Miracle-dz/UniFAR-FTUs huggingface dataset:
Fully automated digital holographic interferometer for 360 deg contour and displacement measurements

Abstract. A fully automated optomechatronic system based on an out-of-plane sensitivity digital holographic interferometer is proposed to measure both the 360-deg object’s contour and its surface displacements due to sound stimulation. The digital holograms to measure the surface contour are acquired using the two points of illumination method whose optimal height sensitivity for this particular case is Δz=2.98 mm. This method renders a phase map that has a tilt produced by the angle change of the object beam relative to the optical axis, a tilt that is removed by subtracting the phase difference from a physical reference plane tangentially located at the back of the object, which contrasts with former methods that locate this plane usually in the middle portion of the object. By using rotation and averaging matrices, the 360-deg object’s contour digital reconstruction was obtained, and with it, the displacements around the object can be accurately placed on its surface. The main contribution of the proposed fully automated system is to get a 360-deg object’s contour and its surface displacements in a hands-free rapid and accurate evaluation.
Clinical and inflammation marker features of cancer patients with COVID-19: data of Istanbul, Turkey multicenter cancer patients (2020–2022)

Abstract Objective We aimed to identify a rapid, accurate, and accessible biomarker in the early stages of COVID-19 that can determine the prognosis of the disease in cancer patients. Methods A total number of 241 patients with solid cancers who had a COVID-19 diagnosis between March 2020 and February 2022 were included in the study. Factors and ten different markers of inflammation were analyzed by year of diagnosis of COVID-19 and grouped by severity of infection. Results Hospitalization, referral to the intensive care unit (ICU), mechanical ventilation, and death were more frequent in 2020 than in 2021 and 2022 (mortality rates, respectively, were 18.8%, 3.8%, and 2.5%). Bilateral lung involvement and chronic lung disease were independent risk factors for severe disease in 2020. In 2021–2022, only bilateral lung involvement was found as an independent risk factor for severe disease. The neutrophil-to-lymphocyte platelet ratio (NLPR) with the highest area under the curve (AUC) value in 2020 had a sensitivity of 71.4% and specificity of 73.3% in detecting severe disease (cut-off > 0.0241, Area Under the Curve (AUC) = 0.842, p <. 001). In 2021–2022, the sensitivity of the C-reactive protein-to-lymphocyte ratio (CRP/L) with the highest AUC value was 70.0%, and the specificity was 73.3% (cut-off > 36.7, AUC = 0.829, p = .001). Conclusions This is the first study to investigate the distribution and characteristics of cancer patients, with a focus on the years of their COVID-19 diagnosis. Based on the data from our study, bilateral lung involvement is an independent factor for severe disease, and the CRP/L inflammation index appears to be the most reliable prognostic marker.
Fourier ptychographic and deep learning using breast cancer histopathological image classification

Automated, as well as accurate classification with breast cancer histological images, was crucial for medical applications because of detecting malignant tumors via histopathological images. In this work create a Fourier ptychographic (FP) and deep learning using breast cancer histopathological image classification. Here the FP method used in the process begins with such a random guess that builds a high‐resolution complex hologram, subsequently uses iterative retrieval using FP constraints to stitch around each other low‐resolution multi‐view means of production owned from either the hologram's high‐resolution hologram's elemental images captured via integral imaging. Next, the feature extraction process includes entropy, geometrical features, and textural features. The entropy‐based normalization is used to optimize the features. Finally, it attains the classification process of the proposed ENDNN classifies the breast cancer images into normal or abnormal. The experimental outcomes demonstrate that our presented technique overtakes the traditional techniques.
A bioengineered pseudovirus nanoparticle displaying SARS‐CoV 2 RBD fully protects mice from mortality and weight loss caused by SARS‐CoV 2 challenge

