gebhart/patrepeval huggingface dataset:
Learning Factorized Multimodal Representations (2018)

Learning multimodal representations is a fundamentally complex research problem due to the presence of multiple heterogeneous sources of information. Although the presence of multiple modalities provides additional valuable information, there are two key challenges to address when learning from multimodal data: 1) models must learn the complex intra-modal and cross-modal interactions for prediction and 2) models must be robust to unexpected missing or noisy modalities during testing. In this paper, we propose to optimize for a joint generative-discriminative objective across multimodal data and labels. We introduce a model that factorizes representations into two sets of independent factors: multimodal discriminative and modality-specific generative factors. Multimodal discriminative factors are shared across all modalities and contain joint multimodal features required for discriminative tasks such as sentiment prediction. Modality-specific generative factors are unique for each modality and contain the information required for generating data. Experimental results show that our model is able to learn meaningful multimodal representations that achieve state-of-the-art or competitive performance on six multimodal datasets. Our model demonstrates flexible generative capabilities by conditioning on independent factors and can reconstruct missing modalities without significantly impacting performance. Lastly, we interpret our factorized representations to understand the interactions that influence multimodal learning.
Organic Photovoltaic Performance Resiliency: Role of Molecular Weight in a PM7 Derivative (2023)

Batch-to-batch variations remain a challenge for organic photovoltaics (OPVs) that must be solved for widespread commercialization. This work addresses the role of the molecular weight (MW), introducing a new donor polymer PM7-D5 with an extended thiophene bridge compared to that of PM6 or PM7. Devices comprising PM7-D5 and the nonfullerene acceptor L8-BO are relatively insensitive to a significant molecular weight variation and result in OPVs with photoconversion efficiencies (PCEs) of 11.4% and 12.4%, when using polymers with 26 and 125 kDa. We elucidate the origins of the small performance change and systematically address morphology, charge generation, recombination, and extraction, combining optical simulations and experimental techniques. The comprehensive analysis emphasizes the complexity of the photoelectric processes and confirms the high robustness to MW variations of this blend system. Lastly, we review reported blends and suggest systematic research of the structural parameters that lead to an increased robustness to MW changes.
Collaborative sequential detection of Gaussian models from observed data and the value of information exchanged (2017)

We consider the problem of detecting which Gaussian model generates an observed time series data. We consider as possible generative models two linear systems driven by white Gaussian noise with Gaussian initial conditions. We also consider two collaborating observers. The observers observe a function of the state of the systems. Using these observations, the aim is to find which one of the two Gaussian models has generated the observations. For each observer we formulate a sequential hypothesis testing problem. Each observer computes its own likelihood ratio based on its own observations. Using the likelihood ratio, each observer performs sequential probability ratio test (SPRT) to arrive at its decision on the hypothesis. Taking into account the random and asymmetric stopping times of the two observers, we present a consensus algorithm which guarantees asymptotic convergence to the true hypothesis. The consensus algorithm involves exchange of information, i.e., the decision of the observers. Through simulations, the “value” of the information exchanged, probability of error and average time to consensus are computed.
Developmental trajectory of the healthy human gut microbiota during the first 5 years of life (2021)

The gut is inhabited by a densely populated ecosystem, the gut microbiota, that is established at birth. However, the succession by which different bacteria are incorporated into the gut microbiota is still relatively unknown. Here, we analyze the microbiota from 471 Swedish children followed from birth to 5 years of age, collecting samples after 4 and 12 months and at 3 and 5 years of age as well as from their mothers at birth using 16S rRNA gene profiling. We also compare their microbiota to an adult Swedish population. Genera follow 4 different colonization patterns during establishment where Methanobrevibacter and Christensenellaceae colonize late and do not reached adult levels at 5 years. These late colonizers correlate with increased alpha diversity in both children and adults. By following the children through age-specific community types, we observe that children have individual dynamics in the gut microbiota development trajectory.
Lipid bilayer nanodisc platform for investigating polyprenol-dependent enzyme interactions and activities (2013)

