Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards high-throughput automated targeted femtosecond laser-based transfection of adherent cells

Femtosecond laser induced cell membrane poration has proven to be an attractive alternative to the classical methods of drug and gene delivery. It is a selective, sterile, non-contact technique that offers a highly localized operation, low toxicity and consistent performance. However, its broader application still requires the development of robust, high-throughput and user-friendly systems. We present a system capable of unassisted enhanced targeted optoinjection and phototransfection of adherent mammalian cells with a femtosecond laser. We demonstrate the advantages of a dynamic diffractive optical element, namely a spatial light modulator (SLM) for precise three dimensional positioning of the beam. It enables the implementation of a "point-and-shoot" system in which using the software interface a user simply points at the cell and a predefined sequence of precisely positioned doses can be applied. We show that irradiation in three axial positions alleviates the problem of exact beam positioning on the cell membrane and doubles the number of viably optoinjected cells when compared with a single dose. The presented system enables untargeted raster scan irradiation which provides transfection of adherent cells at the throughput of 1 cell per second.
Anomalous conductivity in Hall thrusters: Effects of the non-linear coupling of the electron-cyclotron drift instability with secondary electron emission of the walls

With the help of an implicit particle-in-cell code, we have shown in a previous paper that the electron-cyclotron drift instability was able to induce anomalous conductivity as well as anomalous heating. As such it can be a major actor among the mechanisms involved in the operation of Hall thrusters. However, experimental results show that the nature of wall material has a significant effect on the behavior of the thruster. The purpose of this paper is to study the plasma-wall interaction in the case where the plasma is heated self-consistently by electrostatic fluctuations induced by the electron-cyclotron drift instability.
The Refined Theory of Thermoelastic Plane Problems

Based on thermoelastic theory, various two-dimensional equations and solutions for plane problems have been deduced systematically and directly from thick plate theory by using Biot's solution and Lur'e method without ad hoc assumptions. These equations and solutions can be used to construct the refined theory for the plane problems. In the case of homogeneous boundary conditions, the exact governing differential equations and solutions for the plate are derived, which consist of four governing differential equations. It is important note that the refined theory is consistent with the decomposition theorem by Gregory. In the case of non-homogeneous boundary conditions, the approximate governing differential equations and solutions for the plate are accurate up to the second-order terms. The correctness of the stress assumptions in the classic plane stress problems is revised.
KINEMATIC OSCILLATIONS OF POST-CME BLOBS DETECTED BY K-COR ON 2017 SEPTEMBER 10

: We investigate 20 post-coronal mass ejection (CME) blobs formed in the post-CME current sheet (CS) that were observed by K-Cor on 2017 September 10. By visual inspection of the trajectories and projected speed variations of each blob, we ﬁnd that all blobs except one show irregular “zigzag” trajectories resembling transverse oscillatory motions along the CS, and have at least one oscillatory pattern in their instantaneous radial speeds. Their oscillation periods are ranging from 30 to 91 s and their speed amplitudes from 128 to 902 km s − 1 . Among 19 blobs, 10 blobs have experienced at least two cycles of radial speed oscillations with diﬀerent speed amplitudes and periods, while 9 blobs undergo one oscillation cycle. To examine whether or not the apparent speed oscillations can be explained by vortex shedding, we estimate the quantitative parameter of vortex shedding, the Strouhal number, by using the observed lateral widths, linear speeds, and oscillation periods of the blobs. We then compare our estimates with theoretical and experimental results from MHD simulations and ﬂuid dynamic experiments. We ﬁnd that the observed Strouhal numbers range from 0.2 to 2.1, consistent with those (0.15–3.0) from ﬂuid dynamic experiments of bluﬀ spheres, while they are higher than those (0.15–0.25) from MHD simulations of cylindrical shapes. We thus ﬁnd that blobs formed in a post-CME CS undergo kinematic oscillations caused by ﬂuid dynamic vortex shedding. The vortex shedding is driven by the interaction of the outward-moving blob having a bluﬀ spherical shape with the background plasma in the post-CME CS.
Quiet-Sun Connection between Intensity, Doppler Shift, and Line Broadening in Solar Ultraviolet Emission Lines

