Miracle-dz/UniFAR-FTUs huggingface dataset:
Surface seismic imaging with multi-frequency full-waveform amplitude inversion

Numerical experiments have been performed to test three inversion schemes for the imaging of surface seismic data. Three shallow subsurface models were considered: buried karst topography, dipping blocks, and isolated waste ponds. The synthetic experiments involved only a limited number of ‘surveys’ with just 8, 3, or 1 shots into variable length geophone arrays. In all cases, conventional seismic data processing hardly recovers the structure. The inversion algorithm works in the frequency domain and relies on a finite element method to do the 2D/2.5D acoustic wave modelling. Our original inversion scheme used the known source signature (KSS), whereas the other two schemes either estimate it from the various shot gathers (ESI), or perform a normalised data inversion (NDI). The spectral inversions typically worked over 50-400 Hz and involved about 3500 data points. The features in the models typically have dimension of 5-20 m, which can be compared with the geophone spread length of 40 m (8 shots) to 100 m (3 or 1 shots). The 8 shot inversion performed best for all the models. In fact, it was not possible to recover the karst structure with just 1 or 3 shots, but the other models were recovered, albeit with less accuracy, using such a small number of shots. ESI and NDI perform remarkably well on the dipping block and waste pond models. KSS yielded superior results to the other two schemes. The estimated source spectra were close to but did not exactly match the known wavelets.
2 The 2-matrix model , definitions and loop equations 2 . 1 Partition function

Using loop equation technics, we compute all mixed traces correlation functions of the 2-matrix model to large N leading order. The solution turns out to be a sort of Bethe Ansatz, i.e. all correlation functions can be decomposed on products of 2-point functions. We also find that, when the correlation functions are written collectively as a matrix, the loop equation are equivalent to commutation relations.
Automatic Test Value Generation for Ada

This article introduces novel tools to automatically generate pertinent Ada values in order to produce higher quality tests for Ada subprograms. A first tool will generate valid Ada values based on a structural analysis of the types of the parameters of the subprogram under test following various customizable strategies. Those values will then be filtered in order to satisfy the specifications of the subprogram, and new coverage criteria for executable specifications will be used to assess the relevance of the generated testsuite. This first set of values will then be used as seeds both for a fuzzing process, and a symbolic execution campaign, from which values of interest will be then extracted. This integrated process will enable users to generate a high value starting test corpus, which can then be expanded upon by domain-specific tests.
A novel duplex qualitative real-time PCR assay for the detection and differentiation of Plasmodium ovale curtisi and Plasmodium ovale wallikeri malaria

Background P. ovale spp. infections are endemic across multiple African countries and are caused by two distinct non-recombining species, P. ovale curtisi (Poc) and P. ovale wallikeri (Pow). These species are thought to differ in clinical symptomatology and latency, but existing diagnostic assays have limited ability to detect and distinguish them. In this study, we developed a new duplex assay for the detection and differentiation of Poc and Pow that can be used to improve our understanding of these parasites. Methods Repetitive sequence motifs were identified in available Poc and Pow genomes and used for assay development and validation. We evaluated the analytical sensitivity and specificity of the best-performing assay using a panel of samples from Tanzania and the Democratic Republic of the Congo (DRC), then validated its performance using 55 P. ovale spp. samples and 40 non-ovale Plasmodium samples from the DRC. Poc and Pow prevalence among symptomatic individuals sampled across three provinces of the DRC were estimated. Results The best-performing Poc and Pow targets had 9 and 8 copies within the reference genomes, respectively. Our duplex assay had 100% specificity and 95% confidence lower limits of detection of 4.2 and 41.2 parasite genome equivalents/{micro}l for Poc and Pow, respectively. Species was determined in 80% of all P. ovale spp. -positive field samples and 100% of those with >10 parasites/{micro}l. Most P. ovale spp. field samples from the DRC were found to be Poc infections. Conclusions We identified promising multi-copy targets for molecular detection and differentiation of Poc and Pow and used them to develop a new duplex real-time PCR assay that performed well when applied to diverse field samples. Though low-density Pow infections are not reliably detected, the assay is highly specific and can be used for high-throughput studies of P. ovale spp. epidemiology among symptomatic cases in malaria-endemic countries like the DRC.
Aberrant Local Synchrony in Distinct Mouse Models of Epileptic Encephalopathy

