Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncertainty estimation in spatial interpolation of satellite precipitation with ensemble learning

Predictions in the form of probability distributions are crucial for decision-making. Quantile regression enables this within spatial interpolation settings for merging remote sensing and gauge precipitation data. However, ensemble learning of quantile regression algorithms remains unexplored in this context. Here, we address this gap by introducing nine quantile-based ensemble learners and applying them to large precipitation datasets. We employed a novel feature engineering strategy, reducing predictors to distance-weighted satellite precipitation at relevant locations, combined with location elevation. Our ensemble learners include six stacking and three simple methods (mean, median, best combiner), combining six individual algorithms: quantile regression (QR), quantile regression forests (QRF), generalized random forests (GRF), gradient boosting machines (GBM), light gradient boosting machines (LightGBM), and quantile regression neural networks (QRNN). These algorithms serve as both base learners and combiners within different stacking methods. We evaluated performance against QR using quantile scoring functions in a large dataset comprising 15 years of monthly gauge-measured and satellite precipitation in contiguous US (CONUS). Stacking with QR and QRNN yielded the best results across quantile levels of interest (0.025, 0.050, 0.075, 0.100, 0.200, 0.300, 0.400, 0.500, 0.600, 0.700, 0.800, 0.900, 0.925, 0.950, 0.975), surpassing the reference method by 3.91% to 8.95%. This demonstrates the potential of stacking to improve probabilistic predictions in spatial interpolation and beyond.
Suffix Stripping Problem as an Optimization Problem

Abstract Stemming or suffix stripping is the problem of removing suffixes from words to get the root word. Word endings can be removed by developing stripping rules dependent on the morphological knowledge of a specific language; obviously such approach cannot flourish in multilingual environment. Statistical approaches survive in multilingual environment but they require significant amount of computing. We define stemming as an optimization problem for the very first time in the literature. An Integer Program is being developed for the stemming problem. We exhibit our approach by applying it to clusters of English and Spanish words; moreover, the proposed method is also being compared with an established technique in the field for English language. An AMPL program of the proposed method has also been given in Appendix (A.2).
Late transplantation of allogeneic bone marrow stromal cells improves neurologic deficits subsequent to intracerebral hemorrhage.

BACKGROUND AIMS Stem cell therapy seems to be a promising therapeutic tool for treating central nervous system (CNS) injuries. Bone marrow stromal cell (BMSC) transplantation influences functional outcome subsequent to intracerebral hemorrhage (ICH), and enhances endogenous neurogenesis in acute condition studies. We investigated whether late administration of BMSC improves functional deficits subsequent to ICH. METHODS Experimental ICH was induced by stereotactic injection of 0.5 IU collagenase type IV in the striatum of adult female Wistar rats, and 2 months later intralesional administration of 5 × 10(6) allogeneic BMSC from male donors rats in saline (n = 10), or saline only (n = 10), was performed. In the following 6 months, functional outcome was evaluated in each animal by rotarod, modified neurologic severity score (mNSS) and video-tracking box (VTB) tests. To study the behavior of BMSC after transplantation, in situ hybridization studies were performed, with double labeling of the chromosome Y-linked SrY-gene, and neuronal nuclei (NeuN) protein or gliofibrillary acidic protein (GFAP). RESULTS The assessment test revealed significant improvements in functional outcome for the BMSC-treated animals after 2 months of follow-up. Histologic results showed that functional outcome was associated with strong reactivation of endogenous neurogenesis. Furthermore, intralesional BMSC not only integrated in the injured tissue but also showed phenotypic expression of GFAP and NeuN. CONCLUSIONS Late intracerebral transplantation of allogeneic BMSC induces functional recovery after ICH. The possibility of using this type of cell therapy to reverse the consequences of hemorrhagic stroke in humans should be considered.
Fail-Stop Protocols: An Approach to Designing Secure Protocols (Preprint)

