bluuebunny/crossref_metadata_2025 huggingface dataset:
Some Physical Properties of Aflatoxin-Inoculated Cottonseed
Authors: Bridges Catelyn , Moore Janie McClurkin
Published: June 2022

Highlights

The combination of seed dimensions, moisture content, and color were used to indicate microbial spoilage.

Increased water availability in cottonseed stored over time resulted in higher aflatoxin concentrations.

Cottonseed with high microbial levels and aflatoxin could be sorted and removed by size and true density.

Higher aflatoxin levels were correlated to lower true density.

Abstract. Aspergillus flavus is a common field and stored grain fungus that infects cottonseed and other protein-rich grains and oilseeds. This fungus produces aflatoxin, a toxic and carcinogenic mycotoxin, which is initially found in the field and then proliferates during storage as A. flavus metabolizes. When consumed, cottonseed contaminated with aflatoxin has an associated health risk for dairy and beef cattle and poses a cancer threat to humans. There is a need to separate and clean batches of cottonseed before processing. The objective of this study was to determine the key physical properties of contaminated and non-contaminated (healthy) cottonseed. Healthy fuzzy cottonseed (350 g) and cottonseed contaminated with 150 ppb of aflatoxin (350 g), with an initial moisture content of 8.3% dry basis, were stored at 25°C and 85% relative humidity for 21 days. The properties of the healthy and contaminated fuzzy cottonseed after the 21-day storage period that were characterized included sphericity, surface area, individual seed mass, projected area, color, and volume. The presence of aflatoxin and fungus showed significant effects on the density (>1.3 g cm-3), dimensions (>9.8, 5.6, and 4.9 mm for major, intermediate, and minor diameters, respectively), surface area (>368.4 mm2), projected area (>56.7 mm2), and volume (>0.08 cm3) of fuzzy cottonseed. The results of this study provide measurements of physical properties that relate to separating cottonseed contaminated with aflatoxin and fungus during storage and before processing. Keywords: Aflatoxin, Aspergillus flavus, Fuzzy cottonseed, Physical properties, Storage, Surface area, True density.
Environmental Impact Assessment of Tractor Guidance Systems Based on Pasture Management Scenarios
Authors: Ashworth Amanda Joy , Putman William Benjamin , Kharel Tulsi , Thoma Greg , Shew Aaron , Popp Michael , Owens Phillip
Published: June 2022

Highlights

Tractor guidance (TG) reduced the overlaps and gaps during fertilizer and herbicide applications.

Production gains with TG on were 2.7% to 6.5% relative to TG off; however, fuel consumption increased.

A 5% increase in yield is needed to make tractor guidance environmentally remunerating.

Abstract. The use of auto-guidance on tractors and self-propelled machinery improves agricultural production efficiencies by reportedly avoiding negative environmental impacts from over-applying fertilizers and herbicides. Environmental impacts from auto-tractor guidance systems have not been systematically quantified and are difficult to assess at the farm system level. Therefore, this study uses a life cycle-based assessment to quantify the environmental impacts of deploying tractor guidance (TG) over a range of fertility rates, fertilizer sources (organic and inorganic), equipment, and pasture crops through scenarios based on in-field data (collected with and without TG). The use of TG reduced gaps by 7.6% and 10.1% and reduced absolute overlaps by 32.5% and 4.2% during herbicide and fertilizer application, respectively. Estimated production gains with TG on ranged from 2.7% to 6.5% over the baseline (TG off); however, tractor fuel consumption increased when TG was employed. There was high uncertainty for productivity gain estimates; however, under scenario testing with an assumed 15% yield gain, TG resulted in 8% to 12% reduced environmental impacts across all impact categories relative to non-GPS enabled technologies. Future research should be focused on actual yield-based responses from TG, as well as field emissions, operator experience, and resulting water quality. Overall, yield gains were crucial for improved pasture-based system sustainability when using TG because TG results in fewer gaps and overlaps, thereby resulting in greater input use across pasture landscapes. Consequently, more targeted applications of inputs during production may lead to fewer nutrients in water systems and more sustainable production of food. Keywords: Auto-guidance, Forage systems, Life cycle assessment, Poultry litter, Precision agriculture, Small farms.
Enhancement of grayscale image display with amplitude Fourier holograms, employing a limited bandwidth phase
Authors: Cruz Maria-Luisa
Published: June 2022

An alternative method is proposed to generate a modified
random phase that is able to
concentrate the light around a given direction, produces
well-contrasted Fourier amplitude holograms, reduces the quantity and
the randomness of the speckle noise in the image, and decreases the
amount of data necessary for the phase definition. This modified
limited bandwidth random phase uses structured random phase patterns
to control the object dispersion. The resulting hologram displays an
image with structured speckle noise (SSN), exhibiting similar metrics
as the iterative method for hologram generation. A filtering process
eliminates the SSN; the speckle contrast in the final image is reduced
from 0.66 to 0.07; and the peak SNR increases from 7.21 dB to
12.62 dB. This method enhances the fine details and grayscale tone
perception in the final image.
On the optimization of underwater quantum key distribution systems with time-gated SPADs
Authors: Fahim Raouf Amir Hossein , Uysal Murat
Published: June 2022