The quiet-Sun relations between the C IV line parameters, intensity, wavelength shift, and line broadening, are studied with high spatial and spectral resolution. The material is ordered into equal intervals for one of the line parameters, and conditional probabilities are calculated. As the Doppler velocity increases, we find that redshifted profiles with a large intensity or line width constitute an increasing fraction of the total number of profiles in a given velocity interval. For blueshifted profiles, on the other hand, the conditional probabilities for finding a profile with considerable intensity or line width decrease as the line shift increases. Similar relations are found when the material is ordered according to intensity or line-width values.
Lie ideals: from pure algebra to C*-algebras

How does the associative structure of the algebra A e¤ect the Lie structure of A? In particular, is it possible to describe Lie ideals of A through associative ideals of A? This and related questions such as the link between Lie ideals and conjugate-invariant subspaces of unital algebras, have been an active area of research for more than 50 years. They have been studied in pure algebra (see e.g. [A], [BFM], [H1], [H2], [H3], [JR], [LM], [MM1], [MM2], [Mu]) and, more or less independently, also in functional analysis, particularly in operator algebras (see e.g. [BM], [CY], [FM], [FR], [FMS], [FN], [HMS], [HP], [Ma], [MaMu], [MS], [Mi], [To]). One of the goals of this paper is to ‘‘glue’’ these two areas; that is, we will apply purely algebraic results, derived in the first part of the paper, to the second part dealing with Banach algebras, especially with W -algebras and C -algebras.
Tricycle surveillance in Antananarivo, Madagascar: circulation of both extended-spectrum beta-lactamase producing Escherichia coli strains and plasmids among humans, chickens and the environment

Background: Antimicrobial resistance is a major public health threat, affecting not only humans but also animals and the environment. Although the "One Health" dimension of resistance is well recognized, data are lacking on the circulation of resistance, particularly in low-income countries. The World Health Organization has proposed a protocol called Tricycle, focusing on extended-spectrum beta-lactamase (ESBL)-Escherichia coli surveillance in the three sectors. We implemented Tricycle in Madagascar to assess ESBL-E. coli prevalence and describe intra- and inter-sector circulation of ESBL-E. coli and plasmids. Methods: 289 pregnant women, 246 farm chickens and 28 surface waters were sampled in Antananarivo (the capital city) area and tested for ESBL-E. coli. Isolates were sequenced by short- (Illumina) and long- (Nanopore) read methods. Findings: ESBL-E. coli prevalence was 29.8%, 56.9% and 100% in pregnant women, chickens, and the environment, respectively. The wet season was associated with higher rates of carriage in humans (OR=3.1, 95%CI 1.8-5.3) and animals (OR=2.8 95%CI 1.7-4.8). Sequencing of 277 non-duplicated isolates (82, 118 and 77 from each sector, respectively) showed high genetic diversity (90 STs identified) with differences between sectors. Single nucleotide polymorphism (SNP) analysis revealed 169/277 (61%) isolates grouped into 44 clusters ([≥]2 isolates) of closely related isolates (<40 SNPs), of which 24 contained isolates from two sectors and five contained isolates from all three sectors. ESBL genes were all blaCTX-M (77.6% blaCTX-M-15), chromosomally integrated in 57.4% (159/277) of isolates, and plasmidic in 40.8% (113/277). The 114 ESBL-carrying plasmids were mainly IncF (55.2%, n=63) and IncY (36.8%, n=42). The F31/36:A4:B1 (n=13) and F-:A-:B53 (n=8) subtypes, and all IncY plasmids, highly conserved, were observed in isolates of differing genetic backgrounds from all sectors. Interpretation: Despite varying strain population structures in the three sectors, both ESBL-E. coli strains and plasmids are circulating among humans, chickens and the environment in the capital of Madagascar. Funding: Fondation Merieux, INSERM, Universite Paris Cite. Keywords: Extended spectrum beta-lactamase (ESBL), Escherichia coli, Tricycle, One Health, circulation
Prevalence of adequately iodized salt and its determinants in Gambela district, Southwest Ethiopia