Identifying and quantifying synchronous activity of primary neuronal networks using multielectrode arrays (MEAs) can potentially provide a medium-throughput platform to screen potential therapeutics for genetic epileptic encephalopathies (EEs). However, successfully identifying screenable synchrony phenotypes in vitro poses significant experimental and analytical challenges. Primary neuronal cultures quickly become highly synchronous and certain measures of synchrony tend to peak and plateau, while other network activity features remain dynamic. High levels of synchrony may confound the ability to identify reproducible phenotypes in vitro for a subset of EEs. Reducing, or delaying the onset of, high levels of synchrony in vitro may increase the dynamic range of global synchrony measures to identify disease-relevant phenotypes in vitro, but such measures have not been established. We hypothesized that an emphasis on local (nearby) connectivity could elucidate reproducible disease-relevant synchrony phenotypes in cortical cultures not identified by current approaches. We show clear evidence of enriched local synchrony in 48-well MEAs that varies in amplitude during development of neuronal networks. Then, we show new topological-based measures are capable of identifying novel phenotypes of aberrant synchrony in distinct mouse models of EEs. Such topological synchrony measures may provide screenable phenotypes for certain brain diseases and may be further enhanced by experimental innovation reducing global levels of synchrony in primary neuronal networks. Significance In vitro synchrony phenotypes may provide disease-relevant features that can be used for screening potential therapeutic candidates for epileptic encephalopathies. Here, we incorporate inter-electrode distance to generate tools capable of identifying novel synchrony phenotypes in distinct neurodevelopmental disorders. We additionally report robust topological and global in vitro synchrony phenotypes, alongside in vivo synchrony phenotypes in Stxbp1+/- mice. While singular features of disease in an in vitro model are unlikely to effectively test therapeutic candidates, compounds that reverse a larger subset of distinct features may translate to human patients, suggesting such a model may be ideally suited for therapeutic development using MEAs. Across multiple disease models, the topological tools developed here are complimentary to and expand upon those within meaRtools (Gelfman 2018), which is a suite of computational tools to identify network phenotypes using MEAs.
Sclerotherapy and Resection of a Giant Lymphatic Malformation of the Head in a Neonate

Lymphatic malformations, sometimes referred to as “lymphangiomas” are composed of malformed, dilated lymphatic channels. They should be removed either for cosmesis or function when located in the head and neck region. They have traditionally been approached surgically. However, high recurrence rates with surgery alone have caused multimodal therapy to be an attractive approach. We present a case report of a giant macrocystic lesion of the head approached with staged therapy, in an attempt to salvage the patient’s involved ear.
Information Needs of Coastal Residents in Louisiana, U.S.A.: Implications for Risk Communication

ABSTRACT Altinay, Z. ; Morris, L.L. , and Reams, M.A., 2023. Information needs of coastal residents in Louisiana, U.S.A. : Implications for risk communication. Journal of Coastal Research, 39(6), 1170–1179. Charlotte (North Carolina), ISSN 0749-0208. This study aims to address the gap between communication practices and adoption of hazard-mitigation behavior in a deltaic land that experiences chronic coastal hazards, including storm surges and shoreline erosion. Focusing on Louisiana's coastal crisis, first, an online questionnaire was distributed to identify hazard mitigation patterns and information needs of a subset of southern Louisiana residents. A follow-up focus-group discussion sought to delve deeper into residents' experiences with community communication practices as well as the obstacles with dissemination of hazard-mitigation information to nontechnical audiences. Participants recommended the establishment of stronger public-private partnerships, increased use of visual information, and the necessity of providing clear and comprehensive details regarding funding and financial assistance programs to communicate hazard mitigation strategies. Findings provide a starting point for building local knowledge through extension engagement related to the delivery of hazard-mitigation information and discuss how to engage in proactive outreach methods to raise awareness about risk and hazard mitigation for both technical and nontechnical audiences. It combines the theoretical framework of community resilience with principles of communication. Results of this study contribute to an understanding of the barriers to household-level mitigation actions within the community; provide community feedback for extension agents and state and local officials; and suggest discussion points in the context of the Louisiana Coastal Master Plans.
Multiple steps of prion strain adaptation to a new host