In this paper, we study the effect of various transmitter and receiver parameters on the quantum bit error rate (QBER) performance of underwater quantum key distribution. We utilize a Monte Carlo approach to simulate the trajectories of emitted photons transmitting in water from the transmitter towards the receiver. Based on propagation delay results, we first determine a proper value for the bit period to avoid intersymbol interference as a result of possible multiple scattering events. Then, based on the angle of arrival of the received photons, we determine a proper field of view to limit the average number of received background noise. Finally, we determine the optimal value for the single photon avalanche diode gate time in the sense of minimizing the QBER for the selected system parameters and given propagation environment.
Temporal reflection of an optical pulse from a short soliton: impact of Raman scattering
Authors: Zhang Junchi , Donaldson William , Agrawal Govind P.
Published: June 2022

We study temporal reflection of an optical pulse from the
refractive-index barrier created by a short pump soliton inside a
nonlinear dispersive medium such as an optical fiber. One feature is
that the soliton’s speed changes continuously as its spectrum
redshifts because of intrapulse Raman scattering. We use the
generalized nonlinear Schrödinger equation to find the shape and
spectrum of the reflected pulse. Both are affected considerably by the
soliton’s trajectory. The reflected pulse can become considerably
narrower compared to the incident pulse under conditions that involve
a type of temporal focusing. This phenomenon is explained through
space–time duality by showing that the temporal situation is analogous
to an optical beam incident obliquely on a parabolic mirror. We obtain
an approximate analytic expression for the reflected pulse’s spectrum
and use it to derive the temporal version of the transformation law
for the

q

parameter associated with a Gaussian
beam.
Surface topography data fusion of additive manufacturing based on confocal and focus variation microscopy
Authors: Zou Yibo , Li JiaQiang , Ju Yusheng
Published: June 2022

In this paper, two innovative data fusion methods are proposed for reconstructing the surfaces produced by directed energy deposition (DED) additive manufacturing. The surface topographic data were obtained from confocal laser scanning microscopy (CLSM) and focus variation microscopy (FV). The first method (competitive data fusion) aims to improve the data quality by combining both the advantages of the CLSM and FV techniques, while the second method (cooperative data integration) is designed for generating a single representation that contains not only global information but also local details. The results show that both fusion methods achieved satisfactory results: in the competitive fusion, the fused data preserved the characteristics of FV data while its vertical resolution is also improved by integrating the short waves from the CLSM data; the cooperative data fusion achieved one pixel precision of the surface registration which adopted the feature-based registration method with the help of color image information. The computational complexity is reduced from O((m×n)2) to O(m×n + k). Both proposed data fusion methods provided innovative solutions for the microscopic surface reconstruction and surface representation in multiscales in the field of additive manufacturing.
Direct generation of continuous-wave and passively Q-switched visible vortex beams from a doughnut-shaped diode-pumped Pr: YLF laser
Authors: Yang Qi , Yang Zixin , Cai Deyu , Ren Xianghe , Li Chun , Zu Yuqian , Ud Din Syed Zaheer , Leng Jiancai , Liu Jie , He Jingliang
Published: June 2022

We demonstrate the direct generation of visible vortex beams (LG01 mode) from a doughnut-shaped diode-pumped Pr:YLF laser. In continuous-wave mode, the maximum vortex output power was 36 mW at 523 nm, 354 mW at 607 nm, 838 mW at 639 nm, 722 mW at 721 nm, respectively. Moreover, based on this operation, the orange and red passively Q-switched vortex lasers were also achieved by inserting a Co:MgAl2O4 crystal into the laser cavity as a saturable absorber. The shortest pulse width of Q-switched vortex laser was 58 ns for 607 nm, and 34 ns for 639 nm, respectively. Our work provides a reliable and efficient method for the direct generation of visible vortex lasers for potential applications.
Second-order topological insulator in periodically driven optical lattices
Authors: Lei Ying , Luo Xi-Wang , Zhang Shaoliang
Published: June 2022

The higher-order topological insulator (HOTI) is a new type of topological system which has special bulk-edge correspondence compared with conventional topological insulators. In this work, we propose a scheme to realize Floquet HOTI with ultracold atoms in optical lattices. With the combination of periodically spin-dependent driving of the superlattices and a long-range coupling term, a Floquet second-order topological insulator with four zero-energy corner states emerges, whose Wannier bands are gapless and exhibit interesting bulk topology. Furthermore, the nearest-neighbor anisotropic coupling term also induced other intriguing topological phenomena, e.g. non-topologically protected corner states and topological semimetal for two different types of lattice structures respectively. Our scheme may give insight into the construction of different types of higher-order topological insulators in synthetic systems. It also provides an experimentally feasible platform to research the relations between different types of topological states and may have a wide range of applications in future.
Improvement of imaging performance of silicon micropore X-ray optics by ultra long-term annealing
Authors: Fukushima Aoto , Ishi Daiki , Ezoe Yuichiro , Ishikawa Kumi , Numazawa Masaki , Sakuda Sae , Uchino Tomoki , Inagaki Ayata , Ueda Yoko , Morishita Hiromi , Sekiguchi Luna , Murakawa Takatoshi , Tsuji Yukine , Mitsuda Kazuhisa , Kanamori Yoshiaki
Published: June 2022

