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**A**: Given RhoFold+’s high accuracy and speed, we finally conducted ablation studies to understand which components and information are important to RhoFold+’s predictions. The architectural components we investigated included 4 different modules (Fig.5a, see Methods)**B**: Ablation studies were performed on 138 PDB ... | BAC | ABC | ACB | BAC | Selection 2 |
**A**: CF identified and developed the connection to ecological orbits and simple harmonic motion via the maternal effect. LP drafted the initial manuscript; both SL and LP edited the first version posted on arXiv [24]. CF, SL, and LP edited the final version and code [12]. The authors are ordered alphabetically.
**B**... | ACB | CAB | BAC | BAC | Selection 2 |
**A**: In Tsamardinos et al. six AutoML tools were compared [14]. Of these, only one had a predictive performance estimation strategy that could adjusts for multiple model validations (limitedly to SO problems and not affecting model selection), while most of the tools have the necessity to withold a test set for an un... | ACB | ACB | ACB | CAB | Selection 4 |
**A**:
In the past few years, state-of-the-art, DNN-based methods were introduced for IVIM parameter estimation. Bertleff et al. [8] demonstrated the ability of supervised DNN to predict the IVIM model parameters from low SNR DWI data**B**: Barbieri et al. [6] proposed an unsupervised, physics-informed DNN (IVIM-NET) ... | ABC | CAB | BAC | ACB | Selection 1 |
**A**: The tasks above concern prediction of static properties, including structures**B**: Because molecular dynamics trajectories consist of sequences of structures, GNNs should be useful for identifying features for computing reaction statistics, and several groups have combined GNNs with VAMP [8] to learn metastable... | ABC | ACB | CBA | ACB | Selection 1 |
**A**: The concomitant impact of public health interventions and disease transmission rates will decrease the population’s hospitalization rate, although it increases with the severity of the disease. Our research highlights that quarantine may be a favourable strategy at the individual level in specific epidemiologica... | BCA | BAC | BCA | CBA | Selection 4 |
**A**:
The estimation of the parameter vector θ𝜃\thetaitalic_θ, as defined in (13), involves maximizing the product of the two likelihood functions (21) and (22)**B**: To enhance numerical stability, it is often advantageous to consider the formulation in terms of the logarithmic transformation (II-B), which involves... | ACB | ACB | BAC | ABC | Selection 4 |
**A**: Most notably, we do not include the PVC and DVA neurons in our core set despite their strong association with locomotion and strong connections with the core set**B**: This is because the PVC and DVA neurons do not appear in the whole-brain imaging datasets we use to fit our model [1], making it infeasible to fi... | ABC | BCA | ACB | BAC | Selection 2 |
**A**: Aside from instantaneous energetics, gait transition from walking to running has been attributed to muscle force-velocity behavior [31], interlimb coordination variability [32], mechanical load or stress [33, 18], and cognitive or perceptual factors [34, 35]; see [36] for a review**B**: And importantly, we know ... | BCA | ACB | ABC | CBA | Selection 2 |
**A**: This is a different cost from our model, which they supported by showing an approximate quadratic scaling of metabolic cost with force frequency**B**: Van der Zee and Kuo [28] proposed a model of metabolic rate proportional to the second derivative of force, which is equivalent to the metabolic cost per movement... | BAC | CBA | BCA | ACB | Selection 1 |
**A**: Common simplifications like considering a population-wide “contact rate” do not take this structure into account. Considering this structure leads to more realistic models of the epidemic.
