Miracle-dz/UniFAR-FTUs huggingface dataset:
Mode-based morphometry: A multiscale approach to mapping human neuroanatomy

Voxel-based morphometry (VBM) and surface-based morphometry (SBM) are two widely used neuroimaging techniques for investigating brain anatomy. These techniques rely on statistical inferences at individual points (voxels or vertices), clusters of points, or a priori regions-of-interest. They are powerful tools for describing brain anatomy, but offer little insights into the generative processes that shape a particular set of findings. Moreover, they are restricted to a single spatial resolution scale, precluding the opportunity to distinguish anatomical variations that are expressed across multiple scales. Drawing on concepts from classical physics, here we develop an approach, called mode-based morphometry (MBM), that can describe any empirical map of anatomical variations in terms of the fundamental, resonant modes––eigenmodes––of brain anatomy, each tied to a specific spatial scale. Hence, MBM naturally yields a multiscale characterization of the empirical map, affording new opportunities for investigating the spatial frequency content of neuroanatomical variability. Using simulated and empirical data, we show that the validity and reliability of MBM are either comparable or superior to classical vertex-based SBM for capturing differences in cortical thickness maps between two experimental groups. Our approach thus offers a robust, accurate, and informative method for characterizing empirical maps of neuroanatomical variability that can be directly linked to a generative physical process.
Revealing the chassis-effect on a broad-host-range genetic switch and its concordance with interspecies bacterial physiologies

Broad-host-range synthetic biology is an emerging frontier that aims to expand our current engineerable domain of microbial hosts for biodesign applications. As more novel species are brought to “model status”, synthetic biologists are discovering that identically engineered genetic circuits can exhibit different performances depending on the organism it operates within, an observation referred to as the “chassis-effect”. It remains a major challenge to uncover which genome encoded and physiological biological determinants will underpin chassis effects that govern the performance of engineered genetic devices. In this study, we compared model and novel bacterial hosts to ask whether phylogenomic relatedness or similarity in host physiology is a better predictor of toggle switch performance. This was accomplished using comparative framework based on multivariate statistical approaches to systematically demonstrate the chassis-effect and characterize the performance dynamics of a genetic toggle switch operating within six Gammaproteobacteria. Our results solidify the notion that genetic devices are significantly impacted by host-context. Furthermore, we formally determined that hosts exhibiting more similar metrics of growth and molecular physiology also exhibit more similar toggle switch performance, indicating that specific bacterial physiology underpins measurable chassis effects. The result of this study contributes to the field of broad-host-range synthetic biology by lending increased predictive power to the implementation of genetic devices in less-established microbial hosts.
Josephson counting analog-to-digital converter

A superconductive analog-to-digital converter which uses a DC SQUID as a quantizer and a flip-flop counter as a digitizer has been designed, fabricated, and tested. The circuit was fabricated using a ten-level niobium process. Tests at 4.2 K demonstrated counting to the full 12-b accuracy of the design, monotonic A/D conversion with linearity to less than 1 LSB over the more than 9-b range of conversion, read-on-the-fly operation with counter overflow, and counter operation with a gate current bus.
Morphosyntaktische Zerlegung von Komposita der medizinischen Sprache

Die Vorteile der Zerlegung von Komposita bei der Klartextanalyse werden dargestellt. Dazu werden verschiedene Wortmodelle erläutert. Für ein Wortmodell, bei dem ein Wort interpretiert wird als Folge von Wortteilen aus drei Typen von Segmenten, wird eine Sprache definiert, die eine formale komprimierte Notation der Regeln für die Wortanalyse erlaubt. Die Implementierung des Verfahrens wird mit einer Beschreibung der Lexika und des Wortsegmentierungsalgorithmus vorgestellt.
An interchangeable prion-like domain is required for Ty1 retrotransposition

