Miracle-dz/UniFAR-FTUs huggingface dataset:
Parameter Estimation and Variable Selection for Big Systems of Linear Ordinary Differential Equations: A Matrix-Based Approach

ABSTRACT Ordinary differential equations (ODEs) are widely used to model the dynamic behavior of a complex system. Parameter estimation and variable selection for a “Big System” with linear ODEs are very challenging due to the need of nonlinear optimization in an ultra-high dimensional parameter space. In this article, we develop a parameter estimation and variable selection method based on the ideas of similarity transformation and separable least squares (SLS). Simulation studies demonstrate that the proposed matrix-based SLS method could be used to estimate the coefficient matrix more accurately and perform variable selection for a linear ODE system with thousands of dimensions and millions of parameters much better than the direct least squares method and the vector-based two-stage method that are currently available. We applied this new method to two real datasets—a yeast cell cycle gene expression dataset with 30 dimensions and 930 unknown parameters and the Standard & Poor 1500 index stock price data with 1250 dimensions and 1,563,750 unknown parameters—to illustrate the utility and numerical performance of the proposed parameter estimation and variable selection method for big systems in practice. Supplementary materials for this article are available online.
Resorption von proteolytischen Enzymen

Magenlu-men sezerniert und auf der Membranoberfläche der Säulenepithelzellen adsorbiert. Spezifische Car-riermoleküle transportieren Aminosäuren durch die Zellen. Dagegen werden unverdaute (aktive) Pro-teine über M-Zellen in den Peyerschen Plaques oder über Endo-/Exozytose Mechanismen über die Säulenepithelzellen aufgenommen. Die Aufnahme von Nahrungsbestandteilen durch Diffusion durch den interzellulären Raum zwischen den Säulenepithelzellen kommt eigentlich nur in Neugeborenen mit einem genetischen Defekt dieser Barrierefunktion vor. Die Persorption erfolgt über Lücken im Epithelium. Zu bedenken sind hier aber auch die absolute Molekülgröße und eine Lockerung der fes-ten Verbindungen auf Grund hoher proteolytischer Aktivität im Lumen z.B. nach Gabe von Enzymen in einer Säure-resistenten Zubereitung.
Graded Self-Reducibility

We introduce two special kinds of self-reducible sets that we call time-graded and space-graded languages. Attaching time and space bounds to them yields a uniform, quantitative definition of resource-bounded self-reducibility that applies to all languages. We apply this to study the relationship between NSPACE[s(n)] and DSPACE[s(n)2], emphasizing the case s(n) = O(log n). We show that the class of logspace-graded languages, which is contained in DSPACE[log n], contains not only NL and uniform NC, but also a class of Aux-PDA languages that is not known to be a subclass of P. We also prove that many-one space-graded classes are many-one equivalent to the special case in which the self-reduction makes one query to a string of strictly shorter length. For this latter idea of “instance contraction,” we note that some NL-complete problems admit n-to-n/2 contraction in logspace, and prove that some NC-complete problems are n-to-n/2 contractible by finite automata that involve only parity counting. 1 Time and Space Graded Languages A language Z is autoreducible if there is an oracle Turing machine M such that for all x, M(x) decides whether x ∈ Z without querying x itself. Placing time and/or space bounds (etc.) on M , and perhaps imposing standard truth-table, disjunctive, conjunctive, many-one (etc.) restrictions on the way M treats its queries, together define kinds of autoreductions. A self-reduction is the special case where all queries y made by M(x) are below x in some partial order. Complexity-bounded self-reductions are commonly defined by placing conditions on the partial order as well as on M . These two concepts—mostly the latter, recently the former—have had wide importance and application in complexity theory. ∗Supported by a US-Japan Co-operative Research grant from the National Science Foundation, NSF Grant INT-9726724. Also partly supported by NSF Grants CCR-9701911 and CCR-9725021. †Also partly supported by NSF grant INT-9726724. Corresponding author—contact: regan@cse.buffalo. edu ‡Also partly supported by NSF grant INT-9726724
Convergence and polynomiality of primal-dual interior-point algorithms for linear programming with selective addition of inequalities

