Search Results (94)

Alfalfa (Medicago sativa) persists for several years but must be rotated to another crop before replanting. Kura clover (T. ambiguum M. Bieb) is a perennial legume that can persist indefinitely without replanting; however, establishment is slow, which limits economic returns during the process. Two studies, each with four randomized complete blocks, were planted in two consecutive years at New Mexico State University’s Rex E. Kirksey Agricultural Science Center at Tucumcari, NM, USA, as the first known assessment evaluating alfalfa as an economic nurse crop during kura clover establishment using various kura clover–alfalfa drilled and broadcast planting arrangements. Irrigation termination due to drought limited yield measurements to three years after seeding. In that time, kura clover–alfalfa mixtures generally yielded equally to monoculture alfalfa, except for alternate row planting. After 5 years, the alfalfa stand percentage remained >80%, except for the alternate row treatment (69% stand). Kura clover monocultures attained about 40% stand, and the mixtures had a <25% stand. Alfalfa may persist for more than 5 years before relinquishing dominance to kura clover in mixtures, but the alfalfa would continue to provide economic returns as kura clover continues stand development with minimal production, but develops its root system to maximize production when released from the alfalfa nurse crop. Full article

RNA-binding proteins (RBPs) are critical regulators of post-transcriptional processes, playing essential roles in nutrient metabolism and metabolic homeostasis. This literature review explores how RBPs influence the metabolism of glucose, lipid, and amino acid metabolism by controlling processes like mRNA stability and translation regulation. The dysregulation of RBPs, including HuR, PTB, and YTHDF1, is linked to metabolic diseases such as obesity, diabetes, and non-alcoholic fatty liver disease. Advances in techniques like TREX technology and transcriptome analysis have deepened our understanding of RBP functions. Additionally, RBPs show promise as potential biomarkers and targets for new therapies. Future research directions in RBPs could focus on tissue-specific regulation and nutrient–RBP interactions. This could pave the way for more personalized treatments and improved metabolic health. Full article

Direct stochastic optical reconstruction microscopy (dSTORM) circumvents the diffraction limit of light, emerging as a powerful superresolution technique for visualizing subcellular structures with a nanoscale resolution of 10–20 nm. Yet achieving ultrastructural resolution using dSTORM alone remains challenging, despite its advantage of requiring only minimal modifications to the imaging setup and sample preparation compared to conventional fluorescence microscopy. A recent advancement that integrates expansion microscopy (ExM), which embeds specimens in a swellable polymer gel, with dSTORM holds promise for attaining imaging resolutions below 10 nm. The combined resolution, however, is governed by the expansion factor of samples, and prior studies have primarily focused on integrations involving approximately 4-fold gel expansion, as dSTORM imaging of high-fold-expanded specimens is still technically demanding. Here, we propose a pragmatic expansion strategy—post-labeling ten-fold robust expansion microscopy (plTREx)—and outline a workflow to facilitate its compatibility with dSTORM, collectively termed plTREx-dSTORM. Specifically, this workflow enhances the mechanical stability of the expansion hydrogel and improves fluorescence signal density across both widefield and dSTORM imaging platforms. Furthermore, we optimize the re-embedding protocol to integrate hydrogel expansion with dSTORM while preventing gel shrinkage. Together, plTREx-dSTORM enables highly refined imaging capable of ultrastructural interpretation of cellular proteins, effectively bridging the resolution gap between electron microscopy and optical microscopy. Full article

Precise and modular reconstruction of 3D tooth structures is crucial for creating interpretable, adaptable models for digital dental applications. To address the limitations of conventional segmentation approaches under conditions such as missing teeth, misalignment, or incomplete anatomical structures, we propose a process-oriented reconstruction pipeline composed of discrete yet integrated modules. The pipeline begins by decomposing 3D dental meshes into a series of 2D projections, allowing multi-view capture of morphological features. A fine-tuned Segment Anything Model (SAM), enhanced with task-specific bounding box prompts, performs segmentation on each view. T-Rex2, a general object detection module, enables automated prompt generation for high-throughput processing. Segmented 2D components are subsequently reassembled and mapped back onto the original 3D mesh to produce complete and anatomically faithful tooth models. This modular approach enables clear separation of tasks—view projection, segmentation, and reconstruction—enhancing flexibility and robustness. Evaluations on the MICCAI 3DTeethSeg’22 dataset show comparable or superior performance to existing methods, particularly in challenging clinical scenarios. Our method establishes a scalable, interpretable framework for 3D dental modeling, supporting downstream applications in simulation, treatment planning, and morphological analysis. Full article