Retrotransposons and retroviruses shape genome evolution and can negatively impact genome function. Saccharomyces cerevisiae and its close relatives harbor several families of LTR-retrotransposons, the most abundant being Ty1 in several laboratory strains. The cytosolic foci that nucleate Ty1 virus-like particle (VLP) assembly are not well-understood. These foci, termed retrosomes or T-bodies, contain Ty1 Gag and likely Gag-Pol and the Ty1 mRNA destined for reverse transcription. Here, we report a novel intrinsically disordered N-terminal prion-like domain (PrLD) within Gag that is required for transposition. This domain contains amino-acid composition similar to known yeast prions and is sufficient to nucleate prionogenesis in an established cell-based prion reporter system. Deleting the Ty1 PrLD results in dramatic VLP assembly and retrotransposition defects but does not affect Gag protein level. Ty1 Gag chimeras in which the PrLD is replaced with other sequences, including yeast and mammalian prionogenic domains, display a range of retrotransposition phenotypes from wildtype to null. We examine these chimeras throughout the Ty1 replication cycle and find that some support retrosome formation, VLP assembly, and retrotransposition, including the yeast Sup35 prion and the mouse PrP prion. Our interchangeable Ty1 system provides a useful, genetically tractable in vivo platform for studying PrLDs, complete with a suite of robust and sensitive assays, and host modulators developed to study Ty1 retromobility. Our work invites study into the prevalence of PrLDs in additional mobile elements. Significance Retrovirus-like retrotransposons help shape the genome evolution of their hosts and replicate within cytoplasmic particles. How their building blocks associate and assemble within the cell is poorly understood. Here, we report a novel prion-like domain (PrLD) in the budding yeast retrotransposon Ty1 Gag protein that builds virus-like particles. The PrLD has similar sequence properties to prions and disordered protein domains that can drive the formation of assemblies that range from liquid to solid. We demonstrate that the Ty1 PrLD can function as a prion and that certain prion sequences can replace the PrLD and support Ty1 transposition. This interchangeable system is an effective platform to study additional disordered sequences in living cells.
Modulation of proximity to criticality enhances slow activity fluctuations during free recall

Categorically bounded free recall allows generating perceptual and cognitive contents within specific categories while avoiding unrelated intrusions. Previous research suggested that this is implemented via amplification of ultra-slow spontaneous activity fluctuations, initiating a spontaneous recall event. However, the underlying amplification mechanism remains unclear. Here, we demonstrate, using a simulation of a simple random recurrent neuronal network operating near a critical point, that such selective amplification can be generated by a small shift towards this critical point, resulting in a dynamical phenomenon termed “critical slowing down”. By fitting physiological parameters and applying stochastic white noise input, we simulated ultra-slow fluctuations observed during rest and categorically bounded visual recall in the human cortex. Our findings suggest that modulation of spontaneous fluctuations linked to free recall can be explained by a stochastically driven recurrent network near a critical point, providing insight into the rapid and flexible formation of categorical boundaries in human cognition.
Zero-shot learning enables instant denoising and super-resolution in optical fluorescence microscopy

Computational super-resolution (SR) methods, including conventional analytical algorithms and deep learning models, have substantially improved optical microscopy. Among them, supervised deep neural networks have demonstrated outstanding SR performance, however, demanding abundant high-quality training data, which are laborious and even impractical to acquire due to the high dynamics of living cells. Here, we develop zero-shot deconvolution networks (ZS-DeconvNet) that instantly enhance the resolution of microscope images by more than 1.5-fold over the diffraction limit with 10-fold lower fluorescence than ordinary SR imaging conditions in an unsupervised manner without the need for either ground truths or additional data acquisition. We demonstrate the versatile applicability of ZS-DeconvNet on multiple imaging modalities, including total internal reflection fluorescence microscopy, three-dimensional (3D) wide-field microscopy, confocal microscopy, lattice light-sheet microscopy, and multimodal structured illumination microscopy (SIM), which enables multi-color, long-term, super-resolution 2D/3D imaging of subcellular bioprocesses from mitotic single cells to multicellular embryos of mouse and C. elegans.
Sex-dimorphic expression of extracellular matrix genes in mouse bone marrow neutrophils

