Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-modal Gaussian Process Variational Autoencoders for Neural and Behavioral Data

Characterizing the relationship between neural population activity and behavioral data is a central goal of neuroscience. While latent variable models (LVMs) are successful in describing high-dimensional time-series data, they are typically only designed for a single type of data, making it difficult to identify structure shared across different experimental data modalities. Here, we address this shortcoming by proposing an unsupervised LVM which extracts temporally evolving shared and independent latents for distinct, simultaneously recorded experimental modalities. We do this by combining Gaussian Process Factor Analysis (GPFA), an interpretable LVM for neural spiking data with temporally smooth latent space, with Gaussian Process Variational Autoencoders (GP-VAEs), which similarly use a GP prior to characterize correlations in a latent space, but admit rich expressivity due to a deep neural network mapping to observations. We achieve interpretability in our model by partitioning latent variability into components that are either shared between or independent to each modality. We parameterize the latents of our model in the Fourier domain, and show improved latent identification using this approach over standard GP-VAE methods. We validate our model on simulated multi-modal data consisting of Poisson spike counts and MNIST images that scale and rotate smoothly over time. We show that the multi-modal GP-VAE (MM-GPVAE) is able to not only identify the shared and independent latent structure across modalities accurately, but provides good reconstructions of both images and neural rates on held-out trials. Finally, we demonstrate our framework on two real world multi-modal experimental settings: Drosophila whole-brain calcium imaging alongside tracked limb positions, and Manduca sexta spike train measurements from ten wing muscles as the animal tracks a visual stimulus.
Double variational principle for mean dimension of $\mathbb{Z}^{K}$-actions

In this paper, we introduce mean dimension and rate distortion dimension for $\mathbb{Z}^{k}$-actions dynamical system $(\mathcal{X},\mathbb{Z}^k,T)$. Suppose $(\mathcal{X},\mathbb{Z}^k,T)$ has the marker property. Taking these two variables, the metric $d$ on $\mathcal{X}$ and $\mathbb{Z}^{k}$-invariant measure $\mu$, into consideration, a minimax-type variational principle for mean dimension of $\mathbb{Z}^{k}$-actions is established. This result extends the double variational principle obtained recently by Lindenstrauss and Tsukamoto \cite{LT19} from $\mathbb{Z}$-actions dynamical systems to $\mathbb{Z}^{k}$-actions dynamical systems.
Deep-sea sedimentation and paleoproductivity in the Paleogene of a Tethyan basin

In the area of Salzburg the Paleogene sediments of the Rhenodanubian flysch attain a thickness of approximately 450 m. These sediments were deposited in an abyssal environment below the calcite compensation depth and they comprise the complete Paleocene and the Ypresian (up to NP11). A composite section was constructed from two outcrop-groups located in the surrounding of the village of Anthering. Predominantly, the older part of the section (Danian) is built up by turbidites which often show Bouma-cycles. Only minor amounts of hemipelagic claystone occur. By far smectite is the most common clay mineral, followed by illite, chlorite, and kaolinite. The turbidites can be attributed to a small deep-sea fan which had its feeder channel 30 km east of the studied outcrops (Egger in prep.). The material of the turbidites was supplied from the southern part of the European plate which was located north of the flysch basin. The deep-sea fan was abandoned within nannoplankton Zone NP3 or NP4 and its deposits were covered by 50 m of claystone (Strubach-Tonstein) with only a few intercalated turbidite layers. It is noteworthy that the base of this prominent lithological shift seems to be coeval with the beginning of the Selandian. Sedimentation of the Strubach-Tonstein ended within Zone NP8. Clay-mineral composition of the StrubachTonstein is characterized by high contents of chlorite and illite which are indicating increased mechanical erosion in the source area whilst no kaolinite was observed in these samples. This erosion is seen as an effect of strong tectonic movements within the European plate in the middle Paleocene which caused inversion and uplifting of major basement blocks at distances up to 1300 km to the north of the present Alpine deformation front (e.g. Ziegler 1987). In the Alpine foreland these deformations gener-
Maximum Likelihood Estimation of Latent Variable Models by SMC with Marginalization and Data Cloning