Background: Iodine deficiency disorders (IDDs) are among the major public health problems for populations all over the world. Even though the recommended strategy for IDD control is universal salt iodization, little was known about availability of adequately iodized salt in Gambela region. Objective: This study was conducted to determine availability of adequately iodized salt and associated factors in Gambela district, Southwest Ethiopia. Methods: A community-based cross-sectional study was conducted in July 2019 in Gambela district. Multistage sampling method was employed to select 422 households. A structured questionnaire and rapid test kits were data collection instruments. Multivariate logistic regression was used to identify association. Results: About 52.8% (95% CI: 0.47, 0.57) of households had adequately iodized salt. College diploma and above educational status (AOR=4.27, 95% CI: 1.47, 12.44), favorable attitude (AOR=5.69, 95% CI: 2.83, 11.42), walking less than 30 minutes to get iodized salt (AOR=4.69, 95% CI: 2.56, 8.60), using packed salt (AOR=2.75, 95% CI: 1.54, 4.93) and using covered salt container (AOR=3.93, 95% CI: 2.21, 6.98) were factors positively associated with availability of adequately iodized salt. Conclusions: The availability of adequately iodized salt in Gambela district is very low. Enhancing community awareness about the benefit and good practice of iodized salt should be emphasized besides improving accessibility.
Special problems in applying the physical optics method for backscatter computations of complicated objects

The backscatter computation of complicated objects is carried by the physical optics (PO) method, known as the vector Kirchoff approximation. The object is described by a geometrical model using flat plates (panels). These panels can be nonperfectly conducting and multilayered. The PO solution for the scattering matrix of a single multilayered panel is evaluated in detail using the Fresnel reflection coefficients. An example of the computed reflection coefficient of a two-layered medium is presented. The phase integral of the PO method is solved analytically. The hidden-surface problem is discussed, and the procedure for the treatment of doubly reflecting panels is described. For an ideal conducting cube with additional surfaces that generate shadow and double-reflection effects, the computed radar cross section (RCS) is compared with measurements. Computational results of the RCS for nonperfectly conducting panels are given. >
Comparison of Disk Diffusion and Agar Dilution Method for the Detection of Mupirocin Resistance in Staphylococcal Isolates from Skin and Soft Tissue Infections

Abstract Aims and Objectives Mupirocin is a widely used topical antibiotic for the treatment of skin and soft tissue infections. This has resulted in resistance leading to treatment failure. Hence, the present study aimed to determine the prevalence of mupirocin resistance among staphylococcal isolates obtained from the skin and soft tissue infections. Also, comparison of disc diffusion and agar dilution method in detecting mupirocin resistance was done. Materials and Methods This cross-sectional study was conducted in the Department of Microbiology of a tertiary health care center in Karnataka from January to December, 2018. Clinical samples such as wound swabs, tissues, and pus were included in the study. All staphylococcal isolates were screened for mupirocin resistance using 5 µg and 200 µg discs for low-level (MuL) and high-level mupirocin resistance (MuH), respectively. Minimum inhibitory concentration (MIC) was determined using the agar dilution method. Results Out of 100 staphylococcal isolates, 68 were Staphylococcus aureus and 32 were CoNS. MuH was detected in 11 isolates. MuH was more common in CoNS (10/11) compared with S. aureus (1/11). MuL was not found in the study. Discussion In our study, 10 out of 11 mupirocin-resistant isolates were methicillin resistant, which is statistically significant ( p < 0.05). The correlation between results of disc diffusion and MIC were appropriate in this study. Conclusion Judicial prescription of mupirocin after knowing the susceptibility report should become the standard practice. Screening for mupirocin resistance can be done by disc diffusion in resource-limited settings.
Aptamer-Assisted Proximity Ligation Assay for Sensitive Detection of Infectious Bronchitis Coronavirus