The mammalian innate immune system is sex-dimorphic. Neutrophils are the most abundant leukocyte in humans and represent innate immunity’s first line of defense. We previously found that primary mouse bone marrow neutrophils show widespread sex-dimorphism throughout life, including at the transcriptional level. Extracellular matrix [ECM]-related terms were observed among the top sex-dimorphic genes. Since the ECM is emerging as an important regulator of innate immune responses, we sought to further investigate the transcriptomic profile of primary mouse bone marrow neutrophils at both the bulk and single-cell level to understand how biological sex may influence ECM component expression in neutrophils throughout life. Here, using curated gene lists of ECM components and unbiased weighted gene co-expression network analysis [WGCNA], we find that multiple ECM-related gene sets show widespread female-bias in expression in primary mouse neutrophils. Since many immune-related diseases (e.g., rheumatoid arthritis) are more prevalent in females, our work may provide insights into the pathogenesis of sex-dimorphic inflammatory diseases.
Convolutional-recurrent neural networks approximate diffusion tractography from T1-weighted MRI and associated anatomical context

Diffusion MRI (dMRI) streamline tractography is the gold-standard for in vivo estimation of white matter (WM) pathways in the brain. However, the high angular resolution dMRI acquisitions capable of fitting the microstructural models needed for tractography are often time-consuming and not routinely collected clinically, restricting the scope of tractography analyses. To address this limitation, we build on recent advances in deep learning which have demonstrated that streamline propagation can be learned from dMRI directly without traditional model fitting. Specifically, we propose learning the streamline propagator from T1w MRI to facilitate arbitrary tractography analyses when dMRI is unavailable. To do so, we present a novel convolutional-recurrent neural network (CoRNN) trained in a teacher-student framework that leverages T1w MRI, associated anatomical context, and streamline memory from data acquired for the Human Connectome Project. We characterize our approach under two common tractography paradigms, WM bundle analysis and structural connectomics, and find approximately a 5-15% difference between measures computed from streamlines generated with our approach and those generated using traditional dMRI tractography. When placed in the literature, these results suggest that the accuracy of WM measures computed from T1w MRI with our method is on the level of scan-rescan dMRI variability and raise an important question: is tractography truly a microstructural phenomenon, or has dMRI merely facilitated its discovery and implementation?
The Emission-Line Properties of Steep Radio Spectrum Quasars

Data on the emission-line properties of a sample of 45 intermediate redshift quasars with steep radio spectra are presented and compared with those of a sample of flat radio spectrum sources of comparable mean luminosity and redshift. The steep-spectrum sources have, on average, smaller widths of the C IV 1549 A and semiforbidden C III 1909 A line profiles, larger Mg II 2800 A equivalent widths, and smaller (He II and semiforbidden O III)/C IV intensity ratios than the flat-spectrum sources. The steep-spectrum sources have C IV profiles that tend to be asymmetric to the red, while those in the flat-spectrum sources are asymmetric to the blue. The Baldwin effect and the correlation between the Mg II-C IV and semiforbidden C III-C IV redshift differences reported elsewhere are also present both within the combined sample and among the steep-spectrum objects alone. These results support proposed unified models of steep and flat radio spectrum quasars. 56 refs.
Technique for the experimental estimation of nonlinear energy transfer in fully developed turbulence

A new procedure for calculating the nonlinear energy transfer and linear growth/damping rate of fully developed turbulence is derived. It avoids the unphysically large damping rates typically obtained using the predecessor method of Ritz [Ch. P. Ritz, E. J. Powers, and R. D. Bengtson, Phys. Fluids B 1, 153 (1989)]. It enforces stationarity of the turbulence to reduce the effects of noise and fluctuations not described by the basic governing equation, and includes the fourth‐order moment to avoid the closure approximation. The new procedure has been implemented and tested on simulated, fully developed two‐dimensional (2‐D) turbulence data from a 2‐D trapped‐particle fluid code, and has been shown to give excellent reconstructions of the input growth rate and nonlinear coupling coefficients with good noise rejection. However, in the experimentally important case where only a one‐dimensional (1‐D) averaged representation of the underlying 2‐D turbulence is available, this technique does not, in general, give.
Genomic Profiling

