistent. Here, we aimed to provide a quantitative synthesis of the literature to identify convergence of the reported findings at both regional and network levels and to examine their associations with neurotransmitter systems. Methods Through a comprehensive search in PubMed and Scopus databases, we reviewed 5,258 abstracts and identified 36 eligible functional neuroimaging studies on antidepressant effects in major depressive disorder. Activation likelihood estimation was used to investigate regional convergence of the reported foci of consistent antidepressant effects, followed by functional decoding and connectivity mapping of the convergent clusters. Additionally, utilizing group-averaged data from the Human Connectome Project, we assessed convergent resting-state functional connectivity patterns of the reported foci. Next, we compared the convergent circuit with the circuits targeted by transcranial magnetic stimulation (TMS) therapy. Last, we studied the association of regional and network-level convergence maps with selected neurotransmitter receptors/transporters maps. Results No regional convergence was found across foci of treatment-associated alterations in functional imaging. Subgroup analysis across the Treated &gt; Untreated contrast revealed a convergent cluster in the left dorsolateral prefrontal cortex, which was associated with working memory and attention behavioral domains. Moreover, we found network-level convergence of the treatment-associated alterations in a circuit more prominent in the frontoparietal areas. This circuit was co-aligned with circuits targeted by “anti-subgenual” and “Beam F3” TMS therapy. We observed no significant correlations between our meta-analytic findings with the maps of neurotransmitter receptors/transporters. Conclusion Our findings highlight the importance of the frontoparietal network and the left dorsolateral prefrontal cortex in the therapeutic effects of antidepressants, which may relate to their role in improving executive functions and emotional processing.
Computed tomography perfusion imaging-guided intravenous thrombolysis in acute minor ischemic stroke
2023-11-27

Background Over 50% of acute ischemic stroke (AIS) patients present with minor neurological deficits, and optimal treatment is still debated. The randomized PRISMS trial did not show beneficial effects of intravenous thrombolysis (IVT) in unselected patients with minor stroke and non-disabling neurological deficits. Purpose The study aimed to evaluate if AIS patients with minor stroke may benefit from computed-tomography-perfusion (CTP)-guided IVT. The primary endpoint was good functional outcomes, defined as a modified Rankin Scale score of 0–2 at 90 days. Methods AIS patients with a NIHSS of ≤5 presenting within 4.5 h underwent multimodal CT-imaging including CTP. CTP mismatch was defined as hypoperfusion on CTP with time-to-peak delay &amp;gt;6 s without corresponding hypoperfusion in cerebral blood volume. IVT decision was left to the attending stroke physicians. Patients with large vessel occlusion (LVO) and absolute contraindications to IVT were excluded. Results In total, 267 consecutive patients were included [mean age: 72 ± 14 years, 45.3% female patients, 75.3% received IVT, median NIHSS on admission: 3 (IQR 2, 4)]. CTP mismatch was detected in 41.8% of IVT− treated patients (IVT+) and 28.8% of standard treatment patients (IVT−) ( p = 0.06). IVT+ had favorable outcomes at 90 days compared to IVT− ( p = 0.006), but no interaction with an existing CTP mismatch was detected (OR adj : 1.676; 95% CI: 0.644–4.364). No symptomatic intracranial hemorrhage according to ECASS-III criteria occurred. Conclusion Although selected AIS patients with minor stroke may benefit from IVT, CTP mismatch does not correlate with functional outcomes. No benefit from CTP mismatch in guiding IVT was detected in patients without LVO presenting with minor neurological deficits.
The second messenger c-di-AMP controls natural competence via ComFB signaling protein
2023-11-27

Natural competence requires a contractile pilus system. Here, we provide evidence that the pilus biogenesis and natural competence in cyanobacteria are regulated by the second messenger c-di-AMP. Furthermore, we show that the ComFB signaling protein is a novel c-di-AMP-receptor protein, widespread in bacterial phyla, and required for pilus biogenesis and DNA uptake.
Compilation and Validation of Two Short Forms to Measure HEXACO Dimensions in Elementary School Children
2023-11-27