Abstract : We present a methodology to facilitate the design and analysis of secure cryptographic protocols. We advocate the general approach, and a new avenue for research, of restricting protocol designs to well-defined practices, instead of ever increasing the complexity of protocol security analysis mechanisms to deal with every newly discovered attack and the endless variations in protocol construction. In particular, we propose a novel notion of a fail-stop protocol, which automatically halts in response to any active attack that interferes with protocol execution, thus reducing protocol security analysis to that of passive attacks only. We suggest types of protocols that are fail-stop, outline some proof techniques for them, and use examples to illustrate how the notion of a fail-stop protocol can make protocol design easier and can provide a more solid basis for some available protocol analysis methods.
Inter-individual differences of spectral cues in the median plane

Head-related transfer functions (HRTFs) reflect the interaction between human anatomical structures and sound waves, and depend on individuals due to differences in anatomical structures among individuals. This work investigates inter-individual differences of spectral cues encoded in median-plane individual HRTFs using principle component analysis (PCA). First, magnitudes of individual HRTFs from the CIPIC database are decomposed and reduced dimensions by PCA. Then, individual expansion weights of PCA are extracted. Finally, the inter-individual differences in expansion weights are analyzed using standard deviation. Results show that the inter-individual spectral difference in HRTFs decreases with increasing expansion degree of PCA, and the spatial distribution of large inter-individual difference is always at low elevations. When the expansion degree is 1 and 2, the mean of individual expansion weights mainly reflects the inter-elevation difference. The same method is also applied to a combined HRTF database including 295 subjects.
Modeling Biological Membranes with Circuit Boards and Measuring Electrical Signals in Axons: Student Laboratory Exercises

This is a demonstration of how electrical models can be used to characterize biological membranes. This exercise also introduces biophysical terminology used in electrophysiology. The same equipment is used in the membrane model as on live preparations. Some properties of an isolated nerve cord are investigated: nerve action potentials, recruitment of neurons, and responsiveness of the nerve cord to environmental factors.
Computational Methods for Knowledge Integration in the Analysis of Large-scale Biological Networks

i ABSTRACT As we migrate into an era of personalized medicine, understanding how bio-molecules interact with one another to form cellular systems is one of the key focus areas of systems biology. Several challenges such as the dynamic nature of cellular systems, uncertainty due to environmental influences, and the heterogeneity between individual patients render this a difficult task. In the last decade, several algorithms have been proposed to elucidate cellular systems from data, resulting in numerous data-driven hypotheses. However, due to the large number of variables involved in the process, many of which are unknown or not measurable, such computational approaches often lead to a high proportion of false positives. This renders interpretation of the data-driven hypotheses extremely difficult. Consequently, a dismal proportion of these hypotheses are subject to further experimental validation, eventually limiting their potential to augment existing biological knowledge. This dissertation develops a framework of computational methods for the analysis of such data-driven hypotheses leveraging existing biological knowledge. Specifically, I show how biological knowledge can be mapped onto these hypotheses and subsequently augmented through novel hypotheses. Biological hypotheses are learnt in three levels of abstraction-individual interactions, functional modules and relationships between pathways, corresponding to three complementary aspects of biological systems. The computational methods developed in this dissertation are applied to high throughput cancer data, resulting in novel hypotheses with potentially significant biological impact. ii To Grandpa iii ACKNOWEDGEMENTS Several faculty, friends and family members have helped me complete this dissertation and I would like to express my gratitude to them for their assistance. I would like to begin by thanking my advisor, Seungchan Kim, for being a supportive advisor through out my graduate education. From coming up with an appropriate topic for my dissertation to helping me prepare for my defense, he has been instrumental in seeing me through completion of this program. I am grateful to him for his guidance, mentoring and most importantly, being available for discussions on an almost daily basis, in spite of his busy schedule. His emphasis on quality and excellence has made a significant impact on my work and I am indebted to him for this. Special thanks to Pat Langley, member of my dissertation committee. He has worked with me patiently, reviewing my writing and providing me with several painstaking comments. While working on solutions towards a specific application (such as a biological problem) one often forgets the bigger picture. However, …
Form and function of the bulbus arteriosus in yellowfin tuna (Thunnus albacares), bigeye tuna (Thunnus obesus) and blue marlin (Makaira nigricans): static properties