Neuronal death is a central event in spinal cord injury (SCI) pathophysiology. Despite its importance, we have a fragmentary vision of the process. In our opinion, the research community has accumulated enough information to provide a more detailed, integrated vision of neuronal death after SCI. This work embeds this vision by creating an open repository to store and share data and results from their analysis. We have employed this repository to upload raw images of spinal cord sections from a mouse model of contusive SCI and used this information to compare manual-, threshold-, and neural network-based neuron identifications and to explore neuronal death at the injury penumbra 21 days after injury and the effects of the anti-apoptotic drug ucf-101. Results indicate that, whereas the three identification methods assayed yield coherent estimates of the total number of neurons per section, neural network (NN) outperforms the other two methods. Combining NN identification and image registration has allowed us to characterize neuron distribution among Rexed laminae in the mice T11, revealing spatial patterns in the neuronal death that follows injury and in their survival following ucf-101 treatment. Full article

Background: The heterogeneity of sarcomas and resulting distinct sub-type specific characteristics, their high recurrence rates, and tendency for distant metastasis, continue to present significant challenges to providing optimal treatments. Objective: To provide a comprehensive review of current literature and clinical trials in gene and cell therapies for sarcomas. Methods: A comprehensive literature search was conducted utilizing the following databases: PubMed, Medline, Google Scholar and clinicaltrials.gov. Search terms included “gene therapy”, “cell therapy”, “NK cell therapy, “CAR-T therapy”, “virotherapy”, “sarcoma”, “gene therapy”, and “solid tumors”. Additional sources were identified through manual searching for references of relevant studies. No language restrictions were set. The NCT number, study status, condition, and phase were noted for clinical trials. Results: There are only three gene and cell therapies for sarcomas that have been approved by a federal regulatory agency. Rexin-G: the first tumor-targeted gene therapy vector designed to target all advanced solid malignancies, including chemo-refractory osteosarcomas and soft tissue sarcomas, was approved by the Philippine FDA in 2007. Gendicine was the first oncolytic virus approved for intratumoral delivery in China in 2003. Afami-cel, an innovative chimeric antigen receptor (CAR) T cell therapy, was approved for synovial sarcoma in the United States in 2024. Other promising therapies are discussed in the text. Conclusions: The future of gene and cell therapy for sarcomas holds great promise, as research moves to late-stage clinical development. The integration of gene and cell therapies into standard sarcoma treatment protocols has the potential to significantly improve the quality of life and outcomes for patients with this rare and challenging group of cancers. Full article

This study assesses the environmental status and water quality of the Saraswati River, an ancient and endangered waterway in Bengal, using an integrated approach. By combining traditional knowledge, advanced geospatial tools, and field analysis, it examines natural and human-induced factors driving the river’s degradation and proposes sustainable restoration strategies. Tools such as the Garmin Global Positioning System (GPS) eTrex10, Google Earth Pro, Landsat imagery, ArcGIS 10.8, and Google Earth Engine (GEE) were used to map the river’s trajectory and estimate its water quality. Remote sensing-derived indices, including the Normalized Difference Water Index (NDWI), Modified Normalized Difference Water Index (MNDWI), Normalized Difference Salinity Index (NDSI), Normalized Difference Turbidity Index (NDTI), Floating Algae Index (FAI), and Normalized Difference Chlorophyll Index (NDCI), Total Dissolved Solids (TDS), were computed to evaluate parameters such as the salinity, turbidity, chlorophyll content, and water extent. Additionally, field data from 27 sampling locations were analyzed for 11 critical water quality parameters, such as the pH, Total Dissolved Solids (TDS), Electrical Conductivity (EC), Dissolved Oxygen (DO), Biochemical Oxygen Demand (BOD), and microbial content, using an arithmetic weighted water quality index (WQI). The results highlight significant spatial variation in water quality, with WQI values ranging from 86.427 at Jatrasudhi (indicating relatively better conditions) to 358.918 at Gobra Station Road (signaling severe contamination). The pollution is primarily driven by urban solid waste, industrial effluents, agricultural runoff, and untreated sewage. A microbial analysis revealed the presence of harmful species, including Escherichia coli (E. coli), Bacillus, and Entamoeba, with elevated concentrations in regions like Bajra, Chinsurah, and Chandannagar. The study detected heavy metals, fertilizers, and pesticides, highlighting significant anthropogenic impacts. The recommended mitigation measures include debris removal, silt extraction, riverbank stabilization, modern hydraulic structures, improved waste management, systematic removal of water hyacinth and decomposed materials, and spoil bank design in spilling zones to restore the river’s natural flow. Full article

