Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonlocal gap solitons in parity-time symmetric coupler with transverse real potential

In this work, we study the nonlocal gap solitons in a parity-time symmetric coupler with transverse real periodic potential having defocusing nonlocal nonlinearity. The propagation-invariant solutions show that the system supports both high-frequency and low-frequency modes as long as the gain/loss coefficient is less than the coupling coefficient. The high-frequency and low-frequency modes with single-hump, double-hump, and triple-hump structures are obtained. The high-frequency multi-hump modes are observed in the first band gap. The low-frequency single-hump modes lie in the semi-infinite band gap whereas low-frequency double-hump and triple-hump modes lie in the first band gap. The single-hump modes are trapped in the minimum of the potential. The double-hump modes spread through the two consecutive lattices while triple-hump modes lie across three consecutive lattices. As the range of the nonlocal nonlinearity varies, the propagation constants corresponding to different modes also change. Both the linear and dynamical stability analysis of the high-frequency and low-frequency modes have been done. The single-hump and double-hump modes are stable. The triple-hump modes may be stable or unstable. Studies on propagation dynamics reveal that when the range of the nonlocality increases, the width increases and the amplitude decreases, resulting in constant power propagation.
SAMPLER: Empirical distribution representations for rapid analysis of whole slide tissue images

Deep learning has revolutionized digital pathology, allowing for automatic analysis of hematoxylin and eosin (H&E) stained whole slide images (WSIs) for diverse tasks. In such analyses, WSIs are typically broken into smaller images called tiles, and a neural network backbone encodes each tile in a feature space. Many recent works have applied attention based deep learning models to aggregate tile-level features into a slide-level representation, which is then used for slide-level prediction tasks. However, training attention models is computationally intensive, necessitating hyperparameter optimization and specialized training procedures. Here, we propose SAMPLER, a fully statistical approach to generate efficient and informative WSI representations by encoding the empirical cumulative distribution functions (CDFs) of multiscale tile features. We demonstrate that SAMPLER-based classifiers are as accurate or better than state-of-the-art fully deep learning attention models for classification tasks including distinction of: subtypes of breast carcinoma (BRCA: AUC=0.911 ± 0.029); subtypes of non-small cell lung carcinoma (NSCLC: AUC=0.940±0.018); and subtypes of renal cell carcinoma (RCC: AUC=0.987±0.006). A major advantage of the SAMPLER representation is that predictive models are >100X faster compared to attention models. Histopathological review confirms that SAMPLER-identified high attention tiles contain tumor morphological features specific to the tumor type, while low attention tiles contain fibrous stroma, blood, or tissue folding artifacts. We further apply SAMPLER concepts to improve the design of attention-based neural networks, yielding a context aware multi-head attention model with increased accuracy for subtype classification within BRCA and RCC (BRCA: AUC=0.921±0.027, and RCC: AUC=0.988±0.010). Finally, we provide theoretical results identifying sufficient conditions for which SAMPLER is optimal. SAMPLER is a fast and effective approach for analyzing WSIs, with greatly improved scalability over attention methods to benefit digital pathology analysis.
Tailored photoacoustic apertures with superimposed optical holograms

A new method of generating potentially arbitrary photoacoustic wavefronts with optical holograms is presented. This method uses nanosecond laser pulses at 1064 nm that are split into four time-delayed components by means of a configurable multipass optical delay apparatus which serves to map the pulses onto phase-delayed regions of a given acoustic wavefront. A single spatial light modulator generates separate holograms for each component which are imaged onto a photoacoustic transducer comprised of a thermoelastic polymer. The spatially- and temporally-modulated holograms facilitate a phased array effect which enables beam steering of the resulting acoustic pulse. For a first experimental demonstration of the method, as verified by simulation, an acoustic beam is steered in four directions by around 5 degrees.
Elucidating the activation mechanism for GBP1 oligomerization

The dynamin-related human guanylate-binding protein 1 (GBP1) mediates host defense against microbial pathogens. Upon GTP binding and hydrolysis, auto-inhibited GBP1 monomers dimerize and assemble into soluble and membrane-bound oligomers, which are crucial for innate immune responses. How higher-order GBP1 oligomers are built from dimers and how assembly is coordinated with nucleotide-dependent conformational changes has remained elusive. Here, we present cryo-electron microscopy-based structural data of the soluble and membrane-bound GBP1 oligomers demonstrating that GBP1 assembles in an outstretched dimeric conformation. We identify a surface-exposed helix in the large GTPase domain, which contributes to the oligomerization interface, and probe its nucleotide- and dimerization-dependent movements facilitating the formation of an antimicrobial protein coat on a Gram-negative bacterial pathogen. Our results reveal a sophisticated activation mechanism for GBP1 in which nucleotide-dependent structural changes coordinate dimerization, oligomerization, and membrane binding to allow encapsulation of pathogens with an antimicrobial protein coat.
Combining video telemetry and wearable MEG for naturalistic imaging