SUMMARY The juxtaposition of heart and gills in teleost fish means that the Windkessel function characteristic of the whole mammalian arterial tree has to be subserved by the extremely short ventral aorta and bulbus arteriosus. Over the functional pressure range, arteries from blue marlin (Makaira nigricans) and yellowfin tuna (Thunnus albacares) have J-shaped pressure-volume (P-V) loops, while bulbi from the same species have r-shaped P-V loops, with a steep initial rise followed by a compliant plateau phase. The steep initial rise in pressure is due to the geometry of the lumen. The interactions between radius, pressure and tension require a large initial pressure to open the bulbar lumen for flow. The plateau is due to the unique organization of the bulbar wall. The large elastin:collagen ratio, limited amount of collagen arranged cirumferentially, lack of elastin lamellae and low hydrophobicity of the elastin itself all combine to lower stiffness, increase extensibility and allow efficient recoil. Even though the modulus of bulbus material is much lower than that of an artery, at large volumes the overall stiffness of the bulbus increases rapidly. The morphological features that give rise to the special inflation characteristics of the bulbus help to extend flow and maintain pressure during diastole.
Child Support Compliance among Discretionary and Nondiscretionary Obligors

This article documents patterns and correlates of child support compliance among fathers of welfare recipients in Wisconsin. We introduce the concept of discretionary obligors (because payment results in part from voluntary cooperation) and nondiscretionary obligors (because payment results from routine enforcement mechanisms) to differentiate between fathers with weak versus strong connections to formal employment, and we demonstrate that different factors underlie the compliance patterns of these groups.
Behaviour problems in childhood and stressors in early adult life. I. A 20 year follow-up of London school children

Synopsis The research presented in this paper examined the relationship between the presence of childhood behaviour problems and the rate of life events and difficulties in early adult life. Data are presented from a 20 year follow-up study of a sample of inner London school children first studied when they were aged 10. The key finding was that emotional or behavioural disturbance in childhood was associated with a marked increase in the rate of severely negative events and difficulties some two decades later. This increase was only obtained for stressors with severe negative impact of the type shown in previous investigations to be associated with the onset of psychiatric disorder. Additional results demonstrated that this main finding could not be accounted for by stressors that were a result of adult psychiatric disorder, by the respondent's own behaviour, or by continuing association with the family of origin. The need for a lifespan developmental approach to the well-established stressor-illness link is discussed.
Communicating and trusting proofs: The case for foundational proof certificates

It is well recognized that proofs serve two different goals. On one hand, they can serve the didactic purpose of explaining why a theorem holds: that is, a proof has a message that is meant to describe the ''why'' behind a theorem. On the other hand, proofs can serve as certificates of validity. In this case, once a certificate is checked for its syntactic correctness, one can then trust that the theorem is, in fact, true. In this paper, we argue that structural proof theory and computer automation have matured to such a level that they can be used to provide a flexible and universal approach to proof-as-certificate. In contrast, the notion of proof-as-message is still evolving and deals with structures, such as diagrams and natural language texts, that are not yet well formalized.
Multiphysics Neuron Model for Cellular Volume Dynamics

Even though cellular volume dynamics has been linked to cell apoptosis and intrinsic optical signals, there is no quantitative model for describing neuronal volume dynamics on the millisecond time scale. This study introduces a multiphysics neuron model, where the cell volume is a time-varying variable and multiple physical principles are combined to build governing equations. Using this model, we analyzed neuronal volume responses during excitation, which elucidated the variety of optical signals observed experimentally across the literature. Several physiological conditions were examined to investigate their effect on the pattern of volume response. In addition, we analyzed volume responses on a longer time scale with repetitive stimulation to study the characteristics of slow cell swelling. This multiscale analysis of the multiphysics model will provide not only a novel quantitative elucidation of physiologically important issues related with cellular volume dynamics but also a chance for further studies, such as the interesting possibility of inferring the balance of ion flux from plateau volume changes.
Semantic multimedia information analysis for retrieval applications

