Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated Three-Dimensional Identification and Tracking of Micro/Nanobiological Organisms by Computational Holographic Microscopy

The ability to sense, track, identify, and monitor biological micro/nanoorganisms in a real-time, automated, and integrated system is of great importance from both scientific and technological standpoints. Such a system and its possible variants would have numerous applications in a wide spectrum of fields, including defense against biological warfare, disease control, environmental health and safety, and medical treatments. In this paper, we review a comprehensive mixture of optical and computational tools developed in our group aiming at real-time sensing and recognition of biological microorganisms. Digital in-line holographic microscopy is used with both coherent and partially coherent illumination to probe the specimen interferometrically. The interference pattern is then recorded on an optoelectronic image sensor and transferred to a computer where special statistical algorithms are performed to segment, recognize, and track the microorganisms within the field of view of the microscope. The advantages of proposed holographic sensing are described compared to conventional two-dimensional imaging systems. In addition, the theoretical aspects and fundamental limitations of digital in-line holographic microscopy are discussed, which determine the relationship between system parameters and achievable performance. The proposed optical-digital integrated system for automated, real-time sensing and recognition of biological microorganisms has been deemed promising with the potential of widespread application. We demonstrate how the proposed techniques function together in a series of experiments.
Integrating population modeling into ecological risk assessment

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Neuronal toxicity of expanded polyglutamine depends on intracellular distribution in addition to the expression level

The proteins that accumulate in pathologic lesions of neurodegenerative disorders are thought to be closely associated with neuronal cell damage. However, whether or not the formation of cytoplasmic or nuclear inclusions by expanded polyglutamine (polyQ) is directly toxic to neurons has been controversial to date. We prepared a culture model system in which polyQ tracts were transfected into Neuro2a, cells of neuronal origin, to study novel factors involved in cell toxicity of polyQ tracts to neuronal cells. Pathogenic polyQ tracts of 79 repeats (Q79C) when expressed in cytoplasm of Neuro2a cells changed in their intracellular distribution patterns from homogeneous, via punctate aggregates, to massive aggregates with incubation time. Some polyQ tracts formed nuclear inclusions. Cytoplasmic massive aggregates of Q79C tended to be associated with apoptotic fate of Neuro2a cells. Cells exhibiting cytoplasmic massive inclusions had the highest expression level of polyQ tracts among cells with four patterns of intracellular distribution. The elevation in the expression levels of polyQ tracts was not due to the difference in the initial transfection efficiency. When compared among cells expressing polyQ tracts at similar levels, damages were most remarkable in cells with cytoplasmic massive aggregate in terms of shrunken cellular and nuclear sizes. Cells with the other patterns of polyQ tract distribution such as cytoplasmic homogeneous, cytoplasmic punctate and nuclear inclusions were relatively spared. These data suggest that the severity of cell damages depends on the type of intracellular distribution of polyQ tracts, in addition to the expression level of polyQ tracts.
Characteristic sequence motifs located at the genomic breakpoints of the translocation t(12;16) and t(12;22) in myxoid liposarcoma

Aims: To analyse the characteristic sequence motifs around genomic breakpoints of translocations, t(12;16) and t(12;22), and to study the mechanisms underlying these chromosomal translocations in myxoid liposarcomas (MLS). Methods: Genomic DNA sequences derived from t(12;16) and t(12;22) were amplified by long‐distance polymerase chain reaction (PCR) in six cases of MLS, and the DNA sequences around the breakpoints were analysed. Results: Genomic sequences of the FUS‐CHOP or EWS‐CHOP fusion gene were amplified in five and one MLS, respectively. Our sequence analysis revealed that the gene fusions were generated between intron 1 of the CHOP and either intron 5 (type II) or 7 (type I), or 8 (type III) of the FUS, or intron 7 of the EWS. The breakpoints in intron 1 of the CHOP were located near or within Alu repetitive sequences in the six cases. Sequences homologous to consensus recognition motifs of Translin were present adjacent to the breakpoints in the FUS, EWS, and CHOP genes. Sequences homologous to the topoisomerase II consensus site and palindromic oligomer sequences were also frequently found around the breakpoints in these genes. Moreover, Chi or Chi‐like sequences were found in three cases, alternating purine‐pyrimidine tracts and polyadenine/polythymine sequences were each found in one case. Conclusions: Our results suggest that characteristic sequence motifs located at the FUS, EWS and CHOP breakpoint regions, including Alu and palindromic oligomer sequences, are involved in the mechanisms creating chromosomal translocations in MLS.
Automatic pattern recognition of epileptiform discharges using morphological descriptors and linear discriminant analysis

