Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversification in Functions and Expressions of Soybean FLOWERING LOCUS T Genes Fine-Tunes Seasonal Flowering

The proper timing of flowering in response to environmental changes is critical for ensuring crop yields. FLOWERING LOCUS T (FT) homologs of the phosphatidylethanolamine-binding protein family play important roles as floral integrators in many crops. In soybean, we identified 17 genes of this family, and characterized biological functions in flowering for ten FT homologs. Overexpression of GmFT homologs in Arabidopsis revealed that a set of GmFT homologs, including GmFT2a/2b, GmFT3a/3b, and GmFT5a/5b, promoted flowering similar to FT; in contrast, GmFT1a/1b, GmFT4, and GmFT6 delayed flowering. Consistently, expressions of GmFT2a, GmFT2b, and GmFT5a were induced in soybean leaves in response to floral inductive short days, whereas expressions of GmFT1a and GmFT4 were induced in response to long days. Exon swapping analysis between floral activator GmFT2a and floral repressor GmFT4 revealed that the segment B region in the fourth exon is critical for their antagonistic functions. Finally, expression analysis of GmFT2a, GmFT5a, and GmFT4 in soybean accessions exhibiting various flowering times indicated that the mRNA levels of GmFT2a and GmFT5a were higher in early flowering accessions than in late-flowering accessions, while GmFT4 showed the opposite pattern. Moreover, the relative mRNA levels between GmFT2a/GmFT5a and GmFT4 was important in determining day length-dependent flowering in soybean accessions. Taken together, our results suggest that the functions of GmFT homologs have diversified into floral activators and floral repressors during soybean evolution, and the timing of flowering in response to changing day length is determined by modulating the activities of antagonistic GmFT homologs.
Quietly queer(ing): the normative value of sutura and its potential for young women in urban Senegal

Abstract Sutura (discretion, modesty) is a central element in Senegalese Wolof culture that, among other things, promotes feminine honour through chastity, silence with regard to discussing sexuality with elders, and refraining from articulating same-sex desires in general. Consequently, sutura is seen as limiting the space for non-normative sexualities. However, lesbiennes in Senegal strategically employ sutura to navigate this gender and sexual normativity, whereby they queer the initially heteronormative framework. This article explores how, at the frontiers of international sexual rights activism and its antithetical Islamic social code, young women open new avenues for thinking queer Africa. The article explores young women's diverse tactics to turn sutura from a heteronormative framework into a vehicle for queer expression. These women demonstrate the constant yet indeterminate possibilities to negotiate between normative expectations and queer lives. They furthermore propose an alternative to the international queer frontier of overt resistance and protest, and suggest that the silences that sutura prescribe are more productive for queering their urban environment. By balancing the simultaneous desires of same-sex intimacies, family life, societal expectations and urban success, these women are pioneers in offering new routes for ‘queering queer Africa’, as Stella Nyanzi has described it.
Effective impregnation for the preparation of magnetic mesoporous carbon: application to dye adsorption

BACKGROUND In this study, magnetic mesoporous activated carbons were synthesized either via co-precipitation of iron salts onto activated carbon or via impregnation of activated carbon with magnetic nanoparticles by sonication. The resulted impregnated carbons were examined as adsorbents for the removal of Reactive Black 5 (RB5) from aqueous solutions. RESULTS The magnetic nanocomposites were characterized by various techniques (nitrogen adsorption, Fourier transform infrared spectroscopy, X-ray diffraction, vibrating sample magnetometry, and scanning electron microscope measurements). The results of characterization analyses revealed that co-precipitation found to be unsuccessful for the preparation of magnetic carbon while sonication led to a super-paramagnetic activated carbon. Adsorption studies revealed that although magnetic carbon presented a decreased adsorption capacity compared to the raw carbon, it was a sufficient dye adsorbent. High pH and high ionic strength values favored dye adsorption, while the data of adsorption isotherms and kinetics were better fitted by Freundlich isotherm model and the pseudo second-order kinetic model, respectively. Regeneration of dye-loaded activated carbons by thermal re-activation and re-use of regenerated samples were also succeeded. CONCLUSION Mesoporous magnetic activated carbon, with a saturation magnetization of 18 emu/g, was successfully synthesized by sonication of activated carbon and magnetite nanoparticles. The magnetic carbon found to be a sufficient dye adsorbent with a maximum adsorption capacity of 445.294 mg/g.
GPU-accelerated real-time reconstruction in Python of three-dimensional datasets from structured illumination microscopy with hexagonal patterns