Neuroimaging studies have typically relied on rigorously controlled experimental paradigms to probe cognition, in which movement is primitive, an afterthought or merely used to indicate a subject’s choice. Whilst powerful, these paradigms often do not resemble how we behave in everyday life, so a new generation of ecologically valid experiments are being developed. Magnetoencephalography (MEG) measures neural activity by sensing extracranial magnetic fields. It has recently been transformed from a large, static imaging modality to a wearable method where participants can freely move. This makes wearable MEG systems a candidate for naturalistic experiments going forward. Additional measures that capture information about complex behaviours that are compatible with neuroimaging techniques, such as MEG, will benefit researchers therefore needed for naturalistic experiments using naturalistic paradigms. Here we use video data from multi-limb dance moves, processed with open-source machine learning methods, to directly cue the timings of task onset and offset in wearable MEG data In a first step, we compare a traditional, block-designed analysis of limb movements, where the times of interest are based on stimulus presentation, to an analysis pipeline based on hidden Markov model states derived from the video telemetry. We then show that by observing the participants choreographed movement in a dancing paradigm, it is possible to express modes of neuronal activity related to specific limbs and body posture. This demonstrates the potential of combing video telemetry with mobile neuroimaging for future studies of complex and naturalistic behaviours.
Body weight, gonadectomy, and other risk factors for diagnosis of osteoarthritis in companion dogs

OBJECTIVE To evaluate age, sex, body weight, breed, neuter status, and age at neutering as risk factors for diagnosis of osteoarthritis in companion dogs ANIMALS Dogs seen as patients at Banfield Pet Hospital in the United States from 1998-2019 with a date of death in 2019. The final cohort consisted of 131,140 dogs. METHODS In this retrospective cohort study, Cox proportional hazard models were used to test for associations between osteoarthritis incidence and age at baseline, sex, maximum body weight, maximum body condition score, neuter status, and age at neutering. The same model was used to test these associations in 12 representative breeds, chosen based on breed weight and sample size. RESULTS Older age, higher adult body weight, gonadectomy, and younger age at gonadectomy were significantly associated with higher risks of osteoarthritis in the total cohort and in all 12 breeds evaluated. Higher body condition score and sex were also significantly associated with osteoarthritis but with minimal effect sizes in the overall cohort, and these risk factors were not consistently significant in all breeds tested. CLINICAL RELEVANCE These results will assist veterinarians in identifying dogs at higher risk for osteoarthritis and applying appropriate diagnostic, preventative, and treatment interventions. An understanding of potentially modifiable risk factors, such as body condition, and neutering, will support evidence-based discussions with dog owners about risk management in individual patients.
Metabolic reprogramming during Candida albicans planktonic-biofilm transition is modulated by the ZCF15 and ZCF26 paralogs

Candida albicans is a commensal of the human microbiota that can form biofilms on implanted medical devices. These biofilms are tolerant to antifungals and to the host immune system. To identify novel genes modulating C. albicans biofilm formation, we performed a large-scale screen with 2454 C. albicans doxycycline-dependent overexpression strains and identified 16 genes whose overexpression significantly hampered biofilm formation. Among those, overexpression of the ZCF15 and ZCF26 paralogs that encode transcription factors and have orthologs only in biofilm-forming species of the Candida clade, caused impaired biofilm formation both in vitro and in vivo. Interestingly, overexpression of ZCF15 specifically impeded biofilm formation without any defect in hyphal growth. Transcript profiling, transcription factor binding, and phenotypic microarray analyses conducted upon overexpression of ZCF15 and ZCF26 demonstrated their direct role in reprogramming cellular metabolism by regulating glycolytic cycle and tricarboxylic acid cycle genes. Taken together, this study has identified a new set of biofilm regulators, including ZCF15 and ZCF26, that appear to control biofilm development through their specific role in metabolic remodeling.
Time-deterministic cryo-optical microscopy

We developed a technique to rapidly freeze biological systems during observation under an optical microscope, which allows for detailed optical observation at a precise time in the biological dynamics at high spatial resolution and quantifiability under low-temperature conditions. Our study further found that ion distributions and molecular conformations can be fixed in space and time, demonstrated by visualization of calcium waves rapid-frozen at an instant using fluorescent ion indicators. These results show that time-deterministic cryo-optical microscopy can suspend cellular dynamics while maintaining molecular and ionic states, allowing us to view cellular dynamics in a way that has not been possible before. One-Sentence Summary Rapid freezing of dynamic biological systems during optical observation presents time information to the fixed samples
Presence of the ER-Golgi intermediate compartment that matures into the Golgi in yeast