The transmission of prions across species is a critical aspect of their dissemination among mammalian hosts, including humans. This process often necessitates strain adaptation. In this study, we sought to investigate the mechanisms underlying prion adaptation while mitigating biases associated with the history of cross-species transmission of natural prion strains. To achieve this, we utilized the synthetic hamster prion strain S05. Propagation of S05 using mouse PrPC in Protein Misfolding Cyclic Amplification did not immediately overcome the species barrier. This finding underscores the involvement of factors beyond disparities in primary protein structures. Subsequently, we performed five serial passages to stabilize the incubation time to disease in mice. The levels of PrPSc increased with each passage, reaching a maximum at the third passage, and declining thereafter. This suggests that only the initial stage of adaptation is primarily driven by an acceleration in PrPSc replication. During the protracted adaptation to a new host, we observed significant alterations in the glycoform ratio and sialylation status of PrPSc N-glycans. These changes support the notion that qualitative modifications in PrPSc contribute to a more rapid disease progression. Furthermore, consistent with the decline in sialylation, a cue for “eat me” signaling, the newly adapted strain exhibited preferential colocalization with microglia. In contrast to PrPSc dynamics, the intensity of microglia activation continued to increase after the third passage in the new host. In summary, our study elucidates that the adaptation of a prion strain to a new host is a multi-step process driven by several factors.
A viral-specific CD4+ T cell response protects female mice from Coxsackievirus B3 infection

Background Biological sex plays an integral role in the immune response to various pathogens. The underlying basis for these sex differences is still not well defined. Here, we show that Coxsackievirus B3 (CVB3) induces a viral-specific CD4+ T cell response that can protect female mice from mortality. Methods We inoculated C57BL/6 Ifnar-/- mice with CVB3. We investigated the T cell response in the spleen and mesenteric lymph nodes in male and female mice following infection. Results We found that CVB3 can induce expansion of CD62Llo CD4+ T cells in the mesenteric lymph node and spleen of female but not male mice as early as 5 days post-inoculation, indicative of activation. Using a recombinant CVB3 virus expressing a model CD4+ T cell epitope, we found that this response is due to viral antigen and not bystander activation. Finally, the depletion of CD4+ T cells before infection increased mortality in female mice, indicating that CD4+ T cells play a protective role against CVB3 in our model. Conclusions Overall, these data demonstrated that CVB3 can induce an early CD4 response in female but not male mice and further emphasize how sex differences in immune responses to pathogens affect disease.
Comparative profiling of cellular gait on adhesive micropatterns defines statistical patterns of activity that underlie native and cancerous cell dynamics

Cell dynamics are powered by patterns of activity, but it is not straightforward to quantify these patterns or compare them across different environmental conditions or cell-types. Here we digitize the long-term shape fluctuations of metazoan cells grown on micropatterned fibronectin islands to define and extract statistical features of cell dynamics without the need for genetic modification or fluorescence imaging. These shape fluctuations generate single-cell morphological signals that can be decomposed into two major components: a continuous, slow-timescale meandering of morphology about an average steady-state shape; and short-lived “events” of rapid morphology change that sporadically occur throughout the timecourse. By developing statistical metrics for each of these components, we used thousands of hours of single-cell data to quantitatively define how each axis of cell dynamics was impacted by environmental conditions or cell-type. We found the size and spatial complexity of the micropattern island modulated the statistics of morphological events—lifetime, frequency, and orientation—but not its baseline shape fluctuations. Extending this approach to profile a panel of triple negative breast cancer cell-lines, we found that different cell-types could be distinguished from one another along specific and unique statistical axes of their behavior. Our results suggest that micropatterned substrates provide a generalizable method to build statistical profiles of cell dynamics to classify and compare emergent cell behaviors.
Mutations upstream from sdaC and malT in Escherichia coli uncover a complex interplay between the cAMP receptor protein and different sigma factors