Summary Objectives: The current literature on the use of micro-arrays to generate prognostic profiles is still a methodological wasteland. Many valid questions, such as how profiling studies should be evaluated and what conclusions can be drawn, remain unanswered. Or how can flaws in the collection, analysis and interpretation of data be detected? Undiscovered imperfections can lead to a waste of valuable resources as well as be a latent source of false conclusions. Methods: Three seminal papers on the prognosis of breast cancer using genomic profiling will be discussed. Six principles of good experimental design will be used for methodological guidance: defining relevant endpoints, avoiding systematic bias, generalizability of results, appropriately sized samples to achieve sufficient power, simple design to improve interpretability, and avoiding artificial assumptions. Results: Severe violations of at least one of the six principles of good experimental design can be found in each of the three papers. A strategy is presented to assess whether a study has achieved a high level of methodological quality. This strategy also helps to establish a suitable protocol for future profiling projects. Conclusions: Determining the design of a study in a protocol is a first step to avoid impending pitfalls. The protocol should deal with the problem of understanding the complex reality behind genomic profiling. There are basic guiding principles which can help handle the complex task of designing prognostic studies to find genomic signatures.
On the Use of Double Sampling Schemes in Analyzing Categorical Data with Misclassification Errors

Abstract In order to resolve the difficulties involved in inference from a sample of categorical data obtained by using a fallible classifying mechanism (usually inexpensive), we consider, as in Tenenbein (1970, 1971, 1972), the utilization of an additional sample. The second sample is subjected to a simultaneous cross-classification of its elements by the fallible mechanism and by some true (usually expensive) classifying mechanism. The setup is general; i.e., the discussion can be applied to any multidimensional cross-classified data obtained by unrestricted random sampling. Two methodologies are presented: (i) a combined maximum likelihood (ML) and least squares (LS) approach and (ii) a complete-LS approach. Both methodologies are illustrated using real data.
On the competitive fitness of baculoviruses in insects

Mixed infections of baculoviruses in insect hosts are quite common in nature. This leads to ‘within-host’ and ‘between-host’ competition between virus variants. Because both levels of selection will contribute to overall biological fitness, both must be included in assessments of the fitness of fast-acting recombinant baculoviruses. We investigated baculovirus fitness parameters in single and mixed infection of insect larvae, in single and serial passage experiments in lepidopteran hosts (Helicoverpa armigera, Spodoptera exiqua and Trichoplusia ni) in laboratory, greenhouse and field settings. Median time to death in third instar larvae of H. armigera (Hubner) was lower in insects challenged with a mixture of wild type (HaSNPV-wt) and mutant (_egt, HaSNPV-LM2) Helicoverpa armigera SNPV, than in larvae infected with only HaSNPV-wt. The results from a behavioral study on cotton (glasshouse, field) indicated that the transmission of HaSNPV-LM2 is not modified by the absence of the egt gene, whereas in the case of the HaSNPV-AaIT (_egt, + AaIT) lower virus yield as well as altered caterpillar behavior could compromise virus fitness. Virus transmission in greenhouse and field was not reduced, when HaSNPV-LM2 was used in mixed infections with HaSNPV-wt. However, a reduction of ‘between host’ transmission was recorded when H. armigera larvae were co-infected with HaSNPV-wt and HaSNPVAaIT. Serial passage experiments with S. exigua and T. ni showed positive selection for wild type SeMNPV and AcMNPV over genetically modified variants (_egt, + AaIT in the case of SeMNPV, and _egt in the case of AcMNPV) over passages. These findings can help to understand long-term dynamics of virus genotypes in virus-insect-host plant systems. They can also help foresee potential consequences of the introduction of genetically-modified or exotic baculoviruses in agro-ecosystems.
New Numerical Method for Two-Dimensional Partially Wrinkled Membranes