Cargo traffic through the Golgi apparatus is mediated by cisternal maturation, but it remains largely unclear how the cis-cisternae, the earliest Golgi sub-compartment, is generated. Here, we use high-speed, high-resolution confocal microscopy to analyze the spatiotemporal dynamics of a diverse set of proteins that reside in and around the Golgi in budding yeast. We find many mobile punctate structures that harbor yeast counterparts of mammalian endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC) proteins, which we term “yeast ERGIC”. It occasionally attaches onto the ER exit sites and gradually matures into the cis-Golgi. Upon treatment with the Golgi-disrupting agent brefeldin A, the ERGIC proteins form larger aggregates corresponding to the Golgi entry core compartment in plants, while cis- and medial-Golgi proteins are absorbed into the ER. We further analyze the dynamics of several late Golgi proteins. Together with our previous studies, we demonstrate a detailed spatiotemporal profile of the cisternal maturation process from ERGIC to Golgi and further to the trans-Golgi network. Summary Tojima et al. perform spatiotemporal mapping of a variety of proteins residing in and around the Golgi apparatus in budding yeast using super-resolution live imaging microscopy. They identified the ER-Golgi intermediate compartment that matures into the Golgi.
CONNECTED DOMINATION GAME

In this paper we introduce a domination game based on the notion of connected domination. Let G = ( V, E ) be a connected graph of order at least 2. We deﬁne a connected domination game on G as follows: The game is played by two players, Dominator and Staller. The players alternate taking turns choosing a vertex of G (Dominator starts). A move of a player by choosing a vertex v is legal, if (1) the vertex v dominates at least one additional vertex that was not dominated by the set of previously chosen vertices and (2) the set of all chosen vertices induces a connected subgraph of G . The game ends when none of the players has a legal move (i.e., G is dominated). The aim of Dominator is to ﬁnish as soon as possible, Staller has an opposite aim. Let D be the set of played vertices obtained at the end of the connected domination game ( D is a connected dominating set of G ). The connected game domination number of G , denoted γ cg ( G ), is the minimum cardinality of D , when both players played optimally on G . We provide an upper bound on γ cg ( G ) in terms of the connected domination number. We also give a tight upper bound on this parameter for the class of 2-trees. Next, we investigate the Cartesian product of a complete graph and a tree, and we give exact values of the connected game domination number for such a product, when the tree is a path or a star. We also consider some variants of the game, in particular, a Staller-start game.
Parameter Identification of Static Friction Based on An Optimal Exciting Trajectory

In this paper, we focus on how to improve the identification efficiency of friction parameters in a robot joint. First, the static friction model that has only linear dependencies with respect to their parameters is adopted so that the servomotor dynamics can be linearized. In this case, the traditional exciting trajectory based on Fourier series is modified by replacing the constant term with quintic polynomial to ensure the boundary continuity of speed and acceleration. Then, the Fourier-related parameters are optimized by genetic algorithm(GA) in which the condition number of regression matrix is set as the fitness function. At last, compared with the constant-velocity tracking experiment, the friction parameters from the exciting trajectory experiment has the similar result with the advantage of time reduction.
Confluent boundary layer flow development with arbitrary pressure distribution

In presenting the dissertation as a partial fulfillment of the requirements or an advanced degree from the Georgia Institute of Technology, I agree that the Library of the Institute shall laake it available for inspection and circulation in accordance with its regulations governing materials of this type. I agree that permission to copy from, or Lo publish :rom, this dissertation may be granted by the professor under whose direction it was written, or, in his absence, by the Dean of the Graduate Division when such copying or publication is solely for scholarly purposes and do_s not involve potential financial, gain. It is understood tha any copying from, or publication of, this dissertation which invoi /es potential financial gain will not be allowed without written permission.
New modified moment estimators for the two-parameter weighted Lindley distribution

ABSTRACT We propose a modification of the moment estimators for the two-parameter weighted Lindley distribution. The modification replaces the second sample moment (or equivalently the sample variance) by a certain sample average which is bounded on the unit interval for all values in the sample space. In this method, the estimates always exist uniquely over the entire parameter space and have consistency and asymptotic normality over the entire parameter space. The bias and mean squared error of the estimators are also examined by means of a Monte Carlo simulation study, and the empirical results show the small-sample superiority in addition to the desirable large sample properties. Monte Carlo simulation study showed that the proposed modified moment estimators have smaller biases and smaller mean-square errors than the existing moment estimators and are compared favourably with the maximum likelihood estimators in terms of bias and mean-square error. Three illustrative examples are finally presented.
Monorhinal and Birhinal Odor Processing in Humans: an fMRI investigation