We present a structured illumination microscopy system that projects a hexagonal pattern by the interference among three coherent beams, suitable for implementation in a light-sheet geometry. Seven images acquired as the illumination pattern is shifted laterally can be processed to produce a super-resolved image that surpasses the diffraction-limited resolution by a factor of over 2 in an exemplar light-sheet arrangement. Three methods of processing data are discussed depending on whether the raw images are available in groups of seven, individually in a stream or as a larger batch representing a three-dimensional stack. We show that imaging axially moving samples can introduce artefacts, visible as fine structures in the processed images. However, these artefacts are easily removed by a filtering operation carried out as part of the batch processing algorithm for three-dimensional stacks. The reconstruction algorithms implemented in Python include specific optimizations for calculation on a graphics processing unit and we demonstrate its operation on experimental data of static objects and on simulated data of moving objects. We show that the software can process over 239 input raw frames per second at 512 × 512 pixels, generating over 34 super-resolved frames per second at 1024 × 1024 pixels. This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 1)’.
Bletilla striata Polysaccharide Promotes Diabetic Wound Healing Through Inhibition of the NLRP3 Inflammasome

The aim of this study was to evaluate the therapeutic effects of Bletilla striata polysaccharide (BSP) on wound healing in diabetes mellitus (DM) and to explore the underlying mechanisms. DM mouse models were induced by high fat-diet feeding combined with low-dose streptozocin injection. To establish diabetic foot ulcer (DFU) models, DM mice were wounded on the dorsal surface. Subsequently, mice were treated with vehicle or BSP for 12 days and wound healing was monitored. The effects of BSP on the production of interleukin-1β (IL-1β), tumor necrosis factor-α, macrophages infiltration, angiogenesis, the activation of nucleotide-binding and oligomerization (NACHT) domain, leucine-rich repeat (LRR), and pyrin domain (PYD)-containing protein 3 (NLRP3) inflammasome, and insulin sensitivity in wound tissues were subsequently evaluated. Separated- and cultured- bone marrow-derived macrophages (BMDMs) and cardiac microvascular endothelial cells (CMECs) were isolated from mice and used to investigate the effects of BSP on cell viability, reactive oxygen species (ROS) generation, NLRP3 inflammasome activation and insulin sensitivity in vitro following exposure to high glucose (HG). BSP administration accelerated diabetic wound healing, suppressed macrophage infiltration, promoted angiogenesis, suppressed NLRP3 inflammasome activation, decreased IL-1β secretion, and improved insulin sensitivity in wound tissues in DM mice. In vitro, co-treatment with BSP protected against HG-induced ROS generation, NLRP3 inflammasome activation, and IL-1β secretion in BMDMs, and improved cell viability and decreased ROS levels in CMECs. Moreover, in HG exposed BMDMs-CMECs cultures, BSP treatment suppressed NLRP3 inflammasome activation and IL-1β secretion in BMDMs, and improved cell viability and insulin sensitivity in CMECs. Furthermore, treatment with IL-1β almost completely suppressed the beneficial effects of BSP on the NLRP3 inflammasome, IL-1β secretion, and insulin sensitivity in HG-treated BMDMs-CMECs. BSP promotes DFU healing through inhibition of the HG-activated NLRP3 inflammasome.
The Ontology of the Amphioxus Anatomy and Life Cycle (AMPHX)