We have been developing a light-weight X-ray telescope using micro electro mechanical systems technologies for future space missions. Micropores of 20 µm width are formed in a 4-inch Si wafer with deep reactive ion etching, and their sidewalls are used as X-ray reflection mirrors. The flatness of the sidewall is an important factor to determine the imaging performance, angular resolution. It is known that hydrogen annealing is effective to smooth a Si surface. We tested 150 hour annealing to achieve the ultimately smooth sidewalls. After 50 hour, 100 hour, and 150 hour annealing, the angular resolution improved 10.3, 4.0, and 2.6 arcmin in full width at half maximum (FWHM) and 17.0, 14.5, and 10.8 arcmin in half-power width (HPW). In spite of this improvement, the edge shapes of the sidewall were rounded. Therefore, both edges of the sidewall were ground and polished, and then the angular resolution was improved further to 3.2 arcmin (FWHM) and 5.4 arcmin (HPW).
Designing concentric nanoparticles for surface-enhanced light-matter interaction in the mid-infrared
Authors: Khodasevych Iryna , Rufangura Patrick , Iacopi Francesca
Published: June 2022

Nanosized particles with high responsivity in the infrared spectrum are of great interest for biomedical applications. We derive a closed-form expression for the polarizability of nanoparticles made of up to three concentric nanolayers consisting of a frequency dependent polar dielectric core, low permittivity dielectric spacer shell and conductive graphene outer shell, using the electrostatic Mie theory in combination with conductive layer in a dipole approximation. We use the obtained formula to investigate SiC, GaN and hBN as core materials, and graphene as conductive shell, separated by a low-permittivity dielectric spacer. Three-layer nanoparticles demonstrate up to a 12-fold increased mid-infrared (MIR) absorption as compared to their monolithic polar dielectrics, and up to 1.7 as compared to two-layer (no spacer) counterparts. They also show orders of magnitude enhancement of the nanoparticle scattering efficiency. The enhancement originates from the phonon-plasmon hybridization thanks to the graphene and polar dielectric combination, assisted by coupling via the low permittivity spacer, resulting in the splitting of the dielectric resonance into two modes. Those modes extend beyond the dielectric’s Reststrahlen band and can be tuned by tailoring the nanoparticles characteristics as they can be easily calculated through the closed-form expression. Nanoparticles with dual band resonances and enhanced absorption and scattering efficiencies in the MIR are of high technological interest for biomedical applications, such as surface -enhanced vibrational spectroscopies allowing simultaneous imaging and spectroscopy of samples, as well as assisting guided drug delivery.
Twisted light Michelson interferometer for high precision refractive index measurements
Authors: Kerschbaumer Nicola M. , Fochler Lucas I. , Reichenspurner Michael , Rieger Sebastian , Fedoruk Michael , Feldmann Jochen , Lohmüller Theobald
Published: June 2022

Using orbital angular momentum beams in a Michelson interferometer opens the possibility for non-invasive measurements of refractive index changes down to 10−6 refractive index units. We demonstrate the application of a twisted light interferometer to directly measure the concentration of NaCl and glucose solutions label-free and in situ and to monitor temperature differences in the mK-µK range. From these measurements we can extract a correlation of the refractive index to concentration and to temperature from a liquid sample which is in good agreement with literature. Applying this type of twisted light interferometry yields a novel, robust, and easily implementable method for in situ monitoring of concentration and temperature changes in microfluidic samples.
Color gamut change by optical crosstalk in high-resolution organic light-emitting diode microdisplays
Authors: Sim Soobin , Ryu Jinha , Ahn Dae Hyun , Cho Hyunsu , Kang Chan-mo , Shin Jin-Wook , Joo Chul Woong , Kim Gi Heon , Byun Chun-Won , Cho Nam Sung , Youn Hyoc Min , An Young Jae , Kim Jin Sun , Jung Hanyung , Lee Hyunkoo
Published: June 2022

Herein, the color gamut change by optical crosstalk between sub-pixels in high-resolution full-color organic light-emitting diode (OLED) microdisplays was numerically investigated. The color gamut of the OLED microdisplay decreased dramatically as the pixel density of the panel increased from 100 pixels per inch (PPI) to 3000 PPI. In addition, the increase in thickness of the passivation layer between the bottom electrode and the top color filter results in a decrease in the color gamut. We also calculated the color gamut change depending on the pixel structures in the practical OLED microdisplay panel, which had an aspect ratio of 32:9 and a pixel density of 2,490 PPI. The fence angle and height, refractive index of the passivation layer, black matrix width, and white OLED device structure affect the color gamut of the OLED microdisplay panel because of the optical crosstalk effect.
Ultra-dense moving cascaded metasurface holography by using a physics-driven neural network
Authors: Zhou Hongqiang , Li Xin , Wang He , Zhang Shifei , Su Zhaoxian , Jiang Qiang , Ullah Naqeeb , Li Xiaowei , Wang Yongtian , Huang Lingling
Published: June 2022

Metasurfaces are promising platforms for integrated compact optical systems. Traditional metasurface holography design algorithms are limited to information capacity due to finite spatial bandwidth production, which is insufficient for the growing demand for big data storage and encryption. Here, we propose and demonstrate deep learning empowered ultra-dense complex-amplitude holography using step-moving cascaded metasurfaces. Using deep learning artificial intelligence optimization strategy, the barriers of traditional algorithms can be conquered to meet diverse practical requirements. Two metasurfaces are cascaded to form the desired holography. One of them can move to switch the reconstruction images due to diffraction propagation accumulated during the cascaded path. The diffraction pattern from the first metasurface propagates at a different distance and meets with the second metasurface, reconstructing the target holographic reconstructions in the far-field. Such a technique can provide a new solution for multi-dimensional beam shaping, optical encryption, camouflage, integrated on-chip ultra-high-density storage, etc.
Multi-channel higher-order OAM generation and switching based on a mode selective interferometer
Authors: Wu Guowei , Wu Xiaowen , Gao Shecheng , Tu Jiajing , Zhou Ji , Sui Qi , Liu Weiping , Li Zhaohui
Published: June 2022