**B**: This trend also intensified during the Covid-19 pandemic, where network based epidemic models were applied and develo... | CAB | BAC | ABC | BAC | Selection 1 |
**A**: This binding can be represented as pHLAhaplo𝑝𝐻𝐿subscript𝐴ℎ𝑎𝑝𝑙𝑜pHLA_{haplo}italic_p italic_H italic_L italic_A start_POSTSUBSCRIPT italic_h italic_a italic_p italic_l italic_o end_POSTSUBSCRIPT
rather than pHLAallele𝑝𝐻𝐿subscript𝐴𝑎𝑙𝑙𝑒𝑙𝑒pHLA_{allele}italic_p italic_H italic_L italic... | ACB | ABC | BAC | CAB | Selection 3 |
**A**: In summary, we have shown that fast antigenic drift can induce selection for complex adaptive immune responses, in line with our general picture of complexity in dynamical recognition systems**B**: These processes depend on the long-term co-evolution of host immune systems and multiple viral pathogens [86], whic... | CAB | BAC | ACB | ABC | Selection 3 |
**A**:
Table 3: Relative expression (RE) of genes in TLL1-transduced MT-2 cells over MT-2 cells transduced with an empty vector**B**: Genes were picked up if the RE of type 1 was larger than 11111111 and the RE of type 2 was smaller than 3333 or if the RE of type 1 was smaller than 1111 and the RE of type 2 was larger... | BCA | ACB | CAB | CAB | Selection 2 |
**A**: (2019). Our study expands the concept of brain metastable states to multi-person interactions, providing a novel perspective without relying on millisecond time-scale synchronization**B**: Our work offers a fresh perspective on inter-brain connectivity by analyzing a hyperscanning neuroimaging dataset through mu... | BCA | BAC | ABC | CBA | Selection 2 |
**A**: The output special nodes and pair embedding of Co-Former are employed dependent on different tasks, including two pre-training tasks and two downstream affinity tasks. CN, PN, and RN are the special nodes for complex, protein, and RNA, respectively.**B**:
Figure 2: Overview of CoPRA. Given a protein-RNA complex... | ACB | ABC | CAB | ACB | Selection 3 |
**A**: Artifacts in this dataset include out-of-focus areas, tissue folds, cover slips, air bubbles, pen marks, and areas with extreme over- or under-staining, which were carefully labeled to aid in quality control for pathology image analysis. We trained our network using 1500 artifact-free patches from epithelium and... | ACB | CBA | ABC | BCA | Selection 2 |
**A**:
Empirical validation of the urban scaling hypothesis has driven numerous studies using data from multiple countries and examining a wide array of urban indicators. In the realm of disease incidence, the seminal work by Bettencourt et al. reported that HIV/AIDS cases in the USA scale superlinearly with populatio... | ABC | BCA | CBA | ACB | Selection 4 |
**A**: The results show the promising value of GAN-TAT, both through computational performance and validation against clinical data. However, inherent limitations of PIN embedding, such as imbalance, sparsity, and potential overfitting, could effect GAN-TAT’s efficacy. Despite these challenges, this work provided an in... | ABC | CBA | CAB | ACB | Selection 2 |
**A**: In order to capture the hierarchical nature of GO labels, labels are represented as a directed acyclic graph and embedded as an additional feature input. They were able to achieve state-of-the-art results for 2 out of 3 problem subclasses and competitive results with NetGO and GOLabeler for the remainder. Notabl... | ACB | ACB | BAC | CBA | Selection 4 |
**A**:
VNN architecture and training**B**: The VNN model was pre-trained on a healthy population to glean information about healthy aging**C**: To facilitate ΔΔ\Deltaroman_Δ-Age that is transparent and methodologically interpretable, we used a multi-layer VNN model that yielded representations from the input cortical ... | ABC | BAC | BCA | BCA | Selection 1 |
**A**:
Now, we discuss the conditions regarding the non-existence of spatially heterogeneous steady states**B**: For this purpose, first, we deduce a priori estimates for non-negative solutions of the system (17).**C**: The following two lemmas can be found in [37, 65], respectively | ABC | BAC | CAB | ACB | Selection 4 |
**A**: Building on this, Wu et al. (2023, CcBHLA) used BiLSTM, while TransPHLA (Chu et al., 2022; 2021) incorporated self-attention modules to capture complex dependencies**B**: Ye et al. (2023, STMHCpan) modeled peptide-MHC interactions as graphs, introducing graph neural networks to the field.
**C**: With advances in... | ACB | BAC | BCA | CBA | Selection 3 |
**A**: The data generated and used within this work can be found at the Open Science Framework repository (Lluís Hernández-Navarro, Kenneth Distefano, Uwe C**B**: 2024.