An ontology is a computable representation of the different parts of an organism and its different developmental stages as well as the relationships between them. The ontology of model organisms is therefore a fundamental tool for a multitude of bioinformatics and comparative analyses. The cephalochordate amphioxus is a marine animal representing the earliest diverging evolutionary lineage of chordates. Furthermore, its morphology, its anatomy and its genome can be considered as prototypes of the chordate phylum. For these reasons, amphioxus is a very important animal model for evolutionary developmental biology studies aimed at understanding the origin and diversification of vertebrates. Here, we have constructed an amphioxus ontology (AMPHX) which combines anatomical and developmental terms and includes the relationships between these terms. AMPHX will be used to annotate amphioxus gene expression patterns as well as phenotypes. We encourage the scientific community to adopt this amphioxus ontology and send recommendations for future updates and improvements.
The Effects of Viewing Cute Pictures on Performance During a Basketball Free-Throw Task

Previous studies have shown that viewing cute pictures leads to performance improvement in a subsequent fine motor task. We examined the beneficial effects of viewing cute pictures in a more complex sporting skill (i.e., basketball free throws) by comparing three conditions (viewing baby animal pictures, adult animal pictures, and no pictures) and two tests (no-pressure and pressure). The participants, all of whom were college basketball players, performed 16 free throws in each condition. In the no-pressure test, male participants improved performance after viewing pictures of baby animals but not after adult animals and no pictures. In the pressure test, no significant improvement was observed. For female participants, the cuteness-viewing effect was not observed in both tests. The results suggest that viewing cute pictures may improve performance during basketball free throws in a low-pressure situation by narrowing the breadth of attentional focus and inducing approach motivation and caregiving behaviors.
CSim2

To make feasible and scalable the verification of large and complex concurrent systems, it is necessary the use of compositional techniques even at the highest abstraction layers. When focusing on the lowest software abstraction layers, such as the implementation or the machine code, the high level of detail of those layers makes the direct verification of properties very difficult and expensive. It is therefore essential to use techniques allowing to simplify the verification on these layers. One technique to tackle this challenge is top-down verification where by means of simulation properties verified on top layers (representing abstract specifications of a system) are propagated down to the lowest layers (that are an implementation of the top layers). There is no need to say that simulation of concurrent systems implies a greater level of complexity, and having compositional techniques to check simulation between layers is also desirable when seeking for both feasibility and scalability of the refinement verification. In this article, we present CSim2 a (compositional) rely-guarantee-based framework for the top-down verification of complex concurrent systems in the Isabelle/HOL theorem prover. CSim2 uses CSimpl, a language with a high degree of expressiveness designed for the specification of concurrent programs. Thanks to its expressibility, CSimpl is able to model many of the features found in real world programming languages like exceptions, assertions, and procedures. CSim2 provides a framework for the verification of rely-guarantee properties to compositionally reason on CSimpl specifications. Focusing on top-down verification, CSim2 provides a simulation-based framework for the preservation of CSimpl rely-guarantee properties from specifications to implementations. By using the simulation framework, properties proven on the top layers (abstract specifications) are compositionally propagated down to the lowest layers (source or machine code) in each concurrent component of the system. Finally, we show the usability of CSim2 by running a case study over two CSimpl specifications of an Arinc-653 communication service. In this case study, we prove a complex property on a specification, and we use CSim2 to preserve the property on lower abstraction layers.
Species composition of Trichoderma isolates from the rhizosphere of vegetables grown in Hungarian soils