High-grade B-cell lymphoma (HGBL), not otherwise specified (NOS), is a rare entity within the spectrum of B-cell lymphomas. HGBL, NOS remains a diagnosis of exclusion with limited data available on the optimal clinical approach. We report a case of a 67-year-old man with HGBL, NOS with a germinal center B-cell (GCB) immunophenotype. The disease was characterized by an aggressive clinical course, refractory to multiple lines of cytotoxic chemotherapy, immunotargeted treatment, therapy with a PD-1 inhibitor, and haploidentical hematopoietic stem cell transplantation (haplo-HSCT). Ultimately, the disease progression led to the patient’s death nine months post-diagnosis. A FISH assay identified a sole genetic rearrangement: BCL2/IGH. Whole-exome sequencing revealed a number of significant somatic mutations, such as TP53 p.C238G, B2M p.L12R, STAT6 p.D419G, STAT3 p.S614R, TREX1 p.T49fs, and CREBBP p.C367Ter, as well as a high focal amplification of the MUC3A gene and the deletion of the short arm of chromosome 17 (del(17p)). An inactivating somatic mutation in the TREX1 gene (p.T49fs) has not been previously described in patients with non-Hodgkin lymphomas. Additionally, our analysis uncovered a key cancer hallmark: tumor genomic instability, manifested as a high tumor mutational burden, which likely contributed to the aggressive disease course. Full article

Oases are part of the natural wealth and heritage of Morocco and contribute to the social, economic, and touristic environment. Morocco has lost more than 2/3 of its oases during the past century due to water scarcity, succession of drought periods, climate change and over-exploitation of groundwater resources. Palm trees are strongly dependent on irrigation and availability of surface water as soon as the water table depth falls below the root zone of 9 m. Improving management and monitoring of oasis ecosystems is strongly encouraged by UNESCO Biosphere Reserve and RAMSAR guidelines. The Boudenib and Tafilalet oases are among the biggest palm groves located in the south-eastern part of Morocco. These oases belong to catchments of the rivers Guir and Ziz, respectively. This paper uses remotely sensed data from PROBA-V for monitoring vegetation in oases, and linking vegetation characteristics to water availability, water management and quality and quantity of date crops. The Normalized Differential Vegetation Index (NDVI) derived from optical images provides a good estimation of changes in vegetation cover over time. Images of various spatial resolutions (100 m, 300 m and 1 km) obtained with the frequently revisiting Belgian satellite PROBA-V and available since 2014, can be successfully used for deriving time series of vegetation dynamics. TREX—Tool for Raster data Exploration—is a Python-GDAL processing tool of PROBA-V NDVI images for analyzing vegetation dynamics, developed at the Vrije Universiteit Brussel and available online. TREX has various applications, but the main functionality is to provide an automatic processing of PROBA-V satellite images into time series of NDVI and LAI, used in vegetation monitoring of user-defined points of interest. This study presents the results of application of TREX in the arid ecosystems of the Boudenib oasis for the period 2014–2018. The resulting NDVI and LAI time series are also compared to time series of groundwater depth and date crops quantity and quality. Low LAI is observed when water depth is low, and the palm trees lose their greenery. Low LAI is also correlated to low quantity and quality of dates in October 2015 and October 2017. PROBA-V images can therefore be used for monitoring the health of palm trees in oasis environments. However, considering the fact that the PROBA-V satellite mission has ended, this approach could instead be applied to Sentinel-3 data using the same analysis. These results have important implications for water management in the area and can help decision-makers to make better decisions about prevention of water scarcity in the region. Full article