Membrane-bound polyprenol-dependent pathways are important for the assembly of essential glycoconjugates in all domains of life. However, despite their prevalence, the functional significance of the extended linear polyprenyl groups in the interactions of the glycan substrates, the biosynthetic enzymes that act upon them, and the membrane bilayer in which they are embedded remains a mystery. These interactions are investigated simultaneously and uniquely through application of the nanodisc membrane technology. The Campylobacter jejuni N-linked glycosylation pathway has been chosen as a model pathway in which all of the enzymes and substrates are biochemically accessible. We present the functional reconstitution of two enzymes responsible for the early membrane-committed steps in glycan assembly. Protein stoichiometry analysis, fluorescence-based approaches, and biochemical activity assays are used to demonstrate the colocalization of the two enzymes in nanodiscs. Isotopic labeling of the substrates reveals that undecaprenyl-phosphate is coincorporated into discs with the two enzymes, and furthermore, that both enzymes are functionally reconstituted and can sequentially convert the coembedded undecaprenyl-phosphate into undecaprenyl-diphosphate-linked disaccharide. These studies provide a proof-of-concept demonstrating that the nanodisc model membrane system represents a promising experimental platform for analyzing the multifaceted interactions among the enzymes involved in polyprenol-dependent glycan assembly pathways, the membrane-associated substrates, and the lipid bilayer. The stage is now set for exploration of the roles of the conserved polyprenols in promoting protein-protein interactions among pathway enzymes and processing of substrates through sequential steps in membrane-associated glycan assembly.
Risk of being seropositive for multiple HPV types among Finnish and Ugandan women (2010)

Background: Although infections with multiple HPV types have been readily reported, more information is needed for occurrence of the different types at individual or at the population level, e.g., across countries Objective: We determined the distribution of seroprevalences to multiple HPV types in Finland and Uganda to compare epidemiology of the different HPV types in the two populations. Methods: Cross-sectional seroprevalence study of antenatal clinic attendants. In Finland serum samples were randomly drawn from a subset of samples collected between 1995 -2007 for the Finnish Maternity cohort and in Uganda, samples were collected (between 2004-2008) from women enrolled after consenting. The serum samples were stored and analysed for HPV antibodies against seven HPV types; 6, 11, 16, 18, 31, 33, and 45 using direct VLP ELISA. Results: Sera were analysed for 2 784 Finnish and 1 964 Ugandan women (mean ages 22 and 25 years) of whom 44% and 57% had antibodies to at least one of the seven HPV types (6/11/16/18/31/33/45) tested (p < 0.001). Multiple HPV antibody positivity was common. Finnish women, who were HPV45 seropositive (F-HPV45), had higher adjusted risk estimates of having antibodies to most of the other HPV types (HPV18, 31 and 33) than comparable Ugandan women (U-HPV45): F-HPV45:HPV18 (OR = 10.9, 95% CI 5.3-23) vs. U-HPV45:HPV18 (OR = 3.4, 95% CI 2.3-5.0), F-HPV45:HPV31 (OR = 6.1, 95% CI 2.8-13.4) vs. U-HPV45:HPV31 (OR = 2.2, 95% CI 1.6-3.0), and F-HPV45:HPV33 (OR = 12.2, 95% CI 5.8-26) vs. U-HPV45:HPV33 (OR = 3.3, 95% CI 2.4-4.5). This was true also for antibodies to HPV31 and HPV33 among HPV18 seropositive Finnish women (F-HPV18) vs. HPV18 seropositive Ugandan women (U-HPV18) albeit with somewhat overlapping confidence intervals: F-HPV18:HPV31 (OR = 5.2, 95% CI 3.0-9.0) vs. U-HPV18:HPV31 (OR = 3.1, 95% CI 2.2-4.4), F-HPV18:HPV33 (OR = 6.9, 95% CI 4.1-11.7) vs. U-HPV18:HPV33 (OR = 3.3, 95% CI 2.3-4.6). In general, among the HPV16 seropositives increased risk estimates for being seropositive for a second HPV type were observed but major differences were not observed between the Finns and the Ugandans. Conclusion: We observed remarkably increased risk estimates for being double HPV antibody positive among HPV45 and HPV18 seropositive Finns as compared to the Ugandans. In conclusion, biological, behavioral factors, iatrogenic and societal factors (screening vs no screening) may result in the different occurrence of infections with the high risk HPV types in Finland and Uganda. Abstracts for SupplementInternational Journal of Infectious DiseasesVol. 14Preview Full-Text PDF Open Archive
Functor Categories and Store Shapes (1997)

An intuitive grasp of the nature of variable declarations and of what is happening as one enters and exits from blocks is essential to programming in an Algol-like language. However, a precise semantic description of the constructs involved is difficult, and it is particularly difficult if one wants semantics for block structure that mesh elegantly with semantics for procedures.
Nociceptin/Orphanin FQ Receptor Agonists Attenuate l-DOPA-Induced Dyskinesias (2012)