Infectious bronchitis virus (IBV) causes high morbidity and mortality and large economic losses in the poultry industry. The virus has the ability to genetically mutate into new IBV strains, causing devastating disease and outbreaks. ABSTRACT Infectious bronchitis virus (IBV) is a coronavirus responsible for major health problems in the poultry industry. New virus strains continue to appear, causing large economic losses. To develop a rapid and accurate new quantitative assay for diagnosis of the virus without DNA extraction, we selected highly specific single-stranded DNA (ssDNA) aptamers with a high affinity to IBV, using the systematic evolution of ligands by exponential enrichment (SELEX) technology for aptamer screening, followed by high-throughput sequencing technology. Two of these aptamers, AptIBV5 and AptIBV2, were used to establish homogenous and solid-phase proximity ligation assays (PLAs). The developed assays were evaluated for their sensitivity and specificity using collected field samples and then compared to the newly developed sandwich enzyme-linked aptamer assay (ELAA) and reverse transcription-quantitative PCR (qRT-PCR), as the gold-standard method. The solid-phase PLA showed a lower limit of detection and a broader dynamic range than the two other assays. The developed technique may serve as an alternative assay for the diagnosis of IBV, with the potential to be extended to the detection of other important animal or human viruses. IMPORTANCE Infectious bronchitis virus (IBV) causes high morbidity and mortality and large economic losses in the poultry industry. The virus has the ability to genetically mutate into new IBV strains, causing devastating disease and outbreaks. To better monitor the emergence of this virus, the development of a rapid and highly sensitive diagnostic method should be implemented. For this, we generated aptamers with high affinity and specificity to the IBV in an ssDNA library. Using two high-affinity aptamers, we developed a sandwich ELAA and a very sensitive aptamer-based proximity ligation assay (PLA). The new assay showed high sensitivity and specificity and was used to detect IBV in farm samples. The PLA was compared to the newly developed sandwich ELAA and qRT-PCR, as the gold-standard technique.
“Failure To Launch”: Development of a Reproductive Organ Linked to Symbiotic Bacteria

Microbiota have profound effects on animal and plant development. Hosts raised axenically or without symbionts often suffer negative outcomes resulting in developmental defects or reduced organ function. ABSTRACT Developmental processes in animals are influenced by colonization and/or signaling from microbial symbionts. Here, we show that bacteria from the environment are linked to development of a symbiotic organ that houses a bacterial consortium in female Hawaiian bobtail squid, Euprymna scolopes. In addition to the well-characterized light organ association with the bioluminescent bacterium Vibrio fischeri, female E. scolopes house a simple bacterial community in a reproductive organ, the accessory nidamental gland (ANG). In order to understand the influences of bacteria on ANG development, squid were raised in the laboratory under conditions where exposure to environmental microorganisms was experimentally manipulated. Under conditions where hosts were exposed to depleted environmental bacteria, ANGs were completely absent or stunted, a result independent of the presence of the light organ symbiont V. fischeri. When squid were raised in the laboratory with substrate from the host’s natural environment containing the native microbiota, normal ANG development was observed, and the bacterial communities were similar to wild-caught animals. Analysis of the bacterial communities from ANGs and substrates of wild-caught and laboratory-raised animals suggests that certain bacterial groups, namely, the Verrucomicrobia, are linked to ANG development. The ANG community composition was also experimentally manipulated. Squid raised with natural substrate supplemented with a specific ANG bacterial strain, Leisingera sp. JC1, had high proportions of this strain in the ANG, suggesting that once ANG development is initiated, specific strains can be introduced and subsequently colonize the organ. Overall, these data suggest that environmental bacteria are required for development of the ANG in E. scolopes. IMPORTANCE Microbiota have profound effects on animal and plant development. Hosts raised axenically or without symbionts often suffer negative outcomes resulting in developmental defects or reduced organ function. Using defined experimental conditions, we demonstrate that environmental bacteria are required for the formation of a female-specific symbiotic organ in the Hawaiian bobtail squid, Euprymna scolopes. Although nascent tissues from this organ that are involved with bacterial recruitment formed initially, the mature organ failed to develop and was absent or severely reduced in sexually mature animals that were not exposed to microbiota from the host’s natural environment. This is the first example of complete organ development relying on exposure to symbiotic bacteria in an animal host. This study broadens the use of E. scolopes as a model organism for studying the influence of beneficial bacteria on animal development.
Chaos, Solitons and Fractals