The La-doped ternary Zintl phase Ca_10.43(3)La_0.57Sb_9.69(1) was successfully synthesized by arc melting, and the title compound adopted the Ho₁₁Ge₁₀-type structure with a tetragonal I4/mmm space group (Z = 4, Pearson code tI84). The complex crystal structure is composed of (1) the four different kinds of cationic Ca or Ca/La mixed sites surrounded by seven or nine Sb atoms and (2) the 3-dimensional cage-shaped anionic frameworks built by the other two types of Sb atoms. In particular, the La dopants preferred to occupy the Ca4 and Ca1 sites, and this specific cationic-site preference can be rationalized by both electronic and size-factor criteria. Moreover, the ca. 16% occupational deficiency observed at the Sb3 site was attributed to the energetically unfavorable antibonding character of the Sb3–Sb3 bond in the [Sb3]₄ tetramers, according to a series of DFT calculations. A crystal Hamilton overlap population curve analysis also proved that the title compound Ca_10.43(3)La_0.57Sb_9.69(1) tried to keep the valence electron count below 71.02 to remain energetically stable in the Ho₁₁Ge₁₀-type phase. Measurements of temperature-dependent electrical transport properties revealed that the La doping indeed enhanced the electrical conductivity of Ca_10.43(3)La_0.57Sb_9.69(1) compared to the un-doped Ca₁₁Sb₁₀. However, unlike other rare earth metal (RE)-doped compounds in the Ca_11−xRE_xSb₁₀ (RE = Nd and Sm) system that display semiconducting behavior, the La-doped title compound showed poor metallic electrical properties. The positive values of Seebeck coefficients indicated the p-type character of the title compound despite the successful n-type La doping, and this should be attributed to Sb deficiency. Full article

DNA is frequently damaged by genotoxic stresses such as ionizing radiation, reactive oxygen species, and nitrogen species. DNA damage is a key contributor to cancer initiation and progression, and thus the precise and timely repair of these harmful lesions is required. Recent studies revealed transcription as a source of genome instability, and transcription-coupled DNA damage has been a focus in cancer research. Impaired mRNA export is closely related to DNA damage through R-loop formation. The molecular machineries of transcription-coupled DNA damage have been extensively analyzed in Saccharomyces cerevisiae. However, the molecular basis of these phenomena in higher eukaryotes remains elusive. In this review, we focus on the relationship between deregulated mRNA export through the transcription-export-2 (TREX-2) complex and cancer development. Particularly, the expression of germinal center-associated nuclear protein (GANP), a molecular scaffold in the TREX-2 complex, is highly associated with tumorigenesis in mice and humans. Although the deregulated expression of other components in the TREX-2 complex might affect cancer development, we have directly demonstrated the significance of GANP in tumorigenesis using genetically modified mice. Additionally, we describe recent evidence for medical applications demonstrating that the downregulation of the other components may be a good candidate for a chemotherapeutic target in terms of reducing the side effects. Full article