Personality trait measures for children are rarely based on the HEXACO Model of Personality, although research using this framework could provide important insights into the structure and development of children’s personalities. There is no HEXACO measure for elementary school children to date, and existing measures for older children seem not appropriate for this age group (e.g., due to some item content). We thus compiled two HEXACO-based short forms for measuring personality in elementary school children (8-10 years old) via parent reports. We applied a meta-heuristic item sampling algorithm (Ant Colony Optimization) in a training sample with 1,641 parent reports of 122 administered items. We selected a 54-Item Short Form comprising a latent facet structure and an 18-Item Ultra-Short Form comprising a correlated factors model for all six HEXACO dimensions but no facet structure. Both short forms showed good model fit in a holdout sample (n = 411) and sufficiently high re-test correlations after six months. Convergent and divergent validities for maximal performance measures and socio-emotional constructs (also measured six months after the initial personality assessment) were largely in line with theoretical assumptions. Overall, our study provides support for construct, re-test, and (predictive) criterion validity for the selected short forms.
ChemProp2 Dataset: Investigating potential biotransformations with a panel of 45 Drugs on Synthetic Community (Com20) to elucidate Drug-Microbiome-Host Dynamics
2023-11-27

&amp;lt;p&amp;gt;This dataset contains the examination of each of the 45 drugs on the synthetic community Com20, conducted at two distinct timepoints: initially (time 0) and after a 2-hour interval.&amp;lt;br&amp;gt;List of drugs: Ethopropazine, Methotrexate, Felodipine, Miconazole, Floxuridine, Nalidixic acid, Fluconazole, Niclosamide, Ketoconazole, Omeprazole, Lacidipine, Pentamidine isothionate, DMSO, Promethazine, Lansoprazole, Protriptyline, Loratadine, Sertindole, Loxapine, Simvastatin, L-Thyroxine, Streptozotocin, Metformin, Tamoxifen, Tazobactam, Doxorubicin, Telmisartan, Ofloxacin, Terfenadine, Oxolinic acid, Thioguanosine, Tobramycin, Tiratricol, Vancomycin, Water, Rivaroxoban, Metronidazole, Tolfenamic acid, Clarithromycin, Tribenoside, Norfloxacin, Zafirlukast, Montelukast, Sertraline, Fluoxetine, Clomipramin, Novobiocin&amp;lt;/p&amp;gt;
Using Smartphone Sensors for Ataxia Trials: Consensus Guidance by the Ataxia Global Initiative Working Group on Digital-Motor Biomarkers
2023-11-28

Abstract Smartphone sensors are used increasingly in the assessment of ataxias. To date, there is no specific consensus guidance regarding a priority set of smartphone sensor measurements, or standard assessment criteria that are appropriate for clinical trials. As part of the Ataxia Global Initiative Digital-Motor Biomarkers Working Group (AGI WG4), aimed at evaluating key ataxia clinical domains (gait/posture, upper limb, speech and oculomotor assessments), we provide consensus guidance for use of internal smartphone sensors to assess key domains. Guidance was developed by means of a literature review and a two stage Delphi study conducted by an Expert panel, which surveyed members of AGI WG4, representing clinical, research, industry and patient-led experts, and consensus meetings by the Expert panel to agree on standard criteria and map current literature to these criteria. Seven publications were identified that investigated ataxias using internal smartphone sensors. The Delphi 1 survey ascertained current practice, and systems in use or under development. Wide variations in smartphones sensor use for assessing ataxia were identified. The Delphi 2 survey identified seven measures that were strongly endorsed as priorities in assessing 3/4 domains, namely gait/posture, upper limb, and speech performance. The Expert panel recommended 15 standard criteria to be fulfilled in studies. Evaluation of current literature revealed that none of the studies met all criteria, with most being early-phase validation studies. Our guidance highlights the importance of consensus, identifies priority measures and standard criteria, and will encourage further research into the use of internal smartphone sensors to measure ataxia digital-motor biomarkers.
Mass spectrometry data processing in MZmine 3: feature detection and annotation
2023-11-28

Untargeted MS experiments produce complex, multi-dimensional data that are practically impossible to investigate manually. For this reason, computational pipelines are needed to extract relevant information from raw spectral data and convert it into a more comprehensible format. Based on the sample type and/or goal of the study, a variety of MS platforms can be used for such analysis. MZmine is open-source software for the processing of raw spectral data generated by different MS platforms: liquid chromatography–MS (LC–MS), gas chromatography–MS (GC–MS), and MS–imaging. Moreover, the third version of the software, described herein, supports the processing of ion mobility spectrometry (IMS) data. The present protocol provides three distinct procedures to perform feature detection and annotation of untargeted MS data produced by different instrumental setups: LC–(IMS–)MS, GC–MS, and (IMS–)MS imaging. For training purposes, example datasets are provided together with configuration batch files (i.e. list of processing steps and parameters) to allow new users to easily replicate the described workflows. Depending on the number of data files and available computing resources, we anticipate this to take between 2 and 24 hours for new MZmine users and non-experts. Within each procedure, we provide a detailed description for all processing parameters together with instructions/recommendations for their optimization. The main generated outputs are represented by aligned feature tables and fragmentation spectra lists that can be used by other third-party tools for further downstream analysis.
Reactivation strength during cued recall is modulated by graph distance within cognitive maps
2023-11-28