Abstract This paper presents the convergence proof and complexity analysis of an interior-point framework that solves linear programming problems by dynamically selecting and adding relevant inequalities. First, we formulate a new primal–dual interior-point algorithm for solving linear programmes in non-standard form with equality and inequality constraints. The algorithm uses a primal–dual path-following predictor–corrector short-step interior-point method that starts with a reduced problem without any inequalities and selectively adds a given inequality only if it becomes active on the way to optimality. Second, we prove convergence of this algorithm to an optimal solution at which all inequalities are satisfied regardless of whether they have been added by the algorithm or not. We thus provide a theoretical foundation for similar schemes already used in practice. We also establish conditions under which the complexity of such algorithm is polynomial in the problem dimension and address remaining limitations without these conditions for possible further research.
The Discrete Basis Problem and Asso Algorithm for Fuzzy Attributes

We present an extension of the discrete basis problem, recently a profoundly studied problem, from the Boolean setting to the setting of fuzzy attributes, i.e., a setting of ordinal data. Our problem consists in finding for a given object-attribute matrix <inline-formula><tex-math notation="LaTeX">$I$</tex-math></inline-formula> containing truth degrees and a prescribed number <inline-formula><tex-math notation="LaTeX">$k$</tex-math></inline-formula> of factors the best approximate decomposition of <inline-formula><tex-math notation="LaTeX">$I$</tex-math></inline-formula> into an object-factor matrix <inline-formula><tex-math notation="LaTeX">$A$</tex-math></inline-formula> and a factor-attribute matrix <inline-formula><tex-math notation="LaTeX">$B$</tex-math></inline-formula>. Since such matrices represent fuzzy relations, the problem is related to but very different from that of decomposition of fuzzy relations as studied in fuzzy relational equations because neither <inline-formula><tex-math notation="LaTeX">$A$</tex-math></inline-formula> nor <inline-formula><tex-math notation="LaTeX">$B$</tex-math></inline-formula> are supposed to be known in our problem. We observe that our problem is NP-hard as an optimization problem. Consequently, we provide an approximation algorithm for solving this problem and provide its time complexity in the worst case. The algorithm is inspired by the Asso algorithm, which is known for Boolean attributes and is based on new considerations regarding associations among fuzzy attributes. We provide an experimental evaluation on various datasets and demonstrate that our algorithm is capable of extracting informative factors in data. We conclude with a discussion regarding future research issues.
3d face reconstruction from 2d images

A 3D face reconstruction technique using 2D images, such as photographs of a face, is described. Prior face knowledge or a generic face is used to extract sparse 3D information from the images and to identify image pairs. Bundle adjustment is carried out to determine more accurate 3D camera positions, image pairs are rectified, and dense 3D face information is extracted without using the prior face knowledge. Outliers are removed, e.g., by using tensor voting. A 3D surface is extracted from the dense 3D information and surface detail is extracted from the images. ® KIPO & WIPO 2009
The dielectric relaxor behaviour of BaTiO3 based ceramics doped with Bi and Mn

ABSTRACT The dielectric properties of (Ba0.92-xBix)(Ti1-yMny)O3 (BBTM)(x = 0.01–0.03, y = 0.008 or 0.016) ceramics were investigated. For bismuth content smaller than 0.02, BBTM appeared as a normal ferroelectric. For x = 0.02, there exist a clear diffuse phase transition character, associated with a broad permittivity peak vs. temperature without frequency dispersion. For x> 0.02, a relaxor behavior is obtained and frequency dispersion becomes more profound as the bismuth content increases. Atomic computer simulation has been used to predict the energy for different defect associations [], [] and [] which leads to random electrical fields and polar nanoregions (PNRs). The change from normal ferroelectrics to relaxors could be related to the size of PNRs.
Reduced Basis Methods for Option Pricing and Calibration