Chromosomal instability and DNA damage are hallmarks of cancers that can result in the accumulation of micronuclei, cytosolic chromatin fragments (CCFs), or cytosolic DNA species (cytoDNA). The cyclic GMP-AMP synthase (cGAS) is a DNA sensor that recognizes cytosolic DNA and chromatin fragments and subsequently triggers a systemic type I interferon response via the cGAS-STING pathway. Although cancer cells usually contain a high level of chromosomal instability, these cells can avoid the induction of the interferon (IFN) response either by silencing cGAS-STING or the upregulation of the three prime exonuclease 1 (TREX1). TREX1 restricts the spontaneous activation of the cGAS-STING pathway through the degradation of cytoDNA; this in turn limits tumor immunogenicity allowing cancer cells to evade immune detection. Deletion of TREX1 in different cancer types has been shown to decrease tumor growth and increase tumor immune infiltration in pre-clinical mice models. These recent studies also showed the efficacy of TREX1-targeting in combination with anti-PD-1 immune checkpoint blockade. Therefore, targeting TREX1 represents a unique therapeutic strategy to induce an amplified induction of a type I IFN response, promoting the host’s immune response against chromosomally unstable cancer cells. We here discuss these recent advances obtained in preclinical cancer models that pave the way to develop TREX1 inhibitors and to find new avenues to target the broad cGAS-STING pathway signaling in cancer therapy. Full article

Drones are an ecological tool used increasingly in shark research over the past decade. Due to their high-resolution camera and GPS systems, they have been used to estimate the sizes of animals using drone-based photogrammetry. Previous studies have used drone altitude to measure the target size accuracy of objects at the surface; however, target depth and its interaction with altitude have not been studied. We used DJI Mavic 3 video (3960 × 2160 pixel) and images (5280 × 3960 pixel) to measure an autonomous underwater vehicle of known size traveling at six progressively deeper depths to assess how sizing accuracy from a drone at 10 m to 80 m altitude is affected. Drone altitudes below 40 m and target depths below 2 m led to an underestimation of size of 76%. We provide evidence that accounting for the drone’s altitude and the target depth can significantly increase accuracy to 5% underestimation or less. Methods described in this study can be used to measure free-swimming, submerged shark size with accuracy that rivals hand-measuring methods. Full article

Tumors of the spine are rare, with an incidence of 1.0 and 1.5 per 100,000 individuals. A 44-year-old female patient underwent emergency surgery for posterior decompression and tumor resection. A 3-level laminectomy was performed from T6 to T8 using the Medtronic Midas Rex drill and a 5 mm diamond drill, with microsurgical resection of the lesion. A new resection was performed one week later to address a residual tumor located towards the rostral and cephalic levels. A sample of the extradural lesion was obtained and was sent to the Pathology Department of the Hospital Regional de Alta Especialidad de Ixtapaluca (HRAEI) for histopathological diagnosis, reporting Grade 1 psammomatous meningioma according to the WHO’s criteria. Our patient’s rehabilitation treatment consisted of two parts. The first part occurred during her hospital stay, before and after surgery, and upon her discharge. At the first outpatient consultation three weeks after surgery, the patient showed improved strength in the lower extremities, scoring 4/5 on the Daniel’s scale muscle strength test. After one year of follow-up, our patient has recovered muscle strength. This allows her to move freely, scoring 5/5 on the Daniel’s scale muscle strength test. Full article

Begonia rex cv. DS-EYWA is an important plant for indoor and outdoor cultivation, and cv. DS-EYWA is a rare unique cultivar with curly, colorful leaves. Due to their importance, applying plant tissue culture techniques for mass and healthy production in a short period of time without seasonal limitation is of immense economic value. Applying several concentrations of silver nitrate (AgNO₃) in combination with varied concentrations of cytokinins including 6-benzylaminopurine (BAP), thidiazuron (TDZ) (0, 0.5, 1, 1.5 mgL⁻¹), and 1-naphthaleneacetic acid (NAA) auxin (0, 0.5, 1 mgL⁻¹) via focusing on transverse thin cell layer (tTCL) petiole explants for high-scale production was used to establish an efficient in vitro propagation protocol. Our results showed that even low concentrations (25 mgL⁻¹) can control internal bacterial infection and increase shoot direct regeneration efficiency. A combination of 1.5 mgL⁻¹ BAP, 0.5 mgL⁻¹ NAA, and 25 mgL⁻¹ AgNO₃ was the best treatment to increase the number of direct regenerated shoots, and a lower concentration of BAP (0.5 mgL⁻¹) can be suggested for shoot elongation. Elongated shoots were successfully rooted in MS basal medium and acclimatized in a 1:1 peat moss/perlite sterilized pot mixture. Full article