The COVID‐19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has caused considerable morbidity and mortality worldwide. Although authorized COVID‐19 vaccines have been shown highly effective, their significantly lower efficacy against heterologous variants, and the rapid decrease of vaccine‐elicited immunity raises serious concerns, calling for improved vaccine tactics. To this end, a pseudovirus nanoparticle (PVNP) displaying the receptor binding domains (RBDs) of SARS‐CoV‐2 spike, named S‐RBD, was generated and shown it as a promising COVID‐19 vaccine candidate. The S‐RBD PVNP was produced using both prokaryotic and eukaryotic systems. A 3D structural model of the S‐RBD PVNPs was built based on the known structures of the S60 particle and RBDs, revealing an S60 particle‐based icosahedral symmetry with multiple surface‐displayed RBDs that retain authentic conformations and receptor‐binding functions. The PVNP is highly immunogenic, eliciting high titers of RBD‐specific IgG and neutralizing antibodies in mice. The S‐RBD PVNP demonstrated exceptional protective efficacy, and fully (100%) protected K18‐hACE2 mice from mortality and weight loss after a lethal SARS‐CoV‐2 challenge, supporting the S‐RBD PVNPs as a potent COVID‐19 vaccine candidate. By contrast, a PVNP displaying the N‐terminal domain (NTD) of SARS‐CoV‐2 spike exhibited only 50% protective efficacy. Since the RBD antigens of our PVNP vaccine are adjustable as needed to address the emergence of future variants, and various S‐RBD PVNPs can be combined as a cocktail vaccine for broad efficacy, these non‐replicating PVNPs offer a flexible platform for a safe, effective COVID‐19 vaccine with minimal manufacturing cost and time.
Riemann boundary value problems of polyanalytic functions and metaanalytic functions on the closed curves

In this article, Riemann boundary value problems (BVPs) of polyanalytic functions and metaanalytic functions on the closed curve are investigated. Using the theorem of decomposition of polyanalytic functions, the expression of solution and the condition of solvability for Riemann BVP of polyanalytic functions are obtained by reducing the problem to the equivalent Riemann BVP of analytic functions. Then the expression of solution and the condition of solvability for Riemann BVP of metaanalytic functions are obtained by reducing the problem into the equivalent Riemann BVP of polyanalytic functions.
Elliptical Responses to Direct and Indirect Requests for Information.

We present two studies examining the factors that lead speakers to produce elliptical responses to requests for information. Following Clark and Levelt and Kelter, experimenters called businesses and asked about their closing time (e.g., Can you tell me what time you close? ). Participants provided the requested information in full sentence responses (We close at 9) or elliptical responses (At 9). A reanalysis of data from previous experiments using this paradigm shows that participants are more likely to produce an elliptical response when the question is a direct request for information (What time do you close? ) than when the question is an indirect request for information (Can you tell me what time you close? ). Participants were less likely to produce an elliptical response when they began their answer by providing a yes/no response (e.g., Sure . . . we close at 9). A new experiment replicated these findings, and further showed that elliptical responses were less likely when (1) irrelevant linguistic content was inserted between the question and the participant's response, and (2) participants verbalized signs of difficulty retrieving the requested information. This latter effect is most prominent in response to questions that are seen as very polite (May I ask you what time you close? ). We discuss the role that the recoverability of the intended meaning of the ellipsis, the accessibility of potential antecedents for the ellipsis, pragmatic factors, and memory retrieval play in shaping the production of ellipsis.
LncRNA AC012360.1 facilitates growth and metastasis by regulating the miR‐139‐5p/LPCAT1 axis in hepatocellular carcinoma