Most of the research in multimedia retrieval applications has focused on retrieval by content or retrieval by example. Since the classical review by Smeulders, Worring, Santini, Gupta, and Jain (2000), a new interest has grown immensely in the multimedia information retrieval community: retrieval by semantics. This exciting new research area arises as a combination of multimedia understanding, information extraction, information retrieval, and digital libraries. This chapter presents a comprehensive review of analysis algorithms in order to extract semantic information from multimedia content. We discuss statistical approaches to analyze images and video content and conclude with a discussion regarding the described methods.
Comparative Study of W-Shaped Angular Plate and Reconstruction Plate in Treating Posterior Wall Fractures of the Acetabulum

Objective This study aims to assess the medium-term results of the reconstruction of posterior wall fractures using a W-shaped acetabular angular plate (WAAP) compared to those fixed using a reconstruction plate. Methods Between July 2006 and March 2009, we performed a retrospective study, which collected data for any patient treated for a posterior acetabular wall fracture. At the time of treatment, patients were either treated using a WAAP or a pelvic reconstruction plate. The intraoperative fluoroscopic images for both groups were compared. The quality of reduction and radiological grading were assessed according to the criteria developed by Matta. The clinical assessment was based on a modified Merle d’Aubigne and Postel scoring. Results 53 patients met the inclusion criteria and were followed up for an average of 38 months. 25 patients were treated with a WAAP (study group), and 28 patients were treated with a pelvic reconstruction plate (control group). The intraoperative fluoroscopic images of the study group confirmed extra-articular screw placement in all cases. In the control group, intra-articular screw placement was observed intraoperatively in 5 patients (17.86%), and the definitive location of the periarticular hardware could not be determined in 4 patients (14.29%) during the operation. The differences between the two groups were statistically significant (p = 0.002). In contrast, the quality of fracture reduction, clinical outcomes, and radiological grading in the study group were not significantly different from those of the control group (p>0.05). The radiographic grade was strongly associated with the clinical outcomes in both the study and control groups (p<0.05). Conclusion Reconstruction of posterior wall fractures of the acetabulum using a WAAP can help avoid screw penetration of the hip joint, provide a stable fixation of the posterior wall, and ensure good clinical outcomes.
In vitro stimulation of articular chondrocyte differentiated function by 1,25‐dihydroxycholecalciferol or 24R,25‐dihydroxycholecalciferol

The effects of 1,25‐dihydroxycholecalciferol (1,25‐(OH)2D3) (10−13M‐10−8 M) and 24R,25‐dihydroxycholecalciferol (24R,25‐(OH)2D3) (10−12M‐10−7M) on cell proliferation and proteoglycan deposition were examined in our newly developed multilayer culture system for rabbit and human articular chondrocytes. The cells are embedded in an extracellular matrix similar to that seen in vivo and maintain their in vivo phenotype. We extracted and purified native proteoglycans and degraded material from three culture compartments: the medium, intercellular matrix, and cells. Proteoglycan synthesis and deposition were analyzed by measuring 35SO4 incorporation, hexuronic acid, and galactose contents. In both rabbit and human chondrocyte cultures, chronic 1,25‐(OH)2D3 treatment inhibited chondrocyte proliferation and stimulated proteoglycan synthesis and accumulation in the three compartments at 10−12‐10−8M. maximal effect was at 10−10M. Cell proliferation was reduced by 55% and the content of hexuronic acid (or galactose) was increased to about three times that of controls in all compartments. 1,25‐(OH)2D3 did not alter the proteoglycan composition. Chronic 24R,25‐(OH)2D3 treatment induced comparable effects with a maximum at 10−8M. When human dermal fibroblasts were treated as above both vitamin D metabolites increase mitosis. 1,25‐(OH)2D3 mainly reduced the pericellular deposition of proteoglycans, while 24R,25‐(OH)2D3 appeared to reduce their synthesis and deposition in both medium and pericellular compartments. These results suggest that both 1,25‐(OH)2D3 and 24R,25‐(OH)2D3 act specifically on articular chondrocytes to promote phenotype expression.
Iron-dependent gene expression in Actinomyces oris