A data-cloning SMC² method is proposed as a general purpose optimization routine for estimating latent variable models by maximum likelihood. The latent variables are first marginalized out by SMC at any fixed parameter value, and the model parameters are then estimated by density tempered SMC. The data-cloning step is employed to efficiently reduce Monte Carlo errors inherent in the SMC² algorithm and also to effectively address multi-modality present in typical objective functions. This new method has wide applicability and can be massively parallelized to take advantage of typical computers today.
Maximum Likelihood Estimation of the Equity Premium

The equity premium, namely the expected return on the aggregate stock market less the government bill rate, is of central importance to the portfolio allocation of individuals, to the investment decisions of firms, and to model calibration and testing. This quantity is usually estimated from the sample average excess return. We propose an alternative estimator, based on maximum likelihood, that takes into account information contained in dividends and prices. Applied to the postwar sample, our method leads to an economically significant reduction from 6.4% to 5.1%. Simulation results show that our method produces tighter estimates under a range of specifications.
Ice Formation in an Antarctic Glacier-dammed Lake and Implications for Glacier-Lake Interactions

Perennially frozen lakes are common features in the McMurdo Dry Valleys of South Victoria Land in Antarctica. Some of them, called wet based, contain liquid water capped by a permanent ice cover between 2.5 and 6 m in thickness. The others, called dry based, are ice-block lakes. The thickness of the latter may far exceed those of the former. Their level is rising from freezing of the surface flooding of summer meltwater. However, we show here for the first time, using isotopic analyses together with an ionic and gas content and composition study, that the ice of one of these dry-based lakes has been formed by complete freezing from top to bottom of a closed water reservoir and not by successive layers of icings (aufeis) piling on top of each other. We also show how this lake, dammed by a cold-based glacier, has contributed to the formation of the basal ice layer of this glacier.
Global coal gap between Permian-Triassic extinction and Middle Triassic recovery of peat-forming plants

Early Triassic coals are unknown, and Middle Triassic coals are rare and thin. The Early Triassic coal gap began with extinction of peat-forming plants at the end of the Permian (ca. 250 Ma), with no coal known anywhere until Middle Triassic (243 Ma). Permian levels of plant diversity and peat thickness were not recovered until Late Triassic (230 Ma). Tectonic and climatic explanations for the coal gap fail because deposits of fluctuating sea levels and sedimentary facies and paleosols commonly found in coal-bearing sequences are present also in Early Triassic rocks. Nor do we favor explanations involving evolutionary advances in the effectiveness of fungal decomposers, insects or tetrapod herbivores, which became cosmopolitan and much reduced in diversity across the Permian-Triassic boundary. Instead, we favor explanations involving extinction of peat-forming plants at the Permian-Triassic boundary, followed by a hiatus of some 10 m.y. until newly evolved peat-forming plants developed tolerance to the acidic dysaerobic conditions of wetlands. This view is compatible not only with the paleobotanical record of extinction of swamp plants, but also with indications of a terminal Permian productivity crash from {delta}{sup 13}C{sub org} and total organic carbon of both nonmarine and shallow marine shales. 205 refs., 3 figs.,more » 3 tabs. « less
Buoyancy-forced circulations around islands and ridges