Long noncoding RNAs (lncRNAs) participate in tumorigenesis and tumor progression. However, whether lncRNA AC012360.1 contributes to hepatocellular carcinoma (HCC) is unknown. In HCC tissues, differentially expressed lncRNAs were identified by bioinformatics. AC012360.1 level was validated and its role in HCC progression was investigated. Among the top 10 upregulated lncRNAs, AC012360.1 exhibited the greatest increase in HCC tissues. Additionally, AC012360.1 was upregulated in HCC tissues/cells. Moreover, AC012360.1 knockdown refrained cell proliferation/metastasis and tumor growth. Conversely, AC012360.1 overexpression showed an oncogenic role. AC012360.1 and lysophosphatidylcholine acyltransferase 1 (LPCAT1) contained miR‐139‐5p binding sites. Furthermore, miR‐139‐5p silencing partially mitigated the role of AC012360.1 knockdown, while LPCAT1 knockdown partially abolished the tumor‐promoting effect of AC012360.1 overexpression. In conclusion, AC012360.1 exhibited its oncogenic function in HCC through sponging miR‐139‐5p and upregulating LPCAT1 expression.
Toxicity dose descriptors from animal inhalation studies of 13 nanomaterials and their bulk and ionic counterparts and variation with primary particle characteristics

Abstract This study collects toxicity data from animal inhalation studies of some nanomaterials and their bulk and ionic counterparts. To allow potential grouping and interpretations, we retrieved the primary physicochemical and exposure data to the extent possible for each of the materials. Reviewed materials are compounds (mainly elements, oxides and salts) of carbon (carbon black, carbon nanotubes, and graphene), silver, cerium, cobalt, copper, iron, nickel, silicium (amorphous silica and quartz), titanium (titanium dioxide), and zinc (chemical symbols: Ag, C, Ce, Co, Cu, Fe, Ni, Si, Ti, TiO2, and Zn). Collected endpoints are: a) pulmonary inflammation, measured as neutrophils in bronchoalveolar lavage (BAL) fluid at 0-24 hours after last exposure; and b) genotoxicity/carcinogenicity. We present the dose descriptors no-observed-adverse-effect concentrations (NOAECs) and lowest-observed-adverse-effect concentrations (LOAECs) for 88 nanomaterial investigations in data-library and graph formats. We also calculate ‘the value where 25% of exposed animals develop tumors’ (T25) for carcinogenicity studies. We describe how the data may be used for hazard assessment of the materials using carbon black as an example. The collected data also enable hazard comparison between different materials. An important observation for poorly soluble particles is that the NOAEC for neutrophil numbers in general lies around 1 to 2 mg/m3. We further discuss why some materials’ dose descriptors deviate from this level, likely reflecting the effects of the ionic form and effects of the fiber-shape. Finally, we discuss that long-term studies, in general, provide the lowest dose descriptors, and dose descriptors are positively correlated with particle size for near-spherical materials.
Laboratory Studies on the Formation of Three C2H4O Isomers—Acetaldehyde (CH3CHO), Ethylene Oxide (c-C2H4O), and Vinyl Alcohol (CH2CHOH)—in Interstellar and Cometary Ices

Laboratory experiments were conducted to unravel synthetic routes to form three C2H4O isomers—acetaldehyde (CH3CHO), ethylene oxide (c-C2H4O), and vinyl alcohol (CH2CHOH)—in extraterrestrial ices via electronic energy transfer processes initiated by electrons in the track of MeV ion trajectories. Here we present the results of electron irradiation on a 2 : 1 mixture of carbon dioxide (CO2) and ethylene (C2H4). Our studies suggest that suprathermal oxygen atoms can add to the carbon-carbon π bond of an ethylene molecule to form initially an oxirene diradical (addition to one carbon atom) and the cyclic ethylene oxide molecule (addition to two carbon atoms) at 10 K. The oxirene diradical can undergo a [1, 2]-H shift to the acetaldehyde molecule. Both the ethylene oxide and the acetaldehyde isomers can be stabilized in the surrounding ice matrix. To a minor amount, suprathermal oxygen atoms can insert into a carbon-hydrogen bond of the ethylene molecule, forming vinyl alcohol. Once these isomers have been synthesized inside the ice layers of the coated grains in cold molecular clouds, the newly formed molecules can sublime as the cloud reaches the hot molecular core stage. These laboratory investigations help to explain astronomical observations by Nummelin et al. and Ikeda et al. toward massive star-forming regions and hot cores, where observed fractional abundances of these isomers are higher than can be accounted for by gas-phase reactions alone. Similar synthetic routes could help explain the formation of acetaldehyde and ethylene oxide in comet C/1995 O1 (Hale-Bopp) and also suggest a presence of both isomers in Titan's atmosphere.
The problem of the second wind turbine – a note on a common but flawed wind power estimation method