This paper presents the performance analysis of a methodology for automated recognition of epileptiform patterns using morphological descriptors and Linear Discriminant Analysis. Morphological descriptors, in this paper, are parameters related to the morphology of the signal's waveform and Linear Discriminant Analysis (DA) is a method of multivariate statistical analysis commonly used for classification, size reduction and/or feature extraction. Thus, the main purpose of this paper is to analyze the classification performance of the discriminant functions and examine the applicability of Discriminant Analysis in reducing the number of independent variables (in this case morphological descriptors) necessary to obtain a discriminant function with acceptable classification performance. Simulations showed that the best functions exhibited efficiency greater than or equal to 85%, sensitivity of 85-90% and specificity between 80 and 84%.
SIFT – A language technology toolkit to assess the print media coverage of new forms of governance

For social scientists, it is increasingly important to explore large text collections without time-consuming human intervention. We are presenting a language technology tool kit that allows researchers of the NCCR Democracy Module 1 to extract information on various forms of governance from a comprehensive multilingual corpus. The tool kit called SIFT allows searching for governance entities and measuring their salience, tonality, issue context and media frames. In substantial terms, our tool pipeline enables scholars of governance to extend their research focus to the previously neglected area of the public communication of democratic legitimacy and accountability of various forms of governance.
Interaction between chromatin proteins MECP2 and ATRX is disrupted by mutations that cause inherited mental retardation

Mutations in the human methyl-CpG-binding protein gene MECP2 cause the neurological disorder Rett syndrome and some cases of X-linked mental retardation (XLMR). We report that MeCP2 interacts with ATRX, a SWI2/SNF2 DNA helicase/ATPase that is mutated in ATRX syndrome (α-thalassemia/mental retardation, X-linked). MeCP2 can recruit the helicase domain of ATRX to heterochromatic foci in living mouse cells in a DNA methylation-dependent manner. Also, ATRX localization is disrupted in neurons of Mecp2-null mice. Point mutations within the methylated DNA-binding domain of MeCP2 that cause Rett syndrome or X-linked mental retardation inhibit its interaction with ATRX in vitro and its localization in vivo without affecting methyl-CpG binding. We propose that disruption of the MeCP2–ATRX interaction leads to pathological changes that contribute to mental retardation.
Analysis of speedup and communication/computation ratio in multiprocessor systems

The quantitative relationship between speedup and communication is analyzed in terms of the ratio of the communication time to the computation time. An extension to Amdahl's law is proposed to include communication and to estimate the lower and upper bounds on speedup in multiprocessor systems. A method for estimating a response time in a multiprocessor system that incorporates the impact of communication delay is also proposed. <<ETX>>
C‐terminal variations in β‐thymosin family members specify functional differences in actin‐binding properties

Mammalian cells express several isoforms of β‐thymosin, a major actin monomer sequestering factor, including thymosins β4, β10, and β15. Differences in actin‐binding properties of different β‐thymosin family members have not been investigated. We find that thymosin β15 binds actin with a 2.4‐fold higher affinity than does thymosin β4. Mutational analysis was performed to determine the amino acid differences in thymosin β15 that specify its increased actin‐affinity. Previous work with thymosin β4 identified an α‐helical domain, as well as a conserved central motif, as crucial for actin binding. Mutational analysis confirms that these domains are also vital for actin binding in thymosin β15, but that differences in these domains are not responsible for the variation in actin‐binding properties between thymosins β4 and β15. Truncation of the unique C‐terminal residues in thymosin β15 inhibits actin binding, suggesting that this domain also has an important role in mediating actin‐binding affinity. Replacement of the 10 C‐terminal amino acids of thymosin β15 with those of thymosin β4 did, however, reduce the actin‐binding affinity of the hybrid relative to thymosin β15. Similarly, replacement of the thymosin β4 C‐terminal amino acids with those of thymosin β15 led to increased actin binding. We conclude that functional differences between closely related β‐thymosin family members are, in part, specified by the C‐terminal variability between these isoforms. Such differences may have consequences for situations where β‐thymosins are differentially expressed as in embryonic development and in cancer. J. Cell. Biochem. 77:277–287, 2000. © 2000 Wiley‐Liss, Inc.
In Vitro Dissociation of BiP-Peptide Complexes Requires a Conformational Change in BiP after ATP Binding but Does Not Require ATP Hydrolysis (*)