In the present study we investigated whether the neuropeptide nociceptin/orphanin FQ (N/OFQ), previously implicated in the pathogenesis of Parkinson's disease, also affects L-DOPA-induced dyskinesia. In striatal slices of naive rodents, N/OFQ (0.1-1 μm) prevented the increase of ERK phosphorylation and the loss of depotentiation of synaptic plasticity induced by the D1 receptor agonist SKF38393 in spiny neurons. In vivo, exogenous N/OFQ (0.03-1 nmol, i.c.v.) or a synthetic N/OFQ receptor agonist given systemically (0.01-1 mg/Kg) attenuated dyskinesias expression in 6-hydroxydopamine hemilesioned rats primed with L-DOPA, without causing primary hypolocomotive effects. Conversely, N/OFQ receptor antagonists worsened dyskinesia expression. In vivo microdialysis revealed that N/OFQ prevented dyskinesias simultaneously with its neurochemical correlates such as the surge of nigral GABA and glutamate, and the reduction of thalamic GABA. Regional microinjections revealed that N/OFQ attenuated dyskinesias more potently and effectively when microinjected in striatum than substantia nigra (SN) reticulata, whereas N/OFQ receptor antagonists were ineffective in striatum but worsened dyskinesias when given in SN. Quantitative autoradiography showed an increase in N/OFQ receptor binding in striatum and a reduction in SN of both unprimed and dyskinetic 6-hydroxydopamine rats, consistent with opposite adaptive changes of N/OFQ transmission. Finally, the N/OFQ receptor synthetic agonist also reduced dyskinesia expression in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-treated dyskinetic macaques without affecting the global parkinsonian score. We conclude that N/OFQ receptor agonists may represent a novel strategy to counteract L-DOPA-induced dyskinesias. Their action is possibly mediated by upregulated striatal N/OFQ receptors opposing the D1 receptor-mediated overactivation of the striatonigral direct pathway.
Effect of Silica and Tin Oxide Nanoparticles on Properties of Nanofibrous Electrospun Separators (2015)

Innovative separators able to improve the performance and safety of Li-ion batteries are under investigation to meet the growing demand for large-size and high energy density electrochemical cells. In this work, highly porous nanofibrous Poly(vinylidene fluoride) (PVdF) separators loaded with oxide nanoparticles were produced by electrospinning. Silicon oxide and tin oxide nanoparticles were added to PVdF and membranes were characterized by SEM-EDS and TGA. The effect of nanoparticle addition on electrolyte uptake, mechanical properties and conductivity was investigated and such properties were compared to those of a commercial separator (Celgard 2400). Results showed that a small amount of additive can significantly improve the properties of PVdF electrospun membranes and that the different nanoparticles investigated in this work have different effect on membrane performances. In particular, the addition of SiO2 increases the rate of electrolyte uptake and the toughness of the electrospun membrane, while the addition of SnO2 decreases the rate of electrolyte uptake and increases the stiffness of the electrospun membrane. When loaded with nanoparticles, PVdF membranes maintain their insulating character also at high temperature. Preliminary electrochemical results on half-cell vs Li with LiFePO4 and electrospun separators showed good cycling performance, highlighting interesting features of this technology.
Properties of Chemically Cross-Linked Methylcellulose Gels (2019)

Methylcellulose (MC) is widely used as a rheology modifier because, upon heating in aqueous solutions, MC reversibly self-assembles into ∼7–10 nm radius fibrils that percolate into a network, resulting in physical gelation. Here, we have chemically cross-linked both MC solutions at room temperature and MC physical fibril gels at 80 °C and compared the swelling and shear modulus properties of both materials. To achieve this, hydroxyl moieties on MC (Mw ≈ 150 kDa) were substituted with allyl groups, with a degree of substitution of about one pendant carbon–carbon double bond per nine anhydroglucose repeat units. The allyl groups undergo cross-linking in the presence of a photoinitiator and UV light. Chemically cross-linking MC fibril gels (“xfib-MC”) at 80 °C results in opaque solid materials and locks in the fibril structure, which persists even on cooling back to room temperature. From small-angle X-ray scattering analysis, the fibril radius is larger at room temperature ∼20 nm and decreases to ∼10 nm at 80 °C. While the fibrils themselves shrink upon heating, the total volume change of xfib-MC gels is minimal. The dynamic shear modulus G′ increases modestly with increasing temperature despite the lack of volume change, and the volume fraction scaling of the modulus is consistent with previous results for fibril gels. On the other hand, chemically cross-linking MC solutions (“xsol-MC”) at room temperature leads to clear, solid hydrogels, which no longer form fibrils upon heating. Instead, swelling measurements show that the xsol-MC gels shrink by an order of magnitude in volume when the temperature is increased from 25 to 80 °C. The equilibrium polymer volume fraction, ϕe, and G′ are consistent with established theories for cross-linked polymer chains. We conclude that the origin of elasticity at 80 °C for the two solid materials is totally different and highly tunable. For xsol-MC gels, the modulus arises from conformational entropy of the chains, and for xfib-MC gels, the modulus is attributed to the bending modulus of the individual fibrils.
Estimation of fluid status using three multifrequency bioimpedance methods in hemodialysis patients (2022)