Declarative memory retrieval is thought to involve reinstatement of neuronal activity patterns elicited and encoded during a prior learning episode. Furthermore, it is suggested that two mechanisms operate during reinstatement, dependent on task demands: individual memory items can be reactivated simultaneously as a clustered occurrence or, alternatively, replayed sequentially as temporally separate instances. In the current study, participants learned associations between images that were embedded in a directed graph network and retained this information over a brief 8 min consolidation period. During a subsequent cued recall session, participants retrieved the learned information while undergoing magnetoencephalographic recording. Using a trained stimulus decoder, we found evidence for clustered reactivation of learned material. Reactivation strength of individual items during clustered reactivation decreased as a function of increasing graph distance, an ordering present solely for successful retrieval but not for retrieval failure. In line with previous research, we found evidence that sequential replay was dependent on retrieval performance and was most evident in low performers. The results provide evidence for distinct performance-dependent retrieval mechanisms, with graded clustered reactivation emerging as a plausible mechanism to search within abstract cognitive maps.
Intramolecular feedback regulation of the LRRK2 Roc G domain by a LRRK2 kinase-dependent mechanism
2023-11-28

The Parkinson’s disease (PD)-linked protein Leucine-Rich Repeat Kinase 2 (LRRK2) consists of seven domains, including a kinase and a Roc G domain. Despite the availability of several high-resolution structures, the dynamic regulation of its unique intramolecular domain stack is nevertheless still not well understood. By in-depth biochemical analysis, assessing the Michaelis–Menten kinetics of the Roc G domain, we have confirmed that LRRK2 has, similar to other Roco protein family members, a K M value of LRRK2 that lies within the range of the physiological GTP concentrations within the cell. Furthermore, the R1441G PD variant located within a mutational hotspot in the Roc domain showed an increased catalytic efficiency. In contrast, the most common PD variant G2019S, located in the kinase domain, showed an increased K M and reduced catalytic efficiency, suggesting a negative feedback mechanism from the kinase domain to the G domain. Autophosphorylation of the G1+2 residue (T1343) in the Roc P-loop motif is critical for this phosphoregulation of both the K M and the k cat values of the Roc-catalyzed GTP hydrolysis, most likely by changing the monomer–dimer equilibrium. The LRRK2 T1343A variant has a similar increased kinase activity in cells compared to G2019S and the double mutant T1343A/G2019S has no further increased activity, suggesting that T1343 is crucial for the negative feedback in the LRRK2 signaling cascade. Together, our data reveal a novel intramolecular feedback regulation of the LRRK2 Roc G domain by a LRRK2 kinase-dependent mechanism. Interestingly, PD mutants differently change the kinetics of the GTPase cycle, which might in part explain the difference in penetrance of these mutations in PD patients.
The causal involvement of the visual cortex in visual working memory remains unclear: a comment on Phylactou et al., 2023
2023-11-28

The role of the early visual cortex in visual working memory is a matter of current debate (Christophel et al., 2017; Xu 2017). Neuroimaging research has consistently shown that early visual areas (V1, V2 and V3) encode the content of VWM (e.g., Harrison and Tong 2009; Serences et al., 2009). However, we are lacking conclusive evidence supporting the causal role of sensory areas in VWM, not at least because previous transcranial magnetic stimulation (TMS) studies provided incongruent results (e.g., van de Ven et al., 2012; van Lamsweerde et al., 2017; Rademaker et al., 2017). In a recent registered report, Phylactou et al., (2023), sought to tackle this controversy via two well powered TMS experiments, designed to correct possible methodological issues of previous attempts. Unfortunately, a key part of their experimental design was based on the wrong anatomical assumption that a given eye projects input from the center of gaze (i.e., from the central retina) primarily to one hemisphere. They hence disregarded two important anatomical facts, namely that early visual areas of each hemisphere represent the contralateral visual hemifield, and that each hemisphere receives equally strong input from each eye. In what follows, we explain the correct anatomy and describe why their main approach failed to address current issues in the literature.