In the present study, we produced single point mutations in the ATP binding site of hamster BiP, isolated recombinant proteins, and characterized them in terms of their affinity for ATP and ADP, their ability to undergo a conformational change upon nucleotide binding, and their rate of ATP hydrolysis. These analyses allowed us to classify the mutants into three groups: ATP hydrolysis (T229G), ATP binding (G226D, G227D), and ATP-induced conformation (T37G) mutants, and to test the role of these activities in the in vitro ATP-mediated release of proteins from BiP. All three classes of mutants were still able to bind peptide demonstrating that nucleotide is not involved in this function. Addition of ATP to either wild-type BiP or the T229G mutant caused the in vitro release of bound peptide, confirming that ATP hydrolysis is not required for protein release. ATP did not dissociate G226D, G227D, or T37G mutant BiP-peptide complexes, suggesting that ATP binding to BiP is not sufficient for the release of bound peptides, but that an ATP-induced conformational change in BiP is necessary. The identification of BiP mutants that are defective in each of these steps of ATP hydrolysis will allow the in vivo dissection of the role of nucleotide in BiP's activity.
Exchange Rate Fluctuations and Macroeconomic Performance in Sub-Saharan Africa: A Dynamic Panel Cointegration Analysis

In the light of the widespread effects of the recent global financial crisis on exchange rate and other macroeconomic developments, this paper investigates the implications of exchange rate fluctuations on output and other critical determining factors of exchange rates. We use Panel data set containing 40 countries from Sub-Saharan Africa (SSA) over a period of 13 years: 1995-2007. In the paper, we employ the dynamic generalized methods of moments (GMM) panel data framework using the xtabond2 Difference/ System GMM. We also examine the panel co-integration properties of the variables in order to establish long-run relationship between exchange rate and other macroeconomic variables in the SSA countries. The Panel Granger Causality test confirms the bilateral relationships between some variables in the model. Though the results of the study are tentative, in view of the many assumptions underlying the methods used, they reveal their potency to determine exchange rate (EER), a long-run relationship with variables of the model and bidirectional relationships.
Contribution of visual rhythmic information to speech perception in noise

Visual speech information helps listeners perceive speech in noise. The cues underpinning this visual advantage appear to be global and distributed, and previous research hasn't succeeded in pinning down simple dimensions to explain the effect. In this study we focus on the temporal aspects of visual speech cues. In comparison to a baseline of auditory only sentences mixed with noise, we tested the effect of making available a visual speech signal that carries the rhythm of the spoken sentence, through a temporal visual mask function linked to the times of the auditory p-centers, as quantified by stressed syllable onsets. We systematically varied the relative alignment of the peaks of the maximum exposure of visual speech cues with the presumed anchors of sentence rhythm and contrasted these speech cues against an abstract visual condition, whereby the visual signal consisted of a stylised moving curve with its dynamics determined by the mask function. We found that both visual signal types provided a significant benefit to speech recognition in noise, with the speech cues providing the largest benefit. The benefit was largely independent of the amount of delay in relation to the auditory p-centers. Taken together, the results call for further inquiry into temporal dynamics of visual and auditory speech.
Efficient Computation of the Latent Vectors of a Matrix.