In this thesis, a reduced basis framework for the pricing of European and American options is developed. The underlying problems are described by parametrized time-dependent variational (in-)equalities. Corresponding reduced problem formulations are introduced, a posteriori error estimates are derived, and the construction of suitable reduced spaces is worked out. The efficiency of the resulting method is demonstrated in the context of calibrating to market data and by comparing it with existing methods used in practice.
Transcription factor-mediated direct cellular reprogramming yields cell-type specific DNA methylation signature

Direct reprogramming, inducing the conversion of one type of somatic cell into another by the forced expression of defined transcription factors, is a technology with anticipated medical applications. However, due to the many unresolved aspects of the induction mechanisms, it is essential to thoroughly analyze the epigenomic state of the generated cells. Here, we performed comparative genome-wide DNA methylation analyses of mouse embryonic fibroblasts (MEFs) and cells composing organoids formed by intestinal stem cells (ISCs) or induced ISCs (iISCs) that were directly induced from MEFs. We found that the CpG methylation state was similar between cells forming ISC organoids and iISC organoids, while they differed widely from those in MEFs. Moreover, genomic regions that were differentially methylated between ISC organoid- and iISC organoid-forming cells did not significantly affect gene expression. These results demonstrate the accuracy and safety of iISC induction, leading to the medical applications of this technology.
A porous thermoviscoelastic mixture problem: numerical analysis and computational experiments

ABSTRACT In this paper, we study, from the numerical point of view, a porous thermoviscoelastic mixture problem. The mechanical problem is written as a linear coupled system of two hyperbolic partial differential equations for the porosities and a parabolic partial differential equation for the temperature field. An existence and uniqueness result and an energy decay property are stated. Then, fully discrete approximations are introduced by using the finite element method to approximate the spatial variable and the backward Euler scheme to discretize the time derivatives. A priori error estimates are proved from which, under suitable regularity conditions, the linear convergence of the algorithm is derived. Finally, some numerical simulations are presented to demonstrate the accuracy of the approximations in an academical one-dimensional example and the behaviour of the solutions in one- and two-dimensional problems.
The Gaussian channel with intermittent feedback

Sk ∼ Ber(ρ) where at time-k Xk is the channel input, Zk ∼ N (0, σ2) is i.i. d. Gaussian noise, Yk is the channel output. The transmitter receives intermittent feedback in the sense that Yk is revealed to it strictly causally if, and only if, Sk = 1 with Pr(Sk = 1) = 1− Pr(Sk = 0) = ρ for all k. The receiver has no information about S = (S1, . . . ,Sn). We impose the average power constraint for some P > 0
Eine neue und vereinfachte Methode zum Nachweis des LP-X, eines cholestasespezifischen Lipoproteins

Die Erkennung einer Cholestase als Ursache eines Ikterus stützte sich bisher auf Anamnese, klinische Symptomatik, Laparoskopie, Leberbiopsie, auf radiologische Untersuchungen wie auf bestimmte Konstellationen von Laboratoriumsdaten. Eine erhöhte alkalische Phosphatase und Leucin-Aminopeptidase, erhöhte Bilirubinwerte bei nur leicht erhöhten bis normalen Serumtransaminasen sowie ein normaler Eisenspiegel im Serum gelten bei vorliegendem Ikterus als Hinweise auf eine Cholestase. Keiner der genannten blutchemischen Parameter ist jedoch hinreichend spezifisch und empfindlich, um eine sichere Aussage bezüglich einer Cholestase zu gewährleisten. In letzter Zeit schenkte man der Plasmalipiderhöhung bei Ikterus besondere Aufmerksamkeit und fand, daß die bekannte Vermehrung des unveresterten Cholesterins und der Phospholipide im Plasma von Patienten mit Cholestase durch das Auftreten eines abnormen Lowdensity-Lipoproteins bedingt ist (Zusammenfassung: 1). Dieses abnorme Lipoprotein wurde als LP-X bezeichnet (2). Es unterscheidet sich von den normalen Lipoproteinen des Nüchternplasmas durch seinen hohen Gehalt an Phospholipiden und unverestertem Cholesterin, einen geringen Proteinanteil von weniger als 6% Redaktion:
Development and Validation of a Quasi-Dimensional Dual Fuel (Diesel – Natural Gas) Combustion Model