A multi-channel orbital angular momentum (OAM) mode generation and switching scheme is proposed and demonstrated based on an in-fiber mode selective interferometer (MSI), which is formed in a four-mode fiber. The MSI consists of two strong modulated long-period fiber gratings (LPFGs), which realizes the mode selected coupling between a target mode pair. With the optimized structural parameters, the MSI can couple a launched LP01 (or OAM0) into a desired higher-order azimuthal mode (HAM, LP
l
1 or OAM±l, l≥1) at multiple wavelength channels and generate the HAM with high-purity. To verify this concept, we fabricate two LPFGs in a four-mode fiber with designed distance and hence realize a MSI which can generate the second-order HAM (OAM2 or LP21) at 17 wavelength channels. The mode conversion efficiency is more than 90% at 17 wavelengths and the corresponding mode purity is no less than 97%, respectively. In addition, we also demonstrate that the selected mode pair (OAM0 and OAM2) can be switched at multiple channels by changing the state of the MSI. This MSI can also be used as a wavelength band-rejection filter on different spatial modes and find potential applications in optical communications and sensing.
Detecting the transverse spin density of light via electromagnetically induced transparency
Authors: Liu Jinhong , Wu Jinze
Published: June 2022

For light that is transversely confined, its field vector spins in a plane not orthogonal to the propagation direction, leading to the presence of transverse spin, which plays a fundamental role in the field of chiral quantum optics. Here, we theoretically propose a scheme to detect the transverse spin density (TSD) of light by utilizing a multilevel atomic medium. The scheme is based on the electromagnetically induced transparency effect, which enables the TSD-dependent modulation of the susceptibility of the atomic medium by using a coupling field whose TSD is to be detected. The modulated susceptibility results in a spin-dependent absorption for a probe beam passing through the atomic medium. We show that there exists a corresponding relationship between the TSD distribution of the coupling field and the polarization distribution of the transmitted probe beam through a theoretical study of two typical cases, in which the coupling field is provided by a tightly focused field and a two-beam interference field, respectively. Based on this relationship, the key features of the TSD of the coupling field, such as the spatial distribution, the symmetry property, and the spin-momentum locking, can be inferred from the transmitted probe beam. Benefiting from the fast response of the atomic medium to the variation of the coupling field, the present scheme is capable of detecting the TSD in real time, offering new possibilities for developing transverse-spin-based techniques.
The obligations of the scientific research community to society: an introduction to the report on methane production and mitigation
Authors: Leger James R.
Published: June 2022

The Editor-in-Chief of Optics Express introduces a new science and policy report prepared by the American Physical Society and Optica on “Monitoring Methane Emissions from Oil and Gas Operations.”
Experimental demonstration of high-rate discrete-modulated continuous-variable quantum key distribution system
Authors: Pan Yan , Wang Heng , Shao Yun , Pi Yaodi , Li Yang , Liu Bin , Huang Wei , Xu Bingjie
Published: June 2022

A high-rate continuous-variable quantum key distribution (CV-QKD) system based on high-order discrete modulation is experimentally investigated. With the help of the novel system scheme, effective digital signal processing (DSP) algorithms and advanced analytical security proof methods, the transmission results of 5.059 km, 10.314 km, 24.490 km, and 50.592 km are achieved for 1 GBaud optimized quantum signals. Correspondingly, the asymptotic secret key rates (SKRs) are 292.185 Mbps, 156.246 Mbps, 50.491 Mbps, and 7.495 Mbps for discrete Gaussian (DG) 64QAM, and 328.297 Mbps, 176.089 Mbps, 51.304 Mbps, and 9.193 Mbps for DG 256QAM, respectively. Under the same parameters, the achieved SKRs of DG 256QAM is almost same as ideal Gaussian modulation. In this case, the demonstrated high-rate discrete-modulated CV-QKD system has the application potential for high-speed security communication under tens of kilometers.
Parallel creation of propagable integer- and fractional-order vector vortex beams using mode extraction principle
Authors: Miao Yu , Weng Xiaoyu , Wang Yihui , Wang Lingyu , Wang Guanxue , Gao Xiumin , Zhuang Songlin
Published: June 2022

Propagable fractional-order vector vortex beams with fractional topological charge provide new possibilities in optics. However, their complicated polarizations give rise to a big challenge in creating multiple vector vortex beam channels. Here, we solve this scientific problem by generating fractional- and integer-order vector vortex beams in parallel using the mode extraction principle along with an optical pen. Based on the principle of mode extraction, integer- and fractional-order vector vortex beams can be extracted in the focal region of an objective lens directly from a single m = 30-order vector vortex beam. Their number, position, amplitude, and phase are further controlled by the parameters of an optical pen. This work not only presents an example of how to manipulate the polarization and phase of a light beam simultaneously using the principle of mode extraction, but also may open new avenues for the applications of integer- and fractional-order vector vortex beams.
Topologically enabled ultrahigh-Q chiroptical resonances by merging bound states in the continuum
Authors: Wan Shun , Wang Keda , Wang Fatian , Guan Chunying , Li Wenjia , Liu Jianlong , Bogdanov Andrey , Belov Pavel A. , Shi Jinhui
Published: June 2022