' This argument is to be modified as follows: After the second sentence interpolate "Suppose either X denotes A and Y denotes C or X denotes B and Y denotes F. If X belongs to T let rx denote XY plus the continuum of the collection G that contains X. If the interval t of the collection T has one end-point at X, let rT denote t + xi + ya where xi is the continuum of the collection T that contains the other end-point of t and y, is eitherXY orXY plus the continuum of Gl that intersects XY according as XY and G*1 are or are not mutually exclusive. " In the third sentence, after "T", interpolate "distinct from A and from B. " Instead of the sentence beginning in the 18th line of page 381, write "In the space Z1, for each continuum q of the collection Q, let gq denote the boundary of q, plus the set of all points of g, if there are any, which either (a) belong to H or (b) are points of M which in 2 belong to no continuum of the collection H. Let G denote the collection of all such gq's. " 4 See theorem 16 of chapter V. ' Let M denote a continuum formed by a sequence of right pyramids all with the same square base a, their vertices converging to that of the outermost one. Let t4 and t2 denote two adjacent sides of a and let Hi denote the set of all intersections of M with planes perpendicular to ti. Both H1 and H2 are arcs with respect to their elements but M is not a continuous curve.
A Lipoprotein Receptor Cluster IV Mutant Preferentially Binds Amyloid-β and Regulates Its Clearance from the Mouse Brain*

Background: Wild type LRP1 cluster IV (WT-LRPIV) binds plasma Aβ and reduces Aβ-related pathology in APPsw+/0 mice. Results: A novel LRPIV-D3674G mutant binds Aβ with a higher affinity than WT-LRPIV and clears brain Aβ better than WT-LRPIV. LRPIV-D3674G reduces effectively Aβ pathology in APPsw+/0 mice. Conclusion: LRPIV-D3674G is an efficient Aβ clearance agent. Significance: Aβ clearance therapy is critical for treatment of Alzheimer disease. Soluble low density lipoprotein receptor-related protein-1 (sLRP1) binds ∼70% of amyloid β-peptide (Aβ) in human plasma. In Alzheimer disease (AD) and individuals with mild cognitive impairment converting to AD, plasma sLRP1 levels are reduced and sLRP1 is oxidized, which results in diminished Aβ peripheral binding and higher levels of free Aβ in plasma. Experimental studies have shown that free circulating Aβ re-enters the brain and that sLRP1 and/or its recombinant wild type cluster IV (WT-LRPIV) prevent Aβ from entering the brain. Treatment of Alzheimer APPsw+/0 mice with WT-LRPIV has been shown to reduce brain Aβ pathology. In addition to Aβ, LRPIV binds multiple ligands. To enhance LRPIV binding for Aβ relative to other LRP1 ligands, we generated a library of LRPIV-derived fragments and full-length LRPIV variants with glycine replacing aspartic acid residues 3394, 3556, and 3674 in the calcium binding sites. Compared with WT-LRPIV, a lead LRPIV-D3674G mutant had 1.6- and 2.7-fold higher binding affinity for Aβ40 and Aβ42 in vitro, respectively, and a lower binding affinity for other LRP1 ligands (e.g. apolipoprotein E2, E3, and E4 (1.3–1.8-fold), tissue plasminogen activator (2.7-fold), matrix metalloproteinase-9 (4.1-fold), and Factor Xa (3.8-fold)). LRPIV-D3674G cleared mouse endogenous brain Aβ40 and Aβ42 25–27% better than WT-LRPIV. A 3-month subcutaneous treatment of APPsw+/0 mice with LRPIV-D3674G (40 μg/kg/day) reduced Aβ40 and Αβ42 levels in the hippocampus, cortex, and cerebrospinal fluid by 60–80% and improved cerebral blood flow responses and hippocampal function at 9 months of age. Thus, LRPIV-D3674G is an efficient new Aβ clearance therapy.
Effect of Corilagin on Membrane Permeability of Escherichia coli, Staphylococcus aureus and Candida albicans