This paper presents a newly developed quasi- dimensional multi-zone dual fuel combustion model, which has been integrated within the commercial engine system simulation framework. Model is based on the modified Multi-Zone Combustion Model and Fractal Combustion Model. Modified Multi-Zone Combustion Model handles the part of the combustion process that is governed by the mixing-controlled combustion, while the modified Fractal Combustion Model handles the part that is governed by the flame propagation through the combustion chamber. The developed quasi-dimensional dual fuel combustion model features phenomenological description of spray processes, i.e. liquid spray break-up, fresh charge entrainment, droplet heat-up and evaporation process. In order to capture the chemical effects on the ignition delay, special ignition delay table has been made. Additionally, to capture the effect of entrained methane on the chemical reaction rate, special table that features chemical reaction time scale has also been made. The start of flame propagation is calculated through the newly developed sub- model based on knock integral calculation. The existing k-e turbulence model has been extended to account for the effect of diesel pilot injection on the increase of in-cylinder turbulence level. Since in the conventional dual fuel combustion process multiple flames propagate through the combustion chamber, multiple flame propagation model has been developed. This model can describe arbitrary number of flames that propagate through the combustion chamber. The validation data for the developed quasi-dimensional dual fuel combustion model have been acquired on a 2.0 liter Diesel engine, which has been modified to operate in the conventional dual fuel combustion mode. The presented model has been validated at different loads and diesel substitution ratios, and there is a good fit between the measured and cycle-simulation data.
Generation of an induced pluripotent stem cell line from a healthy adult indigenous Nigerian participant

Genetic backgrounds contribute to cellular phenotypes, drug responsiveness, and health outcomes. However, the majority of human induced pluripotent stem cell (iPSC) lines are derived from individuals of European descent. Thus, there is a major, unmet need in the generation, characterisation, and distribution of iPSCs from diverse ancestries. To begin to address this need, we have generated iPSCs from dermal fibroblasts isolated from a healthy 60-year-old indigenous Nigerian male belonging to the Babur ethnic group. The iPSCs were generated using Sendai virus, and copy number variation (CNV) analysis revealed no new major abnormalities compared to the parental fibroblasts. The iPSCs have been characterised for pluripotency markers and morphology and successfully differentiated into neural progenitor cells and astrocytes. This iPSC line could serve as a healthy control in comparative studies and can be used in disease modelling, toxicity assessments, genetic analyses, and drug discovery processes within an African genetic background. To bolster the inclusion of African models in biomedical research, this iPSC line will be made available to the broader scientific community. Ongoing efforts focus on generating more lines from diverse indigenous populations towards creating a dedicated open-access African iPSC biobank.
Efficient protein structure archiving using ProteStAr

Motivation The introduction of Deep Minds’ Alpha Fold 2 enabled prediction of protein structures at unprecedented scale. AlphaFold Protein Structure Database and ESM Metagenomic Atlas contain hundreds of millions of structures stored in CIF and/or PDB formats. When compressed with a general-purpose utility like gzip, this translates to tens of terabytes of data which hinders the effective use of predicted structures in large-scale analyses. Results Here, we present ProteStAr, a compressor dedicated to CIF/PDB as well as, supplementary PAE files. Its main contribution is a novel approach to predict atom coordinates on the basis of the previously analyzed atoms. This allows efficient encoding of the coordinates which are the largest component of the protein structure files. By default, the compression is lossless, though the lossy mode with a controlled maximum error of coordinates reconstruction is also present. Compared to the competing packages, i.e., BinaryCIF, Foldcomp, PDC, our approach offers superior compression ratio at established reconstruction accuracy. By the efficient use of threads at both compression and decompression stages, the algorithm takes advantage of multicore architecture of current central processing units and operates with speeds about 1 GB/s. The presence of C++ API further increases the usability of the presented method. Availability and implementation The source code of ProteStAr is available at https://github.com/refresh-bio/protestar.
Neural representation of phonological wordform in bilateral posterior temporal cortex