Although segmental eight-point bioimpedance techniques provided comparable TBW measurements not affected by standing over a period of 10-15 min, the ECW/TBW ratio appeared to be significantly lower in InBody compared with Seca and Hydra. Results from our study showed lack of agreement between different bioimpedance devices; direct comparison of ECW, ICW, and ECW/TBW between different devices should be avoided and clinicians should use the same device to track the fluid status in their HD population in a longitudinal direction.
Multicohort Analysis of Publicly-available Monocyte Expression Data Identifies Gene Signatures to Accurately Monitor Subset-specific Changes in Human Diseases (2020)

Monocytes and monocyte-derived cells play important roles in the regulation of inflammation, both as precursors as well as effector cells. Monocytes are heterogeneous and characterized by three distinct subsets in humans. Classical and non-classical monocytes represent the most abundant subsets, each carrying out distinct biological functions. Consequently, altered frequencies of different subsets have been associated with inflammatory conditions, such as infections and autoimmune disorders including lupus, rheumatoid arthritis, inflammatory bowel disease, and, more recently, COVID-19. Dissecting the contribution of different monocyte subsets to disease is currently limited by samples and cohorts, often resulting in underpowered studies and, consequently, poor reproducibility. Public transcriptomes provide an alternative source of data characterized by high statistical power and real world heterogeneity. However, most transcriptome datasets profile bulk blood or tissue samples, requiring the use of in silico approaches to quantify changes in the levels of specific cell types. Here, we integrated 853 publicly available microarray expression profiles of sorted human monocyte subsets from 45 independent studies to identify robust and parsimonious gene expression signatures, consisting of 10 genes specific to each subset. These signatures, although derived using only datasets profiling healthy individuals, maintain their accuracy independent of the disease state in an independent cohort profiled by RNA-sequencing (AUC = 1.0). Furthermore, we demonstrate that our signatures are specific to monocyte subsets compared to other immune cells such as B, T, dendritic cells (DCs) and natural killer (NK) cells (AUC = 0.87~0.88, p&lt;2.2e-16). This increased specificity results in estimated monocyte subset levels that are strongly correlated with cytometry-based quantification of cellular subsets (r = 0.69, p = 6.7e-4). Consequently, we show that these monocyte subset-specific signatures can be used to quantify changes in monocyte subsets levels in expression profiles from patients in clinical trials. Finally, we show that proteins encoded by our signature genes can be used in cytometry-based assays to specifically sort monocyte subsets. Our results demonstrate the robustness, versatility, and utility of our computational approach and provide a framework for the discovery of new cellular markers.
Pulmonary physiology, airway responsiveness and asthma (2002)

What we know: Tests that have allowed the measurement of lung function in infants have greatly enhanced our understanding of early pulmonary development and the pathophysiology of early respiratory disease. Airway responsiveness in infancy appears to be an independent determinant of symptoms and lung function later in childhood. New tests of airway responsiveness hold the promise of predicting, with increased specificity, infants at risk of developing asthma. What we need to know: What are the factors that determine airway responsiveness soon after birth? Why does airway responsiveness in the first weeks of life relate to lung function many years later? Do different challenge agents reflect different pathophysiological processes involved in the development of persistent asthma?
Bilevel Formulation for Optimal Traffic-Information Dissemination (2003)

With the fast-growing telematics market and maturing traffic-information services, telematics devices provide a feasible means with which to manage traffic more efficiently. The provision of traffic information to travelers usually involves different parties that have distinctive objectives: travelers are concerned with benefits of travel-time savings at an affordable service charge, private information service providers (ISPs) seek to provide marketable information services from which they can derive a profit, and traffic management centers (TMCs) have the responsibility to maintain and improve system performance, especially to minimize the total system travel time. How transportation system managers can analyze the trade-offs among these objectives and adjust this new traffic-information flow diagram to improve system performance remains an open question. The trade-offs needed among the conflicting multiple objectives of different parties are studied, and traffic system performance is analyzed. The complex traffic network is formulated as a bilevel program. The upper level can be formulated by using various objective functions, such as the objectives for ISP and TMC. The lower level is a multiclass dynamic traffic-assignment model, which determines dynamic traffic flows in the network by considering the information dissemination strategies provided by the upper-level model. Numerical results of a small network are provided to illustrate the behavior of this model, and they prove that when there is congestion in the dynamic transportation network, appropriate subscribed rates benefit both all travelers and system performance, while the ISPs’ information influences little without congestion in the transportation network.