The olfactory nerve, also known as cranial nerve I, is known to have exclusive ipsilateral projections to primary olfactory cortical structures. It is still unclear whether these projections also correspond to functional pathways of odor processing. In an olfactory functional magnetic resonance imaging (fMRI) study of twenty young healthy subjects with a normal sense of smell, we tested whether nostril specific stimulation with phenyl ethyl alcohol (PEA), a pure olfactory stimulant, asymmetrically activates primary or secondary olfactory-related brain structures such as primary olfactory cortex, entorhinal cortex, and orbitofrontal cortex. The results indicated that without a challenging olfactory task, passive (no sniffing) and active (with sniffing) nostril-specific PEA stimulation did not produce asymmetrical fMRI activation in olfactory cortical structures.
Heterotic supergravity on manifolds with Killing spinors

The present work deals with the construction of heterotic string backgrounds on manifolds with real Killing spinors. The latter have played an important role in string theory for a long time, mainly due to Bär’s correspondence between Killing spinors on a manifold M and parallel spinors on the cone over M . Given the fact that parallel spinors always lead to exact supergravity BPS backgrounds, it implies that the cone admits a solution of the BPS equations. Furthermore, in type II string theory and in M-theory it is possible to place a brane at the tip of the cone, in appropriate dimensions, and the resulting supergravity solutions are exactly known. In the limit far away from the brane they converge to the empty space solution, whereas in the near horizon limit one obtains a so-called Freund-Rubin solutions, consisting of an anti-de Sitter space times our base manifold M . In heterotic supergravity on the other hand two types of brane-like solutions are known; the NS5-brane, consisting of an R4-factor with fluxes and a transverse 6dimensional Minkowski space, and what is sometimes called the gauge solitonic branes. These come equipped with an instanton gauge field on some Euclidean space Rp, which carries further non-vanishing fluxes, and again a transverse (10−p)dimensional Minkowski space. The possible values for p that appeared in the literature so far are p = 4, 7 and 8, and the corresponding instantons are the famous BPST and octonionic instantons. Manifolds with real Killing spinors have been classified: besides the round spheres they are either 6-dimensional nearly Kähler, 7-dimensional nearly parallelG2, SasakiEinstein, or 3-Sasakian. I present a generalization of the gauge solitonic branes to the cone over any real Killing spinor manifold, based upon this classification. In particular, this involves the construction of instantons on the cone. Additionally, I show that for homogeneous manifolds with real Killing spinors there is a solution similar to the near horizon limit of the NS5-brane. Finally, the instanton equation on the cylinder over the cone over a 6-dimensional nearly Kähler manifold is investigated. Several instanton solutions exist, and to embed these into heterotic supergravity is an interesting problem for future work. Besides the cone, the so-called sine-cone over a Killing spinor manifold is important. For instance, it is known that the sine-cone over a 5-dimensional Sasaki-Einstein manifold is nearly Kähler, and the one over a nearly Kähler manifold is nearly parallel G2. I generalize these results by proving that the sine-cone over an arbitrary real Killing spinor manifold has a real Killing spinor again. It is shown in particular, that the iterated sine-cone over a Sasaki-Einstein manifold also carries a SasakiEinstein-structure.
Public health intelligence challenges for local public health authorities responding to disease outbreaks: a mixed-methods systematic review protocol

Background Information management capacity is crucial for controlling risks from health emergencies. But little is known about how sub-national public health bodies overcome public health intelligence challenges when responding to disease outbreaks. This paper describes a protocol for a mixed-methods systematic review to fill this knowledge gap. In addition to describing the evidence base and characterising public health intelligence responses, it will explore reported facilitators and barriers to response. Methods Research on sub-national Public Health Intelligence disease outbreak responses will be synthesised. The review will be limited to articles published in English, during or after 2019. Key electronic databases will be searched for peer-reviewed, primary research studies. Two reviewers will independently screen articles for relevance. Articles that refer to a public health intelligence response to a propagated disease outbreak by a sub-national Public Health Authority will be included. Quality assessment of included articles will be undertaken using published tools. Data integration will be by the Pillar Integration Process (PIP). Discussion This review will describe and synthesise the recent literature on sub-national Public Health Authorities’ responses to propagated disease outbreaks. The systematic design will limit bias and the inclusion of data from quantitative, qualitative and mixed-methods studies will ensure relevant evidence is considered regardless of the methodology used to produce it. The review is part of a larger research project which aims to explore the role of sub-national public health intelligence during the COVID-19 pandemic and investigate how public health intelligence preparedness could be improved in the future. This could provide information to support the development of training, preparedness indicators and/or ways of implementing directives. PROSPERO registration CRD42022308042 (08/02/2022)