Observations, theory, and modeling studies indicate that dominant components of both the upwelling and downwelling limbs of the thermohaline circulation take place near boundaries and in regions of steep and/or rough topography. Analytic and numerical results are used here to show that the interaction of upwelling regions with lateral boundaries fundamentally alters the resulting large-scale circulation compared to cases of open ocean upwelling. For narrow upwelling regions, viscous fluxes emerge as a leading term in the potential vorticity budget. The strong horizontal recirculation gyres that are found for sub-basin-scale open ocean upwelling (β-plumes) are replaced by weak, unidirectional flow into or out of the region of vertical motion. If the upwelling is located near an island or mid-ocean ridge, potential vorticity budgets require that a strong, large-scale recirculation develop around the topography, sometimes far from the region of mixing. The resulting boundary layers provide an important dynamic link between the large-scale horizontal components of the thermohaline circulation and the small-scale regions of strong vertical motions.
“Is This A Joke?”: A Large Humor Classification Dataset

Humor is an essential characteristic of language. It has been a topic of research in linguistics and philosophy from historical times. In computer science, computational humor, as a part of Natural Language Processing, is a growing area of research. Social Media is rapidly growing as a platform for communication but processing of social media, owing to its semantic perplexity, is still a challenge. These two facts lead us to present a novel dataset for humor classiﬁcation which captures diversity in humor on web resources. The large size of this dataset is to meet the data requirements for modern machine learning algorithms. This paper also deals with creating a model for detecting and analyzing humor in social media text extracted from eclectic sources on the Internet.
Velocity of compressional waves in various minerals at pressures to 10 kilobars

The velocity of compressional waves in several minerals, as a function of pressure to 10 kb, has been measured. Data for single-crystal microcline suggest that measurements of elastic constants should be made under hydrostatic pressure for all material not of gem quality. Velocities for some rocks with high calcium content suggest a correction to the velocity-density-mean atomic weight relationship of Birch for content of CaO according to Vp := a + 4.60 [CaO] + bρ, where the brackets indicate weight fraction.
Hybrid API Migration: A Marriage of Small API Mapping Models and Large Language Models

API migration is an essential step for code migration between libraries or programming languages, and it is a challenging task as it requires detailed comprehension of both source and target APIs. The existing work either recommends mapped API names only and requires developers to select specific parameters and return value, or uses encoder-decoder models to directly “translate” the source API code into the target API code without considering the characteristics of APIs. In this paper, we propose a hybrid approach that combines small API mapping models with Large Language Models (LLMs). Specifically, the small API mapping model is employed to embed API semantics through their usages and declarations, enabling accurate inference of API mappings across different libraries and programming languages. The inferred mappings are subsequently used as part of the prompts to guide LLMs to generate the target API code corresponding to the source API code. Experimental evaluations demonstrate the effectiveness of our approach in comparison to existing approaches w.r. t. both cross-library and cross-language API migration.
Drawgasms: Playing with expectations and experiences of pleasure through multimodal accounts

Drawing on a study consisting of 29 multimodal accounts of orgasms, we make visible processes, emotions, and notions of playfulness that highlight the critical role of orgasms in transcending the fleeting distinction between reality and play. As sexual pleasure does not necessarily result from experiencing an orgasm, our data also reveals how playful strategies are enacted in order to mitigate ambiguity and societal norms. Instead of seeing the orgasm as a physiological or psychological change in an individual or as an epitome of “good” sex, the multimodal accounts employed in the study reveal attitudes, assumptions, and expectations related to playful pleasure.
Microphysical and radiative properties of boundary layer stratiform clouds deduced from ground‐based measurements