Ultrahigh-Q chiroptical resonance metasurfaces based on merging bound states in the continuum (BICs) are investigated and numerically demonstrated. The destruction of C2 symmetry results in the leakage of BICs into quasi-BICs, and a chiral quasi-BIC is obtained by oblique incidence or continuous destruction of the mirror symmetry of the structure. Due to the significant topological properties of merging BICs, the Q factor (over 2 × 105) of the chiral resonance peak obtained is much higher than that of the previous work. Moreover, the proposed structure is easy to fabricate because no additional out-of-plane asymmetry is introduced. The proposed scheme is of importance in chiral biosensing applications.
Demonstration of a diode-pumped plasma jet-type rare gas laser
Authors: Wang Rui , Yang Zining , Liu Qingshan , Han Kai , Wang Hongyan , Xu Xiaojun
Published: June 2022

The diode-pumped metastable rare gas laser (DPRGL) is showing potential for high-power operation. A key issue in developing this concept is to produce high-density metastables in a large volume. To achieve this goal, we propose a new, to the best of our knowledge, architecture by extracting laser power from a diode-pumped plasma jet. In this scheme, the discharge and gain regions are separated, avoiding the negative effects of discharges in confined regions. A diode-pumped plasma jet-type Ar laser is demonstrated with 466-mW output and 33% slope efficiency. The gain volume can be increased with multi-jets, providing a better scaling potential for the DPRGL system.
Chocolate inspection by means of phase-contrast imaging using multiple-plane terahertz phase retrieval
Authors: Agour Mostafa , Falldorf Claas , Taleb Fatima , Koch Martin , Bergmann Ralf B. , Castro-Camus Enrique
Published: June 2022

Terahertz (THz) radiation has shown enormous potential for non-destructive inspection in many contexts. Here, we present a method for imaging defects in chocolate bars that can be extended to many other materials. Our method requires only a continuous wave (CW) monochromatic source and detector at relatively low frequencies (280 GHz) corresponding to a relatively long wavelength of 1.1 mm. These components are used to construct a common-path configuration enabling the capturing of several images of THz radiation diffracted by the test object at different axial depths. The captured diffraction-rich images are used to constrain the associated phase retrieval problem enabling full access to the wave field, i.e., real amplitude and phase distributions. This allows full-field diffraction-limited phase-contrast imaging. Thus, we experimentally demonstrate the possibility of identifying contaminant particles with dimensions comparable to the wavelength.
The polyol pathway is an evolutionarily conserved system for sensing glucose uptake
Authors: Sano Hiroko , Nakamura Akira , Yamane Mariko , Niwa Hitoshi , Nishimura Takashi , Araki Kimi , Takemoto Kazumasa , Ishiguro Kei-ichiro , Aoki Hiroki , Kato Yuzuru , Kojima Masayasu
Published: June 2022

Cells must adjust the expression levels of metabolic enzymes in response to fluctuating nutrient supply. For glucose, such metabolic remodeling is highly dependent on a master transcription factor ChREBP/MondoA. However, it remains elusive how glucose fluctuations are sensed by ChREBP/MondoA despite the stability of major glycolytic pathways. Here, we show that in both flies and mice, ChREBP/MondoA activation in response to glucose ingestion involves an evolutionarily conserved glucose-metabolizing pathway: the polyol pathway. The polyol pathway converts glucose to fructose via sorbitol. It has been believed that this pathway is almost silent, and its activation in hyperglycemic conditions has deleterious effects on human health. We show that the polyol pathway regulates the glucose-responsive nuclear translocation of Mondo, a Drosophila homologue of ChREBP/MondoA, which directs gene expression for organismal growth and metabolism. Likewise, inhibition of the polyol pathway in mice impairs ChREBP’s nuclear localization and reduces glucose tolerance. We propose that the polyol pathway is an evolutionarily conserved sensing system for glucose uptake that allows metabolic remodeling.
Sex-specific variation in R-loop formation in Drosophila melanogaster
Authors: Stanek Timothy J. , Cao Weihuan , Mehra Rohan M , Ellison Christopher E.
Published: June 2022