Abstract. Several recent wind power estimates suggest that this renewable energy resource can meet all of the current and future global energy demand with little impact on the atmosphere. These estimates are calculated using observed wind speeds in combination with specifications of wind turbine size and density to quantify the extractable wind power. However, this approach neglects the effects of momentum extraction by the turbines on the atmospheric flow that would have effects outside the turbine wake. Here we show with a simple momentum balance model of the atmospheric boundary layer that this common methodology to derive wind power potentials requires unrealistically high increases in the generation of kinetic energy by the atmosphere. This increase by an order of magnitude is needed to ensure momentum conservation in the atmospheric boundary layer. In the context of this simple model, we then compare the effect of three different assumptions regarding the boundary conditions at the top of the boundary layer, with prescribed hub height velocity, momentum transport, or kinetic energy transfer into the boundary layer. We then use simulations with an atmospheric general circulation model that explicitly simulate generation of kinetic energy with momentum conservation. These simulations show that the assumption of prescribed momentum import into the atmospheric boundary layer yields the most realistic behavior of the simple model, while the assumption of prescribed hub height velocity can clearly be disregarded. We also show that the assumptions yield similar estimates for extracted wind power when less than 10% of the kinetic energy flux in the boundary layer is extracted by the turbines. We conclude that the common method significantly overestimates wind power potentials by an order of magnitude in the limit of high wind power extraction. Ultimately, environmental constraints set the upper limit on wind power potential at larger scales rather than detailed engineering specifications of wind turbine design and placement.
Heat stress and amphibian immunity in a time of climate change

As a class of vertebrates, amphibians, are at greater risk for declines or extinctions than any other vertebrate group, including birds and mammals. There are many threats, including habitat destruction, invasive species, overuse by humans, toxic chemicals and emerging diseases. Climate change which brings unpredictable temperature changes and rainfall constitutes an additional threat. Survival of amphibians depends on immune defences functioning well under these combined threats. Here, we review the current state of knowledge of how amphibians respond to some natural stressors, including heat and desiccation stress, and the limited studies of the immune defences under these stressful conditions. In general, the current studies suggest that desiccation and heat stress can activate the hypothalamus pituitary–interrenal axis, with possible suppression of some innate and lymphocyte-mediated responses. Elevated temperatures can alter microbial communities in amphibian skin and gut, resulting in possible dysbiosis that fosters reduced resistance to pathogens. This article is part of the theme issue ‘Amphibian immunity: stress, disease and ecoimmunology’.
ON THE CLASSICAL SOLUTION TO 3-DIMENSIONAL QUASI-GEOSTROPHIC EQUATIONS WITH POTENTIAL VORTICITY

The three-dimensional quasi-geostrophic flow model has been widely used to study basic mechanisms in oceanic flows and climate dynamics. From the mathematical point of view, twodimensional quasi-geostrophic equation (surface quasi-geostrophic equation) is strongly studied by many authors due to the similarity with three dimensional Euler equations. We survey the derivation of the three dimensional quasi-geostrophic equation. Then we discuss the global (in time) existence of the smooth solutions to the three dimensional quasi-geostrophic equation with trivial boundary data.
Shipping stocks as lotteries