Supplementary data, code, and videos for “Slow spatial migration can help eradicate cooperative antimicrobial resistance in time-varying environments”.... | ACB | BCA | CAB | CAB | Selection 1 |
**A**: (2021) and how to identify the effect of ionization on receptor proteins.
The examples reproduce existing results, confirming the reliability of our approach, but also demonstrate additional new discoveries made possible by systematic comparison of molecular simulations.**B**: (2020) how to quantify the influenc... | CAB | ABC | CAB | CBA | Selection 4 |
**A**: Figure 4 represents the scalp topographies of the grand average difference ERP**B**: We can see from figure 4 that the effect starts being significant from the timepoint 500 ms to 800 ms (p<0.001𝑝0.001p<0.001italic_p < 0.001) at the parietal region. In each topography, there is also another significant cluster ... | ABC | BAC | ACB | CBA | Selection 3 |
**A**: An extensive body of theoretical — and some experimental — work on proofreading reports the intuitive speed-accuracy trade-off.
How might our work, motivated by experimental observations of stalling [33, 34, 35, 36, 45, 38], be consistent with such prior work? Prior studies consider only the impact of a few muta... | CBA | BCA | ABC | CBA | Selection 3 |
**A**: DICOM pixel intensities were rescaled, and the image was resized to a smaller size of 224 x 224 to fit on the GPU. A pretrained Efficient-Net model was used for image processing, and extracted features were then concatenated with LSTM/Neural CDE’s features and passed through a final fully connected linear layer ... | ACB | ACB | CBA | CAB | Selection 3 |
**A**: Figure S11: The FI predicts future FPFP5 deficits better than NFPFP5. HRS, sex-stratified**B**: The curves are similar between sexes. Visually, individual points appear to agree between sexes within error**C**: The AUC is the probability that a metric will correctly rank positive individuals as higher than negat... | BCA | BCA | ABC | CAB | Selection 3 |
**A**: (2023), which includes genomic sequences from known organisms—both from human genomes and a curated selection of genomes from multiple species (e.g., fungi, mammalian, invertebrate, bacteria)—and shuffle it into our metagenomic reads at a 1:8 ratio.
**B**: For this, we sample sequences from the dataset provided ... | CAB | CBA | BAC | BCA | Selection 2 |
**A**: Specifically, DNA methylation levels change rapidly during early development and adolescence, stabilize during adulthood, and may alter again in older ages [3, 4]. This nonlinearity[5] poses significant challenges for traditional age prediction models, which often assume a uniform rate of change across the lifes... | BAC | BCA | CAB | BCA | Selection 1 |
**A**:
Furthermore, we compute the reconstruction error as a measure of encoding quality (for details see Appendix E1) and observe that the continuous model is more unstable in terms of representation quality (Fig**B**: This may be due to a continuous drift of neuronal selectivity, which does not appear to be a featur... | BCA | BCA | BAC | ACB | Selection 4 |
**A**: We demonstrate the wide applicability of UniGuide by tackling a variety of geometry-constrained drug discovery tasks**B**: With performance either on par with or superior to tailored models, we conclude that UniGuide offers advantages beyond its unification**C**: Firstly, while the novelty of conditional models ... | ACB | BAC | ABC | BCA | Selection 3 |
**A**: DynamicBind predicts the ligand-specific protein-ligand complex structure with a deep equivariant generative model.**B**:
NeuralPlexer (Qiao et al., 2023) incorporates essential biophysical constraints and a multi-scale geometric deep learning system for the diffusion process**C**: For generating the ligand-spe... | CAB | CBA | ACB | ACB | Selection 1 |
**A**: SCN9A encodes the Nav1.7 sodium channel, which plays a crucial role in pain perception and anesthetic analgesia. CNR1 encodes the cannabinoid receptor type 1, influencing pain and the effects of cannabinoid anesthetics. SLC6A3 and SLC6A5 encode dopamine and glycine transporters, respectively, which are involved ... | CAB | BCA | BAC | CBA | Selection 1 |
**A**:
We systematically trained the model to reconstruct images using sets of 4, 16, 32, and 64 learnable attention maps**B**: This approach allows us to evaluate the optimal number of features required for effective reconstruction**C**: The quality of the reconstructions is quantitatively compared with a baseline mo... | CBA | BAC | ACB | ABC | Selection 4 |