R-loops are three-stranded nucleotide structures consisting of a DNA:RNA hybrid and a displaced ssDNA non-template strand. Previous work suggests that R-loop formation is primarily determined by the thermodynamics of DNA:RNA binding, which are governed by base composition (e.g., GC skew) and transcription-induced DNA superhelicity. However, R-loops have been described at genomic locations that lack these properties, suggesting that they may serve other context-specific roles. To better understand the genetic determinants of R-loop formation, we have characterized the Drosophila melanogaster R-loop landscape across strains and between sexes using DNA:RNA immunoprecipitation followed by high-throughput sequencing (DRIP-seq). We find that R-loops are associated with sequence motifs that are G-rich or exhibit G/C skew, as well as highly expressed genes, tRNAs, and small nuclear RNAs, consistent with a role for DNA sequence and torsion in R-loop specification. However, we also find motifs associated with R-loops that are A/T-rich and lack G/C skew as well as a subset of R-loops that are enriched in polycomb-repressed chromatin. Differential enrichment analysis reveals a small number of sex-biased R-loops: while non-differentially enriched and male-enriched R-loops form at similar genetic features and chromatin states and contain similar sequence motifs, female-enriched R-loops form at unique genetic features, chromatin states, and sequence motifs and are associated with genes that show ovary-biased expression. Male-enriched R-loops are most abundant on the dosage-compensated X chromosome, where R-loops appear stronger compared to autosomal R-loops. R-loop-containing genes on the X chromosome are dosage-compensated yet show lower MOF binding and reduced H4K16ac compared to R-loop-absent genes, suggesting that H4K16ac or MOF may attenuate R-loop formation. Collectively, these results suggest that R-loop formation in vivo is not fully explained by DNA sequence and topology and raise the possibility that a distinct subset of these hybrid structures plays an important role in the establishment and maintenance of epigenetic differences between sexes.
On-farm hydro and nutri-priming increases yield of rainfed pearl millet through physio-biochemical adjustments and anti-oxidative defense mechanism
Authors: Gupta N. K. , Gupta Sunita , Singh Jogendra , Garg Nitin K. , Saha Debanjana , Singhal Rajesh Kumar , Javed Talha , Al-Huqail Asma A. , Ali Hayssam M. , Kumar Ritesh , Siddiqui Manzer H.
Published: June 2022

Seed priming technique has a marvelous potential in enhancing seed germination and crop establishment under limited soil moisture conditions, which ultimately increases yield. Therefore, we investigated the effects of seed priming on physiology, growth, yield and antioxidant defense system of pearl millet (Pennisetum glaucum L.) under rain-fed condition. The experiments were conducted under laboratory as well as field conditions comprising three treatments i.e., non-primed seeds (control, T0), priming with tap water (hydropriming) (T1) and priming with 2% KNO3 2% for 6 hours at 25°C followed by shade drying (T2). The results showed that chlorophyll content (10.37–14.15%) and relative water content (RWC) (12.70–13.01%) increased whereas proline (-19.44 to -25%) and soluble sugar (-15.51 to -29.13%) contents decreased on account of seed priming in pearl millet under field conditions. The seed priming significantly improved the plant height, final plant stand and grain weight which resulted in increased yield. Enhanced activities of superoxide dismutase (SOD) (5.89 to 8.10 unit/g/seed/min), catalase (CAT) (22.54 to 39.67 µmol/min/g/seed) and ascorbate peroxidase (APX) (8.92 to 22.10 µmol/cm/min/g) and concomitant decrease in H2O2 and malondialdehyde (MDA) content suggests their role in imparting oxidative tolerance at initial stages of growth in primed seed. The lab studies suggest that the improved yield might be attributes to increased seed germination and seedling vigor. It is recommended that the hydropriming (tap water) or KNO3 (2%) priming of seeds for 6 hours under ambient conditions is effective to enhance growth and yield of pearl millet under rainfed conditions.
Effects of plant diversity and abiotic factors on the multifunctionality of an arid desert ecosystem
Authors: Shu Yulin , Jiang Lamei , Liu Feiyi , Lv Guanghui
Published: June 2022

Many studies suggest that species diversity and abiotic factors promote ecosystem multifunctionality. However, whether ecosystem multifunctionality is impacted by phylogenetic diversity remains controversial. The present study tested this in an arid desert ecosystem in Ebinur Lake Basin using soil C:N ratio, soil pH, and soil salinity as abiotic factors, and species diversity and phylogenetic diversity as indicators of plant diversity. The effects of plant diversity and abiotic factors on single ecosystem functions (nutrient cycling, carbon stocks, water regulation, and wood production) and ecosystem multifunctionality were studied. We used structural equation modeling to assess the relationships among different functional groups and factors. The results showed that: (1) abiotic factors, particularly pH and C:N ratio in soil, had the strongest positive impact on multifunctionality (P< 0.001). The phylogenetic diversity and species diversity showed inconsistent changes, and their contribution to multifunctionality were not outstanding. (2) Abiotic factors were closely related to different ecosystem functions. Soil C:N had a significant positive effect on carbon stocks (P< 0.001), with an effect index of 0.89. Soil pH significantly enhanced nutrient cycling and water regulation. The role of plant diversity varied with the combination of different ecosystem functions. Phylogenetic diversity and species diversity influenced wood production, but showed opposite functions. (3) The importance of four single-ecosystem functions in an arid region was ranked as follows: carbon stocks > water regulation > nutrient cycling > wood production, emphasizing the importance of carbon elements in these ecosystems. These results improve our understanding of the drivers of multifunctionality in arid ecosystems, facilitating the elucidation of the influence of abiotic factors and phylogenetic diversity.
Socioeconomic status differences in psychological responses to unfair treatments: Behavioral evidence of a vicious cycle
Authors: Kim Youngju , Jung Jaewuk , Na Jinkyung
Published: June 2022

Two studies investigated whether lower socioeconomic status (SES) would be associated with greater tolerance for unfair treatments. Specifically, we hypothesized that individuals with lower SES would be less likely to perceive apparent injustice as unfair than those with higher SES, and furthermore, such differences in perception would lead to the corresponding differences in ensuing psychological responses. In support of the hypotheses, we found that (Study 1, N = 326; Study 2, N = 130), compared with higher SES participants, lower SES participants perceived one-sidedly disadvantageous distribution during the dictator game as less unfair. Moreover, a behavioral experiment in Study 2 showed that such tolerance for unfair treatments were associated with subsequent passive reactions in the ultimatum game. Taken together, the results imply a vicious cycle whereby the SES differences in a tendency to accept unfair treatments lead to psychological responses that may maintain or even strengthen the existing social disparities.
Downsizing of COVID-19 contact tracing in highly immune populations
Authors: Martignoni Maria M. , Renault Josh , Baafi Joseph , Hurford Amy
Published: June 2022