The species composition of Trichoderma isolates from the rhizosphere of different vegetables collected at different locations in Hungary was examined during this study. Trichoderma strains were isolated from the rhizosphere samples on dichloran-rose bengal medium. After purification of genomic DNA, the PCR amplification of the internal transcribed spacer (ITS1-5.8S rDNA-ITS2) region and its sequence analysis were used for the identification of the isolates at the species level. Altogether, 45 Trichoderma isolates were identified from the examined samples. The detected Trichoderma species were T. asperellum, T. atroviride, T. citrinoviride, T. gamsii, T. hamatum, T. harzianum, T. koningiopsis/T. ovalisporum, T. longibrachiatum/H. orientalis, T. pleuroticola and T. virens. Besides species known as opportunistic pathogens of humans (T. longibrachiatum / H. orientalis, T. citrinoviride) or as causative agents of mushroom green mould disease (T. pleuroticola), beneficial taxa (T. harzianum, T. virens, T. atroviride) widely used for the biological control of plant pathogenic fungi could also be identified in the examined samples, suggesting that the rhizosphere of vegetables may be a rich source of potential biocontrol agents. In vitro antagonism was examined in dual culture tests and the Biocontrol Index (BCI) values were determined for the particular isolates. Certain T. asperellum, T. virens and T. atroviride isolates proved to possess good in vitro antagonistic activities against plant pathogenic Fusarium solani and F. oxysporum strains, suggesting that they might be promising for the development of Trichoderma-based biocontrol strategies for the suppression of plant pathogenic fungi in the rhizosphere of vegetables produced in organic farmland soils.
Machining behavior of AA6351–SiC–B4C hybrid composites fabricated by stir casting method

ABSTRACT This study presents an effective approach to assess the machinability of 6351 aluminum alloy matrix, reinforced with 5 wt. % silicon carbide (SiC) and (0, 5, and 10 wt.%) boron carbide (B4C) particles. The turning tests are carried out with a polycrystalline diamond (PCD) tool to identify the effect of the B4C particles addition to the composite, with an objective to improve the material removal rate (MRR) and to reduce the surface roughness (Ra) and power consumption (P). The significant level of each factor, which contributes to affect the output response, is found through analysis of variance (ANOVA). The results show that the inclusion of B4C particles in the hybrid composite significantly affects the machinability, with a contribution to the surface roughness by 7.87% and P by 6.36%. The increase in MRR affects the quality of the material, irrespective of the composites.
Polymersomes for biotechnological applications: Large‐scale production of nano‐scale vesicles

Polymersomes have some fundamental advantages compared to their liposomal counterparts. Due to the increased stability of the polymeric membrane, polymersomes are intended to be reasonably applicable as carrier‐systems and universal reaction compartments for diverse medical and biotechnological applications. Regardless of the application area, suitable methods to produce large vesicle quantities in a controlled and cost‐effective manner have to be developed to put polymersome technology into action at the industrial scale. In this work, the amphiphilic triblock copolymer poly(2‐methyloxazoline)15‐poly(dimethylsiloxane)68‐poly(2‐methyloxazoline)15 was formed into uniform polymersomes. A recently established production process, based on the use of miniaturized stirred‐tank reactors at the milliliter‐scale (12 mL), was successfully scaled‐up to the liter‐scale (1.5 L) based on solid process engineering parameters. Dynamic light scattering measurements show that using standard propeller stirrers with a dimensionless diameter dD−1 ≥0.65 in an unbaffled stirred‐tank reactor led to a narrow particle size distribution when providing a Froude number of Fr = 6.52 at the same time. Polymersomes with a mean diameter of 180 nm and a low polydispersity index (PDI<0.2) were generated within about 1 h in one single production step. Thus, this work provides the fundamental basis for further scale‐up purposes, regarding polymersome production in stirred‐tank reactors at the industrial scale.
FABM-NflexPD 1.0: Assessing an Instantaneous Acclimation
Approach for Modelling Phytoplankton Growth