**A**: One great source of explanations is illusions and disorders of body representation. The human brain constantly sends and receives a flow of multisensory information**B**: We’ve already finished defining our model and we want to get a further step on rationality. For human beings, the most classical perspective w... | BAC | ACB | ABC | ACB | Selection 1 |
**A**: demonstrate their emergence within a relatively simple setup: a ring network of N𝑁Nitalic_N FHN units with symmetric connections but non-uniform parameters**B**:
Contrary to the assumption that complex networks are essential for chimera states, Omelchenko et al**C**: The dynamics of each node in the network ar... | BAC | ACB | ABC | ACB | Selection 1 |
**A**: 6, a simulation within a one-dimensional linear system illustrates the effect of a driving traveling pulse (panel A) - characterized by a constant velocity and width, and a heaviside-like profile - on an oscillatory system with a period of T≈186𝑇186T\approx 186italic_T ≈ 186**B**:
In Fig**C**: The interaction ... | BAC | ABC | CBA | CBA | Selection 1 |
**A**: However, its limited reconstruction performance constrains its applicability. Lin et al**B**:
More closely related to our work, Gao et al. (2023) adapts VQ-VAE (van den Oord et al., 2017) for protein structures**C**: (2023a) explores discrete structural representation learned by such VQ-VAEs (van den Oord et al... | BAC | BCA | ACB | CAB | Selection 1 |
**A**:
A modified version [8] of the de Gruijl model [7] was implemented in Arbor-Pycat. The morphology of mouse IO neuron C4A was used [25]**B**: For programming ease, these default values were scaled by the parameter θ𝜃\thetaitalic_θ, which was thus a vector of ones, initially. Optimization was performed against th... | ABC | ACB | CBA | CAB | Selection 2 |
**A**:
Phages infect host cells by adsorbing (attaching) to receptors on the host cell wall and then delivering the genomic content into the host cytoplasm. Phages are much smaller than bacteria and each host cell presents multiple receptors that phages can bind to, so multiple phages can adsorb to a single host cell,... | BAC | BCA | ABC | BAC | Selection 3 |
**A**:
In this chapter, I have provided a brief introduction to neural networks consisting of DNA, using as an example the winner-take-all network proposed in Ref. Cherry and Qian (2018). The input data is provided as a DNA strand and is processed via biochemical reactions**B**: (2013). Such approaches constitute a pr... | BCA | BAC | CBA | ACB | Selection 4 |
**A**: Positive correlations are observed in the temporal and parietal regions, indicating theta rhythms’ role in auditory information processing and memory integration**B**: The Text model shows reduced but still present positive correlations in the temporal lobe, highlighting the involvement of theta rhythms in cogni... | BCA | ABC | ABC | ACB | Selection 1 |
**A**: Even when the initial position of the agent is uniformly distributed throughout the system, the agent is not able to learn about its complete environment and gets trapped in nearest attractant peak, for low exploration rate and high learning rate**B**: When the attractant profile has peaks of different sizes, th... | CAB | CBA | BAC | BCA | Selection 3 |
**A**: We plotted the correlation values for all the best performing models from conv1, conv2 and conv3 layers. Each point represents a signal-wise model, and the color represents the model type (blue is AFRT, red is Linear-AlexNet)**B**:
Our analysis shows that the predicted activity from the AFRT model correlate hig... | BAC | ABC | ACB | CBA | Selection 1 |
**A**: Genes that have been previously shown to be downregulated in HD from which we obtain a negative correlation between SHAP and gene expression in SPN clusters are: Pde10A [19] or Scnb4 [20]. We have validated other lower rank genes previously described in different HD models, such as Penk1 (cluster iSPN), Gria3 (c... | BAC | CAB | BAC | BCA | Selection 2 |
**A**: For instance, the file parsing is highly optimized and executed with asynchronous buffers**B**: All data is read in streams, so that the number of input files, and their sizes, do not significantly affect the amount of required memory. Processor-intensive steps, such as file parsing and the statistics computatio... | CBA | ACB | CAB | BCA | Selection 4 |
**A**: Our training data was obtained by extracting 50,000 pairs of conformations and molecules from this dataset**B**:
The GEOM-QM9 dataset is an extension of the original QM9 dataset, enriched with multiple conformations for each molecule, primarily focusing on smaller compounds with a maximum of 9 heavy atoms**C**:... | CBA | BCA | ACB | BAC | Selection 4 |
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