Corilagin is a member of polyphenolic tannins. Its antimicrobial activity and action mechanism against Escherichia coli, Staphylococcus aureus and Candida albicans were investigated through membrane permeability. Crystal violet staining determination, outer membrane (OM) and inner membrane (IM) permeability, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS‐PAGE) and atomic force microscopy (AFM) were used as methods for our investigation. The minimum inhibitory concentrations were 62.5, 31.25 and 62.5 µg/mL for E. coli, S. aureus and C. albicans, respectively. Crystal violet results and SDS‐PAGE of supernatant proteins showed that corilagin dose‐dependently affected membrane permeability of E. coli and C. albicans but not of S. aureus. OM and IM permeability assays revealed comparable results for E. coli. By using AFM, we demonstrated extensive cell surface alterations of corilagin‐treated E. coli and C. albicans. SDS‐PAGE of precipitated proteins revealed possible targets of corilagin, i.e. Fib, Sae R, Sar S in S. aureus and Tye 7p in C. albicans. In conclusion, corilagin inhibited the growth of E. coli and C. albicans by disrupting their membrane permeability and that of S. aureus by acting on Fib, Sae R and Sar S but not on membrane integrity. Copyright © 2012 John Wiley & Sons, Ltd.
Device mismatch analysis and effect compensation in fundamental analog cells

The operation of highly complex analog ICs is strongly affected by the non-idealities inherently induced in modern sub-micron production technologies. Extensive testing has proven that process mismatch of small geometry transistors has the strongest effect on production yield. The aim of this article is to propose a methodology to analyze and compensate the effects of mismatch on the functionality of basic analog building blocks, which will be reflected in the operation and performance of more complex analog ICs. The novelty of this paper is the bi-univocal treatment of mismatch cause and effect, along with the appropriate optimization strategy. The analysis methodology is developed around Monte Carlo simulation to estimate statistical data regarding post-production IC performance, and consequently production yield. Further on, means of compensation towards error enhancement are investigated and proven on basic analog building blocks, as well as on a fully differential folded-cascode operational transconductance amplifier.
Stator Harmonic Currents in VSI-Fed Synchronous Motors With Multiple Three-Phase Armature Windings

Electric motors equipped with multiple three-phase windings are often used for the advantages they offer in terms of reliability, performance, and inverter power segmentation. When the windings are fed by independent voltage-source inverters (VSIs), circulation harmonic currents can occur in stator phases. If the motor is an induction machine, circulation currents are known to originate form transient imbalances in the applied voltages due to inverter switching. This paper investigates the problem when a synchronous machine is used and shows how additional (and possibly major) sources for circulation currents can arise in this case (even with a round-rotor design) due to the nonsinusoidal air-gap flux distribution. The phenomenon is illustrated for a 45-MW quadruple three-phase synchronous motor supplied by four medium-voltage (MV) multilevel VSIs. Its circulation currents are predicted with two alternative methods, i.e., analytically and from time-stepping finite-element simulation. The results obtained in both ways are shown to well match measurement results collected on the actual motor during full-load system testing.
Chronic hypoxia increases rat diaphragm muscle endurance and sodium–potassium ATPase pump content

The effects of chronic hypoxia (CH) on respiratory muscle are poorly understood. The aim of the present study was to examine the effects of CH on respiratory muscle structure and function, and to determine whether nitric oxide is implicated in respiratory muscle adaptation to CH. Male Wistar rats were exposed to CH for 1–6 weeks. Sternohyoid and diaphragm muscle contractile properties, muscle fibre type and size, the density of fibres expressing sarco/endoplasmic reticulum calcium-ATPase (SERCA) 2 and sodium–potassium ATPase (Na+,K+-ATPase) pump content were determined. Muscle succinate dehydrogenase (SDH) and reduced nicotinamide adenine dinucleotide phosphate (NADPH) dehydrogenase activities were also assessed. Acute and chronic blockade of nitric oxide synthase (NOS) was employed to determine whether or not NO is critically involved in functional remodelling in CH muscles. CH improved diaphragm, but not sternohyoid, fatigue tolerance in a time-dependent fashion. This adaptation was not attributable to increased SDH or NADPH dehydrogenase activities. The areal density of muscle fibres and relative area of fibres expressing SERCA2 were unchanged. Na+,K+-ATPase pump content was significantly increased in CH diaphragm. Chronic NOS inhibition decreased diaphragm Na+,K+-ATPase pump content and prevented CH-induced increase in muscle endurance. This study provides novel insight into the mechanisms involved in CH-induced muscle plasticity. The results may be of relevance to respiratory disorders characterised by CH, such as chronic obstructive pulmonary disease.