ABSTRACT While shipping stocks are risky investments, their realized returns are found to be consistently lower than expectations derived from a mean-variance framework. The objective of the paper is to examine whether additional characteristics of the return distribution, in particular, extreme positive (maximum) return, are significant in the pricing of shipping stocks. Using U.S. data of publicly listed firms, we find that shipping stocks with a higher daily maximum return in the previous month exhibit significantly lower subsequent returns, suggesting that investors are willing to pay a higher price and accept a lower expected return for such stocks. Our results are robust at portfolio and firm levels after controlling for a barrage of risk factors. Consistent with prospect theory, we corroborate evidence of preference among shipping investors towards lottery-like payoffs. The implications of our work are relevant to investment managers who consider including shipping stocks in their portfolios, to investment bankers providing valuations for the pricing of shipping initial and secondary public offerings, or for mergers and acquisitions, and to shipping firms seeking to estimate their cost of capital in the context of investment appraisal.
Impact of Point Mutation on Shiga-like Toxin 1: A Molecular Dynamics Simulation Study

The causative agent of gastroenteritis is Shiga toxin, which belongs to a functionally and structurally associated protein family despite each individual having a unique amino acid sequence. After entering the ER lumen and relocating the toxic domain to the cytoplasm, they alter the large subunit of rRNA, preventing protein synthesis and ribosomal damage. Shiga-like toxin-1 (SLT-1) subunit B targets glycolipid receptor Gb3, which plays a significant role in cytotoxicity. Though the mutational effect on subunit B is important for cytotoxicity study, we lack better understanding. Our present study targets the mutational impact of glycine protein at their 62th amino acid sequence of subunit B. For example, how it can alter the receptor-binding capacity and virulence. We used in silico method with GROMACS software suite (version 5.2, 2020.1) on Google Colab for a 100ns (100,000ps) simulation period and UCSF Chimera software for visualizing mutant and wild-type structure similarities. Surprisingly, RMSD, RMSF, and Rg trajectories from the simulation analysis indicated a more stable and compact mutant structure than the wild type. Principle component analysis (PCA) and SASA were visualized for the entire 100ns, which pointed towards homogeneity between both structures and more solvent accessibility in the mutant structure. This mutation may elevate receptor-binding and virulence capacity. Moreover, this finding can offer a better insight for future vaccine production.
Evaluation of abstract rule-based associations in the human premotor cortex during passive observation

Decision-making often manifests in behavior, typically yielding overt motor actions. This complex process requires the registration of sensory information with one’s internal representation of the current context, before a categorical judgment of the most appropriate motor behavior can be issued. The construct concept of embodied decision-making encapsulates this sequence of complex processes, whereby behaviorally salient information from the environment is represented in an abstracted space of potential motor actions rather than only in an abstract cognitive “decision” space. Theoretical foundations and some empirical evidence account for support the involvement of premotor cortical circuits in embodied cognitive functions. Animal models show that premotor circuits participate in the registration and evaluation of actions performed by peers in social situations, that is, prior to controlling one’s voluntary movements guided by arbitrary stimulus-response rules. However, such evidence from human data is currently limited. Here we used time-resolved magnetoencephalography imaging to characterize activations of the premotor cortex as human participants observed arbitrary, non-biological visual stimuli that either respected or violated a simple stimulus-response association rule. The participants had learned this rule previously, either actively, by performing a motor task (active learning), or passively, by observing a computer perform the same task (passive learning). We discovered that the human premotor cortex is activated during the passive observation of the correct execution of a sequence of events according to a rule learned previously. Premotor activation also differs when the subjects observe incorrect stimulus sequences. These premotor effects are present even when the observed events are of a non-motor, abstract nature, and even when the stimulus-response association rule was learned via passive observations of a computer agent performing the task, without requiring overt motor actions from the human participant. We found evidence of these phenomena by tracking cortical beta-band signaling in temporal alignment with the observation of task events and behavior. We conclude that premotor cortical circuits that are typically engaged during voluntary motor behavior are also involved in the interpretation of events of a non-ecological, unfamiliar nature but related to a learned abstract rule. As such, the present study provides the first evidence of neurophysiological processes of embodied decision-making in human premotor circuits when the observed events do not involve motor actions of a third party.