Background Actinomyces oris is a Gram-positive bacterium that has been associated with healthy and diseased sites in the human oral cavity. Most pathogenic bacteria require iron to survive, and in order to acquire iron in the relatively iron-scarce oral cavity A. oris has been shown to produce iron-binding molecules known as siderophores. The genes encoding these siderophores and transporters are thought to be regulated by the amount of iron in the growth medium and by the metal-dependent repressor, AmdR, which we showed previously binds to the promoter of proposed iron-regulated genes. Objective The purpose of this study was to characterize siderophore and associated iron transport systems in A. oris. Design We examined gene expression of the putative iron transport genes fetA and sidD in response to low- and high-iron environments. One of these genes, sidD, encoding a putative Fe ABC transporter protein, was insertionally inactivated and was examined for causing growth defects. To gain a further understanding of the role of iron metabolism in oral diseases, clinical isolates of Actinomyces spp. were examined for the presence of the gene encoding AmdR, a proposed global regulator of iron-dependent gene expression in A. oris. Results When A. oris was grown under iron-limiting conditions, the genes encoding iron/siderophore transporters fetA and sidD showed increased expression. One of these genes (sidD) was mutated, and the sidD::Km strain exhibited a 50% reduction in growth in late log and stationary phase cells in media that contained iron. This growth defect was restored when the sidD gene was provided in a complemented strain. We were able to isolate the AmdR-encoding gene in seven clinical isolates of Actinomyces. When these protein sequences were aligned to the laboratory strain, there was a high degree of sequence similarity. Conclusions The growth of the sidD::Km mutant in iron-replete medium mirrored the growth of the wild-type strain grown in iron-limiting medium, suggesting that the sidD::Km mutant was compromised in iron uptake. The known iron regulator AmdR is well conserved in clinical isolates of A. oris. This work provides additional insight into iron metabolism in this important oral microbe.
Numerical Method for Darcy Flow Derived Using Discrete Exterior Calculus

We derive a numerical method for Darcy flow, and also for Poisson’s equation in mixed (first order) form, based on discrete exterior calculus (DEC). Exterior calculus is a generalization of vector calculus to smooth manifolds and DEC is one of its discretizations on simplicial complexes such as triangle and tetrahedral meshes. DEC is a coordinate invariant discretization, in that it does not depend on the embedding of the simplices or the whole mesh. We start by rewriting the governing equations of Darcy flow using the language of exterior calculus. This yields a formulation in terms of flux differential form and pressure. The numerical method is then derived by using the framework provided by DEC for discretizing differential forms and operators that act on forms. We also develop a discretization for a spatially dependent Hodge star that varies with the permeability of the medium. This also allows us to address discontinuous permeability. The matrix representation for our discrete non-homogeneous Hodge star is diagonal, with positive diagonal entries. The resulting linear system of equations for flux and pressure are saddle type, with a diagonal matrix as the top left block. The performance of the proposed numerical method is illustrated on many standard test problems. These include patch tests in two and three dimensions, comparison with analytically known solutions in two dimensions, layered medium with alternating permeability values, and a test with a change in permeability along the flow direction. We also show numerical evidence of convergence of the flux and the pressure. A convergence experiment is included for Darcy flow on a surface. A short introduction to the relevant parts of smooth and discrete exterior calculus is included in this article. We also include a discussion of the boundary condition in terms of exterior calculus.