Abstract. Coupled physical-biogeochemical models can generally reproduce large-scale patterns of primary production and biogeochemistry, but they often underestimate observed variability and gradients. This is partially caused by insufficient representation of systematic variations in the elemental composition and pigment density of phytoplankton. Although progress has been made through approaches accounting for the dynamics of phytoplankton composition with additional state variables, formidable computational challenges arise when these are applied in spatially explicit setups. The Instantaneous Acclimation (IA) approach addresses these challenges by assuming that Chl : C : nutrient ratios are instantly optimized locally (within each modelled grid cell, at each timestep), such that they can be resolved as diagnostic variables. Here we present the first tests of IA in an idealized, 1D setup: we implemented the IA in the Framework for Aquatic Biogeochemical Models (FABM), and coupled it with the General Ocean Turbulence Model (GOTM) to simulate the spatio-temporal dynamics in a 1-D water column. We show that the IA model and a fully dynamic, otherwise equivalently acclimative (DA) variant with an additional state variable behave similarly, and both resolve nutrient and growth dynamics not captured by a third, non-acclimative and fixed-stoichiometry (FS) variant.
MYCOREMEDIATION OF HEAVY METALS PRESENT IN CONTAMINATED AGRICULTURAL SOIL

In this study, Mycoremediation technique was used to analyse the potential of mushroom in absorbing heavy metals from contaminated soil. A small village Sitagarha located in Hazaribag, Jharkhand was selected as sampling site. Soil sample was collected from two different sites – from field where cow manure was used as fertilizer and the other soil sample where chemical fertilizer was mixed. A control sample was also collected from nearby barren land where no cultivation was carried out since decades. After initial screening, three heavy metals Cu, Cd and Zn were selected to carry out further studies. The soil sample was processed in laboratory and analysed in AAS to detect the concentration of heavy metals. Results showed the presence of heavy metals as – Cd > Cu > Zn. Further these soil samples were mixed along with straw and spawn to prepare a mushroom cultivation bag as mushroom has the property to absorb heavy metals. The result of absorbance of heavy metals by mushroom was somewhere an indication that mycoremediation proofs to be an important tool to fight against heavy metals.
Evaluating the Concentration of Ions in Liquid Crystal Cells: Hidden Factors and Useful Techniques

Many liquid crystal devices are driven by electric fields. Ions, typically present in molecular liquid crystal materials in minute quantities, can compromise the performance of mesogenic materials (in the simplest case, through a well-known screening effect). Even highly purified liquid crystals can be contaminated with ions during their production and handling. Therefore, measurements of the concentration of ions have become an important part of the material characterization of liquid crystals. Interestingly, even a brief analysis of existing publications can reveal a quite broad variability of the values of the concentration of ions measured by different research groups for the same liquid crystals. This reflects the complexity of ion generation mechanisms in liquid crystal materials and their dependence on numerous factors. In this paper, an overview of ion generation mechanisms in liquid crystals and modern ion measurement techniques is followed by the discussion of frequently overlooked factors affecting the measured values of the ion concentration. Ion-generating and ion-capturing properties of the alignment layers (or substrates) of liquid crystal cells are considered and used to evaluate a true concentration of ions in liquid crystals. In addition, practical recommendations aimed at improving the measurements of the ion density in liquid crystals are also discussed.
Occurrence of calcium oxalate crystals in some wild plants used in traditional medicine in Saudi Arabia

Plants are widely used in traditional medicine, but could be detrimental to patients, due to the presence of some harmful substances such as calcium oxalate (CaOx) C2CaO4 crystals. The presence, morphology and distribution of CaOx crystals were investigated in 60 wild, herbal plant species from the Al Qussim Region, Saudi Arabia. This was done via light microscopy of transverse sections of stems and leaves using light microscopy. Different types of CaOx crystals were found in only 24 of the plant species studied, the rest had no CaOx crystals. The stems of 12 plant species under study contained different types of CaOx crystals, with crystal sand being the most common. In the leaves of four plant species, druses and solitary crystals were the most frequently found types. In addition, eight species had different types of crystals in their respective stems and leaves. Rumex vesicarius had the most crystals in both its stems and leaves from all investigated species, followed by Asphodelus tenuifolius. Key words: Ca-oxalate crystals, light microscope, plant leaves, stems, Al Qussim Region.