ABSTRACT In Escherichia coli, one of the best understood microorganisms, much can still be learned about the basic interactions between transcription factors and promoters. When a cAMP-deficient cya mutant is supplied with maltose as the main carbon source, mutations develop upstream from the two genes malT and sdaC. Here, we explore the regulation of the two promoters, using fluorescence-based genetic reporters in combination with both spontaneously evolved and systematically engineered cis-acting mutations. We show that in the cya mutant, regulation of malT and sdaC evolves toward cAMP-independence and increased expression in the stationary phase. Furthermore, we show that the location of the cAMP receptor protein (Crp) binding site upstream of malT is important for alternative sigma factor usage. This provides new insights into the architecture of bacterial promoters and the global interplay between Crp and sigma factors in different growth phases. IMPORTANCE This work provides new general insights into (1) the architecture of bacterial promoters, (2) the importance of the location of Class I Crp-dependent promoters, and (3) the global interplay between Crp and sigma factors in different growth phases. This work provides new general insights into (1) the architecture of bacterial promoters, (2) the importance of the location of Class I Crp-dependent promoters, and (3) the global interplay between Crp and sigma factors in different growth phases.
Electrical Resistance Heating of Clay Layers in Water‐Saturated Sand

Electrical resistance heating (ERH) experiments were performed in a two‐dimensional water‐saturated porous medium comprising an electrically conductive, low‐permeability clay lens embedded within a less electrically conductive, higher permeability silica sand. These were compared to experiments performed in homogeneous silica sand. All experiments were performed in the absence of a non‐aqueous phase liquid (NAPL) or dissolved volatile organic compound (VOC). Temperature monitoring showed preferential heating in the clay lens and higher overall heating rates throughout the test cell compared to the homogeneous case. Gas production was localized around the sand–clay interface due to high temperature and low capillary displacement pressure. Above the clay lens, unexpected temperature plateaus were observed, similar to those observed in previous experiments during NAPL–water co‐boiling. A conceptual model based on the consumption of thermal energy as latent heat of vaporization in the highly localized heating and gas production region adjacent to the clay lens is proposed to explain the temperature plateaus. Supporting data is drawn from images of the gas phase and electric current measurements. These results show that the use of co‐boiling plateaus as an indicator of NAPL–water co‐boiling could be misleading during applications of ERH at sites containing electrically conductive, low‐permeability clay lenses embedded within less electrically conductive, higher‐permeability sands.
性 : 淨誘因效果或是淨侵權效果 ? The Asymmetric distribution between Stock Bonus and Stock Dividends : Net Incentives or Entrenchments ? 許文馨

Employee profit sharing stock bonus has always been regarded as the main contributor to the success of the high-tech indus仕y in Taiwan. As profit sharing bonus and shareholder dividends are determined at the same time at the shareholder meeting under the Corporation Law in Taiwan, and can be distributed in either cash or shares, many investors question the fairness to distribute profit sharing bonus (dividends) more (less) in stocks than in cash (Chung, 2004). This study examines whether the high stockJcash proportion in employee bonus, relative to the proportion in shareholder dividends (i.e., asymmetric distribution) represents management's net incentive or entrenchment effects. Consistent with net incentive theo旬, the result show that firm performance, as measured by Tobin's Q and ROA, can increase with the asymmetric dis仕ibution. The results infer that the incentive effect in the asymmetric distribution dominates the entrenchment effect.
Intelligent Prediction Method for Linear Wave Load Based on Deep Neural Network