Two methods for retrieving the microphysical and radiative properties of marine and continental boundary layer stratiform clouds from ground-based measurements are implemented. The first method uses measurements of the cloud liquid water path and the cloud nadir radiance at 1 μm to infer the cloud optical depth, cloud droplet effective radius, and cloud droplet concentration. In the second method a <52-stream radiative transfer model is used to retrieve the microphysical and radiative properties of stratiform clouds from measurements of the cloud liquid water path, the cloud geometric thickness, the downward shortwave irradiance at the surface, and atmospheric profiles of temperature, pressure, and relative humidity. In all of the retrievals the cloud droplets are assumed to have a lognormal size distribution with a logarithmic width of 0.35; the cloud droplet modal radius and cloud droplet concentration are free parameters. Data obtained in the Azores and Oklahoma from marine and continental boundary layer stratiform clouds, respectively, are used in the study. Results of the analysis demonstrated that the retrieved cloud droplet effective radii from the marine clouds (13 μm) were generally larger than the values from continental clouds (7 μm), while cloud droplet number concentrations were much less in marine clouds (150 cm−3) than in continental clouds (500 cm−3). The retrieved cloud droplet effective radius had a strong negative correlation with the cloud droplet concentration. The effects of uncertainties in the measurements, the cloud droplet distribution width, and the surface albedo on the retrieved properties were evaluated by using the 52-stream model. The errors in the retrieved cloud radiative properties were generally less than 5%, while the errors in the retrieved cloud microphysical properties were considerably larger.
Towards a characteristic equation for permeability

Towards a Characteristic Equation for Permeability. (August 2008) Adil Ahmed Siddiqui, B.E. , National University of Sciences & Technology, Pakistan Chair of Advisory Committee: Dr. Thomas A. Blasingame The characterization of reservoir permeability (k) remains the elusive challenge in reservoir engineering. This work considers prior developments in an evolutionary sense, and, as with prior work, our goal is the development of a "characteristic permeability relation" (CPR). To this end, we have developed 5 CPR formulations — 3 of which could be considered modifications of "historical" models and 2 of which are "weighted" power law-exponential models. In this work, we consider permeability to be only a function of two variables; k = f(φ,z) — porosity (φ) and z, where z is either the water saturation (Sw) or the Archie Formation Factor (F). Our rationale in considering k = f(φ,z) is two-fold — first, such a formulation is a fundamental extension of the k = f(φ) correlation work by Archie (and countless others); and second, our validation datasets are limited to literature cases and cases obtained from industry sources — none of which would be considered suitable for extension beyond porosity and another variable. We demonstrate and validate our concept of a characteristic permeability relation using various datasets obtained from the literature and from industry sources. In this work we show that each proposed relation has a unique character and performance — depending on primarily on the data, rather than the functional form of the permeability relation. Using the characteristic permeability relations developed in this work — the proposed permeability relations can be extended to other and other data types. It may also be possible to develop so-called "hydraulic flow unit" methods which segregate petrophysical data into depositional flow sequences.
A new high‐resolution central and western Saharan summertime dust source map from automated satellite dust plume tracking

In this paper, we outline a new objective dust source detection method for the central and western Sahara (CWS), based on the automated tracking of individual dust plumes in data from the Spinning Enhanced Visible and Infrared Imager, available every 15 mins. at ~0.03° spatial resolution. The method is used to map the origin of summertime dust storms in the CWS for June – August 2004 – 2010. It reveals the sources of these events in unprecedented detail, allowing for the identification of specific, highly active source areas. The study of collocated surface features reveals that many of the dominant sources are likely associated with paleolakes and outwash plains, many in close proximity to the Saharan mountains. Extensive nonsource areas are associated with low albedo and elevated terrain, pointing to the mountainous regions of the Sahara. Additionally, sand seas are not identified as important source areas, but their margins sometimes are. The automated tracking method also facilitates analysis of the transport direction of dust plumes from key source regions and the inference of emission mechanisms. It is found that there are two broad domains within the CWS: one in southwest Algeria and northwest Mali, characterized primarily by transport toward the southwest and very likely dominated by low‐level jets embedded in the northeasterly Harmattan winds; and a second in southern Algeria, northwest Niger, and northeast Mali where there is no preferred transport direction and a strong potential association between dust events and deep convection, pointing toward cold pool outflows as the likely deflation mechanism.
North Pacific Decadal Variability and Climate Change in the IPCC AR4 Models