Based on the introduction of a nonnegative adjustable parameter into Poisson's ratio, a new numerical method is proposed to solve numerically the partially wrinkled membrane problems with arbitrary complex shapes. Three fundamental issues in this new method are addressed. First, a nonnegative adjustable parameter is introduced into the constitutive law, automatically representing unwrinkled (taut) and wrinkled states of a membrane. Second, a parametric variational principle is developed for the new membrane model. Third, by the variational principle, the original membrane problem is converted to a nonlinear mathematical programming problem. The variational principle and the mathematical programming formulation lay a foundation for efficient numerical analysis of wrinkled membrane structures using finite element discretization. Three typical examples are given to show the effectiveness of this method.
HURRICANES AND TROPICAL STORMS OF THE WEST COAST OF MEXICO

Records of the Mexican Weather Service for the period 1921 to 1969 show that the West Coast of Mexico is affected more by hurricanes and tropical storms than is the East Coast. Using an arbitrary but probably reasonable criterion of 200 n.mi. as the effective radius of such storms, although there are some smaller storms, we found that the probability of a t least one storm per year affecting the West Coast of Mexico is 90 percent or greater in five of the 10 States studied and 74 percent or greater in nine of the 10 States. The trajectories observed during the months of maximum activity-August, September, and October-are mapped, and a gross climatological storm trajectory is presented. Recommendations for further studies are included.
Computer simulation of liquid crystal spatial light modulator based on surface plasmon resonance

Spatial resolution is an important performance characteristic of spatial light modulators (SLM). This parameter depends on the physical properties of the electro-optical material, as well as on the design features of the SLM. One of the key factors affecting the spatial resolution of liquid crystal (LC)-based SLM is the fringing field effect. This effect can be reduced in thin LC cells with corresponding reduction in the electro-optical response. A strong electro-optic response in thin LC layer can be attained using the Surface Plasmon Resonance (SPR) phenomenon. While SPR-based LC SLMs were already demonstrated about 15 years ago, their development has been hampered by the fact that these devices are expected to have a relatively low resolution, due to the finite propagation length (several tens of micrometers) of the surface plasmons (SP). This study is aimed at improving the spatial resolution of the SPR-SLM by optimizing the metal-dielectric structure of the device. In particular, a small-scale patterning of the metal layer supporting the propagation of SPs is considered a possible solution for reducing the spatial blurring associated with long propagation length of SPs. Detailed computer simulations of the spatial resolution of the SPR-based LC SLM structure have been carried out using both the rigorous coupled wave analysis (RCWA) and the finite difference time domain (FDTD) method. These simulations were performed for an SLM structure based on the well-known prism-type, Kretschmann excitation configuration. The SLM performance for various spatial resolutions was simulated by introducing a dielectric layer with periodically modulated refractive index. The RCWA technique was used for an initial estimate of the SP excitation angle and the optimal thickness of the silver layer supporting the SP propagation. The FDTD method was used for detailed analysis of near and far field spatial distribution of the modulated light. The results of this study showing improved resolution LC-SP-SLM are presented here.r
Novel hydrophone for two dimensional imaging of wideband acoustic pulses

The use of very wideband ultrasonic imaging systems for clinical medicine and industrial NDE (nondestructive evaluation) applications has stimulated a requirement for hydrophones capable of evaluating very-high-performance transducer arrays. It is demonstrated that two-dimensional scans of submicrosecond pulsed acoustic fields with carrier frequencies around 5 MHz can be achieved using an optically scanned hydrophone. Real-time imaging of pulsed acoustic fields in water, including the capability of displaying acoustic waveforms at any point in the plane, is shown to be achieved with signal-to-noise ratio in excess of 50 dB. These hydrophones must be able to respond at frequencies well above 20 MHz because of the nonlinear behaviour of aqueous media. The ultimate limitations of both the hydrophone package and the differential time domain sampling signal-processing scheme used are discussed with this requirement in mind. <<ETX>>