ABSTRACT Chen, S. ; Jiang, C. ; Wang, Z. ; Zhang, F. ; Xia, J., and Li, F. , 2023. Intelligent prediction method for linear wave load based on deep neural network. Journal of Coastal Research, 39(6), 1158–1169. Charlotte (North Carolina), ISSN 0749-0208. To more efficiently and accurately calculate the linear wave load response of a ship at any section position under different speeds, wave periods, wave heights, and wave directions, a linear wave load intelligent prediction (LWLIP) method is established by combining the experimental design, data processing and analysis, strip theory, and deep neural network methods. Taking a ship as an example, the LWLIP analysis was carried out, and the application of the LWLIP method was verified. The results show that, under any sea conditions, the LWLIP method is an alternative to the strip theory program for wave load prediction with high accuracy, it expands the calculation limitations of strip theory, such as section position and wave angle, and it improves the calculation efficiency. The prediction time of the model is 1 ms. The results of this study are of great significance for the rapid assessment of ship global wave loads.
Detection of Change in Flood Return Levels under Global Warming

Using recent advancements in the statistical extreme value theory, this study proposes a methodology for detection of change in flood return levels under climate change. Nonstationary scaling of regional projected peak flows with global warming is first tested by a likelihood ratio test. For nonstationary possible future realizations, the authors then investigate how long the stationary historical design magnitudes or return levels of floods will remain valid, taking into account the uncertainties in the estimation of observed and projected return levels. Although some flood projections are found to be nonstationary, many are stationary in nature. No coherent change in flood return level across the projections is detected in the case study of floods in the Columbia River using available streamflow projections. Most projections yield flood quantiles that are not likely to be critical in the coming century. However, for some simulations detection is achieved, with earlier detection in design magnitudes of lower return periods. A possible worst-case scenario considering the maximum of all the projections shows detection of change in floods of higher return periods in the 21st century.
The Minerals , Metals & Materials Series

The lack of a reliable theoretical model of the processing-microstructure relationship of AM (Additive Manufacturing) material is preventing AM technology from being widely adopted by the manufacturing community. The goal of this work is to establish the link between the microstructure (texture) and the process parameters of metal AM processes. A quantitative method based on the epitaxial growth of columnar grains within and across melt pools is proposed to predict the texture formation during a metal AM process. The state-of-the-art CALPHAD-informed FEM (finite element method) simulation has been used to predict the geometry and thermal profile of the quasi-steady melt pool. The thermal gradient distribution within the 3D melt pool determines the crystallography direction and growth direction of the columnar grains within each deposited single tracks. The single tracks with the predicted geometry are amalgamated together to represent the bulk part, and the epitaxial growth of grains across the boundary of neighboring tracks are quantitatively modeled. The proposed method is calibrated and validated by experimental studies of metal AM processed Alloy 718.
Turn-On Protein Switches for Controlling Actin Binding in Cells

Within a shared cytoplasm, filamentous actin (F-actin) plays numerous and critical roles across the cell body. Cells rely on actin-binding proteins (ABPs) to organize F-actin and to integrate its polymeric characteristics into diverse cellular processes. Yet, the multitude of ABPs that engage with and shape F-actin make studying a single ABP’s influence on cellular activities a significant challenge. Moreover, without a means of manipulating actin-binding subcellularly, harnessing the F-actin cytoskeleton for synthetic biology purposes remains elusive. Here, we describe a suite of designed proteins, Controllable Actin-binding Switch Tools (CASTs), whose actin-binding behavior can be controlled with external stimuli. CASTs were developed that respond to different external inputs, providing options for turn-on kinetics and enabling orthogonality. Being genetically encoded, we show that CASTs can be inserted into native protein sequences to control F-actin association locally and engineered into new structures to control cell and tissue shape and behavior.