Contact tracing is a key component of successful management of COVID-19. Contacts of infected individuals are asked to quarantine, which can significantly slow down (or prevent) community spread. Contact tracing is particularly effective when infections are detected quickly, when contacts are traced with high probability, when the initial number of cases is low, and when social distancing and border restrictions are in place. However, the magnitude of the individual contribution of these factors in reducing epidemic spread and the impact of population immunity (due to either previous infection or vaccination), in determining contact tracing outputs is not fully understood. We present a delayed differential equation model to investigate how the immunity status and the relaxation of social distancing requirements affect contact tracing practices. We investigate how the minimal contact tracing efficiency required to keep an outbreak under control depends on the contact rate and on the proportion of immune individuals. Additionally, we consider how delays in outbreak detection and increased case importation rates affect the number of contacts to be traced daily. We show that in communities that have reached a certain immunity status, a lower contact tracing efficiency is required to avoid a major outbreak, and delayed outbreak detection and relaxation of border restrictions do not lead to a significantly higher risk of overwhelming contact tracing. We find that investing in testing programs, rather than increasing the contact tracing capacity, has a larger impact in determining whether an outbreak will be controllable. This is because early detection activates contact tracing, which will slow, and eventually reverse exponential growth, while the contact tracing capacity is a threshold that will easily become overwhelmed if exponential growth is not curbed. Finally, we evaluate quarantine effectiveness in relation to the immunity status of the population and for different viral variants. We show that quarantine effectiveness decreases with increasing proportion of immune individuals, and increases in the presence of more transmissible variants. These results suggest that a cost-effective approach is to establish different quarantine rules for immune and nonimmune individuals, where rules should depend on viral transmissibility after vaccination or infection. Altogether, our study provides quantitative information for contact tracing downsizing in vaccinated populations or in populations that have already experienced large community outbreaks, to guide COVID-19 exit strategies.
Identification of four serum miRNAs as potential markers to screen for thirteen cancer types
Authors: Chen Joe W. , Dhahbi Joseph
Published: June 2022

Introduction

Cancer consistently remains one of the top causes of death in the United States every year, with many cancer deaths preventable if detected early. Circulating serum miRNAs are a promising, minimally invasive supplement or even an alternative to many current screening procedures. Many studies have shown that different serum miRNAs can discriminate healthy individuals from those with certain types of cancer. Although many of those miRNAs are often reported to be significant in one cancer type, they are also altered in other cancer types. Currently, very few studies have investigated serum miRNA biomarkers for multiple cancer types for general cancer screening purposes.

Method

To identify serum miRNAs that would be useful in screening multiple types of cancers, microarray cancer datasets were curated, yielding 13 different types of cancer with a total of 3352 cancer samples and 2809 non-cancer samples. The samples were divided into training and validation sets. One hundred random forest models were built using the training set to select candidate miRNAs. The selected miRNAs were then used in the validation set to see how well they differentiate cancer from normal samples in an independent dataset. Furthermore, the interactions between these miRNAs and their target mRNAs were investigated.

Result

The random forest models achieved an average of 97% accuracy in the training set with 95% bootstrap confidence interval of 0.9544 to 0.9778. The selected miRNAs were hsa-miR-663a, hsa-miR-6802-5p, hsa-miR-6784-5p, hsa-miR-3184-5p, and hsa-miR-8073. Each miRNA exhibited high area under the curve (AUC) value using receiver operating characteristic analysis. Moreover, the combination of four out of five miRNAs achieved the highest AUC value of 0.9815 with high sensitivity of 0.9773, indicating that these miRNAs have a high potential for cancer screening. miRNA-mRNA and protein-protein interaction analysis provided insights into how these miRNAs play a role in cancer.
Effects of different stent wire mesh densities on hemodynamics in aneurysms of different sizes
Authors: Masuda Shunsuke , Fujimura Soichiro , Takao Hiroyuki , Takeshita Kohei , Suzuki Takashi , Uchiyama Yuya , Karagiozov Kostadin , Ishibashi Toshihiro , Fukudome Koji , Yamamoto Makoto , Murayama Yuichi
Published: June 2022

Background

Intracranial stents are used to treat aneurysms by diverting the blood flow from entering into the aneurysmal dome. Although delayed rupture is rare, clinical outcomes are extremely poor in such cases. Hemodynamics after stent deployment may be related to delayed rupture and a better understanding of the basic characteristics of pressure changes resulting from stent deployment is needed; therefore, this study investigated the relationships between hemodynamics in aneurysms of different sizes treated using stents of different wire mesh densities.

Methods

Using computational fluid dynamics analysis, parameters related to velocity, volume flow rate, pressure, and residual volume inside the aneurysm were evaluated in digital models of 5 basic aneurysms of differing sizes (Small, Medium, Medium-Large, Large, and Giant) and using 6 different types of stent (varying number of wires, stent pitch and wire mesh density) for each aneurysm.