While the neural bases of the earliest stages of speech categorization have been widely explored using neural decoding methods, there is still a lack of consensus on questions as basic as how wordforms are represented and in what way this word-level representation influences downstream processing in the brain. Isolating and localizing the neural representations of wordform is challenging because spoken words evoke activation of a variety of representations (e.g., segmental, semantic, articulatory) in addition to form-based representations. We addressed these challenges through a novel integrated neural decoding and effective connectivity design using region of interest (ROI)-based, source reconstructed magnetoencephalography/electroencephalography (MEG/EEG) data collected during a lexical decision task. To localize wordform representations, we trained classifiers on words and nonwords from different phonological neighborhoods and then tested the classifiers’ ability to discriminate between untrained target words that overlapped phonologically with the trained items. Training with either word or nonword neighbors supported decoding in many brain regions during an early analysis window (100-400 ms) reflecting primarily incremental phonological processing. Training with word neighbors, but not nonword neighbors, supported decoding in a bilateral set of temporal lobe ROIs, in a later time window (400-600 ms) reflecting activation related to word recognition. These ROIs included bilateral posterior temporal regions implicated in wordform representation. Effective connectivity analyses among regions within this subset indicated that word-evoked activity influenced the decoding accuracy more than nonword-evoked activity did. Taken together, these results evidence functional representation of wordforms in bilateral temporal lobes isolated from phonemic or semantic representations.
Mutational profile of the regenerative process and de novo genome assembly of the planarian Schmidtea polychroa

Planarians are organisms with a unique capacity to regenerate any part of their body. New tissues are generated in a process that requires many swift cell divisions. How costly is this process to an animal in terms of mutational load remains unknown. Using whole genome sequencing, we defined the mutational profile of the process of regeneration in the planarian species Schmidtea polychroa. We assembled de novo the genome of S. polychroa and analyzed mutations in animals that have undergone regeneration. We observed a threefold increase in the number of mutations and an altered mutational spectrum. High allele frequencies of subclonal mutations in regenerated animals suggested that relatively few stem cells with high expansion potential regenerated the animal. We provide, for the first time, the draft genome assembly of S. polychroa, an estimation of the germline mutation rate for a planarian species and the mutational spectrum of the regeneration process of a living organism.
Continuous endosomes form functional subdomains and orchestrate rapid membrane trafficking in trypanosomes

Endocytosis is a common process observed in most eukaryotic cells, although its complexity varies among different organisms. In Trypanosoma brucei, the endocytic machinery is under special selective pressure because rapid membrane recycling is essential for immune evasion. This unicellular parasite effectively removes host antibodies from its cell surface through hydrodynamic drag and fast endocytic internalization. The entire process of membrane recycling occurs exclusively through the flagellar pocket, an extracellular organelle situated at the posterior pole of the spindle-shaped cell. The high-speed dynamics of membrane flux in trypanosomes do not seem compatible with the conventional concept of distinct compartments for early, late and recycling endosomes. To investigate the underlying structural basis for the remarkably fast membrane traffic in trypanosomes, we employed advanced techniques in light and electron microscopy to examine the three-dimensional architecture of the endosomal system. Our findings reveal that the endosomal system in trypanosomes exhibits a remarkably intricate structure. Instead of being compartmentalized, it constitutes a continuous membrane system, with specific functions of the endosome segregated into membrane subdomains enriched with classical markers for early, late, and recycling endosomes. These membrane subdomains can partly overlap or are interspersed with areas that are negative for endosomal markers. This continuous endosome allows fast membrane flux by facilitated diffusion that is not slowed by multiple fission and fusion events.