AbstractThe two leading modes of North Pacific sea surface temperature (SST) and sea level pressure (SLP), as well as their connections to tropical variability, are explored in the 24 coupled climate models used in the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4) to evaluate North Pacific decadal variability (NPDV) in the past [twentieth century; climate of the twentieth century (20C3M) scenario] and future [twenty-first century; Special Report on Emissions Scenarios (SRES) A1B scenario] climate. Results indicate that the two dominant modes of North Pacific oceanic variability, the Pacific decadal oscillation (PDO) and the North Pacific Gyre Oscillation (NPGO), do not exhibit significant changes in their spatial and temporal characteristics under greenhouse warming. However, the ability of the models to capture the dynamics associated with the leading North Pacific oceanic modes, including their link to the corresponding atmospheric forcing patterns and to tropical varia.
Analysis of ductal carcinoma in situ by self-reported race reveals molecular differences related to outcome

Ductal carcinoma in situ (DCIS) is a non-obligate precursor to invasive breast cancer (IBC). Studies have indicated differences in DCIS outcome based on race or ethnicity, but molecular differences have not been investigated. We examined the molecular profile of DCIS by self-reported race (SRR) and outcome groups in Black (n=99) and White (n=191) women with DCIS in a large DCIS case-control cohort with longitudinal follow up. Gene expression and pathway analyses indicated that different genes and pathways are involved in ipsilateral breast outcome (DCIS or IBC) after DCIS treatment in White versus Black women. We identified differences in ER and HER2 expression, tumor microenvironment composition, and copy number variations by SRR and outcome groups. Our results suggest that different molecular mechanisms drive subsequent ipsilateral breast events in Black versus White women.
T cells in testicular germ cell tumors: new evidence of fundamental contributions by rare subsets

BACKGROUND Immune cell infiltration is heterogeneous but common in testicular germ cell tumors (TGCT) and pre-invasive germ cell neoplasia in situ (GCNIS). Tumor-infiltrating T cells including regulatory T (Treg) and follicular helper T (Tfh) cells are found in other cancer entities, but their contributions to TGCT are unknown. METHODS Human testis specimens from independent patient cohorts were analyzed using immunohistochemistry, flow cytometry and single-cell RNA sequencing (scRNA-seq) with special emphasis on delineating T cell subtypes. RESULTS Profound changes in immune cell composition within TGCT, shifting from macrophages in normal testes to T cells plus B and dendritic cells in TGCT, were documented. In most samples (96%), the CD4+ T cell frequency exceeded that of CD8+ cells, with decreasing numbers from central to peripheral tumor areas, and to tumor-free, contralateral testes. T cells including Treg and Tfh were most abundant in seminoma compared to mixed tumors and embryonal carcinoma. CONCLUSION Despite considerable heterogeneity between patients, T cell subtypes form a key part of the TGCT microenvironment. The novel finding of rare Treg and Tfh cells in human testis suggests their involvement in TGCT pathobiology, with implications for understanding tumor progression, to assess patients’ prognosis, and as putative targets for personalized immunotherapy.
PRCnet: An Efficient Model for Automatic Detection of Brain Tumor in MRI Images

Brain tumors are the most prevalent and life-threatening cancer; an early and accurate diagnosis of brain tumors increases the chances of patient survival and treatment planning. However, manual tumor detection is a complex, cumbersome and time-consuming task and is prone to errors, which relies on the radiologist’s experience. As a result, the development of accurate and automatic system for tumor detection is critical. In this paper, we proposed a new model called Parallel Residual Convolutional Network (PRCnet) model to classify brain tumors from Magnetic Resonance Imaging. The PCRnet model uses several techniques (such as filters of different sizes with parallel layers, connections between layers, batch normalization layer, and ReLU) and dropout layer to overcome the over-fitting problem, for achieving accurate and automatic classification of brain tumors. The PRCnet model is trained and tested on two different datasets and obtained an accuracy of 94.77% and 97.1% for dataset A and dataset B, respectively which is way better as compared to the state-of-the-art models.