Results

Regardless of the aneurysm size, the velocity inside the aneurysm and the volume flow rate into the aneurysm were observed to continuously decrease up to 89.2% and 78.1%, respectively, with increasing stent mesh density. In terms of pressure, for giant aneurysms, the pressure on the aneurysmal surface elevated to 10.3%, then decreased to 5.1% with increasing stent mesh density. However, in smaller aneurysms, this pressure continuously decreased with increasing stent mesh density. The flow-diverting effect of the stents was limited when a stent with low mesh density (under 20%) was used with a giant aneurysm.

Conclusions

The present results indicate that the selection of appropriate stents according to aneurysm size may contribute to reduced risks of hemodynamic alternations related to stent deployment, which could reduce the incidence of delayed rupture.
A small molecule that disrupts S. Typhimurium membrane voltage without cell lysis reduces bacterial colonization of mice
Authors: Dombach Jamie L. , Quintana Joaquin LJ , Allgood Samual C. , Nagy Toni A. , Gustafson Daniel L. , Detweiler Corrella S.
Published: June 2022

As pathogenic bacteria become increasingly resistant to antibiotics, antimicrobials with mechanisms of action distinct from current clinical antibiotics are needed. Gram-negative bacteria pose a particular problem because they defend themselves against chemicals with a minimally permeable outer membrane and with efflux pumps. During infection, innate immune defense molecules increase bacterial vulnerability to chemicals by permeabilizing the outer membrane and occupying efflux pumps. Therefore, screens for compounds that reduce bacterial colonization of mammalian cells have the potential to reveal unexplored therapeutic avenues. Here we describe a new small molecule, D66, that prevents the survival of a human Gram-negative pathogen in macrophages. D66 inhibits bacterial growth under conditions wherein the bacterial outer membrane or efflux pumps are compromised, but not in standard microbiological media. The compound disrupts voltage across the bacterial inner membrane at concentrations that do not permeabilize the inner membrane or lyse cells. Selection for bacterial clones resistant to D66 activity suggested that outer membrane integrity and efflux are the two major bacterial defense mechanisms against this compound. Treatment of mammalian cells with D66 does not permeabilize the mammalian cell membrane but does cause stress, as revealed by hyperpolarization of mitochondrial membranes. Nevertheless, the compound is tolerated in mice and reduces bacterial tissue load. These data suggest that the inner membrane could be a viable target for anti-Gram-negative antimicrobials, and that disruption of bacterial membrane voltage without lysis is sufficient to enable clearance from the host.
La educación del gusto en las comunidades rurales chiquitanas localizadas en la frontera Brasil-Bolivia
Authors: Paipilla Fernández Stephany , Saléte Grando Beleni
Published: June 2022

Se considera la educación del gusto de las comunidades chiquitanas, ubicadas en la frontera entre el Estado de Mato Grosso (Brasil) y la provincia de José Miguel de Velasco (Bolivia), en relación con la educación del cuerpo para el pueblo indígena en Brasil. La metodología está fundamentada en la investigación cualitativa en educación, enfocada en los conocimientos y capacidades de las comunidades, y específicamente en la etnografía sensorial y la investigación documental como métodos para la recolección y análisis de las informaciones. Como resultados, se encuentra que el cuerpo-investigador está atravesado por el cruce de fronteras coloniales; desde un enfoque anticolonial, se hacen visibles las tradiciones cientificistas y universalistas sobre los sentidos, los apagones en la historia local y en la memoria alimentaria, y las posturas descoloniales para atender diversas epistemologías sobre la experiencia gustativa, que en el caso chiquitano están vinculadas a la relación cuerpo, territorio y espíritu. Se destaca el papel de la familia y de las celebraciones comunitarias en la formación del gusto chiquitano y de las escuelas del área rural para acoger las diferencias y hacer frente a las desigualdades sociales en el contexto de frontera.
Educação antirracista e decolonialidade na educação brasileira: memórias e experiências de professoras e professores
Authors: Beloni de Paula Josiane , Magalhães Pinheiro Patrícia , Paim Elison Antonio
Published: June 2022

Este artigo elucida a urgência em se debater e ampliar a educação antirracista na sociedade brasileira, tendo em vista a realidade que experienciamos desde acolonização, se estendendo para as colonialidades que abrangem o poder, o saber, o ser e a natureza (Quijano, 2005; Lugones, 2014), compreendendo o racismo como pedra angular da colonialidade (Quijano, 2010; Grosfoguel, 2019). Optando, então, pela transformação de uma sociedade no caminho da decolonialidade, por meio de uma pedagogia propositiva e decolonial (Walsh, 2013), ou seja, que faz uma denúncia e um anúncio (Freire, 1987), denunciando o racismo, que estrutura nossa sociedade e anunciando práticas de resistências educacionais antirracistas, que enfrentam e combatem o racismo individual, institucional e estrutural (Almeida, 2018), mantendo a centralidade da educação das relações étnico-raciais na escola. Tomaremos como base para esta construção do artigo as reflexões desenvolvidas nas pesquisas de doutoramento das autoras, ambas defendidas pelo Programa de Pós-graduação em Educação da Universidade Federal de Santa Catarina (UFSC) no ano de 2020, sob orientação do autor do artigo. Nestes trabalhos acadêmicos privilegiamos a escuta das narrativas, vozes (Ribeiro, 2017), memórias e experiências (Benjamin, 2012) de professoras/es comprometidas/os com a luta antirracista e, por consequente, em uma sociedade democrática, equânime e fraterna.