In this paper, we investigate the effectiveness of COVID-19 vaccination in controlling the infectivity and mortality of the SARS-CoV-2. Two major variants Delta and Omicron are investigated respectively. The main method used in the research is the multifractal detrended fluctuation analysis (MF-DFA). We use 𝛥𝛼 as the evaluation of control effectiveness. In the transmission stages of Delta and Omicron, we observe whether 𝛥𝛼 shows a downward trend by gradually expanding the length of time series. Vaccine effectiveness is evaluated using a time series of newly diagnosed patients and newly reported deaths. Data samples are taken from 9 different countries. According to the obtained results, the vaccine controls infectivity and mortality of the virus in the Delta transmission stage, but infectivity control is less effective than mortality. In the Omicron transmission stage, the immune effect of the vaccine is not obvious, which may be related to the high infectivity of Omicron. However, the vaccine is still effective in controlling mortality. We also find that the immune effect of vaccine on Omicron was lower than that of Delta. Finally, we observe that the immune effect of the vaccine in ‘Poland’ was abnormal. By analyzing the vaccination curve, we conclude that in ‘Poland’, when the growth rate of vaccination rate slowed down, the immune effect of the vaccine was very poor in terms of pathogenicity and lethality. Therefore, we suggest that all countries should continue to strengthen the vaccination rate. A higher or faster growth rate of vaccination rate will help control the infectivity and mortality rate, especially in the effectiveness of controlling mortality. Our research can be used to evaluate the effectiveness of vaccines for epidemic prevention and control, the formulation of epidemic prevention measures and vaccination policies for different countries with respect to their current pandemic situation accordingly.
Damage caused by Tuckerella ornata (Acari: Tuckerellidae) on cocoa fruits (Theobroma cacao) in the Amazon region, state of Pará, Brazil

Abstract The study aimed to report peacock mites (Acari: Tuckerellidae) on cocoa fruits (Theobroma cacao L.; Malvaceae) in the northeast Bragantina region, state of Pará, Brazil. Two mite species were identified, Tuckerella ornata, with 149 specimens, 32.89% on leaves and 67.11% on fruits, and Tuckerella knorri, with only two specimens on leaves. It was found that green fruits with T. ornata significantly reduced the size and weight of seeds. More attacked fruits, with more severe damage, showed deformations and thick cracks. Significant damage was noted in the Forastero cocoa seeds, visible to the naked eye, with light brown spots and a fine crack on the epidermis.
Morphological ontogeny of Pilogalumna kazakhstanica sp. nov. (Acari, Oribatida, Galumnidae) from Kazakhstan

Abstract The morphological ontogeny of Pilogalumna kazakhstanica sp. nov. from Kazakhstan is described and illustrated. The adult stage of this species is most similar to P. ornatula Grandjean, 1956, but differs from it mainly by slightly smaller body size and by having two postanal porose areas, whereas P. ornatula has usually a single porose area. In P. kazakhstanica the prodorsal porose area Ad and all notogastral porose areas are framed by dark brown integument, whereas in P. ornatula framed is usually porose area A1. The larva of P. kazakhstanica has 12 pairs of gastronotal setae, most are short and smooth, except for medium-sized and barbed c2, c3, h1 and h2, and minute, smooth h3, the nymphs have 15 pairs, most are short and smooth, except for medium-sized and barbed c2 and c3. In the juvenile instars the gastronotal shield is poorly developed, bearing setae of d-, l-series and h1 in the larva, and setae of d-, l-, h-series and p1 in the nymphs. In all juveniles, a humeral organ is present, and setae of c-, ad-series and p2 and p3 are with microsclerites.
Reproductive Biology and Population Structure of Eurycea chamberlaini in North Carolina

Eurycea chamberlaini (Chamberlain's Dwarf Salamander) is a small spelerpine salamander with scant reproductive and life-history data available. Therefore, the objectives of our study were to examine the reproductive life history and population structure of E. chamberlaini from a North Carolina population. From February 2008 to February 2009, monthly collections were made in Craven County, North Carolina. All specimens (n = 392) were histologically examined for reproductive life history and population characteristics by month. Overall, male and female E. chamberlaini follow a reproductive cycle similar to other spelerpine species with sperm in the Wolffian ducts of specimens from September to February; however, spermatidogenesis was delayed until August and September with the presence of mature sperm in testes from August through November. We captured 201 female salamanders of which 36 were considered immature. We caught 191 males of which 27 were considered immature. The mean snout–vent length (SVL±1 SD) of mature females (27.13±2.33 mm) and males (25.84±2.03 mm) was statistically different from one another. Females tended to be larger than males from our monthly samples, with a greater proportion of the largest specimens being female. Overall, population structure of E. chamblerlaini appears similar to other coastal plain salamander species.